The non-uniformity of fossil preservation

PubMed Central

2016-01-01

The fossil record provides the primary source of data for calibrating the origin of clades. Although minimum ages of clades are given by the oldest preserved fossil, these underestimate the true age, which must be bracketed by probabilistic methods based on multiple fossil occurrences. Although most of these methods assume uniform preservation rates, this assumption is unsupported over geological timescales. On geologically long timescales (more than 10 Myr), the origin and cessation of sedimentary basins, and long-term variations in tectonic subsidence, eustatic sea level and sedimentation rate control the availability of depositional facies that preserve the environments in which species lived. The loss of doomed sediments, those with a low probability of preservation, imparts a secular trend to fossil preservation. As a result, the fossil record is spatially and temporally non-uniform. Models of fossil preservation should reflect this non-uniformity by using empirical estimates of fossil preservation that are spatially and temporally partitioned, or by using indirect proxies of fossil preservation. Geologically, realistic models of preservation will provide substantially more reliable estimates of the origination of clades. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. PMID:27325828

Biogeographic Dating of Speciation Times Using Paleogeographically Informed Processes

PubMed Central

Landis, Michael J.

2017-01-01

Abstract Standard models of molecular evolution cannot estimate absolute speciation times alone, and require external calibrations to do so, such as fossils. Because fossil calibration methods rely on the incomplete fossil record, a great number of nodes in the tree of life cannot be dated precisely. However, many major paleogeographical events are dated, and since biogeographic processes depend on paleogeographical conditions, biogeographic dating may be used as an alternative or complementary method to fossil dating. I demonstrate how a time-stratified biogeographic stochastic process may be used to estimate absolute divergence times by conditioning on dated paleogeographical events. Informed by the current paleogeographical literature, I construct an empirical dispersal graph using 25 areas and 26 epochs for the past 540 Ma of Earth’s history. Simulations indicate biogeographic dating performs well so long as paleogeography imposes constraint on biogeographic character evolution. To gauge whether biogeographic dating may be of practical use, I analyzed the well-studied turtle clade (Testudines) to assess how well biogeographic dating fares when compared to fossil-calibrated dating estimates reported in the literature. Fossil-free biogeographic dating estimated the age of the most recent common ancestor of extant turtles to be from the Late Triassic, which is consistent with fossil-based estimates. Dating precision improves further when including a root node fossil calibration. The described model, paleogeographical dispersal graph, and analysis scripts are available for use with RevBayes. PMID:27155009

Xenopus in Space and Time: Fossils, Node Calibrations, Tip-Dating, and Paleobiogeography.

PubMed

Cannatella, David

2015-01-01

Published data from DNA sequences, morphology of 11 extant and 15 extinct frog taxa, and stratigraphic ranges of fossils were integrated to open a window into the deep-time evolution of Xenopus. The ages and morphological characters of fossils were used as independent datasets to calibrate a chronogram. We found that DNA sequences, either alone or in combination with morphological data and fossils, tended to support a close relationship between Xenopus and Hymenochirus, although in some analyses this topology was not significantly better than the Pipa + Hymenochirus topology. Analyses that excluded DNA data found strong support for the Pipa + Hymenochirus tree. The criterion for selecting the maximum age of the calibration prior influenced the age estimates, and our age estimates of early divergences in the tree of frogs are substantially younger than those of published studies. Node-dating and tip-dating calibrations, either alone or in combination, yielded older dates for nodes than did a root calibration alone. Our estimates of divergence times indicate that overwater dispersal, rather than vicariance due to the splitting of Africa and South America, may explain the presence of Xenopus in Africa and its closest fossil relatives in South America.

Iterative Calibration: A Novel Approach for Calibrating the Molecular Clock Using Complex Geological Events.

PubMed

Loeza-Quintana, Tzitziki; Adamowicz, Sarah J

2018-02-01

During the past 50 years, the molecular clock has become one of the main tools for providing a time scale for the history of life. In the era of robust molecular evolutionary analysis, clock calibration is still one of the most basic steps needing attention. When fossil records are limited, well-dated geological events are the main resource for calibration. However, biogeographic calibrations have often been used in a simplistic manner, for example assuming simultaneous vicariant divergence of multiple sister lineages. Here, we propose a novel iterative calibration approach to define the most appropriate calibration date by seeking congruence between the dates assigned to multiple allopatric divergences and the geological history. Exploring patterns of molecular divergence in 16 trans-Bering sister clades of echinoderms, we demonstrate that the iterative calibration is predominantly advantageous when using complex geological or climatological events-such as the opening/reclosure of the Bering Strait-providing a powerful tool for clock dating that can be applied to other biogeographic calibration systems and further taxa. Using Bayesian analysis, we observed that evolutionary rate variability in the COI-5P gene is generally distributed in a clock-like fashion for Northern echinoderms. The results reveal a large range of genetic divergences, consistent with multiple pulses of trans-Bering migrations. A resulting rate of 2.8% pairwise Kimura-2-parameter sequence divergence per million years is suggested for the COI-5P gene in Northern echinoderms. Given that molecular rates may vary across latitudes and taxa, this study provides a new context for dating the evolutionary history of Arctic marine life.

Bayesian relaxed clock estimation of divergence times in foraminifera.

PubMed

Groussin, Mathieu; Pawlowski, Jan; Yang, Ziheng

2011-10-01

Accurate and precise estimation of divergence times during the Neo-Proterozoic is necessary to understand the speciation dynamic of early Eukaryotes. However such deep divergences are difficult to date, as the molecular clock is seriously violated. Recent improvements in Bayesian molecular dating techniques allow the relaxation of the molecular clock hypothesis as well as incorporation of multiple and flexible fossil calibrations. Divergence times can then be estimated even when the evolutionary rate varies among lineages and even when the fossil calibrations involve substantial uncertainties. In this paper, we used a Bayesian method to estimate divergence times in Foraminifera, a group of unicellular eukaryotes, known for their excellent fossil record but also for the high evolutionary rates of their genomes. Based on multigene data we reconstructed the phylogeny of Foraminifera and dated their origin and the major radiation events. Our estimates suggest that Foraminifera emerged during the Cryogenian (650-920 Ma, Neo-Proterozoic), with a mean time around 770 Ma, about 220 Myr before the first appearance of reliable foraminiferal fossils in sediments (545 Ma). Most dates are in agreement with the fossil record, but in general our results suggest earlier origins of foraminiferal orders. We found that the posterior time estimates were robust to specifications of the prior. Our results highlight inter-species variations of evolutionary rates in Foraminifera. Their effect was partially overcome by using the partitioned Bayesian analysis to accommodate rate heterogeneity among data partitions and using the relaxed molecular clock to account for changing evolutionary rates. However, more coding genes appear necessary to obtain more precise estimates of divergence times and to resolve the conflicts between fossil and molecular date estimates. Copyright © 2011 Elsevier Inc. All rights reserved.

An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae).

PubMed

Arcila, Dahiana; Alexander Pyron, R; Tyler, James C; Ortí, Guillermo; Betancur-R, Ricardo

2015-01-01

Time-calibrated phylogenies based on molecular data provide a framework for comparative studies. Calibration methods to combine fossil information with molecular phylogenies are, however, under active development, often generating disagreement about the best way to incorporate paleontological data into these analyses. This study provides an empirical comparison of the most widely used approach based on node-dating priors for relaxed clocks implemented in the programs BEAST and MrBayes, with two recently proposed improvements: one using a new fossilized birth-death process model for node dating (implemented in the program DPPDiv), and the other using a total-evidence or tip-dating method (implemented in MrBayes and BEAST). These methods are applied herein to tetraodontiform fishes, a diverse group of living and extinct taxa that features one of the most extensive fossil records among teleosts. Previous estimates of time-calibrated phylogenies of tetraodontiforms using node-dating methods reported disparate estimates for their age of origin, ranging from the late Jurassic to the early Paleocene (ca. 150-59Ma). We analyzed a comprehensive dataset with 16 loci and 210 morphological characters, including 131 taxa (95 extant and 36 fossil species) representing all families of fossil and extant tetraodontiforms, under different molecular clock calibration approaches. Results from node-dating methods produced consistently younger ages than the tip-dating approaches. The older ages inferred by tip dating imply an unlikely early-late Jurassic (ca. 185-119Ma) origin for this order and the existence of extended ghost lineages in their fossil record. Node-based methods, by contrast, produce time estimates that are more consistent with the stratigraphic record, suggesting a late Cretaceous (ca. 86-96Ma) origin. We show that the precision of clade age estimates using tip dating increases with the number of fossils analyzed and with the proximity of fossil taxa to the node under assessment. This study suggests that current implementations of tip dating may overestimate ages of divergence in calibrated phylogenies. It also provides a comprehensive phylogenetic framework for tetraodontiform systematics and future comparative studies. Copyright © 2014 Elsevier Inc. All rights reserved.

Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci.

PubMed

Zhu, Tianqi; Dos Reis, Mario; Yang, Ziheng

2015-03-01

Genetic sequence data provide information about the distances between species or branch lengths in a phylogeny, but not about the absolute divergence times or the evolutionary rates directly. Bayesian methods for dating species divergences estimate times and rates by assigning priors on them. In particular, the prior on times (node ages on the phylogeny) incorporates information in the fossil record to calibrate the molecular tree. Because times and rates are confounded, our posterior time estimates will not approach point values even if an infinite amount of sequence data are used in the analysis. In a previous study we developed a finite-sites theory to characterize the uncertainty in Bayesian divergence time estimation in analysis of large but finite sequence data sets under a strict molecular clock. As most modern clock dating analyses use more than one locus and are conducted under relaxed clock models, here we extend the theory to the case of relaxed clock analysis of data from multiple loci (site partitions). Uncertainty in posterior time estimates is partitioned into three sources: Sampling errors in the estimates of branch lengths in the tree for each locus due to limited sequence length, variation of substitution rates among lineages and among loci, and uncertainty in fossil calibrations. Using a simple but analogous estimation problem involving the multivariate normal distribution, we predict that as the number of loci ([Formula: see text]) goes to infinity, the variance in posterior time estimates decreases and approaches the infinite-data limit at the rate of 1/[Formula: see text], and the limit is independent of the number of sites in the sequence alignment. We then confirmed the predictions by using computer simulation on phylogenies of two or three species, and by analyzing a real genomic data set for six primate species. Our results suggest that with the fossil calibrations fixed, analyzing multiple loci or site partitions is the most effective way for improving the precision of posterior time estimation. However, even if a huge amount of sequence data is analyzed, considerable uncertainty will persist in time estimates. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

Biogeographic Dating of Speciation Times Using Paleogeographically Informed Processes.

PubMed

Landis, Michael J

2017-03-01

Standard models of molecular evolution cannot estimate absolute speciation times alone, and require external calibrations to do so, such as fossils. Because fossil calibration methods rely on the incomplete fossil record, a great number of nodes in the tree of life cannot be dated precisely. However, many major paleogeographical events are dated, and since biogeographic processes depend on paleogeographical conditions, biogeographic dating may be used as an alternative or complementary method to fossil dating. I demonstrate how a time-stratified biogeographic stochastic process may be used to estimate absolute divergence times by conditioning on dated paleogeographical events. Informed by the current paleogeographical literature, I construct an empirical dispersal graph using 25 areas and 26 epochs for the past 540 Ma of Earth's history. Simulations indicate biogeographic dating performs well so long as paleogeography imposes constraint on biogeographic character evolution. To gauge whether biogeographic dating may be of practical use, I analyzed the well-studied turtle clade (Testudines) to assess how well biogeographic dating fares when compared to fossil-calibrated dating estimates reported in the literature. Fossil-free biogeographic dating estimated the age of the most recent common ancestor of extant turtles to be from the Late Triassic, which is consistent with fossil-based estimates. Dating precision improves further when including a root node fossil calibration. The described model, paleogeographical dispersal graph, and analysis scripts are available for use with RevBayes. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Potential for bias and low precision in molecular divergence time estimation of the Canopy of Life: an example from aquatic bird families

PubMed Central

van Tuinen, Marcel; Torres, Christopher R.

2015-01-01

Uncertainty in divergence time estimation is frequently studied from many angles but rarely from the perspective of phylogenetic node age. If appropriate molecular models and fossil priors are used, a multi-locus, partitioned analysis is expected to equally minimize error in accuracy and precision across all nodes of a given phylogeny. In contrast, if available models fail to completely account for rate heterogeneity, substitution saturation and incompleteness of the fossil record, uncertainty in divergence time estimation may increase with node age. While many studies have stressed this concern with regard to deep nodes in the Tree of Life, the inference that molecular divergence time estimation of shallow nodes is less sensitive to erroneous model choice has not been tested explicitly in a Bayesian framework. Because of available divergence time estimation methods that permit fossil priors across any phylogenetic node and the present increase in efficient, cheap collection of species-level genomic data, insight is needed into the performance of divergence time estimation of shallow (<10 MY) nodes. Here, we performed multiple sensitivity analyses in a multi-locus data set of aquatic birds with six fossil constraints. Comparison across divergence time analyses that varied taxon and locus sampling, number and position of fossil constraint and shape of prior distribution showed various insights. Deviation from node ages obtained from a reference analysis was generally highest for the shallowest nodes but determined more by temporal placement than number of fossil constraints. Calibration with only the shallowest nodes significantly underestimated the aquatic bird fossil record, indicating the presence of saturation. Although joint calibration with all six priors yielded ages most consistent with the fossil record, ages of shallow nodes were overestimated. This bias was found in both mtDNA and nDNA regions. Thus, divergence time estimation of shallow nodes may suffer from bias and low precision, even when appropriate fossil priors and best available substitution models are chosen. Much care must be taken to address the possible ramifications of substitution saturation across the entire Tree of Life. PMID:26106406

Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea).

PubMed

Jong, Rienk DE

2017-05-25

Fossil butterflies are extremely rare. Yet, they are the only direct evidence of the first appearance of particular characters and as such, they are crucial for calibrating a molecular clock, from which divergence ages are estimated. In turn, these estimates, in combination with paleogeographic information, are most important in paleobiogeographic considerations. The key issue here is the correct allocation of fossils on the phylogenetic tree from which the molecular clock is calibrated.The allocation of a fossil on a tree should be based on an apomorphic character found in a tree based on extant species, similar to the allocation of a new extant species. In practice, the latter is not done, at least not explicitly, on the basis of apomorphy, but rather on overall similarity or on a phylogenetic analysis, which is not possible for most butterfly fossils since they usually are very fragmentary. Characters most often preserved are in the venation of the wings. Therefore, special attention is given to possible apomorphies in venational characters in extant butterflies. For estimation of divergence times, not only the correct allocation of the fossil on the tree is important, but also the tree itself influences the outcome as well as the correct determination of the age of the fossil. These three aspects are discussed.        All known butterfly fossils, consisting of 49 taxa, are critically reviewed and their relationship to extant taxa is discussed as an aid for correctly calibrating a molecular clock for papilionoid Lepidoptera. In this context some aspects of age estimation and biogeographic conclusions are briefly mentioned in review. Specific information has been summarized in four appendices.

Notes on the birth-death prior with fossil calibrations for Bayesian estimation of species divergence times.

PubMed

Dos Reis, Mario

2016-07-19

Constructing a multi-dimensional prior on the times of divergence (the node ages) of species in a phylogeny is not a trivial task, in particular, if the prior density is the result of combining different sources of information such as a speciation process with fossil calibration densities. Yang & Rannala (2006 Mol. Biol. Evol 23, 212-226. (doi:10.1093/molbev/msj024)) laid out the general approach to combine the birth-death process with arbitrary fossil-based densities to construct a prior on divergence times. They achieved this by calculating the density of node ages without calibrations conditioned on the ages of the calibrated nodes. Here, I show that the conditional density obtained by Yang & Rannala is misspecified. The misspecified density can sometimes be quite strange-looking and can lead to unintentionally informative priors on node ages without fossil calibrations. I derive the correct density and provide a few illustrative examples. Calculation of the density involves a sum over a large set of labelled histories, and so obtaining the density in a computer program seems hard at the moment. A general algorithm that may provide a way forward is given.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. © 2016 The Author(s).

A Simple Method for Estimating Informative Node Age Priors for the Fossil Calibration of Molecular Divergence Time Analyses

PubMed Central

Nowak, Michael D.; Smith, Andrew B.; Simpson, Carl; Zwickl, Derrick J.

2013-01-01

Molecular divergence time analyses often rely on the age of fossil lineages to calibrate node age estimates. Most divergence time analyses are now performed in a Bayesian framework, where fossil calibrations are incorporated as parametric prior probabilities on node ages. It is widely accepted that an ideal parameterization of such node age prior probabilities should be based on a comprehensive analysis of the fossil record of the clade of interest, but there is currently no generally applicable approach for calculating such informative priors. We provide here a simple and easily implemented method that employs fossil data to estimate the likely amount of missing history prior to the oldest fossil occurrence of a clade, which can be used to fit an informative parametric prior probability distribution on a node age. Specifically, our method uses the extant diversity and the stratigraphic distribution of fossil lineages confidently assigned to a clade to fit a branching model of lineage diversification. Conditioning this on a simple model of fossil preservation, we estimate the likely amount of missing history prior to the oldest fossil occurrence of a clade. The likelihood surface of missing history can then be translated into a parametric prior probability distribution on the age of the clade of interest. We show that the method performs well with simulated fossil distribution data, but that the likelihood surface of missing history can at times be too complex for the distribution-fitting algorithm employed by our software tool. An empirical example of the application of our method is performed to estimate echinoid node ages. A simulation-based sensitivity analysis using the echinoid data set shows that node age prior distributions estimated under poor preservation rates are significantly less informative than those estimated under high preservation rates. PMID:23755303

Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating.

PubMed

Barba-Montoya, Jose; Dos Reis, Mario; Yang, Ziheng

2017-09-01

Fossil calibrations are the utmost source of information for resolving the distances between molecular sequences into estimates of absolute times and absolute rates in molecular clock dating analysis. The quality of calibrations is thus expected to have a major impact on divergence time estimates even if a huge amount of molecular data is available. In Bayesian molecular clock dating, fossil calibration information is incorporated in the analysis through the prior on divergence times (the time prior). Here, we evaluate three strategies for converting fossil calibrations (in the form of minimum- and maximum-age bounds) into the prior on times, which differ according to whether they borrow information from the maximum age of ancestral nodes and minimum age of descendent nodes to form constraints for any given node on the phylogeny. We study a simple example that is analytically tractable, and analyze two real datasets (one of 10 primate species and another of 48 seed plant species) using three Bayesian dating programs: MCMCTree, MrBayes and BEAST2. We examine how different calibration strategies, the birth-death process, and automatic truncation (to enforce the constraint that ancestral nodes are older than descendent nodes) interact to determine the time prior. In general, truncation has a great impact on calibrations so that the effective priors on the calibration node ages after the truncation can be very different from the user-specified calibration densities. The different strategies for generating the effective prior also had considerable impact, leading to very different marginal effective priors. Arbitrary parameters used to implement minimum-bound calibrations were found to have a strong impact upon the prior and posterior of the divergence times. Our results highlight the importance of inspecting the joint time prior used by the dating program before any Bayesian dating analysis. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

A total-evidence approach to dating with fossils, applied to the early radiation of the hymenoptera.

PubMed

Ronquist, Fredrik; Klopfstein, Seraina; Vilhelmsen, Lars; Schulmeister, Susanne; Murray, Debra L; Rasnitsyn, Alexandr P

2012-12-01

Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4--20 complete) and 68 extant taxa. In both cases we use molecular data from seven markers (∼5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic. [Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.].

A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

PubMed Central

Ronquist, Fredrik; Klopfstein, Seraina; Vilhelmsen, Lars; Schulmeister, Susanne; Murray, Debra L.; Rasnitsyn, Alexandr P.

2012-01-01

Abstract Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4--20 complete) and 68 extant taxa. In both cases we use molecular data from seven markers (∼5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic. [Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.] PMID:22723471

A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects

PubMed Central

Kay, Kathleen M; Whittall, Justen B; Hodges, Scott A

2006-01-01

Background A full understanding of the patterns and processes of biological diversification requires the dating of evolutionary events, yet the fossil record is inadequate for most lineages under study. Alternatively, a molecular clock approach, in which DNA or amino acid substitution rates are calibrated with fossils or geological/climatic events, can provide indirect estimates of clade ages and diversification rates. The utility of this approach depends on the rate constancy of molecular evolution at a genetic locus across time and across lineages. Although the nuclear ribosomal internal transcribed spacer region (nrITS) is increasingly being used to infer clade ages in plants, little is known about the sources or magnitude of variation in its substitution rate. Here, we systematically review the literature to assess substitution rate variation in nrITS among angiosperms, and we evaluate possible correlates of the variation. Results We summarize 28 independently calibrated nrITS substitution rates ranging from 0.38 × 10-9 to 8.34 × 10-9 substitutions/site/yr. We find that herbaceous lineages have substitution rates almost twice as high as woody plants, on average. We do not find any among-lineage phylogenetic constraint to the rates, or any effect of the type of calibration used. Within life history categories, both the magnitude of the rates and the variance among rates tend to decrease with calibration age. Conclusion Angiosperm nrITS substitution rates vary by approximately an order of magnitude, and some of this variation can be attributed to life history categories. We make cautious recommendations for the use of nrITS as an approximate plant molecular clock, including an outline of more appropriate phylogenetic methodology and caveats against over interpretation of results. We also suggest that for lineages with independent calibrations, much of the variation in nrITS substitution rates may come from uncertainty in calibration date estimates, highlighting the importance of accurate and/or multiple calibration dates. PMID:16638138

Evaluation of Sr/Ca-based paleoclimate reconstructions in modern and Medieval Diploria strigosa corals in the northeastern Caribbean

NASA Astrophysics Data System (ADS)

Xu, Y.; Pearson, S. P.; Kilbourne, K.

2013-12-01

Tropical sea surface temperature (SST) has been implicated as a driver of climate changes during the Medieval Climate Anomaly (MCA, 950-1300 A.D.) but little data exists from the tropical oceans during this time period. We collected three modern and seven sub-fossil Diploria strigosa coral colonies from an overwash deposit on Anegada, British Virgin Islands (18.73 °N, 63.33 °W) in order to reconstruct climate in the northeastern Caribbean and Tropical North Atlantic during the MCA. The first step in our reconstruction was to verify the climate signal from this species at this site. We sub-sampled the modern corals along thecal walls with an average sampling resolution of 11-13 samples per year. Sr/Ca ratios measured in the sub-samples were calibrated to temperature using three different calibration techniques (ordinary least squares, reduced major axis, and weighted least squares (WLS)) on the monthly data that includes the seasonal cycles and on the monthly anomaly data. WLS regression accounts for unequal errors in the x and y terms, so we consider it the most robust technique. The WLS regression slope between gridded SST and coral Sr/Ca is similar to the previous two calibrations of this species. Mean Sr/Ca for each of the three modern corals is 8.993 × 0.004 mmol/mol, 9.127 × 0.003 mmol/mol, and 8.960 × 0.007 mmol/mol. These straddle the mean Diploria strigosa Sr/Ca found by Giry et al., (2010), 9.080 mmol/mol, at a site with nearly the same mean SST as Anegada (27.4 °C vs. 27.5 °C). The climatological seasonal cycles for SST derived from the modern corals are statistically indistinguishable from the seasonal cycles in the instrumental SST data. The coral-based seasonal cycles have ranges of 2.70 × 0.31 °C, 2.65 × 0.08 °C and 2.71 × 0.53 °C. These results indicate that this calibration can be applied to our sub-fossil coral data. We applied the WLS calibration to monthly-resolution Sr/Ca data from multiple sub-fossil corals dating to the medieval period with initial U-series dates near the top of the cores ranging from 1277 × 5 A.D. to 1327 × 5 A.D. Initial Sr/Ca results from the first sub-fossil coral have a seasonal range of 2.65 × 0.27 °C when converted to temperature units with our modern calibration, indicating no significant change from modern times. However, the mean Sr/Ca for this coral is very high (9.388 mmol/mol) compared to the modern corals. We explore the potential causes for this discrepancy in our study. Because reconstructing the mean SST during the Medieval Climate Anomaly may be difficult without temporal overlap with modern corals, our focus is on interannual variability. The coral Sr/Ca based monthly SST anomalies for both modern and sub-fossil corals have larger interannual variances than the instrumental record. One explanation for this is that the SSTs derived from sub-fossil corals are local data for which one expects larger variances than the instrumental data averaged over a 2 x 2 ° grid. This species shows great promise for future paleoclimate reconstructions.

Phylogenetic analysis of molecular and morphological data highlights uncertainty in the relationships of fossil and living species of Elopomorpha (Actinopterygii: Teleostei).

PubMed

Dornburg, Alex; Friedman, Matt; Near, Thomas J

2015-08-01

Elopomorpha is one of the three main clades of living teleost fishes and includes a range of disparate lineages including eels, tarpons, bonefishes, and halosaurs. Elopomorphs were among the first groups of fishes investigated using Hennigian phylogenetic methods and continue to be the object of intense phylogenetic scrutiny due to their economic significance, diversity, and crucial evolutionary status as the sister group of all other teleosts. While portions of the phylogenetic backbone for Elopomorpha are consistent between studies, the relationships among Albula, Pterothrissus, Notacanthiformes, and Anguilliformes remain contentious and difficult to evaluate. This lack of phylogenetic resolution is problematic as fossil lineages are often described and placed taxonomically based on an assumed sister group relationship between Albula and Pterothrissus. In addition, phylogenetic studies using morphological data that sample elopomorph fossil lineages often do not include notacanthiform or anguilliform lineages, potentially introducing a bias toward interpreting fossils as members of the common stem of Pterothrissus and Albula. Here we provide a phylogenetic analysis of DNA sequences sampled from multiple nuclear genes that include representative taxa from Albula, Pterothrissus, Notacanthiformes and Anguilliformes. We integrate our molecular dataset with a morphological character matrix that spans both living and fossil elopomorph lineages. Our results reveal substantial uncertainty in the placement of Pterothrissus as well as all sampled fossil lineages, questioning the stability of the taxonomy of fossil Elopomorpha. However, despite topological uncertainty, our integration of fossil lineages into a Bayesian time calibrated framework provides divergence time estimates for the clade that are consistent with previously published age estimates based on the elopomorph fossil record and molecular estimates resulting from traditional node-dating methods. Copyright © 2015 Elsevier Inc. All rights reserved.

A rich fossil record yields calibrated phylogeny for Acanthaceae (Lamiales) and evidence for marked biases in timing and directionality of intercontinental disjunctions.

PubMed

Tripp, Erin A; McDade, Lucinda A

2014-09-01

More than a decade of phylogenetic research has yielded a well-sampled, strongly supported hypothesis of relationships within the large ( > 4000 species) plant family Acanthaceae. This hypothesis points to intriguing biogeographic patterns and asymmetries in sister clade diversity but, absent a time-calibrated estimate for this evolutionary history, these patterns have remained unexplored. Here, we reconstruct divergence times within Acanthaceae using fossils as calibration points and experimenting with both fossil selection and effects of invoking a maximum age prior related to the origin of Eudicots. Contrary to earlier reports of a paucity of fossils of Lamiales (an order of ∼ 23,000 species that includes Acanthaceae) and to the expectation that a largely herbaceous to soft-wooded and tropical lineage would have few fossils, we recovered 51 reports of fossil Acanthaceae. Rigorous evaluation of these for accurate identification, quality of age assessment and utility in dating yielded eight fossils judged to merit inclusion in analyses. With nearly 10 kb of DNA sequence data, we used two sets of fossils as constraints to reconstruct divergence times. We demonstrate differences in age estimates depending on fossil selection and that enforcement of maximum age priors substantially alters estimated clade ages, especially in analyses that utilize a smaller rather than larger set of fossils. Our results suggest that long-distance dispersal events explain present-day distributions better than do Gondwanan or northern land bridge hypotheses. This biogeographical conclusion is for the most part robust to alternative calibration schemes. Our data support a minimum of 13 Old World (OW) to New World (NW) dispersal events but, intriguingly, only one in the reverse direction. Eleven of these 13 were among Acanthaceae s.s., which comprises > 90% of species diversity in the family. Remarkably, if minimum age estimates approximate true history, these 11 events occurred within the last ∼ 20 myr even though Acanthaceae s.s is over 3 times as old. A simulation study confirmed that these dispersal events were significantly skewed toward the present and not simply a chance occurrence. Finally, we review reports of fossils that have been assigned to Acanthaceae that are substantially older than the lower Cretaceous estimate for Angiosperms as a whole (i.e., the general consensus that has resulted from several recent dating and fossil-based studies in plants). This is the first study to reconstruct divergence times among clades of Acanthaceae and sets the stage for comparative evolutionary research in this and related families that have until now been thought to have extremely poor fossil resources. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders.

PubMed

Wood, Hannah Marie; Matzke, Nicholas J; Gillespie, Rosemary G; Griswold, Charles E

2013-03-01

Incorporation of fossils into biogeographic studies can have a profound effect on the conclusions that result, particularly when fossil ranges are nonoverlapping with extant ranges. This is the case in archaeid spiders, where there are known fossils from the Northern Hemisphere, yet all living members are restricted to the Southern Hemisphere. To better understand the biogeographic patterns of archaeid spiders and their palpimanoid relatives, we estimate a dated phylogeny using a relaxed clock on a combined molecular and morphological data set. Dating information is compared with treating the archaeid fossil taxa as both node calibrations and as noncontemporaneous terminal tips, both with and without additional calibration points. Estimation of ancestral biogeographic ranges is then performed, using likelihood and Bayesian methods to take into account uncertainty in phylogeny and in dating. We find that treating the fossils as terminal tips within a Bayesian framework, as opposed to dating the phylogeny based only on molecular data with the dates coming from node calibrations, removes the subjectivity involved in assigning priors, which has not been possible with previous methods. Our analyses suggest that the diversification of the northern and southern archaeid lineages was congruent with the breakup of Pangaea into Laurasia and Gondwanaland. This analysis provides a rare example, and perhaps the most strongly supported, where a dated phylogeny confirms a biogeographical hypothesis based on vicariance due to the breakup of the ancient continental plates.

Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes.

PubMed

Pozzi, Luca; Hodgson, Jason A; Burrell, Andrew S; Sterner, Kirstin N; Raaum, Ryan L; Disotell, Todd R

2014-06-01

The origins and the divergence times of the most basal lineages within primates have been difficult to resolve mainly due to the incomplete sampling of early fossil taxa. The main source of contention is related to the discordance between molecular and fossil estimates: while there are no crown primate fossils older than 56Ma, most molecule-based estimates extend the origins of crown primates into the Cretaceous. Here we present a comprehensive mitogenomic study of primates. We assembled 87 mammalian mitochondrial genomes, including 62 primate species representing all the families of the order. We newly sequenced eleven mitochondrial genomes, including eight Old World monkeys and three strepsirrhines. Phylogenetic analyses support a strong topology, confirming the monophyly for all the major primate clades. In contrast to previous mitogenomic studies, the positions of tarsiers and colugos relative to strepsirrhines and anthropoids are well resolved. In order to improve our understanding of how fossil calibrations affect age estimates within primates, we explore the effect of seventeen fossil calibrations across primates and other mammalian groups and we select a subset of calibrations to date our mitogenomic tree. The divergence date estimates of the Strepsirrhine/Haplorhine split support an origin of crown primates in the Late Cretaceous, at around 74Ma. This result supports a short-fuse model of primate origins, whereby relatively little time passed between the origin of the order and the diversification of its major clades. It also suggests that the early primate fossil record is likely poorly sampled. Copyright © 2014 Elsevier Inc. All rights reserved.

Conceptual issues in Bayesian divergence time estimation

PubMed Central

2016-01-01

Bayesian inference of species divergence times is an unusual statistical problem, because the divergence time parameters are not identifiable unless both fossil calibrations and sequence data are available. Commonly used marginal priors on divergence times derived from fossil calibrations may conflict with node order on the phylogenetic tree causing a change in the prior on divergence times for a particular topology. Care should be taken to avoid confusing this effect with changes due to informative sequence data. This effect is illustrated with examples. A topology-consistent prior that preserves the marginal priors is defined and examples are constructed. Conflicts between fossil calibrations and relative branch lengths (based on sequence data) can cause estimates of divergence times that are grossly incorrect, yet have a narrow posterior distribution. An example of this effect is given; it is recommended that overly narrow posterior distributions of divergence times should be carefully scrutinized. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. PMID:27325831

Conceptual issues in Bayesian divergence time estimation.

PubMed

Rannala, Bruce

2016-07-19

Bayesian inference of species divergence times is an unusual statistical problem, because the divergence time parameters are not identifiable unless both fossil calibrations and sequence data are available. Commonly used marginal priors on divergence times derived from fossil calibrations may conflict with node order on the phylogenetic tree causing a change in the prior on divergence times for a particular topology. Care should be taken to avoid confusing this effect with changes due to informative sequence data. This effect is illustrated with examples. A topology-consistent prior that preserves the marginal priors is defined and examples are constructed. Conflicts between fossil calibrations and relative branch lengths (based on sequence data) can cause estimates of divergence times that are grossly incorrect, yet have a narrow posterior distribution. An example of this effect is given; it is recommended that overly narrow posterior distributions of divergence times should be carefully scrutinized.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. © 2016 The Author(s).

Estimating Divergence Dates and Substitution Rates in the Drosophila Phylogeny

PubMed Central

Obbard, Darren J.; Maclennan, John; Kim, Kang-Wook; Rambaut, Andrew; O’Grady, Patrick M.; Jiggins, Francis M.

2012-01-01

An absolute timescale for evolution is essential if we are to associate evolutionary phenomena, such as adaptation or speciation, with potential causes, such as geological activity or climatic change. Timescales in most phylogenetic studies use geologically dated fossils or phylogeographic events as calibration points, but more recently, it has also become possible to use experimentally derived estimates of the mutation rate as a proxy for substitution rates. The large radiation of drosophilid taxa endemic to the Hawaiian islands has provided multiple calibration points for the Drosophila phylogeny, thanks to the "conveyor belt" process by which this archipelago forms and is colonized by species. However, published date estimates for key nodes in the Drosophila phylogeny vary widely, and many are based on simplistic models of colonization and coalescence or on estimates of island age that are not current. In this study, we use new sequence data from seven species of Hawaiian Drosophila to examine a range of explicit coalescent models and estimate substitution rates. We use these rates, along with a published experimentally determined mutation rate, to date key events in drosophilid evolution. Surprisingly, our estimate for the date for the most recent common ancestor of the genus Drosophila based on mutation rate (25–40 Ma) is closer to being compatible with independent fossil-derived dates (20–50 Ma) than are most of the Hawaiian-calibration models and also has smaller uncertainty. We find that Hawaiian-calibrated dates are extremely sensitive to model choice and give rise to point estimates that range between 26 and 192 Ma, depending on the details of the model. Potential problems with the Hawaiian calibration may arise from systematic variation in the molecular clock due to the long generation time of Hawaiian Drosophila compared with other Drosophila and/or uncertainty in linking island formation dates with colonization dates. As either source of error will bias estimates of divergence time, we suggest mutation rate estimates be used until better models are available. PMID:22683811

The impact of fossil calibrations, codon positions and relaxed clocks on the divergence time estimates of the native Australian rodents (Conilurini).

PubMed

Nilsson, Maria A; Härlid, Anna; Kullberg, Morgan; Janke, Axel

2010-05-01

The native rodents are the most species-rich placental mammal group on the Australian continent. Fossils of native Australian rodents belonging to the group Conilurini are known from Northern Australia at 4.5Ma. These fossil assemblages already display a rich diversity of rodents, but the exact timing of their arrival on the Australian continent is not yet established. The complete mitochondrial genomes of two native Australian rodents, Leggadina lakedownensis (Lakeland Downs mouse) and Pseudomys chapmani (Western Pebble-mound mouse) were sequenced for investigating their evolutionary history. The molecular data were used for studying the phylogenetic position and divergence times of the Australian rodents, using 12 calibration points and various methods. Phylogenetic analyses place the native Australian rodents as the sister-group to the genus Mus. The Mus-Conilurini calibration point (7.3-11.0Ma) is highly critical for estimating rodent divergence times, while the influence of the different algorithms on estimating divergence times is negligible. The influence of the data type was investigated, indicating that amino acid data are more likely to reflect the correct divergence times than nucleotide sequences. The study on the problems related to estimating divergence times in fast-evolving lineages such as rodents, emphasize the choice of data and calibration points as being critical. Furthermore, it is essential to include accurate calibration points for fast-evolving groups, because the divergence times can otherwise be estimated to be significantly older. The divergence times of the Australian rodents are highly congruent and are estimated to 6.5-7.2Ma, a date that is compatible with their fossil record.

The impact of calibration and clock-model choice on molecular estimates of divergence times.

PubMed

Duchêne, Sebastián; Lanfear, Robert; Ho, Simon Y W

2014-09-01

Phylogenetic estimates of evolutionary timescales can be obtained from nucleotide sequence data using the molecular clock. These estimates are important for our understanding of evolutionary processes across all taxonomic levels. The molecular clock needs to be calibrated with an independent source of information, such as fossil evidence, to allow absolute ages to be inferred. Calibration typically involves fixing or constraining the age of at least one node in the phylogeny, enabling the ages of the remaining nodes to be estimated. We conducted an extensive simulation study to investigate the effects of the position and number of calibrations on the resulting estimate of the timescale. Our analyses focused on Bayesian estimates obtained using relaxed molecular clocks. Our findings suggest that an effective strategy is to include multiple calibrations and to prefer those that are close to the root of the phylogeny. Under these conditions, we found that evolutionary timescales could be estimated accurately even when the relaxed-clock model was misspecified and when the sequence data were relatively uninformative. We tested these findings in a case study of simian foamy virus, where we found that shallow calibrations caused the overall timescale to be underestimated by up to three orders of magnitude. Finally, we provide some recommendations for improving the practice of molecular-clock calibration. Copyright © 2014 Elsevier Inc. All rights reserved.

Nitrogen-Fixing Heterocystous Cyanobacteria in the Tonian Period.

PubMed

Pang, Ke; Tang, Qing; Chen, Lei; Wan, Bin; Niu, Changtai; Yuan, Xunlai; Xiao, Shuhai

2018-02-19

Cyanobacteria were the ultimate ancestor of all plastids and, for much of Earth's history, the only source of biogenic oxygen and a major source of fixed carbon and nitrogen. One cyanobacterial clade, subsections IV+V, is characterized by multicellularity and cell differentiation, with many members bearing specialized nitrogen-fixing (or diazotrophic) heterocysts and encysting akinetes [1-3]. Molecular clock estimates of the divergence time of this clade are highly variable, ranging from ∼2,000 Ma (mega-annum) [4-9] to ∼500 Ma [10]. The older estimates are invariably calibrated by putative akinete fossils from Paleoproterozoic-Mesoproterozoic rocks around 2,100-1,400 Ma [3, 11, 12]. However, the interpretation of these fossils as akinetes has been questioned [13], and the next oldest akinete and heterocyst fossils are ∼410 Ma [14]. Thus, the scarcity of reliable heterocystous cyanobacterial fossils significantly hampers our understanding of the evolution of complex multicellularity among cyanobacteria, their role in regulating geochemical cycles in the geological past, and our ability to calibrate cyanobacterial molecular clocks. Here, we report Tonian (∼1,000-720 Ma) filamentous cyanobacteria that are characterized by large cells, binary fission (for filament elongation), hormogonia (for asexual reproduction and dispersal), probable akinetes (for survival in adverse conditions), and by implication, diazotrophic heterocysts. The new fossils provide a minimum age calibration on the divergence of subsections IV+V and place a firm constraint on the evolution of akinetes and heterocysts. Copyright © 2018 Elsevier Ltd. All rights reserved.

The effects of fossil placement and calibration on divergence times and rates: an example from the termites (Insecta: Isoptera).

PubMed

Ware, Jessica L; Grimaldi, David A; Engel, Michael S

2010-01-01

Among insects, eusocial behavior occurs in termites, ants, some bees and wasps. Isoptera and Hymenoptera convergently share social behavior, and for both taxa its evolution remains poorly understood. While dating analyses provide researchers with the opportunity to date the origin of eusociality, fossil calibration methodology may mislead subsequent ecological interpretations. Using a comprehensive termite dataset, we explored the effect of fossil placement and calibration methodology. A combined molecular and morphological dataset for 42 extant termite lineages was used, and a second dataset including these 42 taxa, plus an additional 39 fossil lineages for which we had only morphological data. MrBayes doublet-model analyses recovered similar topologies, with one minor exception (Stolotermitidae is sister to the Hodotermitidae, s.s., in the 42-taxon analysis but is in a polytomy with Hodotermitidae and (Kalotermitidae + Neoisoptera) in the 81-taxon analysis). Analyses using the r8s program on these topologies were run with either minimum/maximum constraints (analysis a = 42-taxon and analysis c = 81-taxon analyses) or with the fossil taxon ages fixed (ages fixed to be the geological age of the deposit from which they came, analysis b = 81-taxon analysis). Confidence intervals were determined for the resulting ultrametric trees, and for most major clades there was significant overlap between dates recovered for analyses A and C (with exceptions, such as the nodes Neoisoptera, and Euisoptera). With the exception of isopteran and eusiopteran node ages, however, none of the major clade ages overlapped when analysis B is compared with either analysis A or C. Future studies on Dictyoptera should note that the age of Kalotermitidae was underestimated in absence of kalotermitid fossils with fixed ages. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

Improving large-scale groundwater models by considering fossil gradients

NASA Astrophysics Data System (ADS)

Schulz, Stephan; Walther, Marc; Michelsen, Nils; Rausch, Randolf; Dirks, Heiko; Al-Saud, Mohammed; Merz, Ralf; Kolditz, Olaf; Schüth, Christoph

2017-05-01

Due to limited availability of surface water, many arid to semi-arid countries rely on their groundwater resources. Despite the quasi-absence of present day replenishment, some of these groundwater bodies contain large amounts of water, which was recharged during pluvial periods of the Late Pleistocene to Early Holocene. These mostly fossil, non-renewable resources require different management schemes compared to those which are usually applied in renewable systems. Fossil groundwater is a finite resource and its withdrawal implies mining of aquifer storage reserves. Although they receive almost no recharge, some of them show notable hydraulic gradients and a flow towards their discharge areas, even without pumping. As a result, these systems have more discharge than recharge and hence are not in steady state, which makes their modelling, in particular the calibration, very challenging. In this study, we introduce a new calibration approach, composed of four steps: (i) estimating the fossil discharge component, (ii) determining the origin of fossil discharge, (iii) fitting the hydraulic conductivity with a pseudo steady-state model, and (iv) fitting the storage capacity with a transient model by reconstructing head drawdown induced by pumping activities. Finally, we test the relevance of our approach and evaluated the effect of considering or ignoring fossil gradients on aquifer parameterization for the Upper Mega Aquifer (UMA) on the Arabian Peninsula.

The Past Sure is Tense: On Interpreting Phylogenetic Divergence Time Estimates.

PubMed

Brown, Joseph W; Smith, Stephen A

2018-03-01

Divergence time estimation-the calibration of a phylogeny to geological time-is an integral first step in modeling the tempo of biological evolution (traits and lineages). However, despite increasingly sophisticated methods to infer divergence times from molecular genetic sequences, the estimated age of many nodes across the tree of life contrast significantly and consistently with timeframes conveyed by the fossil record. This is perhaps best exemplified by crown angiosperms, where molecular clock (Triassic) estimates predate the oldest (Early Cretaceous) undisputed angiosperm fossils by tens of millions of years or more. While the incompleteness of the fossil record is a common concern, issues of data limitation and model inadequacy are viable (if underexplored) alternative explanations. In this vein, Beaulieu et al. (2015) convincingly demonstrated how methods of divergence time inference can be misled by both (i) extreme state-dependent molecular substitution rate heterogeneity and (ii) biased sampling of representative major lineages. These results demonstrate the impact of (potentially common) model violations. Here, we suggest another potential challenge: that the configuration of the statistical inference problem (i.e., the parameters, their relationships, and associated priors) alone may preclude the reconstruction of the paleontological timeframe for the crown age of angiosperms. We demonstrate, through sampling from the joint prior (formed by combining the tree (diversification) prior with the calibration densities specified for fossil-calibrated nodes) that with no data present at all, that an Early Cretaceous crown angiosperms is rejected (i.e., has essentially zero probability). More worrisome, however, is that for the 24 nodes calibrated by fossils, almost all have indistinguishable marginal prior and posterior age distributions when employing routine lognormal fossil calibration priors. These results indicate that there is inadequate information in the data to over-rule the joint prior. Given that these calibrated nodes are strategically placed in disparate regions of the tree, they act to anchor the tree scaffold, and so the posterior inference for the tree as a whole is largely determined by the pseudodata present in the (often arbitrary) calibration densities. We recommend, as for any Bayesian analysis, that marginal prior and posterior distributions be carefully compared to determine whether signal is coming from the data or prior belief, especially for parameters of direct interest. This recommendation is not novel. However, given how rarely such checks are carried out in evolutionary biology, it bears repeating. Our results demonstrate the fundamental importance of prior/posterior comparisons in any Bayesian analysis, and we hope that they further encourage both researchers and journals to consistently adopt this crucial step as standard practice. Finally, we note that the results presented here do not refute the biological modeling concerns identified by Beaulieu et al. (2015). Both sets of issues remain apposite to the goals of accurate divergence time estimation, and only by considering them in tandem can we move forward more confidently.

Divergence times in the termite genus Macrotermes (Isoptera: Termitidae).

PubMed

Brandl, R; Hyodo, F; Korff-Schmising, M von; Maekawa, K; Miura, T; Takematsu, Y; Matsumoto, T; Abe, T; Bagine, R; Kaib, M

2007-10-01

The evolution of fungus-growing termites is supposed to have started in the African rain forests with multiple invasions of semi-arid habitats as well as multiple invasions of the Oriental region. We used sequences of the mitochondrial COII gene and Bayesian dating to investigate the time frame of the evolution of Macrotermes, an important genus of fungus-growing termites. We found that the genus Macrotermes consists of at least 6 distantly related clades. Furthermore, the COII sequences suggested some cryptic diversity within the analysed African Macrotermes species. The dates calculated with the COII data using a fossilized termite mound to calibrate the clock were in good agreement with dates calculated with COI sequences using the split between Locusta and Chortippus as calibration point which supports the consistency of the calibration points. The clades from the Oriental region dated back to the early Tertiary. These estimates of divergence times suggested that Macrotermes invaded Asia during periods with humid climates. For Africa, many speciation events predated the Pleistocene and fall in range of 6-23 million years ago. These estimates suggest that savannah-adapted African clades radiated with the spread of the semi-arid ecosystems during the Miocene. Apparently, events during the Pleistocene were of little importance for speciation within the genus Macrotermes. However, further investigations are necessary to increase the number of taxa for phylogenetic analysis.

Cretaceous biostratigraphy in the Wyoming thrust belt

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nichols, D.J.; Jacobson, S.R.

Biostratigraphy is essential to exploration for oil and gas in the Wyoming thrust belt because fossils provide a temporal framework for interpretation of events of faulting, erosion, sedimentation, and the development of hydrocarbon traps and migration pathways. In the Cretaceous section, fossils are especially useful for dating and correlating repetitive facies of different ages in structurally complex terrain. The biostratigraphic zonation for the region is based on megafossils (chiefly ammonites), which permit accurate dating and correlation of outcrop sections, and which have been calibrated with the radiometric time scale for the Western Interior. Molluscan and vertebrate zone fossils are difficultmore » to obtain from the subsurface, however, and ammonities are restricted to rocks of margin origin. Palynomorphs (plant microfossils) have proven to be the most valuable fossils in investigations of stratigraphy and structures in the subsurface of the thrust belt because palynomorphs can be recovered from drill cuttings. Palynomorphs also are found in both marine and nonmarine rocks and can be used for correlation between facies. In this paper, stratigraphic ranges of selected Cretaceous marine and nonmarine palynomorphs in previously designated reference sections in Fossil Basin, Wyoming, are correlated with the occurrence of ammonities and other zone fossils in the same sections. These correlations can be related to known isotopic ages, and they contribute to the calibration of palynomorph ranges in the Cretaceous of the Western Interior.« less

A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves).

PubMed

Stein, R Will; Brown, Joseph W; Mooers, Arne Ø

2015-11-01

The phylogeny of Galliformes (landfowl) has been studied extensively; however, the associated chronologies have been criticized recently due to misplaced or misidentified fossil calibrations. As a consequence, it is unclear whether any crown-group lineages arose in the Cretaceous and survived the Cretaceous-Paleogene (K-Pg; 65.5 Ma) mass extinction. Using Bayesian phylogenetic inference on an alignment spanning 14,539 bp of mitochondrial and nuclear DNA sequence data, four fossil calibrations, and a combination of uncorrelated lognormally distributed relaxed-clock and strict-clock models, we inferred a time-calibrated molecular phylogeny for 225 of the 291 extant Galliform taxa. These analyses suggest that crown Galliformes diversified in the Cretaceous and that three-stem lineages survived the K-Pg mass extinction. Ideally, characterizing the tempo and mode of diversification involves a taxonomically complete phylogenetic hypothesis. We used simple constraint structures to incorporate 66 data-deficient taxa and inferred the first taxon-complete phylogenetic hypothesis for the Galliformes. Diversification analyses conducted on 10,000 timetrees sampled from the posterior distribution of candidate trees show that the evolutionary history of the Galliformes is best explained by a rate-shift model including 1-3 clade-specific increases in diversification rate. We further show that the tempo and mode of diversification in the Galliformes conforms to a three-pulse model, with three-stem lineages arising in the Cretaceous and inter and intrafamilial diversification occurring after the K-Pg mass extinction, in the Paleocene-Eocene (65.5-33.9 Ma) or in association with the Eocene-Oligocene transition (33.9 Ma). Copyright © 2015 Elsevier Inc. All rights reserved.

Eocene diversification of crown group rails (Aves: Gruiformes: Rallidae).

PubMed

García-R, Juan C; Gibb, Gillian C; Trewick, Steve A

2014-01-01

Central to our understanding of the timing of bird evolution is debate about an apparent conflict between fossil and molecular data. A deep age for higher level taxa within Neoaves is evident from molecular analyses but much remains to be learned about the age of diversification in modern bird families and their evolutionary ecology. In order to better understand the timing and pattern of diversification within the family Rallidae we used a relaxed molecular clock, fossil calibrations, and complete mitochondrial genomes from a range of rallid species analysed in a Bayesian framework. The estimated time of origin of Rallidae is Eocene, about 40.5 Mya, with evidence of intrafamiliar diversification from the Late Eocene to the Miocene. This timing is older than previously suggested for crown group Rallidae, but fossil calibrations, extent of taxon sampling and substantial sequence data give it credence. We note that fossils of Eocene age tentatively assigned to Rallidae are consistent with our findings. Compared to available studies of other bird lineages, the rail clade is old and supports an inference of deep ancestry of ground-dwelling habits among Neoaves.

Using more than the oldest fossils: dating osmundaceae with three Bayesian clock approaches.

PubMed

Grimm, Guido W; Kapli, Paschalia; Bomfleur, Benjamin; McLoughlin, Stephen; Renner, Susanne S

2015-05-01

A major concern in molecular clock dating is how to use information from the fossil record to calibrate genetic distances from DNA sequences. Here we apply three Bayesian dating methods that differ in how calibration is achieved-"node dating" (ND) in BEAST, "total evidence" (TE) dating in MrBayes, and the "fossilized birth-death" (FBD) in FDPPDiv-to infer divergence times in the royal ferns. Osmundaceae have 16-17 species in four genera, two mainly in the Northern Hemisphere and two in South Africa and Australasia; they are the sister clade to the remaining leptosporangiate ferns. Their fossil record consists of at least 150 species in ∼17 genera. For ND, we used the five oldest fossils, whereas for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils, we included up to 36 rhizomes and frond compression/impression fossils, which for TE dating were scored for 33 morphological characters. We also subsampled 10%, 25%, and 50% of the 36 fossils to assess model sensitivity. FBD-derived divergence ages were generally greater than those inferred from ND; two of seven TE-derived ages agreed with FBD-obtained ages, the others were much younger or much older than ND or FBD ages. We prefer the FBD-derived ages because they best fit the Osmundales fossil record (including Triassic fossils not used in our study). Under the preferred model, the clade encompassing extant Osmundaceae (and many fossils) dates to the latest Paleozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, the FBD approach yielded speciation and extinction rates that overlapped those obtained from just neontological data. However, FBD estimates of speciation and extinction are sensitive to violations in the assumption of continuous fossil sampling; therefore, these estimates should be treated with caution. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale.

PubMed

Foster, Charles S P; Sauquet, Hervê; van der Merwe, Marlien; McPherson, Hannah; Rossetto, Maurizio; Ho, Simon Y W

2017-05-01

The evolutionary timescale of angiosperms has long been a key question in biology. Molecular estimates of this timescale have shown considerable variation, being influenced by differences in taxon sampling, gene sampling, fossil calibrations, evolutionary models, and choices of priors. Here, we analyze a data set comprising 76 protein-coding genes from the chloroplast genomes of 195 taxa spanning 86 families, including novel genome sequences for 11 taxa, to evaluate the impact of models, priors, and gene sampling on Bayesian estimates of the angiosperm evolutionary timescale. Using a Bayesian relaxed molecular-clock method, with a core set of 35 minimum and two maximum fossil constraints, we estimated that crown angiosperms arose 221 (251-192) Ma during the Triassic. Based on a range of additional sensitivity and subsampling analyses, we found that our date estimates were generally robust to large changes in the parameters of the birth-death tree prior and of the model of rate variation across branches. We found an exception to this when we implemented fossil calibrations in the form of highly informative gamma priors rather than as uniform priors on node ages. Under all other calibration schemes, including trials of seven maximum age constraints, we consistently found that the earliest divergences of angiosperm clades substantially predate the oldest fossils that can be assigned unequivocally to their crown group. Overall, our results and experiments with genome-scale data suggest that reliable estimates of the angiosperm crown age will require increased taxon sampling, significant methodological changes, and new information from the fossil record. [Angiospermae, chloroplast, genome, molecular dating, Triassic.]. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Phylogenetic Analysis of Pelecaniformes (Aves) Based on Osteological Data: Implications for Waterbird Phylogeny and Fossil Calibration Studies

PubMed Central

Smith, Nathan D.

2010-01-01

Background Debate regarding the monophyly and relationships of the avian order Pelecaniformes represents a classic example of discord between morphological and molecular estimates of phylogeny. This lack of consensus hampers interpretation of the group's fossil record, which has major implications for understanding patterns of character evolution (e.g., the evolution of wing-propelled diving) and temporal diversification (e.g., the origins of modern families). Relationships of the Pelecaniformes were inferred through parsimony analyses of an osteological dataset encompassing 59 taxa and 464 characters. The relationships of the Plotopteridae, an extinct family of wing-propelled divers, and several other fossil pelecaniforms (Limnofregata, Prophaethon, Lithoptila, ?Borvocarbo stoeffelensis) were also assessed. The antiquity of these taxa and their purported status as stem members of extant families makes them valuable for studies of higher-level avian diversification. Methodology/Principal Findings Pelecaniform monophyly is not recovered, with Phaethontidae recovered as distantly related to all other pelecaniforms, which are supported as a monophyletic Steganopodes. Some anatomical partitions of the dataset possess different phylogenetic signals, and partitioned analyses reveal that these discrepancies are localized outside of Steganopodes, and primarily due to a few labile taxa. The Plotopteridae are recovered as the sister taxon to Phalacrocoracoidea, and the relationships of other fossil pelecaniforms representing key calibration points are well supported, including Limnofregata (sister taxon to Fregatidae), Prophaethon and Lithoptila (successive sister taxa to Phaethontidae), and ?Borvocarbo stoeffelensis (sister taxon to Phalacrocoracidae). These relationships are invariant when ‘backbone’ constraints based on recent avian phylogenies are imposed. Conclusions/Significance Relationships of extant pelecaniforms inferred from morphology are more congruent with molecular phylogenies than previously assumed, though notable conflicts remain. The phylogenetic position of the Plotopteridae implies that wing-propelled diving evolved independently in plotopterids and penguins, representing a remarkable case of convergent evolution. Despite robust support for the placement of fossil taxa representing key calibration points, the successive outgroup relationships of several “stem fossil + crown family” clades are variable and poorly supported across recent studies of avian phylogeny. Thus, the impact these fossils have on inferred patterns of temporal diversification depends heavily on the resolution of deep nodes in avian phylogeny. PMID:20976229

The geological record and phylogeny of spider wasps (Hymenoptera: Pompilidae): A revision of fossil species and their phylogenetic placement.

PubMed

Rodriguez, Juanita; Waichert, Cecilia; von Dohlen, Carol D; Pitts, James P

2017-01-01

Accurate fossil identification has become increasingly relevant with the widespread use of phylogenetic divergence time estimation methods, which rely on fossil data to determine clade hard-minimum ages. Here we revise, diagnose and illustrate known spider wasp (Hymenoptera: Pompilidae) fossil species and place them within the latest Pompilidae phylogenetic hypothesis. Ceropalites infelix Cockerell, from the Florissant Fossil Beds (Priabonian), is no longer recognized as Pompilidae, but as Aulacidae. Agenioideus saxigenus (Cockerell) comb. nov., Deuteragenia wettweri (Statz) comb. nov., Caputelus scudderi (Cockerell, 1906) comb. nov., Pepsinites avitula (Cockerell, 1941) comb. nov., Pepsinites contentus (Theobald, 1937) comb. nov., Pepsinites florissantensis (Cockerell, 1906) comb. nov., Pepsinites laminarum (Rohwer, 1909) comb. nov., Pepsinites scelerosus (Meunier, 1919) comb. nov., Pepsinites cockerellae (Rohwer, 1909) comb. nov., Pompilinites coquandi (Theobald, 1937) comb. nov., Pompilinites depressus (Statz, 1936) comb. nov., Pompilites incertus (Theobald, 1937) comb. nov., Pompilites induratus (Heer, 1849) comb. nov., Pompilites fasciatus (Theobald, 1937) comb. nov., and Pompilites senex comb. nov. are new combinations. Twenty-three fossil species of spider wasps are now recognized in 13 genera. Four new genera are proposed: Caputelus Waichert & Pitts gen. nov., Pompilites Rodriguez gen. nov., Pompilinites Rodriguez & Waichert gen. nov., and Pepsinites Rodriguez & Waichert gen. nov., of which the three latter are collective-group names for fossils with taxonomic uncertainty. One species of fossil spider wasp is described: Deuteragenia catalunyia Rodriguez, Waichert & Pitts sp. nov., from the Bellver deposits in Catalonia, Spain. Five of the 23 known species can be used to determine hard-minimum age for calibrations of genera stem-groups (Agenioideus, Anoplius, Cryptocheilus, Deuteragenia, Priocnemis). The fossil belonging to the stem-group of the tribe Ageniellini (Chubutholites) is not recommended for calibration because of the high uncertainty in its age and taxonomy. The remaining taxa can be assigned to the lineage comprising Pompilinae + Pepsinae (12 species) or crown-group Pompilidae (four species).

The geological record and phylogeny of spider wasps (Hymenoptera: Pompilidae): A revision of fossil species and their phylogenetic placement

PubMed Central

Waichert, Cecilia; von Dohlen, Carol D.; Pitts, James P.

2017-01-01

Accurate fossil identification has become increasingly relevant with the widespread use of phylogenetic divergence time estimation methods, which rely on fossil data to determine clade hard-minimum ages. Here we revise, diagnose and illustrate known spider wasp (Hymenoptera: Pompilidae) fossil species and place them within the latest Pompilidae phylogenetic hypothesis. Ceropalites infelix Cockerell, from the Florissant Fossil Beds (Priabonian), is no longer recognized as Pompilidae, but as Aulacidae. Agenioideus saxigenus (Cockerell) comb. nov., Deuteragenia wettweri (Statz) comb. nov., Caputelus scudderi (Cockerell, 1906) comb. nov., Pepsinites avitula (Cockerell, 1941) comb. nov., Pepsinites contentus (Theobald, 1937) comb. nov., Pepsinites florissantensis (Cockerell, 1906) comb. nov., Pepsinites laminarum (Rohwer, 1909) comb. nov., Pepsinites scelerosus (Meunier, 1919) comb. nov., Pepsinites cockerellae (Rohwer, 1909) comb. nov., Pompilinites coquandi (Theobald, 1937) comb. nov., Pompilinites depressus (Statz, 1936) comb. nov., Pompilites incertus (Theobald, 1937) comb. nov., Pompilites induratus (Heer, 1849) comb. nov., Pompilites fasciatus (Theobald, 1937) comb. nov., and Pompilites senex comb. nov. are new combinations. Twenty-three fossil species of spider wasps are now recognized in 13 genera. Four new genera are proposed: Caputelus Waichert & Pitts gen. nov., Pompilites Rodriguez gen. nov., Pompilinites Rodriguez & Waichert gen. nov., and Pepsinites Rodriguez & Waichert gen. nov., of which the three latter are collective-group names for fossils with taxonomic uncertainty. One species of fossil spider wasp is described: Deuteragenia catalunyia Rodriguez, Waichert & Pitts sp. nov., from the Bellver deposits in Catalonia, Spain. Five of the 23 known species can be used to determine hard-minimum age for calibrations of genera stem-groups (Agenioideus, Anoplius, Cryptocheilus, Deuteragenia, Priocnemis). The fossil belonging to the stem-group of the tribe Ageniellini (Chubutholites) is not recommended for calibration because of the high uncertainty in its age and taxonomy. The remaining taxa can be assigned to the lineage comprising Pompilinae + Pepsinae (12 species) or crown-group Pompilidae (four species). PMID:29020022

Molecules and fossils reveal punctuated diversification in Caribbean “faviid” corals

PubMed Central

2012-01-01

Background Even with well-known sampling biases, the fossil record is key to understanding macro-evolutionary patterns. During the Miocene to Pleistocene in the Caribbean Sea, the fossil record of scleractinian corals shows a remarkable period of rapid diversification followed by massive extinction. Here we combine a time-calibrated molecular phylogeny based on three nuclear introns with an updated fossil stratigraphy to examine patterns of radiation and extinction in Caribbean corals within the traditional family Faviidae. Results Concatenated phylogenetic analysis showed most species of Caribbean faviids were monophyletic, with the exception of two Manicina species. The time-calibrated tree revealed the stem group originated around the closure of the Tethys Sea (17.0 Ma), while the genus Manicina diversified during the Late Miocene (8.20 Ma), when increased sedimentation and productivity may have favored free-living, heterotrophic species. Reef and shallow water specialists, represented by Diploria and Favia, originate at the beginning of the Pliocene (5 – 6 Ma) as the Isthmus of Panama shoaled and regional productivity declined. Conclusions Later origination of the stem group than predicted from the fossil record corroborates the hypothesis of morphological convergence in Diploria and Favia genera. Our data support the rapid evolution of morphological and life-history traits among faviid corals that can be linked to Mio-Pliocene environmental changes. PMID:22831179

When did anoles diverge? An analysis of multiple dating strategies.

PubMed

Román-Palacios, Cristian; Tavera, Jose; Del Rosario Castañeda, María

2018-06-12

Whereas most of the studies that discuss the evolutionary divergence of Anolis lizards have dated the clade's crown group in between 31-64 Ma, a single study has recovered a significantly older age for the same node (87 Ma). These differences also entail notable consequences on the preferred biogeographical hypothesis for the whole clade. Here we analyze a total of seven dating strategies by combining three calibration sources in independent BEAST runs to infer the most probable divergence timing for anole lizards (a mitochondrial rate for ND2 gene, the Anolis dominicanus fossil, and a group of fossils assigned to the Priscagamines, Iguanines, and Idontosaurus clades). Based on the estimated timing, we also addressed whether chronograms differ the most in deeper or shallower nodes by exploring the trend in the standard deviation of mean ages between chronograms across time. Next, we focus on the pattern for a single shallow node by hypothesizing the biogeography of the island-endemic Malpelo anole (Anolis agassizi), and evaluating the temporal congruence between the species' divergence and the island geology. The estimated set of ages suggests that anoles most likely diverged 72 Ma (71-73 Ma), with the crown group established around 58 Ma (51-65 Ma). Dispersal is therefore supported as the major driver in the biogeography of the group (and in Caribbean lineages in particular). Our analyses also indicated that (1) rate-based analyses pulled dates toward younger ages, (2) the differences in node ages between chronograms decrease towards the tips regardless of the position of the constrained node, and that (3) the estimated age for deep nodes (e.g. Anolis stem) is highly influenced when deep nodes are also constrained. The latter two results imply that the estimated age for shallower nodes is largely unaffected by the used temporal constraint. The congruence of all chronograms for the Malpelo anole also support this finding. Anolis agassizi was found to have diverged before the emergence of Malpelo island in each analysis (anole: 19-31 Ma vs. Malpelo island: 16-17 Ma). We recommend when performing absolute dating analyses to first test for sequence saturation in the analyzed dataset (especially when calibrations are based on molecular rates). Our study also points out the importance of using of multiple node constraints, especially when placed deeply in the tree, for fossil-based divergence dating analyses. Copyright © 2018. Published by Elsevier Inc.

Evidence for a recent origin of penguins

PubMed Central

Subramanian, Sankar; Beans-Picón, Gabrielle; Swaminathan, Siva K.; Millar, Craig D.; Lambert, David M.

2013-01-01

Penguins are a remarkable group of birds, with the 18 extant species living in diverse climatic zones from the tropics to Antarctica. The timing of the origin of these extant penguins remains controversial. Previous studies based on DNA sequences and fossil records have suggested widely differing times for the origin of the group. This has given rise to widely differing biogeographic narratives about their evolution. To resolve this problem, we sequenced five introns from 11 species representing all genera of living penguins. Using these data and other available DNA sequences, together with the ages of multiple penguin fossils to calibrate the molecular clock, we estimated the age of the most recent common ancestor of extant penguins to be 20.4 Myr (17.0–23.8 Myr). This time is half of the previous estimates based on molecular sequence data. Our results suggest that most of the major groups of extant penguins diverged 11–16 Ma. This overlaps with the sharp decline in Antarctic temperatures that began approximately 12 Ma, suggesting a possible relationship between climate change and penguin evolution. PMID:24227045

Insect-damaged fossil leaves record food web response to ancient climate change and extinction.

PubMed

Wilf, P

2008-01-01

Plants and herbivorous insects have dominated terrestrial ecosystems for over 300 million years. Uniquely in the fossil record, foliage with well-preserved insect damage offers abundant and diverse information both about producers and about ecological and sometimes taxonomic groups of consumers. These data are ideally suited to investigate food web response to environmental perturbations, and they represent an invaluable deep-time complement to neoecological studies of global change. Correlations between feeding diversity and temperature, between herbivory and leaf traits that are modulated by climate, and between insect diversity and plant diversity can all be investigated in deep time. To illustrate, I emphasize recent work on the time interval from the latest Cretaceous through the middle Eocene (67-47 million years ago (Ma)), including two significant events that affected life: the end-Cretaceous mass extinction (65.5 Ma) and its ensuing recovery; and globally warming temperatures across the Paleocene-Eocene boundary (55.8 Ma). Climatic effects predicted from neoecology generally hold true in these deep-time settings. Rising temperature is associated with increased herbivory in multiple studies, a result with major predictive importance for current global warming. Diverse floras are usually associated with diverse insect damage; however, recovery from the end-Cretaceous extinction reveals uncorrelated plant and insect diversity as food webs rebuilt chaotically from a drastically simplified state. Calibration studies from living forests are needed to improve interpretation of the fossil data.

Dating placentalia: Morphological clocks fail to close the molecular fossil gap.

PubMed

Puttick, Mark N; Thomas, Gavin H; Benton, Michael J

2016-04-01

Dating the origin of Placentalia has been a contentious issue for biologists and paleontologists. Although it is likely that crown-group placentals originated in the Late Cretaceous, nearly all molecular clock estimates point to a deeper Cretaceous origin. An approach with the potential to reconcile this discrepancy could be the application of a morphological clock. This would permit the direct incorporation of fossil data in node dating, and would break long internal branches of the tree, so leading to improved estimates of node ages. Here, we use a large morphological dataset and the tip-calibration approach of MrBayes. We find that the estimated date for the origin of crown mammals is much older, ∼130-145 million years ago (Ma), than fossil and molecular clock data (∼80-90 Ma). Our results suggest that tip calibration may result in estimated dates that are more ancient than those obtained from other sources of data. This can be partially overcome by constraining the ages of internal nodes on the tree; however, when this was applied to our dataset, the estimated dates were still substantially more ancient than expected. We recommend that results obtained using tip calibration, and possibly morphological dating more generally, should be treated with caution. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Dating and biogeographical patterns in the sea slug genus Acanthodoris Gray, 1850 (Mollusca, Gastropoda, Nudibranchia).

PubMed

Hallas, Joshua M; Brian Simison, W; Gosliner, Terrence M

2016-04-01

Recent studies investigating vicariance and dispersal have been focused on correlating major geological events with instances of taxonomic expansion by incorporating the fossil record with molecular clock analyses. However, this approach becomes problematic for soft-bodied organisms that are poorly represented in the fossil record. Here, we estimate the phylogenetic relationships of the nudibranch genus Acanthodoris Gray, 1850 using three molecular markers (16S, COI, H3), and then test two alternative geologically calibrated molecular clock scenarios in BEAST and their effect on ancestral area reconstruction (AAR) estimates employed in LAGRANGE. The global temperate distribution of Acanthodoris spans multiple geological barriers, including the Bering Strait (∼5.32 Mya) and the Baja Peninsula (∼5.5 Mya), both of which are used in our dating estimates. The expansion of the Atlantic Ocean (∼95-105 Mya) is also used to calibrate the relationship between A. falklandica Eliot, 1905 and A. planca Fahey and Valdés, 2005, which are distributed in southern Chile and South Africa respectively. Phylogenetic analyses recovered strong biogeographical signal and recovered two major clades representing northern and southern hemispheric distributions of Acanthodoris. When all three geological events are applied to the calibration analyses, the age for Acanthodoris is estimated to be mid-Cretaceous. When the expansion of the Atlantic Ocean is excluded from our analyses, however, Acanthodoris is estimated to be much younger, with a divergence time estimate during the Miocene. Regardless of divergence estimates, our AAR suggests that Acanthodoris may have origins in the Atlantic Ocean with the Atlantic acting as a dispersal point to the northeastern Pacific. These results suggest that Acanthodoris exhibits a rare instance of western trans-arctic expansion. This study also shows that northeast Pacific specimens of A. pilosa should be regarded as A. atrogriseata and that A. serpentinotus should be regarded as a synonym of A. pina. Copyright © 2016 Elsevier Inc. All rights reserved.

Multiple Threats to Child Health from Fossil Fuel Combustion: Impacts of Air Pollution and Climate Change.

PubMed

Perera, Frederica P

2017-02-01

Approaches to estimating and addressing the risk to children from fossil fuel combustion have been fragmented, tending to focus either on the toxic air emissions or on climate change. Yet developing children, and especially poor children, now bear a disproportionate burden of disease from both environmental pollution and climate change due to fossil fuel combustion. This commentary summarizes the robust scientific evidence regarding the multiple current and projected health impacts of fossil fuel combustion on the young to make the case for a holistic, child-centered energy and climate policy that addresses the full array of physical and psychosocial stressors resulting from fossil fuel pollution. The data summarized here show that by sharply reducing our dependence on fossil fuels we would achieve highly significant health and economic benefits for our children and their future. These benefits would occur immediately and also play out over the life course and potentially across generations. Going beyond the powerful scientific and economic arguments for urgent action to reduce the burning of fossil fuels is the strong moral imperative to protect our most vulnerable populations. Citation: Perera FP. 2017. Multiple threats to child health from fossil fuel combustion: impacts of air pollution and climate change. Environ Health Perspect 125:141-148; http://dx.doi.org/10.1289/EHP299.

Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines).

PubMed

Shaffer, H Bradley; McCartney-Melstad, Evan; Near, Thomas J; Mount, Genevieve G; Spinks, Phillip Q

2017-10-01

Accurate time-calibrated phylogenies are the centerpiece of many macroevolutionary studies, and the relationship between the size and scale of molecular data sets and the density and accuracy of fossil calibrations is a key element of time tree studies. Here, we develop a target capture array specifically for living turtles, compare its efficiency to an ultraconserved element (UCE) dataset, and present a time-calibrated molecular phylogeny based on 539 nuclear loci sequenced from 26 species representing the breadth of living turtle diversity plus outgroups. Our gene array, based on three fully sequenced turtle genomes, is 2.4 times more variable across turtles than a recently published UCE data set for an identical subset of 13 species, confirming that taxon-specific arrays return more informative data per sequencing effort than UCEs. We used our genomic data to estimate the ages of living turtle clades including a mid-late Triassic origin for crown turtles and a mid-Carboniferous split of turtles from their sister group, Archosauria. By specifically excluding several of the earliest potential crown turtle fossils and limiting the age of fossil calibration points to the unambiguous crown lineage Caribemys oxfordiensis from the Late Jurassic (Oxfordian, 163.5-157.3Ma) we corroborate a relatively ancient age for living turtles. We also provide novel age estimates for five of the ten testudine families containing more than a single species, as well as several intrafamilial clades. Most of the diversity of crown turtles appears to date to the Paleogene, well after the Cretaceous-Paleogene mass extinction 66mya. Copyright © 2017 Elsevier Inc. All rights reserved.

Oreopithecus was a bipedal ape after all: Evidence from the iliac cancellous architecture

PubMed Central

Rook, Lorenzo; Bondioli, Luca; Köhler, Meike; Moyà-Solà, Salvador; Macchiarelli, Roberto

1999-01-01

Textural properties and functional morphology of the hip bone cancellous network of Oreopithecus bambolii, a 9- to 7-million-year-old Late Miocene hominoid from Italy, provide insights into the postural and locomotor behavior of this fossil ape. Digital image processing of calibrated hip bone radiographs reveals the occurrence of trabecular features, which, in humans and fossil hominids, are related to vertical support of the body weight, i.e., to bipedality. PMID:10411955

Development and Application of Sr/Ca-δ18O-Sea Surface Temperature calibrations for Last Glacial Maximum-Aged Isopora corals in the Great Barrier Reef

NASA Astrophysics Data System (ADS)

Brenner, L. D.; Linsley, B. K.; Potts, D. C.; Felis, T.; Mcgregor, H. V.; Gagan, M. K.; Inoue, M.; Tudhope, A. W.; Esat, T. M.; Thompson, W. G.; Tiwari, M.; Fallon, S.; Humblet, M.; Yokoyama, Y.; Webster, J.

2016-12-01

Isopora (Acroporidae) are sub-massive to massive corals found on most modern and fossil Indo-Pacific reefs. Despite their abundance, they are largely absent from the paleoceanographic literature but have the potential to provide proxy data where other commonly used corals, such as Porites, are sparse. The retrieval of Isopora fossils during International Ocean Discovery Program Leg 325 in the Great Barrier Reef (GBR) signaled the need to evaluate their possible paleoceanographic utility. We developed modern skeletal Sr/Ca- and δ18O-sea surface temperature (SST) calibrations for six modern Isopora colonies collected at Heron Island in the southern GBR. Pairing the coral Sr/Ca record with monthly SST data yielded Reduced Major Axis Sr/Ca- and δ18O-SST sensitivities of -0.054 mmol/mol/°C and -0.152 ‰/°C, respectively, falling within the range of published Porites values. We applied our Isopora-based regressions and previously published sensitivities from other species to a suite (n=37) of fossil samples collected from IODP 32. The calibrations produced a range of 3-7°C of warming, averaging 5°C, in the GBR from 22 ka to modern climate. This SST change is similar or slightly larger than other coral studies and larger than planktonic foraminifera Mg/Ca records. The planktonic Mg/Ca records from the Indonesian and Western Pacific Warm Pools indicate a warming of 3-3.5°C since 23ka (Linsley et al., 2010) while a fossil coral record from Tahiti indicates a warming of 3.2°C from 9.5ka to present (DeLong et al., 2010) and western Pacific coral records suggest a cooling of 5-6°C (Gagan et al., 2010; Guilderson et al., 1994: Beck et al., 1997), although these value might require rescaling (Gagan et al., 2012) resulting in slightly warmer temperature calculations. Our Isopora fossils from the GBR speak to the spatial heterogeneity of warming since the LGM and the continued need to develop more records for a more comprehensive understanding of the deglaciation.

Multiple Threats to Child Health from Fossil Fuel Combustion: Impacts of Air Pollution and Climate Change

PubMed Central

Perera, Frederica P.

2016-01-01

Background: Approaches to estimating and addressing the risk to children from fossil fuel combustion have been fragmented, tending to focus either on the toxic air emissions or on climate change. Yet developing children, and especially poor children, now bear a disproportionate burden of disease from both environmental pollution and climate change due to fossil fuel combustion. Objective: This commentary summarizes the robust scientific evidence regarding the multiple current and projected health impacts of fossil fuel combustion on the young to make the case for a holistic, child-centered energy and climate policy that addresses the full array of physical and psychosocial stressors resulting from fossil fuel pollution. Discussion: The data summarized here show that by sharply reducing our dependence on fossil fuels we would achieve highly significant health and economic benefits for our children and their future. These benefits would occur immediately and also play out over the life course and potentially across generations. Conclusion: Going beyond the powerful scientific and economic arguments for urgent action to reduce the burning of fossil fuels is the strong moral imperative to protect our most vulnerable populations. Citation: Perera FP. 2017. Multiple threats to child health from fossil fuel combustion: impacts of air pollution and climate change. Environ Health Perspect 125:141–148; http://dx.doi.org/10.1289/EHP299 PMID:27323709

Biofuels, vehicle emissions, and urban air quality.

PubMed

Wallington, Timothy J; Anderson, James E; Kurtz, Eric M; Tennison, Paul J

2016-07-18

Increased biofuel content in automotive fuels impacts vehicle tailpipe emissions via two mechanisms: fuel chemistry and engine calibration. Fuel chemistry effects are generally well recognized, while engine calibration effects are not. It is important that investigations of the impact of biofuels on vehicle emissions consider the impact of engine calibration effects and are conducted using vehicles designed to operate using such fuels. We report the results of emission measurements from a Ford F-350 fueled with either fossil diesel or a biodiesel surrogate (butyl nonanoate) and demonstrate the critical influence of engine calibration on NOx emissions. Using the production calibration the emissions of NOx were higher with the biodiesel fuel. Using an adjusted calibration (maintaining equivalent exhaust oxygen concentration to that of the fossil diesel at the same conditions by adjusting injected fuel quantities) the emissions of NOx were unchanged, or lower, with biodiesel fuel. For ethanol, a review of the literature data addressing the impact of ethanol blend levels (E0-E85) on emissions from gasoline light-duty vehicles in the U.S. is presented. The available data suggest that emissions of NOx, non-methane hydrocarbons, particulate matter (PM), and mobile source air toxics (compounds known, or suspected, to cause serious health impacts) from modern gasoline and diesel vehicles are not adversely affected by increased biofuel content over the range for which the vehicles are designed to operate. Future increases in biofuel content when accomplished in concert with changes in engine design and calibration for new vehicles should not result in problematic increases in emissions impacting urban air quality and may in fact facilitate future required emissions reductions. A systems perspective (fuel and vehicle) is needed to fully understand, and optimize, the benefits of biofuels when blended into gasoline and diesel.

Ceratopetalum (Cunoniaceae) fruits of Australasian affinity from the early Eocene Laguna del Hunco flora, Patagonia, Argentina

PubMed Central

Hermsen, Elizabeth J

2017-01-01

Abstract Background and Aims Radially symmetrical, five-winged fossil fruits from the highly diverse early Eocene Laguna del Hunco flora of Chubut Province, Patagonia, Argentina, are named, described and illustrated. The main goals are to assess the affinities of the fossils and to place them in an evolutionary, palaeoecological and biogeographic context. Methods Specimens of fossil fruits were collected from the Tufolitas Laguna del Hunco. They were prepared, photographed and compared with similar extant and fossil fruits using published literature. Their structure was also evaluated by comparing them with that of modern Ceratopetalum (Cunoniaceae) fruits through examination of herbarium specimens. Key Results The Laguna del Hunco fossil fruits share the diagnostic features that characterize modern and fossil Ceratopetalum (symmetry, number of fruit wings, presence of a conspicuous floral nectary and overall venation pattern). The pattern of the minor wing (sepal) veins observed in the Patagonian fossil fruits is different from that of modern and previously described fossil Ceratopetalum fruits; therefore, a new fossil species is recognized. An apomorphy (absence of petals) suggests that the fossils belong within crown-group Ceratopetalum. Conclusions The Patagonian fossil fruits are the oldest known record for Ceratopetalum. Because the affinities, provenance and age of the fossils are so well established, this new Ceratopetalum fossil species is an excellent candidate for use as a calibration point in divergence dating studies of the family Cunoniaceae. It represents the only record of Ceratopetalum outside Australasia, and further corroborates the biogeographic connection between the Laguna del Hunco flora and ancient and modern floras of the Australasian region. PMID:28110267

The pipid root.

PubMed

Bewick, Adam J; Chain, Frédéric J J; Heled, Joseph; Evans, Ben J

2012-12-01

The estimation of phylogenetic relationships is an essential component of understanding evolution. Accurate phylogenetic estimation is difficult, however, when internodes are short and old, when genealogical discordance is common due to large ancestral effective population sizes or ancestral population structure, and when homoplasy is prevalent. Inference of divergence times is also hampered by unknown and uneven rates of evolution, the incomplete fossil record, uncertainty in relationships between fossil and extant lineages, and uncertainty in the age of fossils. Ideally, these challenges can be overcome by developing large "phylogenomic" data sets and by analyzing them with methods that accommodate features of the evolutionary process, such as genealogical discordance, recurrent substitution, recombination, ancestral population structure, gene flow after speciation among sampled and unsampled taxa, and variation in evolutionary rates. In some phylogenetic problems, it is possible to use information that is independent of fossils, such as the geological record, to identify putative triggers for diversification whose associated estimated divergence times can then be compared a posteriori with estimated relationships and ages of fossils. The history of diversification of pipid frog genera Pipa, Hymenochirus, Silurana, and Xenopus, for instance, is characterized by many of these evolutionary and analytical challenges. These frogs diversified dozens of millions of years ago, they have a relatively rich fossil record, their distributions span continental plates with a well characterized geological record of ancient connectivity, and there is considerable disagreement across studies in estimated evolutionary relationships. We used high throughput sequencing and public databases to generate a large phylogenomic data set with which we estimated evolutionary relationships using multilocus coalescence methods. We collected sequence data from Pipa, Hymenochirus, Silurana, and Xenopus and the outgroup taxon Rhinophrynus dorsalis from coding sequence of 113 autosomal regions, averaging ∼300 bp in length (range: 102-1695 bp) and also a portion of the mitochondrial genome. Analysis of these data using multiple approaches recovers strong support for the ((Xenopus, Silurana)(Pipa, Hymenochirus)) topology, and geologically calibrated divergence time estimates that are consistent with estimated ages and phylogenetic affinities of many fossils. These results provide new insights into the biogeography and chronology of pipid diversification during the breakup of Gondwanaland and illustrate how phylogenomic data may be necessary to tackle tough problems in molecular systematics. [Coalescence; gene tree; high-throughout sequencing; lineage sorting; pipid; species tree; Xenopus.].

Transitional fossils and the origin of turtles

PubMed Central

Lyson, Tyler R.; Bever, Gabe S.; Bhullar, Bhart-Anjan S.; Joyce, Walter G.; Gauthier, Jacques A.

2010-01-01

The origin of turtles is one of the most contentious issues in systematics with three currently viable hypotheses: turtles as the extant sister to (i) the crocodile–bird clade, (ii) the lizard–tuatara clade, or (iii) Diapsida (a clade composed of (i) and (ii)). We reanalysed a recent dataset that allied turtles with the lizard–tuatara clade and found that the inclusion of the stem turtle Proganochelys quenstedti and the ‘parareptile’ Eunotosaurus africanus results in a single overriding morphological signal, with turtles outside Diapsida. This result reflects the importance of transitional fossils when long branches separate crown clades, and highlights unexplored issues such as the role of topological congruence when using fossils to calibrate molecular clocks. PMID:20534602

Passifloraceae seeds from the late Eocene of Colombia.

PubMed

Martínez, Camila

2017-12-01

The plant fossil record for the neotropics is still sparse and temporally discontinuous. The location and description of new fossil material are fundamental for understanding evolutionary and biogeographic patterns of lineages. A new fossil record of Passifloraceae from the late Eocene of Colombia is described in this study. Plant fossils were collected from a new locality from the Eocene Esmeraldas Formation. Eighteen fossil seeds were selected, described, and compared with fossil and extant angiosperm seeds based on the literature and herbarium collections. Taxonomic affinities of the fossil seeds within Passifloraceae s.l. were evaluated by comparing morphological characters of the seeds in a phylogenetic context. Stratigraphic information associated with the fossil locality was used to interpret the environment and taphonomic processes associated with fossil deposition. A new seed fossil genus and species, Passifloroidesperma sogamosense gen. and sp. nov., is described and associated with the subfamily Passifloroideae based on the presence of a foveolate seed surface, ruminate endosperm, and a seed coat with prismatic palisade cells. The depositional environment of the locality is described as a floodplain associated with river channels. A detailed review of the Passifloraceae fossil record indicates that P. sogamosense is the oldest confirmed record of Passifloraceae. Its late Eocene age provides a minimum age that can be used as a calibration point for the crown Passifloroideae node in future dating analyses that together with its neotropical geographic location can shed light on the origin and diversification of the subfamily. © 2017 Botanical Society of America.

The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation

PubMed Central

Roger, Andrew J; Hug, Laura A

2006-01-01

Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes. Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods used and their assumptions. Accurate dating of divergence times among the major eukaryote lineages will require a robust tree of eukaryotes, a much richer Proterozoic fossil record of microbial eukaryotes assignable to extant groups for calibration, more sophisticated relaxed molecular clock methods and many more genes sampled from the full diversity of microbial eukaryotes. PMID:16754613

The first fossil of a bolbitidoid fern belongs to the early-divergent lineages of Elaphoglossum (Dryopteridaceae).

PubMed

Lóriga, Josmaily; Schmidt, Alexander R; Moran, Robbin C; Feldberg, Kathrin; Schneider, Harald; Heinrichs, Jochen

2014-09-01

• Closing gaps in the fossil record and elucidating phylogenetic relationships of mostly incomplete fossils are major challenges in the reconstruction of the diversification of fern lineages through time. The cosmopolitan family Dryopteridaceae represents one of the most species-rich families of leptosporangiate ferns, yet its fossil record is sparse and poorly understood. Here, we describe a fern inclusion in Miocene Dominican amber and investigate its relationships to extant Dryopteridaceae.• The morphology of the fossil was compared with descriptions of extant ferns, resulting in it being tentatively assigned to the bolbitidoid fern genus Elaphoglossum. This assignment was confirmed by reconstructing the evolution of the morphological characters preserved in the inclusion on a molecular phylogeny of 158 extant bolbitidoid ferns. To assess the morphology-based assignment of the fossil to Elaphoglossum, we examined DNA-calibrated divergence time estimates against the age of the amber deposits from which it came.• The fossil belongs to Elaphoglossum and is the first of a bolbitidoid fern. Its assignment to a particular section of Elaphoglossum could not be determined; however, sects. Lepidoglossa, Polytrichia, and Setosa can be discounted because the fossil lacks subulate scales or scales with acicular marginal hairs. Thus, the fossil might belong to either sects. Amygdalifolia, Wrightiana, Elaphoglossum, or Squamipedia or to an extinct lineage.• The discovery of a Miocene Elaphoglossum fossil provides remarkable support to current molecular clock-based estimates of the diversification of these ferns. © 2014 Botanical Society of America, Inc.

Ceratopetalum (Cunoniaceae) fruits of Australasian affinity from the early Eocene Laguna del Hunco flora, Patagonia, Argentina.

PubMed

Gandolfo, María A; Hermsen, Elizabeth J

2017-03-01

Radially symmetrical, five-winged fossil fruits from the highly diverse early Eocene Laguna del Hunco flora of Chubut Province, Patagonia, Argentina, are named, described and illustrated. The main goals are to assess the affinities of the fossils and to place them in an evolutionary, palaeoecological and biogeographic context. Specimens of fossil fruits were collected from the Tufolitas Laguna del Hunco. They were prepared, photographed and compared with similar extant and fossil fruits using published literature. Their structure was also evaluated by comparing them with that of modern Ceratopetalum (Cunoniaceae) fruits through examination of herbarium specimens. The Laguna del Hunco fossil fruits share the diagnostic features that characterize modern and fossil Ceratopetalum (symmetry, number of fruit wings, presence of a conspicuous floral nectary and overall venation pattern). The pattern of the minor wing (sepal) veins observed in the Patagonian fossil fruits is different from that of modern and previously described fossil Ceratopetalum fruits; therefore, a new fossil species is recognized. An apomorphy (absence of petals) suggests that the fossils belong within crown-group Ceratopetalum . The Patagonian fossil fruits are the oldest known record for Ceratopetalum . Because the affinities, provenance and age of the fossils are so well established, this new Ceratopetalum fossil species is an excellent candidate for use as a calibration point in divergence dating studies of the family Cunoniaceae. It represents the only record of Ceratopetalum outside Australasia, and further corroborates the biogeographic connection between the Laguna del Hunco flora and ancient and modern floras of the Australasian region. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company.

Time-calibrated molecular phylogeny of pteropods

PubMed Central

Hörnlein, Christine; Janssen, Arie W.; Hughes, Martin; Bush, Stephanie L.; Marlétaz, Ferdinand; Gasca, Rebeca; Pierrot-Bults, Annelies C.; Michel, Ellinor; Todd, Jonathan A.; Young, Jeremy R.; Osborn, Karen J.; Menken, Steph B. J.

2017-01-01

Pteropods are a widespread group of holoplanktonic gastropod molluscs and are uniquely suitable for study of long-term evolutionary processes in the open ocean because they are the only living metazoan plankton with a good fossil record. Pteropods have been proposed as bioindicators to monitor the impacts of ocean acidification and in consequence have attracted considerable research interest, however, a robust evolutionary framework for the group is still lacking. Here we reconstruct their phylogenetic relationships and examine the evolutionary history of pteropods based on combined analyses of Cytochrome Oxidase I, 28S, and 18S ribosomal rRNA sequences and a molecular clock calibrated using fossils and the estimated timing of the formation of the Isthmus of Panama. Euthecosomes with uncoiled shells were monophyletic with Creseis as the earliest diverging lineage, estimated at 41–38 million years ago (mya). The coiled euthecosomes (Limacina, Heliconoides, Thielea) were not monophyletic contrary to the accepted morphology-based taxonomy; however, due to their high rate heterogeneity no firm conclusions can be drawn. We found strong support for monophyly of most euthecosome genera, but Clio appeared as a polyphyletic group, and Diacavolinia grouped within Cavolinia, making the latter genus paraphyletic. The highest evolutionary rates were observed in Heliconoides inflatus and Limacina bulimoides for both 28S and 18S partitions. Using a fossil-calibrated phylogeny that sets the first occurrence of coiled euthecosomes at 79–66 mya, we estimate that uncoiled euthecosomes evolved 51–42 mya and that most extant uncoiled genera originated 40–15 mya. These findings are congruent with a molecular clock analysis using the Isthmus of Panama formation as an independent calibration. Although not all phylogenetic relationships could be resolved based on three molecular markers, this study provides a useful resource to study pteropod diversity and provides general insight into the processes that generate and maintain their diversity in the open ocean. PMID:28604805

Time-calibrated molecular phylogeny of pteropods.

PubMed

Burridge, Alice K; Hörnlein, Christine; Janssen, Arie W; Hughes, Martin; Bush, Stephanie L; Marlétaz, Ferdinand; Gasca, Rebeca; Pierrot-Bults, Annelies C; Michel, Ellinor; Todd, Jonathan A; Young, Jeremy R; Osborn, Karen J; Menken, Steph B J; Peijnenburg, Katja T C A

2017-01-01

Pteropods are a widespread group of holoplanktonic gastropod molluscs and are uniquely suitable for study of long-term evolutionary processes in the open ocean because they are the only living metazoan plankton with a good fossil record. Pteropods have been proposed as bioindicators to monitor the impacts of ocean acidification and in consequence have attracted considerable research interest, however, a robust evolutionary framework for the group is still lacking. Here we reconstruct their phylogenetic relationships and examine the evolutionary history of pteropods based on combined analyses of Cytochrome Oxidase I, 28S, and 18S ribosomal rRNA sequences and a molecular clock calibrated using fossils and the estimated timing of the formation of the Isthmus of Panama. Euthecosomes with uncoiled shells were monophyletic with Creseis as the earliest diverging lineage, estimated at 41-38 million years ago (mya). The coiled euthecosomes (Limacina, Heliconoides, Thielea) were not monophyletic contrary to the accepted morphology-based taxonomy; however, due to their high rate heterogeneity no firm conclusions can be drawn. We found strong support for monophyly of most euthecosome genera, but Clio appeared as a polyphyletic group, and Diacavolinia grouped within Cavolinia, making the latter genus paraphyletic. The highest evolutionary rates were observed in Heliconoides inflatus and Limacina bulimoides for both 28S and 18S partitions. Using a fossil-calibrated phylogeny that sets the first occurrence of coiled euthecosomes at 79-66 mya, we estimate that uncoiled euthecosomes evolved 51-42 mya and that most extant uncoiled genera originated 40-15 mya. These findings are congruent with a molecular clock analysis using the Isthmus of Panama formation as an independent calibration. Although not all phylogenetic relationships could be resolved based on three molecular markers, this study provides a useful resource to study pteropod diversity and provides general insight into the processes that generate and maintain their diversity in the open ocean.

A revised timescale for human evolution based on ancient mitochondrial genomes

PubMed Central

Johnson, Philip L.F.; Bos, Kirsten; Lari, Martina; Bollongino, Ruth; Sun, Chengkai; Giemsch, Liane; Schmitz, Ralf; Burger, Joachim; Ronchitelli, Anna Maria; Martini, Fabio; Cremonesi, Renata G.; Svoboda, Jiří; Bauer, Peter; Caramelli, David; Castellano, Sergi; Reich, David; Pääbo, Svante; Krause, Johannes

2016-01-01

Summary Background Recent analyses of de novo DNA mutations in modern humans have suggested a nuclear substitution rate that is approximately half that of previous estimates based on fossil calibration. This result has led to suggestions that major events in human evolution occurred far earlier than previously thought. Result Here we use mitochondrial genome sequences from 10 securely dated ancient modern humans spanning 40,000 years as calibration points for the mitochondrial clock, thus yielding a direct estimate of the mitochondrial substitution rate. Our clock yields mitochondrial divergence times that are in agreement with earlier estimates based on calibration points derived from either fossils or archaeological material. In particular, our results imply a separation of non-Africans from the most closely related sub-Saharan African mitochondrial DNAs (haplogroup L3) of less than 62,000-95,000 years ago. Conclusion Though single loci like mitochondrial DNA (mtDNA) can only provide biased estimates of population split times, they can provide valid upper bounds; our results exclude most of the older dates for African and non-African split times recently suggested by de novo mutation rate estimates in the nuclear genome. PMID:23523248

A revised timescale for human evolution based on ancient mitochondrial genomes.

PubMed

Fu, Qiaomei; Mittnik, Alissa; Johnson, Philip L F; Bos, Kirsten; Lari, Martina; Bollongino, Ruth; Sun, Chengkai; Giemsch, Liane; Schmitz, Ralf; Burger, Joachim; Ronchitelli, Anna Maria; Martini, Fabio; Cremonesi, Renata G; Svoboda, Jiří; Bauer, Peter; Caramelli, David; Castellano, Sergi; Reich, David; Pääbo, Svante; Krause, Johannes

2013-04-08

Recent analyses of de novo DNA mutations in modern humans have suggested a nuclear substitution rate that is approximately half that of previous estimates based on fossil calibration. This result has led to suggestions that major events in human evolution occurred far earlier than previously thought. Here, we use mitochondrial genome sequences from ten securely dated ancient modern humans spanning 40,000 years as calibration points for the mitochondrial clock, thus yielding a direct estimate of the mitochondrial substitution rate. Our clock yields mitochondrial divergence times that are in agreement with earlier estimates based on calibration points derived from either fossils or archaeological material. In particular, our results imply a separation of non-Africans from the most closely related sub-Saharan African mitochondrial DNAs (haplogroup L3) that occurred less than 62-95 kya. Though single loci like mitochondrial DNA (mtDNA) can only provide biased estimates of population divergence times, they can provide valid upper bounds. Our results exclude most of the older dates for African and non-African population divergences recently suggested by de novo mutation rate estimates in the nuclear genome. Copyright © 2013 Elsevier Ltd. All rights reserved.

Fossil nutlets of Boraginaceae from the continental Eocene of Hamada of Méridja (southwestern Algeria): The first fossil of the Borage family in Africa.

PubMed

Hammouda, Sid Ahmed; Weigend, Maximilian; Mebrouk, Fateh; Chacón, Juliana; Bensalah, Mustapha; Ensikat, Hans-Jürgen; Adaci, Mohammed

2015-12-01

The Paleogene deposits of the Hamada of Méridja, southwestern Algeria, are currently dated as lower-to-middle Eocene in age based on fossil gastropods and charophytes. Here we report the presence of fruits that can be assigned to the Boraginaceae s.str., apparently representing the first fossil record for this family in Africa, shedding new light on the historical biogeography of this group. Microscopic studies of the fossil nutlets were carried out and compared to extant Boraginaceae nutlets, and to types reported in the literature for this family. The fossils are strikingly similar in general size and morphology, particularly in the finer details of the attachment scar and ornamentation, to nutlets of extant representatives of the Boraginaceae tribe Echiochileae, and especially the genus Ogastemma. We believe that these nutlets represent an extinct member of this lineage. The Ogastemma-like fossils indicate that the Echiochileae, which are most diverse in northern Africa and southwestern Asia, have a long history in this region, dating back to the Eocene. This tribe corresponds to the basal-most clade in Boraginaceae s.str., and the fossils described here agree well with an assumed African origin of the family and the Boraginales I, providing an important additional calibration point for dating the phylogenies of this clade. © 2015 Botanical Society of America.

New Eocene Coleoid (Cephalopoda) Diversity from Statolith Remains: Taxonomic Assignation, Fossil Record Analysis, and New Data for Calibrating Molecular Phylogenies

PubMed Central

Neige, Pascal; Lapierre, Hervé; Merle, Didier

2016-01-01

New coleoid cephalopods are described from statolith remains from the Middle Eocene (Middle Lutetian) of the Paris Basin. Fifteen fossil statoliths are identified and assigned to the Sepiidae (Sepia boletzkyi sp. nov.,? Sepia pira sp. nov.), Loliginidae (Loligo clarkei sp. nov.), and Ommastrephidae (genus indet.) families. The sediments containing these fossils indicate permanent aquatic settings in the infralittoral domain. These sediments range in age from 46 Mya to 43 Mya. Analysis of the fossil record of statoliths (from findings described here, together with a review of previously published data) indicates marked biases in our knowledge. Fossil statoliths are known from as far back as the Early Jurassic (199.3 to 190.8 Mya) but surprisingly, to the best of our knowledge, no record occurs in the Cretaceous. This is a “knowledge bias” and clearly calls for further studies. Finally, we attempt to compare findings described here with fossils previously used to constrain divergence and/or diversification ages of some coleoid subclades in molecular phylogenies. This comparison clearly indicates that the new records detailed here will challenge some estimated divergence times of coleoid cephalopod subclades. PMID:27192490

New Eocene Coleoid (Cephalopoda) Diversity from Statolith Remains: Taxonomic Assignation, Fossil Record Analysis, and New Data for Calibrating Molecular Phylogenies.

PubMed

Neige, Pascal; Lapierre, Hervé; Merle, Didier

2016-01-01

New coleoid cephalopods are described from statolith remains from the Middle Eocene (Middle Lutetian) of the Paris Basin. Fifteen fossil statoliths are identified and assigned to the Sepiidae (Sepia boletzkyi sp. nov.,? Sepia pira sp. nov.), Loliginidae (Loligo clarkei sp. nov.), and Ommastrephidae (genus indet.) families. The sediments containing these fossils indicate permanent aquatic settings in the infralittoral domain. These sediments range in age from 46 Mya to 43 Mya. Analysis of the fossil record of statoliths (from findings described here, together with a review of previously published data) indicates marked biases in our knowledge. Fossil statoliths are known from as far back as the Early Jurassic (199.3 to 190.8 Mya) but surprisingly, to the best of our knowledge, no record occurs in the Cretaceous. This is a "knowledge bias" and clearly calls for further studies. Finally, we attempt to compare findings described here with fossils previously used to constrain divergence and/or diversification ages of some coleoid subclades in molecular phylogenies. This comparison clearly indicates that the new records detailed here will challenge some estimated divergence times of coleoid cephalopod subclades.

Combining fossil and molecular data to date the diversification of New World Primates.

PubMed

Schrago, C G; Mello, B; Soares, A E R

2013-11-01

Recent methodological advances in molecular dating associated with the growing availability of sequence data have prompted the study of the evolution of New World Anthropoidea in recent years. Motivated by questions regarding historical biogeography or the mode of evolution, these works aimed to obtain a clearer scenario of Platyrrhini origins and diversification. Although some consensus was found, disputed issues, especially those relating to the evolutionary affinities of fossil taxa, remain. The use of fossil taxa for divergence time analysis is traditionally restricted to the provision of calibration priors. However, new analytical approaches have been developed that incorporate fossils as terminals and, thus, directly assign ages to the fossil tips. In this study, we conducted a combined analysis of molecular and morphological data, including fossils, to derive the timescale of New World anthropoids. Differently from previous studies that conducted total-evidence analysis of molecules and morphology, our approach investigated the morphological clock alone. Our results corroborate the hypothesis that living platyrrhines diversified in the last 20 Ma and that Miocene Patagonian fossils compose an independent evolutionary radiation that diversified in the late Oligocene. When compared to the node ages inferred from the molecular timescale, the inclusion of fossils augmented the precision of the estimates for nodes constrained by the fossil tips. We show that morphological data can be analysed using the same methodological framework applied in relaxed molecular clock studies. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

The evolution of scarab beetles tracks the sequential rise of angiosperms and mammals

PubMed Central

Ahrens, Dirk; Schwarzer, Julia; Vogler, Alfried P.

2014-01-01

Extant terrestrial biodiversity arguably is driven by the evolutionary success of angiosperm plants, but the evolutionary mechanisms and timescales of angiosperm-dependent radiations remain poorly understood. The Scarabaeoidea is a diverse lineage of predominantly plant- and dung-feeding beetles. Here, we present a phylogenetic analysis of Scarabaeoidea based on four DNA markers for a taxonomically comprehensive set of specimens and link it to recently described fossil evidence. The phylogeny strongly supports multiple origins of coprophagy, phytophagy and anthophagy. The ingroup-based fossil calibration of the tree widely confirmed a Jurassic origin of the Scarabaeoidea crown group. The crown groups of phytophagous lineages began to radiate first (Pleurostict scarabs: 108 Ma; Glaphyridae between 101 Ma), followed by the later diversification of coprophagous lineages (crown-group age Scarabaeinae: 76 Ma; Aphodiinae: 50 Ma). Pollen feeding arose even later, at maximally 62 Ma in the oldest anthophagous lineage. The clear time lag between the origins of herbivores and coprophages suggests an evolutionary path driven by the angiosperms that first favoured the herbivore fauna (mammals and insects) followed by the secondary radiation of the dung feeders. This finding makes it less likely that extant dung beetle lineages initially fed on dinosaur excrements, as often hypothesized. PMID:25100705

Oldest known dinosaurian nesting site and reproductive biology of the Early Jurassic sauropodomorph Massospondylus

PubMed Central

Reisz, Robert R.; Evans, David C.; Roberts, Eric M.; Sues, Hans-Dieter; Yates, Adam M.

2012-01-01

The extensive Early Jurassic continental strata of southern Africa have yielded an exceptional record of dinosaurs that includes scores of partial to complete skeletons of the sauropodomorph Massospondylus, ranging from embryos to large adults. In 1976 an incomplete egg clutch including in ovo embryos of this dinosaur, the oldest known example in the fossil record, was collected from a road-cut talus, but its exact provenance was uncertain. An excavation program at the site started in 2006 has yielded multiple in situ egg clutches, documenting the oldest known dinosaurian nesting site, predating other similar sites by more than 100 million years. The presence of numerous clutches of eggs, some of which contain embryonic remains, in at least four distinct horizons within a small area, provides the earliest known evidence of complex reproductive behavior including site fidelity and colonial nesting in a terrestrial vertebrate. Thus, fossil and sedimentological evidence from this nesting site provides empirical data on reproductive strategies in early dinosaurs. A temporally calibrated optimization of dinosaurian reproductive biology not only demonstrates the primary significance of the Massospondylus nesting site, but also provides additional insights into the initial stages of the evolutionary history of dinosaurs, including evidence that deposition of eggs in a tightly organized single layer in a nest evolved independently from brooding. PMID:22308330

Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution

PubMed Central

Langergraber, Kevin E.; Prüfer, Kay; Rowney, Carolyn; Boesch, Christophe; Crockford, Catherine; Fawcett, Katie; Inoue, Eiji; Inoue-Muruyama, Miho; Mitani, John C.; Muller, Martin N.; Robbins, Martha M.; Schubert, Grit; Stoinski, Tara S.; Viola, Bence; Watts, David; Wittig, Roman M.; Wrangham, Richard W.; Zuberbühler, Klaus; Pääbo, Svante; Vigilant, Linda

2012-01-01

Fossils and molecular data are two independent sources of information that should in principle provide consistent inferences of when evolutionary lineages diverged. Here we use an alternative approach to genetic inference of species split times in recent human and ape evolution that is independent of the fossil record. We first use genetic parentage information on a large number of wild chimpanzees and mountain gorillas to directly infer their average generation times. We then compare these generation time estimates with those of humans and apply recent estimates of the human mutation rate per generation to derive estimates of split times of great apes and humans that are independent of fossil calibration. We date the human–chimpanzee split to at least 7–8 million years and the population split between Neanderthals and modern humans to 400,000–800,000 y ago. This suggests that molecular divergence dates may not be in conflict with the attribution of 6- to 7-million-y-old fossils to the human lineage and 400,000-y-old fossils to the Neanderthal lineage. PMID:22891323

Impacts of the spatial extent of pollen-climate calibration-set on the absolute values, range and trends of reconstructed Holocene precipitation

NASA Astrophysics Data System (ADS)

Cao, X.; Tian, F.; Telford, R.; Ni, J.; Xu, Q.; Chen, F.; Liu, X.; Stebich, M.; Zhao, Y.; Herzschuh, U.

2017-12-01

Pollen-based quantitative reconstructions of past climate variables is a standard palaeoclimatic approach. Despite knowing that the spatial extent of the calibration-set affects the reconstruction result, guidance is lacking as to how to determine a suitable spatial extent of the pollen-climate calibration-set. In this study, past mean annual precipitation (Pann) during the Holocene (since 11.5 cal ka BP) is reconstructed repeatedly for pollen records from Qinghai Lake (36.7°N, 100.5°E; north-east Tibetan Plateau), Gonghai Lake (38.9°N, 112.2°E; north China) and Sihailongwan Lake (42.3°N, 126.6°E; north-east China) using calibration-sets of varying spatial extents extracted from the modern pollen dataset of China and Mongolia (2559 sampling sites and 168 pollen taxa in total). Results indicate that the spatial extent of the calibration-set has a strong impact on model performance, analogue quality and reconstruction diagnostics (absolute value, range, trend, optimum). Generally, these effects are stronger with the modern analogue technique (MAT) than with weighted averaging partial least squares (WA-PLS). With respect to fossil spectra from northern China, the spatial extent of calibration-sets should be restricted to ca. 1000 km in radius because small-scale calibration-sets (<800 km radius) will likely fail to include enough spatial variation in the modern pollen assemblages to reflect the temporal range shifts during the Holocene, while too broad a scale calibration-set (>1500 km radius) will include taxa with very different pollen-climate relationships. Based on our results we conclude that the optimal calibration-set should 1) cover a reasonably large spatial extent with an even distribution of modern pollen samples; 2) possess good model performance as indicated by cross-validation, high analogue quality, and excellent fit with the target fossil pollen spectra; 3) possess high taxonomic resolution, and 4) obey the modern and past distribution ranges of taxa inferred from palaeo-genetic and macrofossil studies.

Dysaerobic trace fossils and ichnofabrics in the upper Jurassic Kimmeridge Clay of southern England

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wignall, P.B.

The trace fossil suite from the Kimmeridge Clay is calibrated against an oxygen gradient derived from previous geochemical, lithological and shelly macrofaunal studies. Several soft-bodied trace markers appear to have tolerated lower oxygen tensions than even the hardiest shelly benthic macrofauna-a common occurrence in both recent and ancient dysaerobic settings. Lowest diversity trace fossil assemblages consist of Astacimorphichnus etchesi (new ichnotaxon), a small endostratal pascichnial trace attributed to pioneering polychaete populations. Ekdale and Masons' (1988) contention that fodinichnia dominate the lowest diversity and lowest oxygen settings is not substantiated as the only example of this feeding strategy, Rhizocorallium irregulare, ismore » encountered in moderately diverse trace fossil assemblages associated with a low diversity shelly macrofauna. Upper dysaerobic conditions are characterized by the development of a surface mixed layer and the consequent destruction of fine lamination. Tiering is only developed under normal oxygen conditions with Chondrites as the deepest trace. In contrast to many previous studies, Chondrites is never found in dysaerobic facies.« less

Empirical and Bayesian approaches to fossil-only divergence times: A study across three reptile clades.

PubMed

Turner, Alan H; Pritchard, Adam C; Matzke, Nicholas J

2017-01-01

Estimating divergence times on phylogenies is critical in paleontological and neontological studies. Chronostratigraphically-constrained fossils are the only direct evidence of absolute timing of species divergence. Strict temporal calibration of fossil-only phylogenies provides minimum divergence estimates, and various methods have been proposed to estimate divergences beyond these minimum values. We explore the utility of simultaneous estimation of tree topology and divergence times using BEAST tip-dating on datasets consisting only of fossils by using relaxed morphological clocks and birth-death tree priors that include serial sampling (BDSS) at a constant rate through time. We compare BEAST results to those from the traditional maximum parsimony (MP) and undated Bayesian inference (BI) methods. Three overlapping datasets were used that span 250 million years of archosauromorph evolution leading to crocodylians. The first dataset focuses on early Sauria (31 taxa, 240 chars.), the second on early Archosauria (76 taxa, 400 chars.) and the third on Crocodyliformes (101 taxa, 340 chars.). For each dataset three time-calibrated trees (timetrees) were calculated: a minimum-age timetree with node ages based on earliest occurrences in the fossil record; a 'smoothed' timetree using a range of time added to the root that is then averaged over zero-length internodes; and a tip-dated timetree. Comparisons within datasets show that the smoothed and tip-dated timetrees provide similar estimates. Only near the root node do BEAST estimates fall outside the smoothed timetree range. The BEAST model is not able to overcome limited sampling to correctly estimate divergences considerably older than sampled fossil occurrence dates. Conversely, the smoothed timetrees consistently provide node-ages far older than the strict dates or BEAST estimates for morphologically conservative sister-taxa when they sit on long ghost lineages. In this latter case, the relaxed-clock model appears to be correctly moderating the node-age estimate based on the limited morphological divergence. Topologies are generally similar across analyses, but BEAST trees for crocodyliforms differ when clades are deeply nested but contain very old taxa. It appears that the constant-rate sampling assumption of the BDSS tree prior influences topology inference by disfavoring long, unsampled branches.

Empirical and Bayesian approaches to fossil-only divergence times: A study across three reptile clades

PubMed Central

Turner, Alan H.; Pritchard, Adam C.; Matzke, Nicholas J.

2017-01-01

Estimating divergence times on phylogenies is critical in paleontological and neontological studies. Chronostratigraphically-constrained fossils are the only direct evidence of absolute timing of species divergence. Strict temporal calibration of fossil-only phylogenies provides minimum divergence estimates, and various methods have been proposed to estimate divergences beyond these minimum values. We explore the utility of simultaneous estimation of tree topology and divergence times using BEAST tip-dating on datasets consisting only of fossils by using relaxed morphological clocks and birth-death tree priors that include serial sampling (BDSS) at a constant rate through time. We compare BEAST results to those from the traditional maximum parsimony (MP) and undated Bayesian inference (BI) methods. Three overlapping datasets were used that span 250 million years of archosauromorph evolution leading to crocodylians. The first dataset focuses on early Sauria (31 taxa, 240 chars.), the second on early Archosauria (76 taxa, 400 chars.) and the third on Crocodyliformes (101 taxa, 340 chars.). For each dataset three time-calibrated trees (timetrees) were calculated: a minimum-age timetree with node ages based on earliest occurrences in the fossil record; a ‘smoothed’ timetree using a range of time added to the root that is then averaged over zero-length internodes; and a tip-dated timetree. Comparisons within datasets show that the smoothed and tip-dated timetrees provide similar estimates. Only near the root node do BEAST estimates fall outside the smoothed timetree range. The BEAST model is not able to overcome limited sampling to correctly estimate divergences considerably older than sampled fossil occurrence dates. Conversely, the smoothed timetrees consistently provide node-ages far older than the strict dates or BEAST estimates for morphologically conservative sister-taxa when they sit on long ghost lineages. In this latter case, the relaxed-clock model appears to be correctly moderating the node-age estimate based on the limited morphological divergence. Topologies are generally similar across analyses, but BEAST trees for crocodyliforms differ when clades are deeply nested but contain very old taxa. It appears that the constant-rate sampling assumption of the BDSS tree prior influences topology inference by disfavoring long, unsampled branches. PMID:28187191

Giving the early fossil record of sponges a squeeze.

PubMed

Antcliffe, Jonathan B; Callow, Richard H T; Brasier, Martin D

2014-11-01

Twenty candidate fossils with claim to be the oldest representative of the Phylum Porifera have been re-analysed. Three criteria are used to assess each candidate: (i) the diagnostic criteria needed to categorize sponges in the fossil record; (ii) the presence, or absence, of such diagnostic features in the putative poriferan fossils; and (iii) the age constraints for the candidate fossils. All three criteria are critical to the correct interpretation of any fossil and its placement within an evolutionary context. Our analysis shows that no Precambrian fossil candidate yet satisfies all three of these criteria to be a reliable sponge fossil. The oldest widely accepted candidate, Mongolian silica hexacts from c. 545 million years ago (Ma), are here shown to be cruciform arsenopyrite crystals. The oldest reliable sponge remains are siliceous spicules from the basal Cambrian (Protohertzina anabarica Zone) Soltanieh Formation, Iran, which are described and analysed here in detail for the first time. Extensive archaeocyathan sponge reefs emerge and radiate as late as the middle of the Fortunian Stage of the Cambrian and demonstrate a gradual assembly of their skeletal structure through this time coincident with the evolution of other metazoan groups. Since the Porifera are basal in the Metazoa, their presence within the late Proterozoic has been widely anticipated. Molecular clock calibration for the earliest Porifera and Metazoa should now be based on the Iranian hexactinellid material dated to c. 535 Ma. The earliest convincing fossil sponge remains appeared at around the time of the Precambrian-Cambrian boundary, associated with the great radiation events of that interval. © 2014 The Authors. Biological Reviews © 2014 Cambridge Philosophical Society.

Myrteae phylogeny, calibration, biogeography and diversification patterns: Increased understanding in the most species rich tribe of Myrtaceae.

PubMed

Vasconcelos, Thais N C; Proença, Carol E B; Ahmad, Berhaman; Aguilar, Daniel S; Aguilar, Reinaldo; Amorim, Bruno S; Campbell, Keron; Costa, Itayguara R; De-Carvalho, Plauto S; Faria, Jair E Q; Giaretta, Augusto; Kooij, Pepijn W; Lima, Duane F; Mazine, Fiorella F; Peguero, Brigido; Prenner, Gerhard; Santos, Matheus F; Soewarto, Julia; Wingler, Astrid; Lucas, Eve J

2017-04-01

Myrteae (c. 2500 species; 51 genera) is the largest tribe of Myrtaceae and an ecologically important groups of angiosperms in the Neotropics. Systematic relationships in Myrteae are complex, hindering conservation initiatives and jeopardizing evolutionary modelling. A well-supported and robust phylogenetic hypothesis was here targeted towards a comprehensive understanding of the relationships within the tribe. The resultant topology was used as a base for key evolutionary analyses such as age estimation, historical biogeography and diversification rate patterns. One nuclear (ITS) and seven chloroplast (psbA-trnH, matK, ndhF, trnl-trnF, trnQ-rps16, rpl16 and rpl32-trnL) DNA regions for 115 taxa representing 46 out of the 51 genera in the tribe were accessed and analysed using maximum likelihood and Bayesian inference tools for phylogenetic reconstruction. Dates of diversification events were estimated and contrasted using two distinct fossil sets (macro and pollen) in BEAST. The subsequent dated phylogenies were compared and analysed for biogeographical patterns using BioGeoBEARS and diversification rates using BAMM. Myrteae phylogeny presents strong statistical support for three major clades within the tribe: Australasian group, Myrtus group and Main Neotropical Lineage. Dating results from calibration using macrofossil are an average of 20 million years older and show an early Paleocene origin of Myrteae, against a mid-Eocene one from the pollen fossil calibration. Biogeographic analysis shows the origin of Myrteae in Zealandia in both calibration approaches, followed by a widespread distribution throughout the still-linked Gondwana continents and diversification of Neotropical endemic lineages by later vicariance. Best configuration shift indicates three points of acceleration in diversification rates, all of them occurring in the Main Neotropical Lineage. Based on the reconstructed topology, several new taxonomic placements were recovered, including: the relative position of Myrtus communis, the placement of the Blepharocalyx group, the absence of generic endemism in the Caribbean, and the paraphyletism of the former Pimenta group. Distinct calibration approaches affect biogeography interpretation, increasing the number of necessary long distance dispersal events in the topology with older nodes. It is hypothesised that biological intrinsic factors such as modifications of embryo type and polyploidy might have played a role in accelerating shifts of diversification rates in Neotropical lineages. Future perspectives include formal subtribal classification, standardization of fossil calibration approaches and better links between diversification shifts and trait evolution. Copyright © 2017 Elsevier Inc. All rights reserved.

Do missing data influence the accuracy of divergence-time estimation with BEAST?

PubMed

Zheng, Yuchi; Wiens, John J

2015-04-01

Time-calibrated phylogenies have become essential to evolutionary biology. A recurrent and unresolved question for dating analyses is whether genes with missing data cells should be included or excluded. This issue is particularly unclear for the most widely used dating method, the uncorrelated lognormal approach implemented in BEAST. Here, we test the robustness of this method to missing data. We compare divergence-time estimates from a nearly complete dataset (20 nuclear genes for 32 species of squamate reptiles) to those from subsampled matrices, including those with 5 or 2 complete loci only and those with 5 or 8 incomplete loci added. In general, missing data had little impact on estimated dates (mean error of ∼5Myr per node or less, given an overall age of ∼220Myr in squamates), even when 80% of sampled genes had 75% missing data. Mean errors were somewhat higher when all genes were 75% incomplete (∼17Myr). However, errors increased dramatically when only 2 of 9 fossil calibration points were included (∼40Myr), regardless of missing data. Overall, missing data (and even numbers of genes sampled) may have only minor impacts on the accuracy of divergence dating with BEAST, relative to the dramatic effects of fossil calibrations. Copyright © 2015 Elsevier Inc. All rights reserved.

A gas chromatograph for quantification of peroxycarboxylic nitric anhydrides calibrated by thermal dissociation cavity ring-down spectroscopy

NASA Astrophysics Data System (ADS)

Tokarek, T. W.; Huo, J. A.; Odame-Ankrah, C. A.; Hammoud, D.; Taha, Y. M.; Osthoff, H. D.

2014-10-01

The peroxycarboxylic nitric anhydrides (PANs, molecular formula: RC(O)O2NO2) can readily be observed by gas chromatography (PAN-GC) coupled to electron capture detection. Calibration of a PAN-GC remains a challenge, because the response factors differ for each of the PANs, and because their synthesis in sufficiently high purity is non-trivial, in particular for PANs containing unsaturated side chains. In this manuscript, a PAN-GC and its calibration using diffusion standards, whose output was quantified by blue diode laser thermal dissociation cavity ring-down spectroscopy (TD-CRDS), are described. The PAN-GC peak areas correlated linearly with total peroxy nitrate (ΣPN) mixing ratios measured by TD-CRDS (r > 0.96). Accurate determination of response factors required the concentrations of PAN impurities in the synthetic standards to be subtracted from ΣPN. The PAN-GC and its TD-CRDS calibration method were deployed during ambient air measurement campaigns in Abbotsford, BC, from 20 July to 5 August 2012, and during the Fort McMurray Oil Sands Strategic Investigation of Local Sources (FOSSILS) campaign at the AMS13 ground site in Fort McKay, AB, from 10 August to 5 September 2013. The PAN-GC limits of detection for PAN, PPN, and MPAN during FOSSILS were 1, 2, and 3 pptv, respectively. For the Abbotsford data set, the PAN-GC mixing ratios were compared, and agreed with those determined in parallel by thermal dissociation chemical ionization mass spectrometry (TD-CIMS). Advantages and disadvantages of the PAN measurement techniques used in this work and the utility of TD-CRDS as a PAN-GC calibration method are discussed.

A critical framework for the assessment of biological palaeoproxies: predicting past climate and levels of atmospheric CO(2) from fossil leaves.

PubMed

Jordan, Gregory J

2011-10-01

This review uses proxies of past temperature and atmospheric CO(2) composition based on fossil leaves to illustrate the uncertainties in biologically based proxies of past environments. Most leaf-based proxies are geographically local or genetically restricted and therefore can be confounded by evolution, extinction, changes in local environment or immigration of species. Stomatal frequency proxies illustrate how genetically restricted proxies can be particularly vulnerable to evolutionary change. High predictive power in the modern world resulting from the use of a very narrow calibration cannot be confidently extrapolated into the past (the Ginkgo paradox). Many foliar physiognomic proxies of climate are geographically local and use traits that are more or less fixed for individual species. Such proxies can therefore be confounded by floristic turnover and biome shifts in the region of calibration. Uncertainty in proxies tends to be greater for more ancient fossils. I present a set of questions that should be considered before using a proxy. Good proxies should be relatively protected from environmental and genetic change, particularly through having high information content and being founded on biomechanical or biochemical principles. Some current and potential developments are discussed, including those that involve more mechanistically sound proxies and better use of multivariate approaches. © 2011 The Author. New Phytologist © 2011 New Phytologist Trust.

Evaluation of NPP-VIIRS Nighttime Light Data for Mapping Global Fossil Fuel Combustion CO2 Emissions: A Comparison with DMSP-OLS Nighttime Light Data.

PubMed

Ou, Jinpei; Liu, Xiaoping; Li, Xia; Li, Meifang; Li, Wenkai

2015-01-01

Recently, the stable light products and radiance calibrated products from Defense Meteorological Satellite Program's (DMSP) Operational Linescan System (OLS) have been useful for mapping global fossil fuel carbon dioxide (CO2) emissions at fine spatial resolution. However, few studies on this subject were conducted with the new-generation nighttime light data from the Visible Infrared Imaging Radiometer Suite (VIIRS) sensor on the Suomi National Polar-orbiting Partnership (NPP) Satellite, which has a higher spatial resolution and a wider radiometric detection range than the traditional DMSP-OLS nighttime light data. Therefore, this study performed the first evaluation of the potential of NPP-VIIRS data in estimating the spatial distributions of global CO2 emissions (excluding power plant emissions). Through a disaggregating model, three global emission maps were then derived from population counts and three different types of nighttime lights data (NPP-VIIRS, the stable light data and radiance calibrated data of DMSP-OLS) for a comparative analysis. The results compared with the reference data of land cover in Beijing, Shanghai and Guangzhou show that the emission areas of map from NPP-VIIRS data have higher spatial consistency of the artificial surfaces and exhibit a more reasonable distribution of CO2 emission than those of other two maps from DMSP-OLS data. Besides, in contrast to two maps from DMSP-OLS data, the emission map from NPP-VIIRS data is closer to the Vulcan inventory and exhibits a better agreement with the actual statistical data of CO2 emissions at the level of sub-administrative units of the United States. This study demonstrates that the NPP-VIIRS data can be a powerful tool for studying the spatial distributions of CO2 emissions, as well as the socioeconomic indicators at multiple scales.

Evaluation of NPP-VIIRS Nighttime Light Data for Mapping Global Fossil Fuel Combustion CO2 Emissions: A Comparison with DMSP-OLS Nighttime Light Data

PubMed Central

Ou, Jinpei; Liu, Xiaoping; Li, Xia; Li, Meifang; Li, Wenkai

2015-01-01

Recently, the stable light products and radiance calibrated products from Defense Meteorological Satellite Program’s (DMSP) Operational Linescan System (OLS) have been useful for mapping global fossil fuel carbon dioxide (CO2) emissions at fine spatial resolution. However, few studies on this subject were conducted with the new-generation nighttime light data from the Visible Infrared Imaging Radiometer Suite (VIIRS) sensor on the Suomi National Polar-orbiting Partnership (NPP) Satellite, which has a higher spatial resolution and a wider radiometric detection range than the traditional DMSP-OLS nighttime light data. Therefore, this study performed the first evaluation of the potential of NPP-VIIRS data in estimating the spatial distributions of global CO2 emissions (excluding power plant emissions). Through a disaggregating model, three global emission maps were then derived from population counts and three different types of nighttime lights data (NPP-VIIRS, the stable light data and radiance calibrated data of DMSP-OLS) for a comparative analysis. The results compared with the reference data of land cover in Beijing, Shanghai and Guangzhou show that the emission areas of map from NPP-VIIRS data have higher spatial consistency of the artificial surfaces and exhibit a more reasonable distribution of CO2 emission than those of other two maps from DMSP-OLS data. Besides, in contrast to two maps from DMSP-OLS data, the emission map from NPP-VIIRS data is closer to the Vulcan inventory and exhibits a better agreement with the actual statistical data of CO2 emissions at the level of sub-administrative units of the United States. This study demonstrates that the NPP-VIIRS data can be a powerful tool for studying the spatial distributions of CO2 emissions, as well as the socioeconomic indicators at multiple scales. PMID:26390037

Experimental taphonomy and the anatomy and diversity of the earliest fossil vertebrates (Chengjiang Biota, Cambrian, China)

NASA Astrophysics Data System (ADS)

Purnell, Mark; Gabbott, Sarah; Murdock, Duncan; Cong, Peiyun

2016-04-01

The oldest fossil vertebrates are from the Lower Cambrian Chengjiang biota of China, which contains four genera of fish-like, primitive vertebrates: Haikouichthys, Myllokunmingia, Zhongjianichthys and Zhongxiniscus. These fossils play key roles in calibrating molecular clocks and informing our view of the anatomy of animals close to the origin of vertebrates, potentially including transitional forms between vertebrates and their nearest relatives. Despite the evident importance of these fossils, the degree to which taphonomic processes have affected their anatomical completeness has not been investigated. For example, some or all might have been affected by stemward slippage - the pattern observed in experimental decay of non-biomineralised chordates in which preferential decay of synapomorphies and retention of plesiomorphic characters would cause fossil taxa to erroneously occupy more basal positions than they should. This hypothesis is based on experimental data derived from decay of non-biomineralised chordates under laboratory conditions. We have expanded this analysis to include a broader range of potentially significant environmental variables; we have also compared and combined the results of experiments from several taxa to identify general patterns of chordate decay. Examination of the Chengjiang vertebrates in the light of these results demonstrates that, contrary to some assertions, experimentally derived models of phylogenetic bias are applicable to fossils. Anatomical and phylogenetic interpretations of early vertebrates that do not take taphonomic biases into account risk overestimating diversity and the evolutionary significance of differences between fossil specimens.

Palynologically calibrated vertebrate record from North Dakota consistent with abrupt dinosaur extinction at the Cretaceous-Tertiary boundary

USGS Publications Warehouse

Pearson, D.A.; Schaefer, T.; Johnson, K.R.; Nichols, D.J.

2001-01-01

New data from 17 Cretaceous-Tertiary (K-T) boundary sections and 53 vertebrate sites in the Hell Creek and Fort Union Formations in southwestern North Dakota document a 1.76 m barren interval between the highest Cretaceous vertebrate fossils and the palynologically recognized K-T boundary. The boundary is above the formational contact at 15 localities and coincident with it at two, demonstrating that the formational contact is diachronous. Dinosaurs are common in the highest Cretaceous vertebrate samples and a partial dinosaur skeleton in the Fort Union Formation is the highest recorded Cretaceous vertebrate fossil in this area.

A roller-like bird (Coracii) from the Early Eocene of Denmark.

PubMed

Bourdon, Estelle; Kristoffersen, Anette V; Bonde, Niels

2016-09-27

The fossil record of crown group birds (Neornithes) prior to the Cretaceous-Paleogene boundary is scarce and fragmentary. Early Cenozoic bird fossils are more abundant, but are typically disarticulated and/or flattened. Here we report the oldest roller (Coracii), Septencoracias morsensis gen. et sp. nov. (Primobucconidae), based on a new specimen from the Early Eocene (about 54 million years ago) Fur Formation of Denmark. The new fossil is a nearly complete, three-dimensionally preserved and articulated skeleton. It lies at the lower end of the size range for extant rollers. Salient diagnostic features of Septencoracias relative to other Coracii include the proportionally larger skull and the small, ovoid and dorsally positioned narial openings. Our discovery adds to the evidence that the Coracii had a widespread northern hemisphere distribution in the Eocene. Septencoracias is the oldest substantial record of the Picocoraciae and provides a reliable calibration point for molecular phylogenetic studies.

A roller-like bird (Coracii) from the Early Eocene of Denmark

PubMed Central

Bourdon, Estelle; Kristoffersen, Anette V.; Bonde, Niels

2016-01-01

The fossil record of crown group birds (Neornithes) prior to the Cretaceous-Paleogene boundary is scarce and fragmentary. Early Cenozoic bird fossils are more abundant, but are typically disarticulated and/or flattened. Here we report the oldest roller (Coracii), Septencoracias morsensis gen. et sp. nov. (Primobucconidae), based on a new specimen from the Early Eocene (about 54 million years ago) Fur Formation of Denmark. The new fossil is a nearly complete, three-dimensionally preserved and articulated skeleton. It lies at the lower end of the size range for extant rollers. Salient diagnostic features of Septencoracias relative to other Coracii include the proportionally larger skull and the small, ovoid and dorsally positioned narial openings. Our discovery adds to the evidence that the Coracii had a widespread northern hemisphere distribution in the Eocene. Septencoracias is the oldest substantial record of the Picocoraciae and provides a reliable calibration point for molecular phylogenetic studies. PMID:27670387

Constraining the Deep Origin of Parasitic Flatworms and Host-Interactions with Fossil Evidence.

PubMed

De Baets, Kenneth; Dentzien-Dias, Paula; Upeniece, Ieva; Verneau, Olivier; Donoghue, Philip C J

2015-01-01

Novel fossil discoveries have contributed to our understanding of the evolutionary appearance of parasitism in flatworms. Furthermore, genetic analyses with greater coverage have shifted our views on the coevolution of parasitic flatworms and their hosts. The putative record of parasitic flatworms is consistent with extant host associations and so can be used to put constraints on the evolutionary origin of the parasites themselves. The future lies in new molecular clock analyses combined with additional discoveries of exceptionally preserved flatworms associated with hosts and coprolites. Besides direct evidence, the host fossil record and biogeography have the potential to constrain their evolutionary history, albeit with caution needed to avoid circularity, and a need for calibrations to be implemented in the most conservative way. This might result in imprecise, but accurate divergence estimates for the evolution of parasitic flatworms. Copyright © 2015 Elsevier Ltd. All rights reserved.

Including Fossils in Phylogenetic Climate Reconstructions: A Deep Time Perspective on the Climatic Niche Evolution and Diversification of Spiny Lizards (Sceloporus).

PubMed

Lawing, A Michelle; Polly, P David; Hews, Diana K; Martins, Emília P

2016-08-01

Fossils and other paleontological information can improve phylogenetic comparative method estimates of phenotypic evolution and generate hypotheses related to species diversification. Here, we use fossil information to calibrate ancestral reconstructions of suitable climate for Sceloporus lizards in North America. Integrating data from the fossil record, general circulation models of paleoclimate during the Miocene, climate envelope modeling, and phylogenetic comparative methods provides a geographically and temporally explicit species distribution model of Sceloporus-suitable habitat through time. We provide evidence to support the historic biogeographic hypothesis of Sceloporus diversification in warm North American deserts and suggest a relatively recent Sceloporus invasion into Mexico around 6 Ma. We use a physiological model to map extinction risk. We suggest that the number of hours of restriction to a thermal refuge limited Sceloporus from inhabiting Mexico until the climate cooled enough to provide suitable habitat at approximately 6 Ma. If the future climate returns to the hotter climates of the past, Mexico, the place of highest modern Sceloporus richness, will no longer provide suitable habitats for Sceloporus to survive and reproduce.

Temperature profile around a basaltic sill intruded into wet sediments

USGS Publications Warehouse

Baker, Leslie; Bernard, Andrew; Rember, William C.; Milazzo, Moses; Dundas, Colin M.; Abramov, Oleg; Kestay, Laszlo P.

2015-01-01

The transfer of heat into wet sediments from magmatic intrusions or lava flows is not well constrained from field data. Such field constraints on numerical models of heat transfer could significantly improve our understanding of water–lava interactions. We use experimentally calibrated pollen darkening to measure the temperature profile around a basaltic sill emplaced into wet lakebed sediments. It is well known that, upon heating, initially transparent palynomorphs darken progressively through golden, brown, and black shades before being destroyed; however, this approach to measuring temperature has not been applied to volcanological questions. We collected sediment samples from established Miocene fossil localities at Clarkia, Idaho. Fossils in the sediments include pollen from numerous tree and shrub species. We experimentally calibrated changes in the color of Clarkia sediment pollen and used this calibration to determine sediment temperatures around a Miocene basaltic sill emplaced in the sediments. Results indicated a flat temperature profile above and below the sill, with T > 325 °C within 1 cm of the basalt-sediment contact, near 300 °C at 1–2 cm from the contact, and ~ 250 °C at 1 m from the sill contact. This profile suggests that heat transport in the sediments was hydrothermally rather than conductively controlled. This information will be used to test numerical models of heat transfer in wet sediments on Earth and Mars.

Calibrating the Ordovician Radiation of marine life: implications for Phanerozoic diversity trends

NASA Technical Reports Server (NTRS)

Miller, A. I.; Foote, M.

1996-01-01

It has long been suspected that trends in global marine biodiversity calibrated for the Phanerozoic may be affected by sampling problems. However, this possibility has not been evaluated definitively, and raw diversity trends are generally accepted at face value in macroevolutionary investigations. Here, we analyze a global-scale sample of fossil occurrences that allows us to determine directly the effects of sample size on the calibration of what is generally thought to be among the most significant global biodiversity increases in the history of life: the Ordovician Radiation. Utilizing a composite database that includes trilobites, brachiopods, and three classes of molluscs, we conduct rarefaction analyses to demonstrate that the diversification trajectory for the Radiation was considerably different than suggested by raw diversity time-series. Our analyses suggest that a substantial portion of the increase recognized in raw diversity depictions for the last three Ordovician epochs (the Llandeilian, Caradocian, and Ashgillian) is a consequence of increased sample size of the preserved and catalogued fossil record. We also use biometric data for a global sample of Ordovician trilobites, along with methods of measuring morphological diversity that are not biased by sample size, to show that morphological diversification in this major clade had leveled off by the Llanvirnian. The discordance between raw diversity depictions and more robust taxonomic and morphological diversity metrics suggests that sampling effects may strongly influence our perception of biodiversity trends throughout the Phanerozoic.

Likelihood of Tree Topologies with Fossils and Diversification Rate Estimation.

PubMed

Didier, Gilles; Fau, Marine; Laurin, Michel

2017-11-01

Since the diversification process cannot be directly observed at the human scale, it has to be studied from the information available, namely the extant taxa and the fossil record. In this sense, phylogenetic trees including both extant taxa and fossils are the most complete representations of the diversification process that one can get. Such phylogenetic trees can be reconstructed from molecular and morphological data, to some extent. Among the temporal information of such phylogenetic trees, fossil ages are by far the most precisely known (divergence times are inferences calibrated mostly with fossils). We propose here a method to compute the likelihood of a phylogenetic tree with fossils in which the only considered time information is the fossil ages, and apply it to the estimation of the diversification rates from such data. Since it is required in our computation, we provide a method for determining the probability of a tree topology under the standard diversification model. Testing our approach on simulated data shows that the maximum likelihood rate estimates from the phylogenetic tree topology and the fossil dates are almost as accurate as those obtained by taking into account all the data, including the divergence times. Moreover, they are substantially more accurate than the estimates obtained only from the exact divergence times (without taking into account the fossil record). We also provide an empirical example composed of 50 Permo-Carboniferous eupelycosaur (early synapsid) taxa ranging in age from about 315 Ma (Late Carboniferous) to 270 Ma (shortly after the end of the Early Permian). Our analyses suggest a speciation (cladogenesis, or birth) rate of about 0.1 per lineage and per myr, a marginally lower extinction rate, and a considerable hidden paleobiodiversity of early synapsids. [Extinction rate; fossil ages; maximum likelihood estimation; speciation rate.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A Late Cretaceous Piper (Piperaceae) from Colombia and diversification patterns for the genus.

PubMed

Martínez, Camila; Carvalho, Mónica R; Madriñán, Santiago; Jaramillo, Carlos A

2015-02-01

Documented fossil floras in the neotropics are sparse, yet their records provide evidence on the spatial and temporal occurrence of taxa, allowing for testing of biogeographical and diversification scenarios on individual lineages. A new fossil Piper from the Late Cretaceous of Colombia is described here, and its importance for assessing diversification patterns in the genus is addressed. Leaf architecture of 32 fossil leaf compressions from the Guaduas Formation was compared with that of 294 extant angiosperm species. The phylogenetic position of the fossil named Piper margaritae sp. nov. was established based on leaf traits and a molecular scaffold of Piper. The age of the fossil was independently used as a calibration point for divergence time estimations. Natural affinities of P. margaritae to the Schilleria clade of Piper indicate that the genus occurred in tropical America by the Late Cretaceous. Estimates of age divergence and lineage accumulation reveal that most of the extant diversity of the genus accrued during the last ∼30 Myr. The recent radiation of Piper is coeval with both the Andean uplift and the emergence of Central America, which have been proposed as important drivers of diversity. This pattern could exemplify a recurrent theme among many neotropical plant lineages. © 2015 Botanical Society of America, Inc.

Global Inventory of Gas Geochemistry Data from Fossil Fuel, Microbial and Burning Sources, version 2017

NASA Astrophysics Data System (ADS)

Sherwood, Owen A.; Schwietzke, Stefan; Arling, Victoria A.; Etiope, Giuseppe

2017-08-01

The concentration of atmospheric methane (CH4) has more than doubled over the industrial era. To help constrain global and regional CH4 budgets, inverse (top-down) models incorporate data on the concentration and stable carbon (δ13C) and hydrogen (δ2H) isotopic ratios of atmospheric CH4. These models depend on accurate δ13C and δ2H end-member source signatures for each of the main emissions categories. Compared with meticulous measurement and calibration of isotopic CH4 in the atmosphere, there has been relatively less effort to characterize globally representative isotopic source signatures, particularly for fossil fuel sources. Most global CH4 budget models have so far relied on outdated source signature values derived from globally nonrepresentative data. To correct this deficiency, we present a comprehensive, globally representative end-member database of the δ13C and δ2H of CH4 from fossil fuel (conventional natural gas, shale gas, and coal), modern microbial (wetlands, rice paddies, ruminants, termites, and landfills and/or waste) and biomass burning sources. Gas molecular compositional data for fossil fuel categories are also included with the database. The database comprises 10 706 samples (8734 fossil fuel, 1972 non-fossil) from 190 published references. Mean (unweighted) δ13C signatures for fossil fuel CH4 are significantly lighter than values commonly used in CH4 budget models, thus highlighting potential underestimation of fossil fuel CH4 emissions in previous CH4 budget models. This living database will be updated every 2-3 years to provide the atmospheric modeling community with the most complete CH4 source signature data possible. Database digital object identifier (DOI): https://doi.org/10.15138/G3201T.

Using DMSP/OLS nighttime imagery to estimate carbon dioxide emission

NASA Astrophysics Data System (ADS)

Desheng, B.; Letu, H.; Bao, Y.; Naizhuo, Z.; Hara, M.; Nishio, F.

2012-12-01

This study highlighted a method for estimating CO2 emission from electric power plants using the Defense Meteorological Satellite Program's Operational Linescan System (DMSP/OLS) stable light image product for 1999. CO2 emissions from power plants account for a high percentage of CO2 emissions from fossil fuel consumptions. Thermal power plants generate the electricity by burning fossil fuels, so they emit CO2 directly. In many Asian countries such as China, Japan, India, and South Korea, the amounts of electric power generated by thermal power accounts over 58% in the total amount of electric power in 1999. So far, figures of the CO2 emission were obtained mainly by traditional statistical methods. Moreover, the statistical data were summarized as administrative regions, so it is difficult to examine the spatial distribution of non-administrative division. In some countries the reliability of such CO2 emission data is relatively low. However, satellite remote sensing can observe the earth surface without limitation of administrative regions. Thus, it is important to estimate CO2 using satellite remote sensing. In this study, we estimated the CO2 emission by fossil fuel consumption from electric power plant using stable light image of the DMSP/OLS satellite data for 1999 after correction for saturation effect in Japan. Digital number (DN) values of the stable light images in center areas of cities are saturated due to the large nighttime light intensities and characteristics of the OLS satellite sensors. To more accurately estimate the CO2 emission using the stable light images, a saturation correction method was developed by using the DMSP radiance calibration image, which does not include any saturation pixels. A regression equation was developed by the relationship between DN values of non-saturated pixels in the stable light image and those in the radiance calibration image. And, regression equation was used to adjust the DNs of the radiance calibration image. Then, saturated DNs of the stable light image was corrected using adjusted radiance calibration image. After that, regression analysis was performed with cumulative DNs of the corrected stable light image, electric power consumption, electric power generation and CO2 emission by fossil fuel consumption from electric power plant each other. Results indicated that there are good relationships (R2>90%) between DNs of the corrected stable light image and other parameters. Based on the above results, we estimated the CO2 emission from electric power plant using corrected stable light image. Keywords: DMSP/OLS, stable light, saturation light correction method, regression analysis Acknowledgment: The research was financially supported by the Sasakawa Scientific Research Grant from the Japan Science Society.

The Effect of Inappropriate Calibration: Three Case Studies in Molecular Ecology

PubMed Central

Ho, Simon Y. W.; Saarma, Urmas; Barnett, Ross; Haile, James; Shapiro, Beth

2008-01-01

Time-scales estimated from sequence data play an important role in molecular ecology. They can be used to draw correlations between evolutionary and palaeoclimatic events, to measure the tempo of speciation, and to study the demographic history of an endangered species. In all of these studies, it is paramount to have accurate estimates of time-scales and substitution rates. Molecular ecological studies typically focus on intraspecific data that have evolved on genealogical scales, but often these studies inappropriately employ deep fossil calibrations or canonical substitution rates (e.g., 1% per million years for birds and mammals) for calibrating estimates of divergence times. These approaches can yield misleading estimates of molecular time-scales, with significant impacts on subsequent evolutionary and ecological inferences. We illustrate this calibration problem using three case studies: avian speciation in the late Pleistocene, the demographic history of bowhead whales, and the Pleistocene biogeography of brown bears. For each data set, we compare the date estimates that are obtained using internal and external calibration points. In all three cases, the conclusions are significantly altered by the application of revised, internally-calibrated substitution rates. Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events. PMID:18286172

The effect of inappropriate calibration: three case studies in molecular ecology.

PubMed

Ho, Simon Y W; Saarma, Urmas; Barnett, Ross; Haile, James; Shapiro, Beth

2008-02-20

Time-scales estimated from sequence data play an important role in molecular ecology. They can be used to draw correlations between evolutionary and palaeoclimatic events, to measure the tempo of speciation, and to study the demographic history of an endangered species. In all of these studies, it is paramount to have accurate estimates of time-scales and substitution rates. Molecular ecological studies typically focus on intraspecific data that have evolved on genealogical scales, but often these studies inappropriately employ deep fossil calibrations or canonical substitution rates (e.g., 1% per million years for birds and mammals) for calibrating estimates of divergence times. These approaches can yield misleading estimates of molecular time-scales, with significant impacts on subsequent evolutionary and ecological inferences. We illustrate this calibration problem using three case studies: avian speciation in the late Pleistocene, the demographic history of bowhead whales, and the Pleistocene biogeography of brown bears. For each data set, we compare the date estimates that are obtained using internal and external calibration points. In all three cases, the conclusions are significantly altered by the application of revised, internally-calibrated substitution rates. Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events.

Memoirs of a frequent flier: Phylogenomics reveals 18 long-distance dispersals between North America and South America in the popcorn flowers (Amsinckiinae).

PubMed

Guilliams, C Matt; Hasenstab-Lehman, Kristen E; Mabry, Makenzie E; Simpson, Michael G

2017-11-23

American amphitropical disjunction (AAD) is an important but understudied New World biogeographic pattern in which related plants occur in extratropical North America and South America, but are absent in the intervening tropics. Subtribe Amsinckiinae (Boraginaceae) is one of the richest groups of plants displaying the AAD pattern. Here, we infer a time-calibrated molecular phylogeny of the group to evaluate the number, timing, and directionality of AAD events, which yields generalizable insights into the mechanism of AAD. We perform a phylogenomic analysis of 139 samples of subtribe Amsinckiinae and infer divergence times using two calibration schemes: with only fossil calibrations and with fossils plus a secondary calibration from a recent family level analysis. Biogeographic analysis was performed in the R package BioGeoBEARS. We document 18 examples of AAD in the Amsinckiinae. Inferred divergence times of these AAD examples were strongly asynchronous, ranging from Miocene (17.1 million years ago [Ma]) to Pleistocene (0.33 Ma), with most (12) occurring <5 Ma. Four events occurred 10-5 Ma, during the second rise of the Andes. All AAD examples had a North America to South America directionality. Second only to the hyperdiverse Poaceae in number of documented AAD examples, the Amsinckiinae is an ideal system for the study of AAD. Asynchronous divergence times support the hypothesis of long-distance dispersal by birds as the mechanism of AAD in the subtribe and more generally. Further comparative phylogenomic studies may permit biogeographic hypothesis testing and examination of the relationship between AAD and fruit morphology, reproductive biology, and ploidy. © 2017 Botanical Society of America.

Multimodal Spatial Calibration for Accurately Registering EEG Sensor Positions

PubMed Central

Chen, Shengyong; Xiao, Gang; Li, Xiaoli

2014-01-01

This paper proposes a fast and accurate calibration method to calibrate multiple multimodal sensors using a novel photogrammetry system for fast localization of EEG sensors. The EEG sensors are placed on human head and multimodal sensors are installed around the head to simultaneously obtain all EEG sensor positions. A multiple views' calibration process is implemented to obtain the transformations of multiple views. We first develop an efficient local repair algorithm to improve the depth map, and then a special calibration body is designed. Based on them, accurate and robust calibration results can be achieved. We evaluate the proposed method by corners of a chessboard calibration plate. Experimental results demonstrate that the proposed method can achieve good performance, which can be further applied to EEG source localization applications on human brain. PMID:24803954

Examining bias in pollen-based quantitative climate reconstructions induced by human impact on vegetation in China

NASA Astrophysics Data System (ADS)

Ding, Wei; Xu, Qinghai; Tarasov, Pavel E.

2017-09-01

Human impact is a well-known confounder in pollen-based quantitative climate reconstructions as most terrestrial ecosystems have been artificially affected to varying degrees. In this paper, we use a human-induced pollen dataset (H-set) and a corresponding natural pollen dataset (N-set) to establish pollen-climate calibration sets for temperate eastern China (TEC). The two calibration sets, taking a weighted averaging partial least squares (WA-PLS) approach, are used to reconstruct past climate variables from a fossil record, which is located at the margin of the East Asian summer monsoon in north-central China and covers the late glacial Holocene from 14.7 ka BP (thousands of years before AD 1950). Ordination results suggest that mean annual precipitation (Pann) is the main explanatory variable of both pollen composition and percentage distributions in both datasets. The Pann reconstructions, based on the two calibration sets, demonstrate consistently similar patterns and general trends, suggesting a relatively strong climate impact on the regional vegetation and pollen spectra. However, our results also indicate that the human impact may obscure climate signals derived from fossil pollen assemblages. In a test with modern climate and pollen data, the Pann influence on pollen distribution decreases in the H-set, while the human influence index (HII) rises. Moreover, the relatively strong human impact reduces woody pollen taxa abundances, particularly in the subhumid forested areas. Consequently, this shifts their model-inferred Pann optima to the arid end of the gradient compared to Pann tolerances in the natural dataset and further produces distinct deviations when the total tree pollen percentages are high (i.e. about 40 % for the Gonghai area) in the fossil sequence. In summary, the calibration set with human impact used in our experiment can produce a reliable general pattern of past climate, but the human impact on vegetation affects the pollen-climate relationship and biases the pollen-based climate reconstruction. The extent of human-induced bias may be rather small for the entire late glacial and early Holocene interval when we use a reference set called natural. Nevertheless, this potential bias should be kept in mind when conducting quantitative reconstructions, especially for the recent 2 or 3 millennia.

Multiple-Objective Stepwise Calibration Using Luca

USGS Publications Warehouse

Hay, Lauren E.; Umemoto, Makiko

2007-01-01

This report documents Luca (Let us calibrate), a multiple-objective, stepwise, automated procedure for hydrologic model calibration and the associated graphical user interface (GUI). Luca is a wizard-style user-friendly GUI that provides an easy systematic way of building and executing a calibration procedure. The calibration procedure uses the Shuffled Complex Evolution global search algorithm to calibrate any model compiled with the U.S. Geological Survey's Modular Modeling System. This process assures that intermediate and final states of the model are simulated consistently with measured values.

Tephrochronology and Stratigraphy of Silicic and Basaltic Volcanic Ash Layers at Hagerman Fossil Beds National Monument, Idaho, USA

NASA Astrophysics Data System (ADS)

Walkup, L. C.; Prassack, K. A.; Hart, W. K.; Wan, E.

2016-12-01

Hagerman Fossil Beds National Monument (HAFO) is home to a diverse early-middle Pliocene ( 4.2-3.0 Ma) faunal assemblage. The Glenns Ferry Formation, exposed within the Monument and in surrounding areas, preserves lacustrine and fluvial deposits interbedded with tephra and lava flows establishing a broad chronostratigraphic context for the fossils. Despite multiple attempts by previous studies to date several volcanic horizons within the Glenns Ferry Formation, the precise chronostratigraphy of specific key fossil localities within the Monument remains poorly constrained. HAFO contains many type specimens, including that of the newly described river otter Lontra weiri (Prassack, 2016). The chronologies of type specimens are especially important because they establish the first and, in some cases, only known occurrence of a species in the fossil record. Refined chronology also allows for community-level reconstructions of fauna across ancient landscapes. Thus, multiple silicic and basaltic tephra distributions were mapped, sampled, petrographically characterized, analyzed by electron microprobe (EMP), and correlated across the Monument to provide a refined spatial and temporal framework for specific fossil localities. Previous tephrochronologic studies focused on the Fossil Gulch and Peters Gulch areas. This investigation extends the mapped distribution extent of the tephra layers identified by other workers. To further support the updated tephrochronologic framework, several tephra samples from type localities were also analyzed using EMP and correlated with samples collected during this study. We also present a new age of 3.07± 0.23 Ma for an upper tephra horizon, measured via ITPFT and DCFT glass fission track methods. This age is in agreement with a previously suggested age of 3.15 Ma for this horizon based on regional tephra correlation and more precisely constrains the age of an important underlying fossil site.

Resolution of ray-finned fish phylogeny and timing of diversification.

PubMed

Near, Thomas J; Eytan, Ron I; Dornburg, Alex; Kuhn, Kristen L; Moore, Jon A; Davis, Matthew P; Wainwright, Peter C; Friedman, Matt; Smith, W Leo

2012-08-21

Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major ray-finned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the "bush at the top of the tree" that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the "Second Age of Fishes."

Resolution of ray-finned fish phylogeny and timing of diversification

PubMed Central

Near, Thomas J.; Eytan, Ron I.; Dornburg, Alex; Kuhn, Kristen L.; Moore, Jon A.; Davis, Matthew P.; Wainwright, Peter C.; Friedman, Matt; Smith, W. Leo

2012-01-01

Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major ray-finned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the “bush at the top of the tree” that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the “Second Age of Fishes.” PMID:22869754

Old Lineages in a New Ecosystem: Diversification of Arcellinid Amoebae (Amoebozoa) and Peatland Mosses

PubMed Central

Leander, Brian S.

2014-01-01

Arcellinid testate amoebae (Amoebozoa) form a group of free-living microbial eukaryotes with one of the oldest fossil records known, yet several aspects of their evolutionary history remain poorly understood. Arcellinids occur in a range of terrestrial, freshwater and even brackish habitats; however, many arcellinid morphospecies such as Hyalosphenia papilio are particularly abundant in Sphagnum-dominated peatlands, a relatively new ecosystem that appeared during the diversification of Sphagnum species in the Miocene (5–20 Myr ago). Here, we reconstruct divergence times in arcellinid testate amoebae after selecting several fossils for clock calibrations and then infer whether or not arcellinids followed a pattern of diversification that parallels the pattern described for Sphagnum. We found that the diversification of core arcellinids occurred during the Phanerozoic, which is congruent with most arcellinid fossils but not with the oldest known amoebozoan fossil (i.e. at ca. 662 or ca. 750 Myr). Overall, Sphagnum and the Hyalospheniidae exhibit different patterns of diversification. However, an extensive molecular phylogenetic analysis of distinct clades within H. papilio species complex demonstrated a correlation between the recent diversification of H. papilio, the recent diversification of Sphagnum mosses, and the establishment of peatlands. PMID:24762929

Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record.

PubMed

Park, Eunji; Hwang, Dae-Sik; Lee, Jae-Seong; Song, Jun-Im; Seo, Tae-Kun; Won, Yong-Jin

2012-01-01

The phylum Cnidaria is comprised of remarkably diverse and ecologically significant taxa, such as the reef-forming corals, and occupies a basal position in metazoan evolution. The origin of this phylum and the most recent common ancestors (MRCAs) of its modern classes remain mostly unknown, although scattered fossil evidence provides some insights on this topic. Here, we investigate the molecular divergence times of the major taxonomic groups of Cnidaria (27 Hexacorallia, 16 Octocorallia, and 5 Medusozoa) on the basis of mitochondrial DNA sequences of 13 protein-coding genes. For this analysis, the complete mitochondrial genomes of seven octocoral and two scyphozoan species were newly sequenced and combined with all available mitogenomic data from GenBank. Five reliable fossil dates were used to calibrate the Bayesian estimates of divergence times. The molecular evidence suggests that cnidarians originated 741 million years ago (Ma) (95% credible region of 686-819), and the major taxa diversified prior to the Cambrian (543 Ma). The Octocorallia and Scleractinia may have originated from radiations of survivors of the Permian-Triassic mass extinction, which matches their fossil record well. Copyright © 2011 Elsevier Inc. All rights reserved.

The origin and early evolution of Sauria: reassessing the permian Saurian fossil record and the timing of the crocodile-lizard divergence.

PubMed

Ezcurra, Martín D; Scheyer, Torsten M; Butler, Richard J

2014-01-01

Sauria is the crown-group of Diapsida and is subdivided into Lepidosauromorpha and Archosauromorpha, comprising a high percentage of the diversity of living and fossil tetrapods. The split between lepidosauromorphs and archosauromorphs (the crocodile-lizard, or bird-lizard, divergence) is considered one of the key calibration points for molecular analyses of tetrapod phylogeny. Saurians have a very rich Mesozoic and Cenozoic fossil record, but their late Paleozoic (Permian) record is problematic. Several Permian specimens have been referred to Sauria, but the phylogenetic affinity of some of these records remains questionable. We reexamine and review all of these specimens here, providing new data on early saurian evolution including osteohistology, and present a new morphological phylogenetic dataset. We support previous studies that find that no valid Permian record for Lepidosauromorpha, and we also reject some of the previous referrals of Permian specimens to Archosauromorpha. The most informative Permian archosauromorph is Protorosaurus speneri from the middle Late Permian of Western Europe. A historically problematic specimen from the Late Permian of Tanzania is redescribed and reidentified as a new genus and species of basal archosauromorph: Aenigmastropheus parringtoni. The supposed protorosaur Eorasaurus olsoni from the Late Permian of Russia is recovered among Archosauriformes and may be the oldest known member of the group but the phylogenetic support for this position is low. The assignment of Archosaurus rossicus from the latest Permian of Russia to the archosauromorph clade Proterosuchidae is supported. Our revision suggests a minimum fossil calibration date for the crocodile-lizard split of 254.7 Ma. The occurrences of basal archosauromorphs in the northern (30°N) and southern (55°S) parts of Pangea imply a wider paleobiogeographic distribution for the group during the Late Permian than previously appreciated. Early archosauromorph growth strategies appear to be more diverse than previously suggested based on new data on the osteohistology of Aenigmastropheus.

The Origin and Early Evolution of Sauria: Reassessing the Permian Saurian Fossil Record and the Timing of the Crocodile-Lizard Divergence

PubMed Central

Ezcurra, Martín D.; Scheyer, Torsten M.; Butler, Richard J.

2014-01-01

Sauria is the crown-group of Diapsida and is subdivided into Lepidosauromorpha and Archosauromorpha, comprising a high percentage of the diversity of living and fossil tetrapods. The split between lepidosauromorphs and archosauromorphs (the crocodile-lizard, or bird-lizard, divergence) is considered one of the key calibration points for molecular analyses of tetrapod phylogeny. Saurians have a very rich Mesozoic and Cenozoic fossil record, but their late Paleozoic (Permian) record is problematic. Several Permian specimens have been referred to Sauria, but the phylogenetic affinity of some of these records remains questionable. We reexamine and review all of these specimens here, providing new data on early saurian evolution including osteohistology, and present a new morphological phylogenetic dataset. We support previous studies that find that no valid Permian record for Lepidosauromorpha, and we also reject some of the previous referrals of Permian specimens to Archosauromorpha. The most informative Permian archosauromorph is Protorosaurus speneri from the middle Late Permian of Western Europe. A historically problematic specimen from the Late Permian of Tanzania is redescribed and reidentified as a new genus and species of basal archosauromorph: Aenigmastropheus parringtoni. The supposed protorosaur Eorasaurus olsoni from the Late Permian of Russia is recovered among Archosauriformes and may be the oldest known member of the group but the phylogenetic support for this position is low. The assignment of Archosaurus rossicus from the latest Permian of Russia to the archosauromorph clade Proterosuchidae is supported. Our revision suggests a minimum fossil calibration date for the crocodile-lizard split of 254.7 Ma. The occurrences of basal archosauromorphs in the northern (30°N) and southern (55°S) parts of Pangea imply a wider paleobiogeographic distribution for the group during the Late Permian than previously appreciated. Early archosauromorph growth strategies appear to be more diverse than previously suggested based on new data on the osteohistology of Aenigmastropheus. PMID:24586565

ARTIP: Automated Radio Telescope Image Processing Pipeline

NASA Astrophysics Data System (ADS)

Sharma, Ravi; Gyanchandani, Dolly; Kulkarni, Sarang; Gupta, Neeraj; Pathak, Vineet; Pande, Arti; Joshi, Unmesh

2018-02-01

The Automated Radio Telescope Image Processing Pipeline (ARTIP) automates the entire process of flagging, calibrating, and imaging for radio-interferometric data. ARTIP starts with raw data, i.e. a measurement set and goes through multiple stages, such as flux calibration, bandpass calibration, phase calibration, and imaging to generate continuum and spectral line images. Each stage can also be run independently. The pipeline provides continuous feedback to the user through various messages, charts and logs. It is written using standard python libraries and the CASA package. The pipeline can deal with datasets with multiple spectral windows and also multiple target sources which may have arbitrary combinations of flux/bandpass/phase calibrators.

Using Multiple Calibration Indices in Order to Capture the Complex Picture of What Affects Students' Accuracy of Feeling of Confidence

ERIC Educational Resources Information Center

Boekaerts, Monique; Rozendaal, Jeroen S.

2010-01-01

The present study used multiple calibration indices to capture the complex picture of fifth graders' calibration of feeling of confidence in mathematics. Specifically, the effects of gender, type of mathematical problem, instruction method, and time of measurement (before and after problem solving) on calibration skills were investigated. Fourteen…

Colonization and diversification in the African 'sky islands': insights from fossil-calibrated molecular dating of Lychnis (Caryophyllaceae).

PubMed

Gizaw, Abel; Brochmann, Christian; Nemomissa, Sileshi; Wondimu, Tigist; Masao, Catherine Aloyce; Tusiime, Felly Mugizi; Abdi, Ahmed Abdikadir; Oxelman, Bengt; Popp, Magnus; Dimitrov, Dimitar

2016-07-01

The flora on the isolated high African mountains or 'sky islands' is remarkable for its peculiar adaptations, local endemism and striking biogeographical connections to remote parts of the world. Ages of the plant lineages and the timing of their radiations have frequently been debated but remain contentious as there are few estimates based on explicit models and fossil-calibrated molecular clocks. We used the plastid region maturaseK (matK) and a Caryophylloflora paleogenica fossil to infer the age of the genus Lychnis, and constructed a data set of three plastid (matK; a ribosomal protein S16 (rps16); and an intergenic spacer (psbE-petL)) and two nuclear (internal transcribed spacer (ITS) and a region spanning exon 18-24 in the second largest subunit of RNA polymerase II (RPB2)) loci for joint estimation of the species tree and divergence time of the African representatives. The time of divergence of the African high-altitude Lychnis was placed in the late Miocene to early Pliocene. A single speciation event was inferred in the early Pliocene; subsequent speciation took place sporadically from the late Pliocene to the middle Pleistocene. We provide further support for a Eurasian origin of the African 'sky islands' floral elements, which seem to have been recruited via dispersals at different times: some old, as in Lychnis, and others very recent. We show that dispersal and diversification within Africa play an important role in shaping these isolated plant communities. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

SSTs from Fossil Corals using Sr-U Thermometry

NASA Astrophysics Data System (ADS)

Cohen, A. L.; Alpert, A.; Soucy, A.; DeCarlo, T. M.; Vasquez-Bedoya, L. F.; Blanchon, P.; Oppo, D.; Gaetani, G. A.

2017-12-01

Earth's climate varies naturally on decadal through millennial timescales. Resolving and attributing the anthropogenic influence on climate therefore, requires accurate, continuous records that exceed the duration of the short observational dataset. Sea surface temperatures (SSTs) of warm tropical regions are especially important because the tropics are regions of deep atmospheric convection that redistribute heat and moisture. The skeletons of long-lived corals are valuable archives of tropical ocean temperature, yet the pre-instrumental SST evolution of the global tropical oceans remains poorly constrained. One reason is the limited lifespan of individual coral colonies, which seldom exceeds 150-200 years. Thus, extending SST records well beyond the observational period requires use of well-dated sub-fossil material but the current coral-based temperature proxy, Sr/Ca, is not well-suited for application to non-living material. The sensitivity of the Sr/Ca-SST relationship can vary from coral to coral, limiting the accuracy with which absolute temperature and trends can be interpreted from non-living corals. To overcome this constraint, we developed a new thermometer, Sr-U, based on a robust understanding of the processes responsible for colony-to-colony variability. Our Sr-U SST calibration is derived from three coral species representing two Atlantic and one Pacific site, validated against the instrumental record of SST and spanning a temperature range of 24.5 through 28.5 °C. We applied Sr-U to U-series dated fossil corals that grew on tropical Atlantic reefs during the Little Ice Age (1450-1650 AD) and Last Interglacial (122 000 yr BP). Our results show that SSTs in the region fluctuated within 1°C of modern values, with much of the late LIA slightly cooler and the LIG slightly warmer than late 20th century SSTs. Each continuous coral-based record spans multiple decades, enabling us to identify multi-decadal AMO-like variability as a persistent characteristic of tropical Atlantic variability.

Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins

PubMed Central

Heath, Tracy A.; Ksepka, Daniel T.; Stadler, Tanja; Welch, David; Drummond, Alexei J.

2017-01-01

The total-evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples, that is, ancestors of fossil or extant species or of clades. The fossilized birth–death (FBD) process explicitly models the diversification, fossilization, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the FBD model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}${\\sim}12.7$\\end{document} Ma and most splits leading to extant species occurring in the last 2 myr. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (version 2.4) software www.beast2.org with packages SA (version at least 1.1.4) and morph-models (version at least 1.0.4) installed. [Birth–death process; calibration; divergence times; MCMC; phylogenetics.] PMID:28173531

Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales

PubMed Central

dos Reis, Mario; Thawornwattana, Yuttapong; Angelis, Konstantinos; Telford, Maximilian J.; Donoghue, Philip C.J.; Yang, Ziheng

2015-01-01

Summary The timing of divergences among metazoan lineages is integral to understanding the processes of animal evolution, placing the biological events of species divergences into the correct geological timeframe. Recent fossil discoveries and molecular clock dating studies have suggested a divergence of bilaterian phyla >100 million years before the Cambrian, when the first definite crown-bilaterian fossils occur. Most previous molecular clock dating studies, however, have suffered from limited data and biases in methodologies, and virtually all have failed to acknowledge the large uncertainties associated with the fossil record of early animals, leading to inconsistent estimates among studies. Here we use an unprecedented amount of molecular data, combined with four fossil calibration strategies (reflecting disparate and controversial interpretations of the metazoan fossil record) to obtain Bayesian estimates of metazoan divergence times. Our results indicate that the uncertain nature of ancient fossils and violations of the molecular clock impose a limit on the precision that can be achieved in estimates of ancient molecular timescales. For example, although we can assert that crown Metazoa originated during the Cryogenian (with most crown-bilaterian phyla diversifying during the Ediacaran), it is not possible with current data to pinpoint the divergence events with sufficient accuracy to test for correlations between geological and biological events in the history of animals. Although a Cryogenian origin of crown Metazoa agrees with current geological interpretations, the divergence dates of the bilaterians remain controversial. Thus, attempts to build evolutionary narratives of early animal evolution based on molecular clock timescales appear to be premature. PMID:26603774

Phylogeny and temporal diversification of darters (Percidae: Etheostomatinae).

PubMed

Near, Thomas J; Bossu, Christen M; Bradburd, Gideon S; Carlson, Rose L; Harrington, Richard C; Hollingsworth, Phillip R; Keck, Benjamin P; Etnier, David A

2011-10-01

Discussions aimed at resolution of the Tree of Life are most often focused on the interrelationships of major organismal lineages. In this study, we focus on the resolution of some of the most apical branches in the Tree of Life through exploration of the phylogenetic relationships of darters, a species-rich clade of North American freshwater fishes. With a near-complete taxon sampling of close to 250 species, we aim to investigate strategies for efficient multilocus data sampling and the estimation of divergence times using relaxed-clock methods when a clade lacks a fossil record. Our phylogenetic data set comprises a single mitochondrial DNA (mtDNA) gene and two nuclear genes sampled from 245 of the 248 darter species. This dense sampling allows us to determine if a modest amount of nuclear DNA sequence data can resolve relationships among closely related animal species. Darters lack a fossil record to provide age calibration priors in relaxed-clock analyses. Therefore, we use a near-complete species-sampled phylogeny of the perciform clade Centrarchidae, which has a rich fossil record, to assess two distinct strategies of external calibration in relaxed-clock divergence time estimates of darters: using ages inferred from the fossil record and molecular evolutionary rate estimates. Comparison of Bayesian phylogenies inferred from mtDNA and nuclear genes reveals that heterospecific mtDNA is present in approximately 12.5% of all darter species. We identify three patterns of mtDNA introgression in darters: proximal mtDNA transfer, which involves the transfer of mtDNA among extant and sympatric darter species, indeterminate introgression, which involves the transfer of mtDNA from a lineage that cannot be confidently identified because the introgressed haplotypes are not clearly referable to mtDNA haplotypes in any recognized species, and deep introgression, which is characterized by species diversification within a recipient clade subsequent to the transfer of heterospecific mtDNA. The results of our analyses indicate that DNA sequences sampled from single-copy nuclear genes can provide appreciable phylogenetic resolution for closely related animal species. A well-resolved near-complete species-sampled phylogeny of darters was estimated with Bayesian methods using a concatenated mtDNA and nuclear gene data set with all identified heterospecific mtDNA haplotypes treated as missing data. The relaxed-clock analyses resulted in very similar posterior age estimates across the three sampled genes and methods of calibration and therefore offer a viable strategy for estimating divergence times for clades that lack a fossil record. In addition, an informative rank-free clade-based classification of darters that preserves the rich history of nomenclature in the group and provides formal taxonomic communication of darter clades was constructed using the mtDNA and nuclear gene phylogeny. On the whole, the appeal of mtDNA for phylogeny inference among closely related animal species is diminished by the observations of extensive mtDNA introgression and by finding appreciable phylogenetic signal in a modest sampling of nuclear genes in our phylogenetic analyses of darters.

European Forest Cover During the Past 12,000 Years: A Palynological Reconstruction Based on Modern Analogs and Remote Sensing

PubMed Central

Zanon, Marco; Davis, Basil A. S.; Marquer, Laurent; Brewer, Simon; Kaplan, Jed O.

2018-01-01

Characterization of land cover change in the past is fundamental to understand the evolution and present state of the Earth system, the amount of carbon and nutrient stocks in terrestrial ecosystems, and the role played by land-atmosphere interactions in influencing climate. The estimation of land cover changes using palynology is a mature field, as thousands of sites in Europe have been investigated over the last century. Nonetheless, a quantitative land cover reconstruction at a continental scale has been largely missing. Here, we present a series of maps detailing the evolution of European forest cover during last 12,000 years. Our reconstructions are based on the Modern Analog Technique (MAT): a calibration dataset is built by coupling modern pollen samples with the corresponding satellite-based forest-cover data. Fossil reconstructions are then performed by assigning to every fossil sample the average forest cover of its closest modern analogs. The occurrence of fossil pollen assemblages with no counterparts in modern vegetation represents a known limit of analog-based methods. To lessen the influence of no-analog situations, pollen taxa were converted into plant functional types prior to running the MAT algorithm. We then interpolate site-specific reconstructions for each timeslice using a four-dimensional gridding procedure to create continuous gridded maps at a continental scale. The performance of the MAT is compared against methodologically independent forest-cover reconstructions produced using the REVEALS method. MAT and REVEALS estimates are most of the time in good agreement at a trend level, yet MAT regularly underestimates the occurrence of densely forested situations, requiring the application of a bias correction procedure. The calibrated MAT-based maps draw a coherent picture of the establishment of forests in Europe in the Early Holocene with the greatest forest-cover fractions reconstructed between ∼8,500 and 6,000 calibrated years BP. This forest maximum is followed by a general decline in all parts of the continent, likely as a result of anthropogenic deforestation. The continuous spatial and temporal nature of our reconstruction, its continental coverage, and gridded format make it suitable for climate, hydrological, and biogeochemical modeling, among other uses. PMID:29568303

European Forest Cover During the Past 12,000 Years: A Palynological Reconstruction Based on Modern Analogs and Remote Sensing.

PubMed

Zanon, Marco; Davis, Basil A S; Marquer, Laurent; Brewer, Simon; Kaplan, Jed O

2018-01-01

Characterization of land cover change in the past is fundamental to understand the evolution and present state of the Earth system, the amount of carbon and nutrient stocks in terrestrial ecosystems, and the role played by land-atmosphere interactions in influencing climate. The estimation of land cover changes using palynology is a mature field, as thousands of sites in Europe have been investigated over the last century. Nonetheless, a quantitative land cover reconstruction at a continental scale has been largely missing. Here, we present a series of maps detailing the evolution of European forest cover during last 12,000 years. Our reconstructions are based on the Modern Analog Technique (MAT): a calibration dataset is built by coupling modern pollen samples with the corresponding satellite-based forest-cover data. Fossil reconstructions are then performed by assigning to every fossil sample the average forest cover of its closest modern analogs. The occurrence of fossil pollen assemblages with no counterparts in modern vegetation represents a known limit of analog-based methods. To lessen the influence of no-analog situations, pollen taxa were converted into plant functional types prior to running the MAT algorithm. We then interpolate site-specific reconstructions for each timeslice using a four-dimensional gridding procedure to create continuous gridded maps at a continental scale. The performance of the MAT is compared against methodologically independent forest-cover reconstructions produced using the REVEALS method. MAT and REVEALS estimates are most of the time in good agreement at a trend level, yet MAT regularly underestimates the occurrence of densely forested situations, requiring the application of a bias correction procedure. The calibrated MAT-based maps draw a coherent picture of the establishment of forests in Europe in the Early Holocene with the greatest forest-cover fractions reconstructed between ∼8,500 and 6,000 calibrated years BP. This forest maximum is followed by a general decline in all parts of the continent, likely as a result of anthropogenic deforestation. The continuous spatial and temporal nature of our reconstruction, its continental coverage, and gridded format make it suitable for climate, hydrological, and biogeochemical modeling, among other uses.

Impacts of curatorial and research practices on the preservation of fossil hominid remains.

PubMed

Le Cabec, Adeline; Toussaint, Michel

2017-12-30

Fossil remains are the only physical evidence of past forms of life which researchers can use to study the evolutionary biology of a species, especially regarding the human lineage. We review and consider the way in which the conditions surrounding a fossil's discovery and its use for scientific research impacts its long-term preservation. The deterioration of the body starts soon after death, continues in the sediments and only a subsample of the anatomical elements will persist and may finally be unearthed by archeologists. From their recovery onwards, fossil remains are exposed to many sources of further damage: from handling, restoration, measuring to invasive sampling. On the one hand, curators are faced with the inherent challenge of balancing their responsibility to protect fossil specimens with allowing researchers to perform specific analyses or invasive sampling detrimental to the preservation of the fossil. On the other hand, scientists may find their analyses complicated by multiple factors including taphonomy, or restoration techniques (e.g., consolidants, cleaning chemicals). We provide several historical examples illustrating the complex nature of the factors acting on fossil preservation. We discuss concerns about producing and sharing (digital) data from fossils. Finally, we also suggest and support some curatorial practices which maximize the traceability of treatments underwent by a fossil.

Phylogeny of Dictyoptera: Dating the Origin of Cockroaches, Praying Mantises and Termites with Molecular Data and Controlled Fossil Evidence

PubMed Central

Legendre, Frédéric; Nel, André; Svenson, Gavin J.; Robillard, Tony; Pellens, Roseli; Grandcolas, Philippe

2015-01-01

Understanding the origin and diversification of organisms requires a good phylogenetic estimate of their age and diversification rates. This estimate can be difficult to obtain when samples are limited and fossil records are disputed, as in Dictyoptera. To choose among competing hypotheses of origin for dictyopteran suborders, we root a phylogenetic analysis (~800 taxa, 10 kbp) within a large selection of outgroups and calibrate datings with fossils attributed to lineages with clear synapomorphies. We find the following topology: (mantises, (other cockroaches, (Cryptocercidae, termites)). Our datings suggest that crown-Dictyoptera—and stem-mantises—would date back to the Late Carboniferous (~ 300 Mya), a result compatible with the oldest putative fossil of stem-dictyoptera. Crown-mantises, however, would be much more recent (~ 200 Mya; Triassic/Jurassic boundary). This pattern (i.e., old origin and more recent diversification) suggests a scenario of replacement in carnivory among polyneopterous insects. The most recent common ancestor of (cockroaches + termites) would date back to the Permian (~275 Mya), which contradicts the hypothesis of a Devonian origin of cockroaches. Stem-termites would date back to the Triassic/Jurassic boundary, which refutes a Triassic origin. We suggest directions in extant and extinct species sampling to sharpen this chronological framework and dictyopteran evolutionary studies. PMID:26200914

Nuclear's role in 21. century Pacific rim energy use

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singer, Clifford; Taylor, J'Tia

2007-07-01

Extrapolations contrast the future of nuclear energy use in Japan and the Republic of Korea (ROK) to that of the Association of Southeast Asian Nations (ASEAN). Japan can expect a gradual rise in the nuclear fraction of a nearly constant total energy use rate as the use of fossil fuels declines. ROK nuclear energy rises gradually with total energy use. ASEAN's total nuclear energy use rate can rapidly approach that of the ROK if Indonesia and Vietnam make their current nuclear energy targets by 2020, but experience elsewhere suggests that nuclear energy growth may be slower than planned. Extrapolations aremore » based on econometric calibration to a utility optimization model of the impact of growth of population, gross domestic product, total energy use, and cumulative fossil carbon use. Fractions of total energy use from fluid fossil fuels, coal, water-driven electrical power production, nuclear energy, and wind and solar electric energy sources are fit to market fractions data. Where historical data is insufficient for extrapolation, plans for non-fossil energy are used as a guide. Extrapolations suggest much more U.S. nuclear energy and spent nuclear fuel generation than for the ROK and ASEAN until beyond the first half of the twenty-first century. (authors)« less

Inferring Arthropod Phylogeny: Fossils and their Interaction with Other Data Sources.

PubMed

Edgecombe, Gregory D

2017-09-01

The past five years have witnessed a renewed interest in discrete morphological characters as a source of phylogenetic data, after a decade or more of their dismissal in favor of molecules-only approaches. This has stemmed in large part from refinements in total evidence dating, which requires morphological character matrices for extinct and extant taxa as well as temporal data from fossils. The unique contribution of palaeontology is stem groups, revealing the sequence of character acquisition in long-branch terminals and otherwise unknown character combinations and/or character states in extinct phenotypes. The origin of mandibles exemplifies an integrative approach to analyzing the origin of a complex phenotypic feature using molecular, anatomical, and palaeontological data: (1) transcriptomics defends a single origin of mandibles in the clade Mandibulata; (2) Cambrian fossils inform on morphological changes in the gnathal appendages in the mandibulate stem group; (3) molecular dating, calibrated by fossils in novel modes of exceptional preservation, draws the mandibulate crown group into the early Cambrian and constrains the timing of character evolution; and (4) functional studies in extant taxa identify genes that specify mandibular identity from a maxilla and, ultimately, a trunk limb-like precursor, as predicted by the serial similarity of these appendages in Cambrian stem-group fossils. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Molecular and Paleontological Evidence for a Post-Cretaceous Origin of Rodents

PubMed Central

Wu, Shaoyuan; Wu, Wenyu; Zhang, Fuchun; Ye, Jie; Ni, Xijun; Sun, Jimin; Edwards, Scott V.; Meng, Jin; Organ, Chris L.

2012-01-01

The timing of the origin and diversification of rodents remains controversial, due to conflicting results from molecular clocks and paleontological data. The fossil record tends to support an early Cenozoic origin of crown-group rodents. In contrast, most molecular studies place the origin and initial diversification of crown-Rodentia deep in the Cretaceous, although some molecular analyses have recovered estimated divergence times that are more compatible with the fossil record. Here we attempt to resolve this conflict by carrying out a molecular clock investigation based on a nine-gene sequence dataset and a novel set of seven fossil constraints, including two new rodent records (the earliest known representatives of Cardiocraniinae and Dipodinae). Our results indicate that rodents originated around 61.7–62.4 Ma, shortly after the Cretaceous/Paleogene (K/Pg) boundary, and diversified at the intraordinal level around 57.7–58.9 Ma. These estimates are broadly consistent with the paleontological record, but challenge previous molecular studies that place the origin and early diversification of rodents in the Cretaceous. This study demonstrates that, with reliable fossil constraints, the incompatibility between paleontological and molecular estimates of rodent divergence times can be eliminated using currently available tools and genetic markers. Similar conflicts between molecular and paleontological evidence bedevil attempts to establish the origination times of other placental groups. The example of the present study suggests that more reliable fossil calibration points may represent the key to resolving these controversies. PMID:23071573

On the importance of stratigraphic control for vertebrate fossil sites in Channel Islands National Park, California, USA: Examples from new Mammuthus finds on San Miguel Island

USGS Publications Warehouse

Pigati, Jeffery S.; Muhs, Daniel R.; McGeehin, John P.

2016-01-01

Quaternary vertebrate fossils, most notably mammoth remains, are relatively common on the northern Channel Islands of California. Well-preserved cranial, dental, and appendicular elements of Mammuthus exilis (pygmy mammoth) and Mammuthus columbi (Columbian mammoth) have been recovered from hundreds of localities on the islands during the past half-century or more. Despite this paleontological wealth, the geologic context of the fossils is described in the published literature only briefly or not at all, which has hampered the interpretation of associated 14C ages and reconstruction of past environmental conditions. We recently discovered a partial tusk, several large bones, and a tooth enamel plate (all likely mammoth) at two sites on the northwest flank of San Miguel Island, California. At both localities, we documented the stratigraphic context of the fossils, described the host sediments in detail, and collected charcoal and terrestrial gastropod shells for radiocarbon dating. The resulting 14C ages indicate that the mammoths were present on San Miguel Island between ∼20 and 17 ka as well as between ∼14 and 13 ka (thousands of calibrated 14C years before present), similar to other mammoth sites on San Miguel, Santa Cruz, and Santa Rosa Islands. In addition to documenting the geologic context and ages of the fossils, we present a series of protocols for documenting and reporting geologic and stratigraphic information at fossil sites on the California Channel Islands in general, and in Channel Islands National Park in particular, so that pertinent information is collected prior to excavation of vertebrate materials, thus maximizing their scientific value.

Multiple calibrator measurements improve accuracy and stability estimates of automated assays.

PubMed

Akbas, Neval; Budd, Jeffrey R; Klee, George G

2016-01-01

The effects of combining multiple calibrations on assay accuracy (bias) and measurement of calibration stability were investigated for total triiodothyronine (TT3), vitamin B12 and luteinizing hormone (LH) using Beckman Coulter's Access 2 analyzer. Three calibration procedures (CC1, CC2 and CC3) combined 12, 34 and 56 calibrator measurements over 1, 2, and 3 days. Bias was calculated between target values and average measured value over 3 consecutive days after calibration. Using regression analysis of calibrator measurements versus measurement date, calibration stability was determined as the maximum number of days before a calibrator measurement exceeded 5% tolerance limits. Competitive assays (TT3, vitamin B12) had positive time regression slopes, while sandwich assay (LH) had a negative slope. Bias values for TT3 were -2.49%, 1.49%, and -0.50% using CC1, CC2 and CC3 respectively, with calibrator stability of 32, 20, and 30 days. Bias values for vitamin B12 were 2.44%, 0.91%, and -0.50%, with calibrator stability of 4, 9, and 12 days. Bias values for LH were 2.26%, 1.44% and -0.29% with calibrator stability of >43, 39 and 36 days. Measured stability was more consistent across calibration procedures using percent change rather than difference from target: 26 days for TT3, 12 days for B12 and 31 days for LH. Averaging over multiple calibrations produced smaller bias, consistent with improved accuracy. Time regression slopes in percent change were unaffected by number of calibration measurements but calibrator stability measured from the target value was highly affected by the calibrator value at time zero.

Mg/Ca-temperature calibration for costate Bulimina species (B. costata, B. inflata, B. mexicana): A paleothermometer for hypoxic environments

NASA Astrophysics Data System (ADS)

Grunert, Patrick; Rosenthal, Yair; Jorissen, Frans; Holbourn, Ann; Zhou, Xiaoli; Piller, Werner E.

2018-01-01

Costate species of Bulimina are cosmopolitan, infaunal benthic foraminifers which are common in the fossil record since the Paleogene. In the present study, we evaluate the temperature dependency of Mg/Ca ratios in Bulimina inflata, B. mexicana and B. costata from an extensive set of core-top samples from the Atlantic, Pacific and Indian Oceans. The results show no significant offset in Mg/Ca values between costate morphospecies when present in the same sample. The apparent lack of significant inter-specific/inter-morphotype differences amongst the analyzed costate buliminids allows for the combined use of their data-sets for our core-top calibration. Over a bottom-water temperature (BWT) range of 3-13 °C, the Bulimina species show a sensitivity of ∼0.12 mmol/mol/°C which is comparable to that of epifaunal Cibicidoides species and higher than that of the shallow infaunal Uvigerina spp., the most commonly used taxon in Mg/Ca-based palaeotemperature reconstruction. The reliability and accuracy of the new Mg/Ca-temperature calibration is corroborated in the fossil record by a case study in the Timor Sea which demonstrates the presence of southern-sourced waters at intermediate depths for the past 26,000 years. Costate species of Bulimina might thus provide a valuable alternative for BWT reconstruction in mesotrophic to eutrophic settings where many of the commonly used (more oligotrophic) species are rare or absent, and be particularly useful in hypoxic settings such as permanent upwelling zones where costate buliminids often dominate foraminiferal assemblages. The evaluation further reveals a mean positive offset of ∼0.2 mmol/mol of the Atlantic data-set over the Indo-Pacific data-set which contributes to the scatter in our calibration. Although an explanation for this offset is not straightforward and further research is necessary, we hypothesize that different levels of export production and carbonate ion concentrations in pore waters are likely reasons.

A timeline for terrestrialization: consequences for the carbon cycle in the Palaeozoic

PubMed Central

Kenrick, Paul; Wellman, Charles H.; Schneider, Harald; Edgecombe, Gregory D.

2012-01-01

The geochemical carbon cycle is strongly influenced by life on land, principally through the effects of carbon sequestration and the weathering of calcium and magnesium silicates in surface rocks and soils. Knowing the time of origin of land plants and animals and also of key organ systems (e.g. plant vasculature, roots, wood) is crucial to understand the development of the carbon cycle and its effects on other Earth systems. Here, we compare evidence from fossils with calibrated molecular phylogenetic trees (timetrees) of living plants and arthropods. We show that different perspectives conflict in terms of the relative timing of events, the organisms involved and the pattern of diversification of various groups. Focusing on the fossil record, we highlight a number of key biases that underpin some of these conflicts, the most pervasive and far-reaching being the extent and nature of major facies changes in the rock record. These effects probably mask an earlier origin of life on land than is evident from certain classes of fossil data. If correct, this would have major implications in understanding the carbon cycle during the Early Palaeozoic. PMID:22232764

Methods for the quantitative comparison of molecular estimates of clade age and the fossil record.

PubMed

Clarke, Julia A; Boyd, Clint A

2015-01-01

Approaches quantifying the relative congruence, or incongruence, of molecular divergence estimates and the fossil record have been limited. Previously proposed methods are largely node specific, assessing incongruence at particular nodes for which both fossil data and molecular divergence estimates are available. These existing metrics, and other methods that quantify incongruence across topologies including entirely extinct clades, have so far not taken into account uncertainty surrounding both the divergence estimates and the ages of fossils. They have also treated molecular divergence estimates younger than previously assessed fossil minimum estimates of clade age as if they were the same as cases in which they were older. However, these cases are not the same. Recovered divergence dates younger than compared oldest known occurrences require prior hypotheses regarding the phylogenetic position of the compared fossil record and standard assumptions about the relative timing of morphological and molecular change to be incorrect. Older molecular dates, by contrast, are consistent with an incomplete fossil record and do not require prior assessments of the fossil record to be unreliable in some way. Here, we compare previous approaches and introduce two new descriptive metrics. Both metrics explicitly incorporate information on uncertainty by utilizing the 95% confidence intervals on estimated divergence dates and data on stratigraphic uncertainty concerning the age of the compared fossils. Metric scores are maximized when these ranges are overlapping. MDI (minimum divergence incongruence) discriminates between situations where molecular estimates are younger or older than known fossils reporting both absolute fit values and a number score for incompatible nodes. DIG range (divergence implied gap range) allows quantification of the minimum increase in implied missing fossil record induced by enforcing a given set of molecular-based estimates. These metrics are used together to describe the relationship between time trees and a set of fossil data, which we recommend be phylogenetically vetted and referred on the basis of apomorphy. Differences from previously proposed metrics and the utility of MDI and DIG range are illustrated in three empirical case studies from angiosperms, ostracods, and birds. These case studies also illustrate the ways in which MDI and DIG range may be used to assess time trees resultant from analyses varying in calibration regime, divergence dating approach or molecular sequence data analyzed. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Quantifying pollen-vegetation relationships to reconstruct ancient forests using 19th-century forest composition and pollen data

USGS Publications Warehouse

Dawson, Andria; Paciorek, Christopher J.; McLachlan, Jason S.; Goring, Simon; Williams, John W.; Jackson, Stephen T.

2016-01-01

Mitigation of climate change and adaptation to its effects relies partly on how effectively land-atmosphere interactions can be quantified. Quantifying composition of past forest ecosystems can help understand processes governing forest dynamics in a changing world. Fossil pollen data provide information about past forest composition, but rigorous interpretation requires development of pollen-vegetation models (PVMs) that account for interspecific differences in pollen production and dispersal. Widespread and intensified land-use over the 19th and 20th centuries may have altered pollen-vegetation relationships. Here we use STEPPS, a Bayesian hierarchical spatial PVM, to estimate key process parameters and associated uncertainties in the pollen-vegetation relationship. We apply alternate dispersal kernels, and calibrate STEPPS using a newly developed Euro-American settlement-era calibration data set constructed from Public Land Survey data and fossil pollen samples matched to the settlement-era using expert elicitation. Models based on the inverse power-law dispersal kernel outperformed those based on the Gaussian dispersal kernel, indicating that pollen dispersal kernels are fat tailed. Pine and birch have the highest pollen productivities. Pollen productivity and dispersal estimates are generally consistent with previous understanding from modern data sets, although source area estimates are larger. Tests of model predictions demonstrate the ability of STEPPS to predict regional compositional patterns.

Quantifying pollen-vegetation relationships to reconstruct ancient forests using 19th-century forest composition and pollen data

NASA Astrophysics Data System (ADS)

Dawson, Andria; Paciorek, Christopher J.; McLachlan, Jason S.; Goring, Simon; Williams, John W.; Jackson, Stephen T.

2016-04-01

Mitigation of climate change and adaptation to its effects relies partly on how effectively land-atmosphere interactions can be quantified. Quantifying composition of past forest ecosystems can help understand processes governing forest dynamics in a changing world. Fossil pollen data provide information about past forest composition, but rigorous interpretation requires development of pollen-vegetation models (PVMs) that account for interspecific differences in pollen production and dispersal. Widespread and intensified land-use over the 19th and 20th centuries may have altered pollen-vegetation relationships. Here we use STEPPS, a Bayesian hierarchical spatial PVM, to estimate key process parameters and associated uncertainties in the pollen-vegetation relationship. We apply alternate dispersal kernels, and calibrate STEPPS using a newly developed Euro-American settlement-era calibration data set constructed from Public Land Survey data and fossil pollen samples matched to the settlement-era using expert elicitation. Models based on the inverse power-law dispersal kernel outperformed those based on the Gaussian dispersal kernel, indicating that pollen dispersal kernels are fat tailed. Pine and birch have the highest pollen productivities. Pollen productivity and dispersal estimates are generally consistent with previous understanding from modern data sets, although source area estimates are larger. Tests of model predictions demonstrate the ability of STEPPS to predict regional compositional patterns.

The emergence of lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (decapoda: achelata, astacidea, glypheidea, polychelida).

PubMed

Bracken-Grissom, Heather D; Ahyong, Shane T; Wilkinson, Richard D; Feldmann, Rodney M; Schweitzer, Carrie E; Breinholt, Jesse W; Bendall, Matthew; Palero, Ferran; Chan, Tin-Yam; Felder, Darryl L; Robles, Rafael; Chu, Ka-Hou; Tsang, Ling-Ming; Kim, Dohyup; Martin, Joel W; Crandall, Keith A

2014-07-01

Lobsters are a ubiquitous and economically important group of decapod crustaceans that include the infraorders Polychelida, Glypheidea, Astacidea and Achelata. They include familiar forms such as the spiny, slipper, clawed lobsters and crayfish and unfamiliar forms such as the deep-sea and "living fossil" species. The high degree of morphological diversity among these infraorders has led to a dynamic classification and conflicting hypotheses of evolutionary relationships. In this study, we estimated phylogenetic relationships among the major groups of all lobster families and 94% of the genera using six genes (mitochondrial and nuclear) and 195 morphological characters across 173 species of lobsters for the most comprehensive sampling to date. Lobsters were recovered as a non-monophyletic assemblage in the combined (molecular + morphology) analysis. All families were monophyletic, with the exception of Cambaridae, and 7 of 79 genera were recovered as poly- or paraphyletic. A rich fossil history coupled with dense taxon coverage allowed us to estimate and compare divergence times and origins of major lineages using two drastically different approaches. Age priors were constructed and/or included based on fossil age information or fossil discovery, age, and extant species count data. Results from the two approaches were largely congruent across deep to shallow taxonomic divergences across major lineages. The origin of the first lobster-like decapod (Polychelida) was estimated in the Devonian (∼409-372 Ma) with all infraorders present in the Carboniferous (∼353-318 Ma). Fossil calibration subsampling studies examined the influence of sampling density (number of fossils) and placement (deep, middle, and shallow) on divergence time estimates. Results from our study suggest including at least 1 fossil per 10 operational taxonomic units (OTUs) in divergence dating analyses. [Dating; decapods; divergence; lobsters; molecular; morphology; phylogenetics.]. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.For Permissions, please email: journals.permissions@oup.com.

Major Radiations in the Evolution of Caviid Rodents: Reconciling Fossils, Ghost Lineages, and Relaxed Molecular Clocks

PubMed Central

Pérez, María Encarnación; Pol, Diego

2012-01-01

Background Caviidae is a diverse group of caviomorph rodents that is broadly distributed in South America and is divided into three highly divergent extant lineages: Caviinae (cavies), Dolichotinae (maras), and Hydrochoerinae (capybaras). The fossil record of Caviidae is only abundant and diverse since the late Miocene. Caviids belongs to Cavioidea sensu stricto (Cavioidea s.s.) that also includes a diverse assemblage of extinct taxa recorded from the late Oligocene to the middle Miocene of South America (“eocardiids”). Results A phylogenetic analysis combining morphological and molecular data is presented here, evaluating the time of diversification of selected nodes based on the calibration of phylogenetic trees with fossil taxa and the use of relaxed molecular clocks. This analysis reveals three major phases of diversification in the evolutionary history of Cavioidea s.s. The first two phases involve two successive radiations of extinct lineages that occurred during the late Oligocene and the early Miocene. The third phase consists of the diversification of Caviidae. The initial split of caviids is dated as middle Miocene by the fossil record. This date falls within the 95% higher probability distribution estimated by the relaxed Bayesian molecular clock, although the mean age estimate ages are 3.5 to 7 Myr older. The initial split of caviids is followed by an obscure period of poor fossil record (refered here as the Mayoan gap) and then by the appearance of highly differentiated modern lineages of caviids, which evidentially occurred at the late Miocene as indicated by both the fossil record and molecular clock estimates. Conclusions The integrated approach used here allowed us identifying the agreements and discrepancies of the fossil record and molecular clock estimates on the timing of the major events in cavioid evolution, revealing evolutionary patterns that would not have been possible to gather using only molecular or paleontological data alone. PMID:23144757

Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time

PubMed Central

O'Connor, Anne; Wills, Matthew A.

2016-01-01

The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpinned claims about temporal and taxonomic patterns of completeness in the fossil record. The most widely used stratigraphic congruence indices are the stratigraphic consistency index (SCI), the modified Manhattan stratigraphic measure (MSM*), and the gap excess ratio (GER) (plus its derivatives; the topological GER and the modified GER). Many factors are believed to variously bias these indices, with several empirical and simulation studies addressing some subset of the putative interactions. This study combines both approaches to quantify the effects (on all five indices) of eight variables reasoned to constrain the distribution of possible values (the number of taxa, tree balance, tree resolution, range of first occurrence (FO) dates, center of gravity of FO dates, the variability of FO dates, percentage of extant taxa, and percentage of taxa with no fossil record). Our empirical data set comprised 647 published animal and plant cladograms spanning the entire Phanerozoic, and for these data we also modeled the effects of mean age of FOs (as a proxy for clade age), the taxonomic rank of the clade, and the higher taxonomic group to which it belonged. The center of gravity of FO dates had not been investigated hitherto, and this was found to correlate most strongly with some measures of stratigraphic congruence in our empirical study (top-heavy clades had better congruence). The modified GER was the index least susceptible to bias. We found significant differences across higher taxa for all indices; arthropods had lower congruence and tetrapods higher congruence. Stratigraphic congruence—however measured—also varied throughout the Phanerozoic, reflecting the taxonomic composition of our sample. Notably, periods containing a high proportion of arthropods had poorer congruence overall than those with higher proportions of tetrapods. [Fossil calibration; gap excess ratio; manhattan stratigraphic metric; molecular clocks; stratigraphic congruence.] PMID:27155010

Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time.

PubMed

O'Connor, Anne; Wills, Matthew A

2016-09-01

The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpinned claims about temporal and taxonomic patterns of completeness in the fossil record. The most widely used stratigraphic congruence indices are the stratigraphic consistency index (SCI), the modified Manhattan stratigraphic measure (MSM*), and the gap excess ratio (GER) (plus its derivatives; the topological GER and the modified GER). Many factors are believed to variously bias these indices, with several empirical and simulation studies addressing some subset of the putative interactions. This study combines both approaches to quantify the effects (on all five indices) of eight variables reasoned to constrain the distribution of possible values (the number of taxa, tree balance, tree resolution, range of first occurrence (FO) dates, center of gravity of FO dates, the variability of FO dates, percentage of extant taxa, and percentage of taxa with no fossil record). Our empirical data set comprised 647 published animal and plant cladograms spanning the entire Phanerozoic, and for these data we also modeled the effects of mean age of FOs (as a proxy for clade age), the taxonomic rank of the clade, and the higher taxonomic group to which it belonged. The center of gravity of FO dates had not been investigated hitherto, and this was found to correlate most strongly with some measures of stratigraphic congruence in our empirical study (top-heavy clades had better congruence). The modified GER was the index least susceptible to bias. We found significant differences across higher taxa for all indices; arthropods had lower congruence and tetrapods higher congruence. Stratigraphic congruence-however measured-also varied throughout the Phanerozoic, reflecting the taxonomic composition of our sample. Notably, periods containing a high proportion of arthropods had poorer congruence overall than those with higher proportions of tetrapods. [Fossil calibration; gap excess ratio; manhattan stratigraphic metric; molecular clocks; stratigraphic congruence.]. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

Livistona palms in Australia: ancient relics or opportunistic immigrants?

PubMed

Crisp, Michael D; Isagi, Yuji; Kato, Yohei; Cook, Lyn G; Bowman, David M J S

2010-02-01

Eighteen of the 34 species of the fan palm genus Livistona (Arecaceae) are restricted to Australia and southern New Guinea, east of Wallace's Line, an ancient biogeographic boundary between the former supercontinents Laurasia and Gondwana. The remaining species extend from SE Asia to Africa, west of Wallace's Line. Competing hypotheses contend that Livistona is (a) ancient, its current distribution a relict of the supercontinents, or (b) a Miocene immigrant from the north into Australia as it drifted towards Asia. We have tested these hypotheses using Bayesian and penalized likelihood molecular dating based on 4Kb of nuclear and chloroplast DNA sequences with multiple fossil calibration points. Ancestral areas and biomes were reconstructed using parsimony and maximum likelihood. We found strong support for the second hypothesis, that a single Livistona ancestor colonized Australia from the north about 10-17Ma. Spread and diversification of the genus within Australia was likely favoured by a transition from the aseasonal wet to monsoonal biome, to which it could have been preadapted by fire-tolerance. Copyright (c) 2009 Elsevier Inc. All rights reserved.

Phylogeny and Divergence Times of Lemurs Inferred with Recent and Ancient Fossils in the Tree.

PubMed

Herrera, James P; Dávalos, Liliana M

2016-09-01

Paleontological and neontological systematics seek to answer evolutionary questions with different data sets. Phylogenies inferred for combined extant and extinct taxa provide novel insights into the evolutionary history of life. Primates have an extensive, diverse fossil record and molecular data for living and extinct taxa are rapidly becoming available. We used two models to infer the phylogeny and divergence times for living and fossil primates, the tip-dating (TD) and fossilized birth-death process (FBD). We collected new morphological data, especially on the living and extinct endemic lemurs of Madagascar. We combined the morphological data with published DNA sequences to infer near-complete (88% of lemurs) time-calibrated phylogenies. The results suggest that primates originated around the Cretaceous-Tertiary boundary, slightly earlier than indicated by the fossil record and later than previously inferred from molecular data alone. We infer novel relationships among extinct lemurs, and strong support for relationships that were previously unresolved. Dates inferred with TD were significantly older than those inferred with FBD, most likely related to an assumption of a uniform branching process in the TD compared with a birth-death process assumed in the FBD. This is the first study to combine morphological and DNA sequence data from extinct and extant primates to infer evolutionary relationships and divergence times, and our results shed new light on the tempo of lemur evolution and the efficacy of combined phylogenetic analyses. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Toward a standard line for use in multibeam echo sounder calibration

NASA Astrophysics Data System (ADS)

Weber, Thomas C.; Rice, Glen; Smith, Michael

2018-06-01

A procedure is suggested in which a relative calibration for the intensity output of a multibeam echo sounder (MBES) can be performed. This procedure identifies a common survey line (i.e., a standard line), over which acoustic backscatter from the seafloor is collected with multiple MBES systems or by the same system multiple times. A location on the standard line which exhibits temporal stability in its seafloor backscatter response is used to bring the intensity output of the multiple MBES systems to a common reference. This relative calibration procedure has utility for MBES users wishing to generate an aggregate seafloor backscatter mosaic using multiple systems, revisiting an area to detect changes in substrate type, and comparing substrate types in the same general area but with different systems or different system settings. The calibration procedure is demonstrated using three different MBES systems over 3 different years in New Castle, NH, USA.

A Complete Fossil-Calibrated Phylogeny of Seed Plant Families as a Tool for Comparative Analyses: Testing the ‘Time for Speciation’ Hypothesis

PubMed Central

Harris, Liam W.; Davies, T. Jonathan

2016-01-01

Explaining the uneven distribution of species richness across the branches of the tree of life has been a major challenge for evolutionary biologists. Advances in phylogenetic reconstruction, allowing the generation of large, well-sampled, phylogenetic trees have provided an opportunity to contrast competing hypotheses. Here, we present a new time-calibrated phylogeny of seed plant families using Bayesian methods and 26 fossil calibrations. While there are various published phylogenetic trees for plants which have a greater density of species sampling, we are still a long way from generating a complete phylogeny for all ~300,000+ plants. Our phylogeny samples all seed plant families and is a useful tool for comparative analyses. We use this new phylogenetic hypothesis to contrast two alternative explanations for differences in species richness among higher taxa: time for speciation versus ecological limits. We calculated net diversification rate for each clade in the phylogeny and assessed the relationship between clade age and species richness. We then fit models of speciation and extinction to individual branches in the tree to identify major rate-shifts. Our data suggest that the majority of lineages are diversifying very slowly while a few lineages, distributed throughout the tree, are diversifying rapidly. Diversification is unrelated to clade age, no matter the age range of the clades being examined, contrary to both the assumption of an unbounded lineage increase through time, and the paradigm of fixed ecological limits. These findings are consistent with the idea that ecology plays a role in diversification, but rather than imposing a fixed limit, it may have variable effects on per lineage diversification rates through time. PMID:27706173

Early evolution of the angiosperm clade Asteraceae in the Cretaceous of Antarctica.

PubMed

Barreda, Viviana D; Palazzesi, Luis; Tellería, Maria C; Olivero, Eduardo B; Raine, J Ian; Forest, Félix

2015-09-01

The Asteraceae (sunflowers and daisies) are the most diverse family of flowering plants. Despite their prominent role in extant terrestrial ecosystems, the early evolutionary history of this family remains poorly understood. Here we report the discovery of a number of fossil pollen grains preserved in dinosaur-bearing deposits from the Late Cretaceous of Antarctica that drastically pushes back the timing of assumed origin of the family. Reliably dated to ∼76-66 Mya, these specimens are about 20 million years older than previously known records for the Asteraceae. Using a phylogenetic approach, we interpreted these fossil specimens as members of an extinct early diverging clade of the family, associated with subfamily Barnadesioideae. Based on a molecular phylogenetic tree calibrated using fossils, including the ones reported here, we estimated that the most recent common ancestor of the family lived at least 80 Mya in Gondwana, well before the thermal and biogeographical isolation of Antarctica. Most of the early diverging lineages of the family originated in a narrow time interval after the K/P boundary, 60-50 Mya, coinciding with a pronounced climatic warming during the Late Paleocene and Early Eocene, and the scene of a dramatic rise in flowering plant diversity. Our age estimates reduce earlier discrepancies between the age of the fossil record and previous molecular estimates for the origin of the family, bearing important implications in the evolution of flowering plants in general.

The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes).

PubMed

Dornburg, Alex; Moore, Jon; Beaulieu, Jeremy M; Eytan, Ron I; Near, Thomas J

2015-01-01

One of the most striking biodiversity patterns is the uneven distribution of marine species richness, with species diversity in the Indo-Australian Archipelago (IAA) exceeding all other areas. However, the IAA formed fairly recently, and marine biodiversity hotspots have shifted across nearly half the globe since the Paleogene. Understanding how lineages have responded to shifting biodiversity hotspots represents a necessary historic perspective on the formation and maintenance of global marine biodiversity. Such evolutionary inferences are often challenged by a lack of fossil evidence that provide insights into historic patterns of abundance and diversity. The greatest diversity of squirrelfishes and soldierfishes (Holocentridae) is in the IAA, yet these fishes also represent some of the most numerous fossil taxa in deposits of the former West Tethyan biodiversity hotspot. We reconstruct the pattern of holocentrid range evolution using time-calibrated phylogenies that include most living species and several fossil lineages, demonstrating the importance of including fossil species as terminal taxa in ancestral area reconstructions. Holocentrids exhibit increased range fragmentation following the West Tethyan hotspot collapse. However, rather than originating within the emerging IAA hotspot, the IAA has acted as a reservoir for holocentrid diversity that originated in adjacent regions over deep evolutionary time scales. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Boom and bust: ancient and recent diversification in bichirs (Polypteridae: Actinopterygii), a relictual lineage of ray-finned fishes.

PubMed

Near, Thomas J; Dornburg, Alex; Tokita, Masayoshi; Suzuki, Dai; Brandley, Matthew C; Friedman, Matt

2014-04-01

Understanding the history that underlies patterns of species richness across the Tree of Life requires an investigation of the mechanisms that not only generate young species-rich clades, but also those that maintain species-poor lineages over long stretches of evolutionary time. However, diversification dynamics that underlie ancient species-poor lineages are often hidden due to a lack of fossil evidence. Using information from the fossil record and time calibrated molecular phylogenies, we investigate the history of lineage diversification in Polypteridae, which is the sister lineage of all other ray-finned fishes (Actinopterygii). Despite originating at least 390 million years (Myr) ago, molecular timetrees support a Neogene origin for the living polypterid species. Our analyses demonstrate polypterids are exceptionally species depauperate with a stem lineage duration that exceeds 380 million years (Ma) and is significantly longer than the stem lineage durations observed in other ray-finned fish lineages. Analyses of the fossil record show an early Late Cretaceous (100.5-83.6 Ma) peak in polypterid genus richness, followed by 60 Ma of low richness. The Neogene species radiation and evidence for high-diversity intervals in the geological past suggest a "boom and bust" pattern of diversification that contrasts with common perceptions of relative evolutionary stasis in so-called "living fossils." © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Ancient origins and multiple appearances of carotenoid-pigmented feathers in birds

PubMed Central

Thomas, Daniel B.; McGraw, Kevin J.; Butler, Michael W.; Carrano, Matthew T.; Madden, Odile; James, Helen F.

2014-01-01

The broad palette of feather colours displayed by birds serves diverse biological functions, including communication and camouflage. Fossil feathers provide evidence that some avian colours, like black and brown melanins, have existed for at least 160 million years (Myr), but no traces of bright carotenoid pigments in ancient feathers have been reported. Insight into the evolutionary history of plumage carotenoids may instead be gained from living species. We visually surveyed modern birds for carotenoid-consistent plumage colours (present in 2956 of 9993 species). We then used high-performance liquid chromatography and Raman spectroscopy to chemically assess the family-level distribution of plumage carotenoids, confirming their presence in 95 of 236 extant bird families (only 36 family-level occurrences had been confirmed previously). Using our data for all modern birds, we modelled the evolutionary history of carotenoid-consistent plumage colours on recent supertrees. Results support multiple independent origins of carotenoid plumage pigmentation in 13 orders, including six orders without previous reports of plumage carotenoids. Based on time calibrations from the supertree, the number of avian families displaying plumage carotenoids increased throughout the Cenozoic, and most plumage carotenoid originations occurred after the Miocene Epoch (23 Myr). The earliest origination of plumage carotenoids was reconstructed within Passeriformes, during the Palaeocene Epoch (66–56 Myr), and not at the base of crown-lineage birds. PMID:24966316

Importance of Calibration/Validation Traceability for Multi-Sensor Imaging Spectrometry Applications

NASA Technical Reports Server (NTRS)

Thome, K.

2017-01-01

Knowledge of calibration traceability is essential for ensuring the quality of data products relying on multiple sensors and especially true for imaging spectrometers. The current work discusses the expected impact that imaging spectrometers have in ensuring radiometric traceability for both multispectral and hyperspectral products. The Climate Absolute Radiance and Refractivity Observatory Pathfinder mission is used to show the role that high-accuracy imaging spectrometers can play in understanding test sites used for vicarious calibration of sensors. The associated Solar, Lunar for Absolute Reflectance Imaging Spectroradiometer calibration demonstration system is used to illustrate recent advances in laboratory radiometric calibration approaches that will allow both the use of imaging spectrometers as calibration standards as well as to ensure the consistency of the multiple imaging spectrometers expected to be on orbit in the next decade.

Consequences of Secondary Calibrations on Divergence Time Estimates.

PubMed

Schenk, John J

2016-01-01

Secondary calibrations (calibrations based on the results of previous molecular dating studies) are commonly applied in divergence time analyses in groups that lack fossil data; however, the consequences of applying secondary calibrations in a relaxed-clock approach are not fully understood. I tested whether applying the posterior estimate from a primary study as a prior distribution in a secondary study results in consistent age and uncertainty estimates. I compared age estimates from simulations with 100 randomly replicated secondary trees. On average, the 95% credible intervals of node ages for secondary estimates were significantly younger and narrower than primary estimates. The primary and secondary age estimates were significantly different in 97% of the replicates after Bonferroni corrections. Greater error in magnitude was associated with deeper than shallower nodes, but the opposite was found when standardized by median node age, and a significant positive relationship was determined between the number of tips/age of secondary trees and the total amount of error. When two secondary calibrated nodes were analyzed, estimates remained significantly different, and although the minimum and median estimates were associated with less error, maximum age estimates and credible interval widths had greater error. The shape of the prior also influenced error, in which applying a normal, rather than uniform, prior distribution resulted in greater error. Secondary calibrations, in summary, lead to a false impression of precision and the distribution of age estimates shift away from those that would be inferred by the primary analysis. These results suggest that secondary calibrations should not be applied as the only source of calibration in divergence time analyses that test time-dependent hypotheses until the additional error associated with secondary calibrations is more properly modeled to take into account increased uncertainty in age estimates.

Deep trees: Woodfall biodiversity dynamics in present and past oceans

NASA Astrophysics Data System (ADS)

Sigwart, Julia D.

2017-03-01

Marine deposits of sunken wood provide an important habitat for deep-sea biota, including an extensive wood-endemic invertebrate fauna. These habitats are important in their own right; many species on organic falls are not able to survive in other deep sea ecosystems. Evolutionary transitions of species among various chemosynthesis-based ecosystems does not proceed deliberately from organic falls toward hydrothermal vents. Polyplacophoran molluscs (chitons) are generally rare in deep-sea systems but are found in comparatively high diversity and abundance on tropical sunken wood. A new time-calibrated phylogeny for the predominantly deep-sea order Lepidopleurida shows the chiton lineages found in sunken wood habitats do not comprise a single clade or radiation, but represents a minimum of three independent radiations in the Pacific alone. Most marine invertebrate groups diversified in the deep sea following the end Cretaceous extinction event; by contrast, sunken-wood chitons may have persisted in these habitats for longer than other animals. Fossil chitons from the early Carboniferous (ca. 350 Mya) have strong similarities to modern wood-endemic taxa, yet the common ancestor of living Lepidopleurida occurred much later in the Triassic and did not apparently rely on woodfall. Clades within Lepidopleurida that occupy wood habitats in the tropical Pacific probably arose in the Jurassic, which corresponds to evidence from the fossil record, but with an additional separate colonisation more recently in the early Paleogene. Wood-endemic chiton species encompass multiple independent evolutionary origins of co-occurring wood species, and these separate lineages correspond to differences in micohabitat and feeding strategies. These patterns demonstrate the ongoing evolutionary linkages between terrestrial and deep marine environments, and the opportunistic adaptations of deep-sea organisms.

Heterogeneous Rates of Molecular Evolution and Diversification Could Explain the Triassic Age Estimate for Angiosperms.

PubMed

Beaulieu, Jeremy M; O'Meara, Brian C; Crane, Peter; Donoghue, Michael J

2015-09-01

Dating analyses based on molecular data imply that crown angiosperms existed in the Triassic, long before their undisputed appearance in the fossil record in the Early Cretaceous. Following a re-analysis of the age of angiosperms using updated sequences and fossil calibrations, we use a series of simulations to explore the possibility that the older age estimates are a consequence of (i) major shifts in the rate of sequence evolution near the base of the angiosperms and/or (ii) the representative taxon sampling strategy employed in such studies. We show that both of these factors do tend to yield substantially older age estimates. These analyses do not prove that younger age estimates based on the fossil record are correct, but they do suggest caution in accepting the older age estimates obtained using current relaxed-clock methods. Although we have focused here on the angiosperms, we suspect that these results will shed light on dating discrepancies in other major clades. ©The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Mid-Cretaceous amber fossils illuminate the past diversity of tropical lizards.

PubMed

Daza, Juan D; Stanley, Edward L; Wagner, Philipp; Bauer, Aaron M; Grimaldi, David A

2016-03-01

Modern tropical forests harbor an enormous diversity of squamates, but fossilization in such environments is uncommon and little is known about tropical lizard assemblages of the Mesozoic. We report the oldest lizard assemblage preserved in amber, providing insight into the poorly preserved but potentially diverse mid-Cretaceous paleotropics. Twelve specimens from the Albian-Cenomanian boundary of Myanmar (99 Ma) preserve fine details of soft tissue and osteology, and high-resolution x-ray computed tomography permits detailed comparisons to extant and extinct lizards. The extraordinary preservation allows several specimens to be confidently assigned to groups including stem Gekkota and stem Chamaleonidae. Other taxa are assignable to crown clades on the basis of similar traits. The detailed preservation of osteological and soft tissue characters in these specimens may facilitate their precise phylogenetic placement, making them useful calibration points for molecular divergence time estimates and potential keys for resolving conflicts in higher-order squamate relationships.

Chlorine-36 in fossil rat urine: an archive of cosmogenic nuclide deposition during the past 40,000 years.

PubMed

Plummer, M A; Phillips, F M; Fabryka-Martin, J; Turin, H J; Wigand, P E; Sharma, P

1997-07-25

Knowledge of the production history of cosmogenic nuclides, which is needed for geological and archaeological dating, has been uncertain. Measurements of chlorine-36/chlorine (36Cl/Cl) ratios in fossil packrat middens from Nevada that are radiocarbon-dated between about 38 thousand years ago (ka) and the present showed that 36Cl/Cl ratios were higher by a factor of about 2 before approximately 11 ka. This raises the possibility that cosmogenic production rates just before the close of the Pleistocene were up to 50% higher than is suggested by carbon-14 calibration data. The discrepancy could be explained by addition of low-carbon-14 carbon dioxide to the atmosphere during that period, which would have depressed atmospheric radiocarbon activity. Alternatively, climatic effects on 36Cl deposition may have enhanced the 36Cl/Cl ratios.

Mid-Cretaceous amber fossils illuminate the past diversity of tropical lizards

PubMed Central

Daza, Juan D.; Stanley, Edward L.; Wagner, Philipp; Bauer, Aaron M.; Grimaldi, David A.

2016-01-01

Modern tropical forests harbor an enormous diversity of squamates, but fossilization in such environments is uncommon and little is known about tropical lizard assemblages of the Mesozoic. We report the oldest lizard assemblage preserved in amber, providing insight into the poorly preserved but potentially diverse mid-Cretaceous paleotropics. Twelve specimens from the Albian-Cenomanian boundary of Myanmar (99 Ma) preserve fine details of soft tissue and osteology, and high-resolution x-ray computed tomography permits detailed comparisons to extant and extinct lizards. The extraordinary preservation allows several specimens to be confidently assigned to groups including stem Gekkota and stem Chamaleonidae. Other taxa are assignable to crown clades on the basis of similar traits. The detailed preservation of osteological and soft tissue characters in these specimens may facilitate their precise phylogenetic placement, making them useful calibration points for molecular divergence time estimates and potential keys for resolving conflicts in higher-order squamate relationships. PMID:26973870

First fossil of an oestroid fly (Diptera: Calyptratae: Oestroidea) and the dating of oestroid divergences.

PubMed

Cerretti, Pierfilippo; Stireman, John O; Pape, Thomas; O'Hara, James E; Marinho, Marco A T; Rognes, Knut; Grimaldi, David A

2017-01-01

Calyptrate flies include about 22,000 extant species currently classified into Hippoboscoidea (tsetse, louse, and bat flies), the muscoid grade (house flies and relatives) and the Oestroidea (blow flies, bot flies, flesh flies, and relatives). Calyptrates are abundant in nearly all terrestrial ecosystems, often playing key roles as decomposers, parasites, parasitoids, vectors of pathogens, and pollinators. For oestroids, the most diverse group within calyptrates, definitive fossils have been lacking. The first unambiguous fossil of Oestroidea is described based on a specimen discovered in amber from the Dominican Republic. The specimen was identified through digital dissection by CT scans, which provided morphological data for a cladistic analysis of its phylogenetic position among extant oestroids. The few known calyptrate fossils were used as calibration points for a molecular phylogeny (16S, 28S, CAD) to estimate the timing of major diversification events among the Oestroidea. Results indicate that: (a) the fossil belongs to the family Mesembrinellidae, and it is identified and described as Mesembrinella caenozoica sp. nov.; (b) the mesembrinellids form a sister clade to the Australian endemic Ulurumyia macalpinei (Ulurumyiidae) (McAlpine's fly), which in turn is sister to all remaining oestroids; (c) the most recent common ancestor of extant Calyptratae lived just before the K-Pg boundary (ca. 70 mya); and (d) the radiation of oestroids began in the Eocene (ca. 50 mya), with the origin of the family Mesembrinellidae dated at ca. 40 mya. These results provide new insight into the timing and rate of oestroid diversification and highlight the rapid radiation of some of the most diverse and ecologically important families of flies. ZooBank accession number-urn:lsid:zoobank.org:pub:0DC5170B-1D16-407A-889E-56EED3FE3627.

First fossil of an oestroid fly (Diptera: Calyptratae: Oestroidea) and the dating of oestroid divergences

PubMed Central

Stireman, John O.; Pape, Thomas; O’Hara, James E.; Marinho, Marco A. T.; Rognes, Knut; Grimaldi, David A.

2017-01-01

Calyptrate flies include about 22,000 extant species currently classified into Hippoboscoidea (tsetse, louse, and bat flies), the muscoid grade (house flies and relatives) and the Oestroidea (blow flies, bot flies, flesh flies, and relatives). Calyptrates are abundant in nearly all terrestrial ecosystems, often playing key roles as decomposers, parasites, parasitoids, vectors of pathogens, and pollinators. For oestroids, the most diverse group within calyptrates, definitive fossils have been lacking. The first unambiguous fossil of Oestroidea is described based on a specimen discovered in amber from the Dominican Republic. The specimen was identified through digital dissection by CT scans, which provided morphological data for a cladistic analysis of its phylogenetic position among extant oestroids. The few known calyptrate fossils were used as calibration points for a molecular phylogeny (16S, 28S, CAD) to estimate the timing of major diversification events among the Oestroidea. Results indicate that: (a) the fossil belongs to the family Mesembrinellidae, and it is identified and described as Mesembrinella caenozoica sp. nov.; (b) the mesembrinellids form a sister clade to the Australian endemic Ulurumyia macalpinei (Ulurumyiidae) (McAlpine’s fly), which in turn is sister to all remaining oestroids; (c) the most recent common ancestor of extant Calyptratae lived just before the K–Pg boundary (ca. 70 mya); and (d) the radiation of oestroids began in the Eocene (ca. 50 mya), with the origin of the family Mesembrinellidae dated at ca. 40 mya. These results provide new insight into the timing and rate of oestroid diversification and highlight the rapid radiation of some of the most diverse and ecologically important families of flies. ZooBank accession number–urn:lsid:zoobank.org:pub:0DC5170B-1D16-407A-889E-56EED3FE3627. PMID:28832610

Specimen-level phylogenetics in paleontology using the Fossilized Birth-Death model with sampled ancestors.

PubMed

Cau, Andrea

2017-01-01

Bayesian phylogenetic methods integrating simultaneously morphological and stratigraphic information have been applied increasingly among paleontologists. Most of these studies have used Bayesian methods as an alternative to the widely-used parsimony analysis, to infer macroevolutionary patterns and relationships among species-level or higher taxa. Among recently introduced Bayesian methodologies, the Fossilized Birth-Death (FBD) model allows incorporation of hypotheses on ancestor-descendant relationships in phylogenetic analyses including fossil taxa. Here, the FBD model is used to infer the relationships among an ingroup formed exclusively by fossil individuals, i.e., dipnoan tooth plates from four localities in the Ain el Guettar Formation of Tunisia. Previous analyses of this sample compared the results of phylogenetic analysis using parsimony with stratigraphic methods, inferred a high diversity (five or more genera) in the Ain el Guettar Formation, and interpreted it as an artifact inflated by depositional factors. In the analysis performed here, the uncertainty on the chronostratigraphic relationships among the specimens was included among the prior settings. The results of the analysis confirm the referral of most of the specimens to the taxa Asiatoceratodus , Equinoxiodus, Lavocatodus and Neoceratodus , but reject those to Ceratodus and Ferganoceratodus . The resulting phylogeny constrained the evolution of the Tunisian sample exclusively in the Early Cretaceous, contrasting with the previous scenario inferred by the stratigraphically-calibrated topology resulting from parsimony analysis. The phylogenetic framework also suggests that (1) the sampled localities are laterally equivalent, (2) but three localities are restricted to the youngest part of the section; both results are in agreement with previous stratigraphic analyses of these localities. The FBD model of specimen-level units provides a novel tool for phylogenetic inference among fossils but also for independent tests of stratigraphic scenarios.

Multielevation calibration of frequency-domain electromagnetic data

USGS Publications Warehouse

Minsley, Burke J.; Kass, M. Andy; Hodges, Greg; Smith, Bruce D.

2014-01-01

Systematic calibration errors must be taken into account because they can substantially impact the accuracy of inverted subsurface resistivity models derived from frequency-domain electromagnetic data, resulting in potentially misleading interpretations. We have developed an approach that uses data acquired at multiple elevations over the same location to assess calibration errors. A significant advantage is that this method does not require prior knowledge of subsurface properties from borehole or ground geophysical data (though these can be readily incorporated if available), and is, therefore, well suited to remote areas. The multielevation data were used to solve for calibration parameters and a single subsurface resistivity model that are self consistent over all elevations. The deterministic and Bayesian formulations of the multielevation approach illustrate parameter sensitivity and uncertainty using synthetic- and field-data examples. Multiplicative calibration errors (gain and phase) were found to be better resolved at high frequencies and when data were acquired over a relatively conductive area, whereas additive errors (bias) were reasonably resolved over conductive and resistive areas at all frequencies. The Bayesian approach outperformed the deterministic approach when estimating calibration parameters using multielevation data at a single location; however, joint analysis of multielevation data at multiple locations using the deterministic algorithm yielded the most accurate estimates of calibration parameters. Inversion results using calibration-corrected data revealed marked improvement in misfit, lending added confidence to the interpretation of these models.

Evolutionary History of the Asian Horned Frogs (Megophryinae): Integrative Approaches to Timetree Dating in the Absence of a Fossil Record.

PubMed

Mahony, Stephen; Foley, Nicole M; Biju, S D; Teeling, Emma C

2017-03-01

Molecular dating studies typically need fossils to calibrate the analyses. Unfortunately, the fossil record is extremely poor or presently nonexistent for many species groups, rendering such dating analysis difficult. One such group is the Asian horned frogs (Megophryinae). Sampling all generic nomina, we combined a novel ∼5 kb dataset composed of four nuclear and three mitochondrial gene fragments to produce a robust phylogeny, with an extensive external morphological study to produce a working taxonomy for the group. Expanding the molecular dataset to include out-groups of fossil-represented ancestral anuran families, we compared the priorless RelTime dating method with the widely used prior-based Bayesian timetree method, MCMCtree, utilizing a novel combination of fossil priors for anuran phylogenetic dating. The phylogeny was then subjected to ancestral phylogeographic analyses, and dating estimates were compared with likely biogeographic vicariant events. Phylogenetic analyses demonstrated that previously proposed systematic hypotheses were incorrect due to the paraphyly of genera. Molecular phylogenetic, morphological, and timetree results support the recognition of Megophryinae as a single genus, Megophrys, with a subgenus level classification. Timetree results using RelTime better corresponded with the known fossil record for the out-group anuran tree. For the priorless in-group, it also outperformed MCMCtree when node date estimates were compared with likely influential historical biogeographic events, providing novel insights into the evolutionary history of this pan-Asian anuran group. Given a relatively small molecular dataset, and limited prior knowledge, this study demonstrates that the computationally rapid RelTime dating tool may outperform more popular and complex prior reliant timetree methodologies. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A volumetric technique for fossil body mass estimation applied to Australopithecus afarensis.

PubMed

Brassey, Charlotte A; O'Mahoney, Thomas G; Chamberlain, Andrew T; Sellers, William I

2018-02-01

Fossil body mass estimation is a well established practice within the field of physical anthropology. Previous studies have relied upon traditional allometric approaches, in which the relationship between one/several skeletal dimensions and body mass in a range of modern taxa is used in a predictive capacity. The lack of relatively complete skeletons has thus far limited the potential application of alternative mass estimation techniques, such as volumetric reconstruction, to fossil hominins. Yet across vertebrate paleontology more broadly, novel volumetric approaches are resulting in predicted values for fossil body mass very different to those estimated by traditional allometry. Here we present a new digital reconstruction of Australopithecus afarensis (A.L. 288-1; 'Lucy') and a convex hull-based volumetric estimate of body mass. The technique relies upon identifying a predictable relationship between the 'shrink-wrapped' volume of the skeleton and known body mass in a range of modern taxa, and subsequent application to an articulated model of the fossil taxa of interest. Our calibration dataset comprises whole body computed tomography (CT) scans of 15 species of modern primate. The resulting predictive model is characterized by a high correlation coefficient (r 2  = 0.988) and a percentage standard error of 20%, and performs well when applied to modern individuals of known body mass. Application of the convex hull technique to A. afarensis results in a relatively low body mass estimate of 20.4 kg (95% prediction interval 13.5-30.9 kg). A sensitivity analysis on the articulation of the chest region highlights the sensitivity of our approach to the reconstruction of the trunk, and the incomplete nature of the preserved ribcage may explain the low values for predicted body mass here. We suggest that the heaviest of previous estimates would require the thorax to be expanded to an unlikely extent, yet this can only be properly tested when more complete fossils are available. Copyright © 2017 Elsevier Ltd. All rights reserved.

Step wise, multiple objective calibration of a hydrologic model for a snowmelt dominated basin

USGS Publications Warehouse

Hay, L.E.; Leavesley, G.H.; Clark, M.P.; Markstrom, S.L.; Viger, R.J.; Umemoto, M.

2006-01-01

The ability to apply a hydrologic model to large numbers of basins for forecasting purposes requires a quick and effective calibration strategy. This paper presents a step wise, multiple objective, automated procedure for hydrologic model calibration. This procedure includes the sequential calibration of a model's simulation of solar radiation (SR), potential evapotranspiration (PET), water balance, and daily runoff. The procedure uses the Shuffled Complex Evolution global search algorithm to calibrate the U.S. Geological Survey's Precipitation Runoff Modeling System in the Yampa River basin of Colorado. This process assures that intermediate states of the model (SR and PET on a monthly mean basis), as well as the water balance and components of the daily hydrograph are simulated, consistently with measured values.

The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record.

PubMed

Hsiang, Allison Y; Field, Daniel J; Webster, Timothy H; Behlke, Adam D B; Davis, Matthew B; Racicot, Rachel A; Gauthier, Jacques A

2015-05-20

The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive analytical reconstruction of the ancestor of crown snakes and the ancestor of the snake total-group, as inferred using multiple methods of ancestral state reconstruction. We use a combined-data approach that includes new information from the fossil record on extinct crown snakes, new data on the anatomy of the stem snakes Najash rionegrina, Dinilysia patagonica, and Coniophis precedens, and a deeper understanding of the distribution of phenotypic apomorphies among the major clades of fossil and Recent snakes. Additionally, we infer time-calibrated phylogenies using both new 'tip-dating' and traditional node-based approaches, providing new insights on temporal patterns in the early evolutionary history of snakes. Comprehensive ancestral state reconstructions reveal that both the ancestor of crown snakes and the ancestor of total-group snakes were nocturnal, widely foraging, non-constricting stealth hunters. They likely consumed soft-bodied vertebrate and invertebrate prey that was subequal to head size, and occupied terrestrial settings in warm, well-watered, and well-vegetated environments. The snake total-group - approximated by the Coniophis node - is inferred to have originated on land during the middle Early Cretaceous (~128.5 Ma), with the crown-group following about 20 million years later, during the Albian stage. Our inferred divergence dates provide strong evidence for a major radiation of henophidian snake diversity in the wake of the Cretaceous-Paleogene (K-Pg) mass extinction, clarifying the pattern and timing of the extant snake radiation. Although the snake crown-group most likely arose on the supercontinent of Gondwana, our results suggest the possibility that the snake total-group originated on Laurasia. Our study provides new insights into when, where, and how snakes originated, and presents the most complete picture of the early evolution of snakes to date. More broadly, we demonstrate the striking influence of including fossils and phenotypic data in combined analyses aimed at both phylogenetic topology inference and ancestral state reconstruction.

Species relationships and divergence times in beeches: new insights from the inclusion of 53 young and old fossils in a birth-death clock model.

PubMed

Renner, S S; Grimm, Guido W; Kapli, Paschalia; Denk, Thomas

2016-07-19

The fossilized birth-death (FBD) model can make use of information contained in multiple fossils representing the same clade, and we here apply this model to infer divergence times in beeches (genus Fagus), using 53 fossils and nuclear sequences for all nine species. We also apply FBD dating to the fern clade Osmundaceae, with about 12 living species and 36 fossils. Fagus nuclear sequences cannot be aligned with those of other Fagaceae, and we therefore use Bayes factors to choose among alternative root positions. The crown group of Fagus is dated to 53 (62-43) Ma; divergence of the sole American species to 44 (51-39) Ma and divergence between Central European F. sylvatica and Eastern Mediterranean F. orientalis to 8.7 (20-1.8) Ma, unexpectedly old. The FBD model can accommodate fossils as sampled ancestors or as extinct or unobserved lineages; however, this makes its raw output, which shows all fossils on short or long branches, problematic to interpret. We use hand-drawn depictions and a bipartition network to illustrate the uncertain placements of fossils. Inferred speciation and extinction rates imply approximately 5× higher evolutionary turnover in Fagus than in Osmundaceae, fitting a hypothesized low turnover in plants adapted to low-nutrient conditions.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. © 2016 The Author(s).

Species relationships and divergence times in beeches: new insights from the inclusion of 53 young and old fossils in a birth–death clock model

PubMed Central

Kapli, Paschalia; Denk, Thomas

2016-01-01

The fossilized birth–death (FBD) model can make use of information contained in multiple fossils representing the same clade, and we here apply this model to infer divergence times in beeches (genus Fagus), using 53 fossils and nuclear sequences for all nine species. We also apply FBD dating to the fern clade Osmundaceae, with about 12 living species and 36 fossils. Fagus nuclear sequences cannot be aligned with those of other Fagaceae, and we therefore use Bayes factors to choose among alternative root positions. The crown group of Fagus is dated to 53 (62–43) Ma; divergence of the sole American species to 44 (51–39) Ma and divergence between Central European F. sylvatica and Eastern Mediterranean F. orientalis to 8.7 (20–1.8) Ma, unexpectedly old. The FBD model can accommodate fossils as sampled ancestors or as extinct or unobserved lineages; however, this makes its raw output, which shows all fossils on short or long branches, problematic to interpret. We use hand-drawn depictions and a bipartition network to illustrate the uncertain placements of fossils. Inferred speciation and extinction rates imply approximately 5× higher evolutionary turnover in Fagus than in Osmundaceae, fitting a hypothesized low turnover in plants adapted to low-nutrient conditions. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. PMID:27325832

Early evolution of the angiosperm clade Asteraceae in the Cretaceous of Antarctica

PubMed Central

Barreda, Viviana D.; Palazzesi, Luis; Tellería, Maria C.; Olivero, Eduardo B.; Raine, J. Ian; Forest, Félix

2015-01-01

The Asteraceae (sunflowers and daisies) are the most diverse family of flowering plants. Despite their prominent role in extant terrestrial ecosystems, the early evolutionary history of this family remains poorly understood. Here we report the discovery of a number of fossil pollen grains preserved in dinosaur-bearing deposits from the Late Cretaceous of Antarctica that drastically pushes back the timing of assumed origin of the family. Reliably dated to ∼76–66 Mya, these specimens are about 20 million years older than previously known records for the Asteraceae. Using a phylogenetic approach, we interpreted these fossil specimens as members of an extinct early diverging clade of the family, associated with subfamily Barnadesioideae. Based on a molecular phylogenetic tree calibrated using fossils, including the ones reported here, we estimated that the most recent common ancestor of the family lived at least 80 Mya in Gondwana, well before the thermal and biogeographical isolation of Antarctica. Most of the early diverging lineages of the family originated in a narrow time interval after the K/P boundary, 60–50 Mya, coinciding with a pronounced climatic warming during the Late Paleocene and Early Eocene, and the scene of a dramatic rise in flowering plant diversity. Our age estimates reduce earlier discrepancies between the age of the fossil record and previous molecular estimates for the origin of the family, bearing important implications in the evolution of flowering plants in general. PMID:26261324

How do geological sampling biases affect studies of morphological evolution in deep time? A case study of pterosaur (Reptilia: Archosauria) disparity.

PubMed

Butler, Richard J; Brusatte, Stephen L; Andres, Brian; Benson, Roger B J

2012-01-01

A fundamental contribution of paleobiology to macroevolutionary theory has been the illumination of deep time patterns of diversification. However, recent work has suggested that taxonomic diversity counts taken from the fossil record may be strongly biased by uneven spatiotemporal sampling. Although morphological diversity (disparity) is also frequently used to examine evolutionary radiations, no empirical work has yet addressed how disparity might be affected by uneven fossil record sampling. Here, we use pterosaurs (Mesozoic flying reptiles) as an exemplar group to address this problem. We calculate multiple disparity metrics based upon a comprehensive anatomical dataset including a novel phylogenetic correction for missing data, statistically compare these metrics to four geological sampling proxies, and use multiple regression modeling to assess the importance of uneven sampling and exceptional fossil deposits (Lagerstätten). We find that range-based disparity metrics are strongly affected by uneven fossil record sampling, and should therefore be interpreted cautiously. The robustness of variance-based metrics to sample size and geological sampling suggests that they can be more confidently interpreted as reflecting true biological signals. In addition, our results highlight the problem of high levels of missing data for disparity analyses, indicating a pressing need for more theoretical and empirical work. © 2011 The Author(s). Evolution © 2011 The Society for the Study of Evolution.

Simultaneous Calibration: A Joint Optimization Approach for Multiple Kinect and External Cameras.

PubMed

Liao, Yajie; Sun, Ying; Li, Gongfa; Kong, Jianyi; Jiang, Guozhang; Jiang, Du; Cai, Haibin; Ju, Zhaojie; Yu, Hui; Liu, Honghai

2017-06-24

Camera calibration is a crucial problem in many applications, such as 3D reconstruction, structure from motion, object tracking and face alignment. Numerous methods have been proposed to solve the above problem with good performance in the last few decades. However, few methods are targeted at joint calibration of multi-sensors (more than four devices), which normally is a practical issue in the real-time systems. In this paper, we propose a novel method and a corresponding workflow framework to simultaneously calibrate relative poses of a Kinect and three external cameras. By optimizing the final cost function and adding corresponding weights to the external cameras in different locations, an effective joint calibration of multiple devices is constructed. Furthermore, the method is tested in a practical platform, and experiment results show that the proposed joint calibration method can achieve a satisfactory performance in a project real-time system and its accuracy is higher than the manufacturer's calibration.

Simultaneous Calibration: A Joint Optimization Approach for Multiple Kinect and External Cameras

PubMed Central

Liao, Yajie; Sun, Ying; Li, Gongfa; Kong, Jianyi; Jiang, Guozhang; Jiang, Du; Cai, Haibin; Ju, Zhaojie; Yu, Hui; Liu, Honghai

2017-01-01

Camera calibration is a crucial problem in many applications, such as 3D reconstruction, structure from motion, object tracking and face alignment. Numerous methods have been proposed to solve the above problem with good performance in the last few decades. However, few methods are targeted at joint calibration of multi-sensors (more than four devices), which normally is a practical issue in the real-time systems. In this paper, we propose a novel method and a corresponding workflow framework to simultaneously calibrate relative poses of a Kinect and three external cameras. By optimizing the final cost function and adding corresponding weights to the external cameras in different locations, an effective joint calibration of multiple devices is constructed. Furthermore, the method is tested in a practical platform, and experiment results show that the proposed joint calibration method can achieve a satisfactory performance in a project real-time system and its accuracy is higher than the manufacturer’s calibration. PMID:28672823

Extreme Ultraviolet Variability Experiment (EVE) Multiple EUV Grating Spectrographs (MEGS): Radiometric Calibrations and Results

NASA Technical Reports Server (NTRS)

Hock, R. A.; Woods, T. N.; Crotser, D.; Eparvier, F. G.; Woodraska, D. L.; Chamberlin, P. C.; Woods, E. C.

2010-01-01

The NASA Solar Dynamics Observatory (SDO), scheduled for launch in early 2010, incorporates a suite of instruments including the Extreme Ultraviolet Variability Experiment (EVE). EVE has multiple instruments including the Multiple Extreme ultraviolet Grating Spectrographs (MEGS) A, B, and P instruments, the Solar Aspect Monitor (SAM), and the Extreme ultraviolet SpectroPhotometer (ESP). The radiometric calibration of EVE, necessary to convert the instrument counts to physical units, was performed at the National Institute of Standards and Technology (NIST) Synchrotron Ultraviolet Radiation Facility (SURF III) located in Gaithersburg, Maryland. This paper presents the results and derived accuracy of this radiometric calibration for the MEGS A, B, P, and SAM instruments, while the calibration of the ESP instrument is addressed by Didkovsky et al. . In addition, solar measurements that were taken on 14 April 2008, during the NASA 36.240 sounding-rocket flight, are shown for the prototype EVE instruments.

Note: Improved calibration of atomic force microscope cantilevers using multiple reference cantilevers.

PubMed

Sader, John E; Friend, James R

2015-05-01

Overall precision of the simplified calibration method in J. E. Sader et al., Rev. Sci. Instrum. 83, 103705 (2012), Sec. III D, is dominated by the spring constant of the reference cantilever. The question arises: How does one take measurements from multiple reference cantilevers, and combine these results, to improve uncertainty of the reference cantilever's spring constant and hence the overall precision of the method? This question is addressed in this note. Its answer enables manufacturers to specify of a single set of data for the spring constant, resonant frequency, and quality factor, from measurements on multiple reference cantilevers. With this data set, users can trivially calibrate cantilevers of the same type.

Meta-analysis of prediction model performance across multiple studies: Which scale helps ensure between-study normality for the C-statistic and calibration measures?

PubMed

Snell, Kym Ie; Ensor, Joie; Debray, Thomas Pa; Moons, Karel Gm; Riley, Richard D

2017-01-01

If individual participant data are available from multiple studies or clusters, then a prediction model can be externally validated multiple times. This allows the model's discrimination and calibration performance to be examined across different settings. Random-effects meta-analysis can then be used to quantify overall (average) performance and heterogeneity in performance. This typically assumes a normal distribution of 'true' performance across studies. We conducted a simulation study to examine this normality assumption for various performance measures relating to a logistic regression prediction model. We simulated data across multiple studies with varying degrees of variability in baseline risk or predictor effects and then evaluated the shape of the between-study distribution in the C-statistic, calibration slope, calibration-in-the-large, and E/O statistic, and possible transformations thereof. We found that a normal between-study distribution was usually reasonable for the calibration slope and calibration-in-the-large; however, the distributions of the C-statistic and E/O were often skewed across studies, particularly in settings with large variability in the predictor effects. Normality was vastly improved when using the logit transformation for the C-statistic and the log transformation for E/O, and therefore we recommend these scales to be used for meta-analysis. An illustrated example is given using a random-effects meta-analysis of the performance of QRISK2 across 25 general practices.

Oldest Known Eucalyptus Macrofossils Are from South America

PubMed Central

Zamaloa, María C.; Nixon, Kevin C.; González, Cynthia C.; Wilf, Peter; Cúneo, N. Rubén; Johnson, Kirk R.

2011-01-01

The evolutionary history of Eucalyptus and the eucalypts, the larger clade of seven genera including Eucalyptus that today have a natural distribution almost exclusively in Australasia, is poorly documented from the fossil record. Little physical evidence exists bearing on the ancient geographical distributions or morphologies of plants within the clade. Herein, we introduce fossil material of Eucalyptus from the early Eocene (ca. 51.9 Ma) Laguna del Hunco paleoflora of Chubut Province, Argentina; specimens include multiple leaves, infructescences, and dispersed capsules, several flower buds, and a single flower. Morphological similarities that relate the fossils to extant eucalypts include leaf shape, venation, and epidermal oil glands; infructescence structure; valvate capsulate fruits; and operculate flower buds. The presence of a staminophore scar on the fruits links them to Eucalyptus, and the presence of a transverse scar on the flower buds indicates a relationship to Eucalyptus subgenus Symphyomyrtus. Phylogenetic analyses of morphological data alone and combined with aligned sequence data from a prior study including 16 extant eucalypts, one outgroup, and a terminal representing the fossils indicate that the fossils are nested within Eucalyptus. These are the only illustrated Eucalyptus fossils that are definitively Eocene in age, and the only conclusively identified extant or fossil eucalypts naturally occurring outside of Australasia and adjacent Mindanao. Thus, these fossils indicate that the evolution of the eucalypt group is not constrained to a single region. Moreover, they strengthen the taxonomic connections between the Laguna del Hunco paleoflora and extant subtropical and tropical Australasia, one of the three major ecologic-geographic elements of the Laguna del Hunco paleoflora. The age and affinities of the fossils also indicate that Eucalyptus subgenus Symphyomyrtus is older than previously supposed. Paleoecological data indicate that the Patagonian Eucalyptus dominated volcanically disturbed areas adjacent to standing rainforest surrounding an Eocene caldera lake. PMID:21738605

Bluetooth wireless monitoring, diagnosis and calibration interface for control system of fuel cell bus in Olympic demonstration

NASA Astrophysics Data System (ADS)

Hua, Jianfeng; Lin, Xinfan; Xu, Liangfei; Li, Jianqiu; Ouyang, Minggao

With the worldwide deterioration of the natural environment and the fossil fuel crisis, the possible commercialization of fuel cell vehicles has become a hot topic. In July 2008, Beijing started a clean public transportation plan for the 29th Olympic games. Three fuel cell city buses and 497 other low-emission vehicles are now serving the Olympic core area and Beijing urban areas. The fuel cell buses will operate along a fixed bus line for 1 year as a public demonstration of green energy vehicles. Due to the specialized nature of fuel cell engines and electrified power-train systems, measurement, monitoring and calibration devices are indispensable. Based on the latest Bluetooth wireless technology, a novel Bluetooth universal data interface was developed for the control system of the fuel cell city bus. On this platform, a series of wireless portable control auxiliary systems have been implemented, including wireless calibration, a monitoring system and an in-system programming platform, all of which are ensuring normal operation of the fuel cell buses used in the demonstration.

Phylogeny, paleontology, and primates: do incomplete fossils bias the tree of life?

PubMed

Pattinson, David J; Thompson, Richard S; Piotrowski, Aleks K; Asher, Robert J

2015-03-01

Paleontological systematics relies heavily on morphological data that have undergone decay and fossilization. Here, we apply a heuristic means to assess how a fossil's incompleteness detracts from inferring its phylogenetic relationships. We compiled a phylogenetic matrix for primates and simulated the extinction of living species by deleting an extant taxon's molecular data and keeping only those morphological characters present in actual fossils. The choice of characters present in a given living taxon (the subject) was defined by those present in a given fossil (the template). By measuring congruence between a well-corroborated phylogeny to those incorporating artificial fossils, and by comparing real vs. random character distributions and states, we tested the information content of paleontological datasets and determined if extinction of a living species leads to bias in phylogeny reconstruction. We found a positive correlation between fossil completeness and topological congruence. Real fossil templates sampled for 36 or more of the 360 available morphological characters (including dental) performed significantly better than similarly complete templates with random states. Templates dominated by only one partition performed worse than templates with randomly sampled characters across partitions. The template based on the Eocene primate Darwinius masillae performs better than most other templates with a similar number of sampled characters, likely due to preservation of data across multiple partitions. Our results support the interpretation that Darwinius is strepsirhine, not haplorhine, and suggest that paleontological datasets are reliable in primate phylogeny reconstruction. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Five-Hole Flow Angle Probe Calibration for the NASA Glenn Icing Research Tunnel

NASA Technical Reports Server (NTRS)

Gonsalez, Jose C.; Arrington, E. Allen

1999-01-01

A spring 1997 test section calibration program is scheduled for the NASA Glenn Research Center Icing Research Tunnel following the installation of new water injecting spray bars. A set of new five-hole flow angle pressure probes was fabricated to properly calibrate the test section for total pressure, static pressure, and flow angle. The probes have nine pressure ports: five total pressure ports on a hemispherical head and four static pressure ports located 14.7 diameters downstream of the head. The probes were calibrated in the NASA Glenn 3.5-in.-diameter free-jet calibration facility. After completing calibration data acquisition for two probes, two data prediction models were evaluated. Prediction errors from a linear discrete model proved to be no worse than those from a full third-order multiple regression model. The linear discrete model only required calibration data acquisition according to an abridged test matrix, thus saving considerable time and financial resources over the multiple regression model that required calibration data acquisition according to a more extensive test matrix. Uncertainties in calibration coefficients and predicted values of flow angle, total pressure, static pressure. Mach number. and velocity were examined. These uncertainties consider the instrumentation that will be available in the Icing Research Tunnel for future test section calibration testing.

A multilocus evaluation of ermine (Mustela erminea) across the Holarctic, testing hypotheses of Pleistocene diversification in response to climate change

USGS Publications Warehouse

Dawson, Natalie G.; Hope, Andrew G.; Talbot, Sandra L.; Cook, Joseph A.

2013-01-01

Aim: We examined data for ermine (Mustela erminea) to test two sets of diversification hypotheses concerning the number and location of late Pleistocene refugia, the timing and mode of diversification, and the evolutionary influence of insularization. Location: Temperate and sub-Arctic Northern Hemisphere. Methods: We used up to two mitochondrial and four nuclear loci from 237 specimens for statistical phylogeographical and demographic analyses. Coalescent species-tree estimation used a Bayesian approach for clade divergence based on external mutation rate calibrations. Approximate Bayesian methods were used to assess population size, timing of divergence and gene flow. Results: Limited structure coupled with evidence of population growth across broad regions, including previously ice-covered areas, indicated expansion from multiple centres of differentiation, but high endemism along the North Pacific coast (NPC). A bifurcating model of diversification with recent growth spanning three glacial cycles best explained the empirical data. Main conclusions: A newly identified clade in North America indicated a fourth refugial area for ermine. The shallow coalescence of all extant ermine reflects a recent history of diversification overlying a deeper fossil record. Post-glacial colonization has led to potential contact zones for multiple lineages in north-western North America. A model of diversification of ermine accompanied by recent gene flow was marginally less well supported than a model of divergence of major clades in response to the most recent glacial cycles.

Multiple transfer standard for calibration and characterization of test setups for LED lamps and luminaires in industry

NASA Astrophysics Data System (ADS)

Sperling, A.; Meyer, M.; Pendsa, S.; Jordan, W.; Revtova, E.; Poikonen, T.; Renoux, D.; Blattner, P.

2018-04-01

Proper characterization of test setups used in industry for testing and traceable measurement of lighting devices by the substitution method is an important task. According to new standards for testing LED lamps, luminaires and modules, uncertainty budgets are requested because in many cases the properties of the device under test differ from the transfer standard used, which may cause significant errors, for example if a LED-based lamp is tested or calibrated in an integrating sphere which was calibrated with a tungsten lamp. This paper introduces a multiple transfer standard, which was designed not only to transfer a single calibration value (e.g. luminous flux) but also to characterize test setups used for LED measurements with additional provided and calibrated output features to enable the application of the new standards.

A new yeti crab phylogeny: Vent origins with indications of regional extinction in the East Pacific

PubMed Central

Liu, Xinming; Lin, Rongcheng; Li, Xinzheng; Won, Yong-Jin

2018-01-01

The recent discovery of two new species of kiwaid squat lobsters on hydrothermal vents in the Pacific Ocean and in the Pacific sector of the Southern Ocean has prompted a re-analysis of Kiwaid biogeographical history. Using a larger alignment with more fossil calibrated nodes than previously, we consider the precise relationship between Kiwaidae, Chirostylidae and Eumunididae within Chirostyloidea (Decapoda: Anomura) to be still unresolved at present. Additionally, the placement of both new species within a new “Bristly” clade along with the seep-associated Kiwa puravida is most parsimoniously interpreted as supporting a vent origin for the family, rather than a seep-to-vent progression. Fossil-calibrated divergence analysis indicates an origin for the clade around the Eocene-Oligocene boundary in the eastern Pacific ~33–38 Ma, coincident with a lowering of bottom temperatures and increased ventilation in the Pacific deep sea. Likewise, the mid-Miocene (~10–16 Ma) rapid radiation of the new Bristly clade also coincides with a similar cooling event in the tropical East Pacific. The distribution, diversity, tree topology and divergence timing of Kiwaidae in the East Pacific is most consistent with a pattern of extinctions, recolonisations and radiations along fast-spreading ridges in this region and may have been punctuated by large-scale fluctuations in deep-water ventilation and temperature during the Cenozoic; further affecting the viability of Kiwaidae populations along portions of mid-ocean ridge. PMID:29547631

Multiple frequency method for operating electrochemical sensors

DOEpatents

Martin, Louis P [San Ramon, CA

2012-05-15

A multiple frequency method for the operation of a sensor to measure a parameter of interest using calibration information including the steps of exciting the sensor at a first frequency providing a first sensor response, exciting the sensor at a second frequency providing a second sensor response, using the second sensor response at the second frequency and the calibration information to produce a calculated concentration of the interfering parameters, using the first sensor response at the first frequency, the calculated concentration of the interfering parameters, and the calibration information to measure the parameter of interest.

Linking Fossil Fish Cyclicity and Paleoenvironmental Proxies in the mid-Devonian

NASA Astrophysics Data System (ADS)

Grogan, D.; Whiteside, J. H.; Trewin, N. H.; Johnson, J. E.

2009-12-01

The significant radiation of fishes throughout the Devonian, combined with the abundance of well-preserved fossil fish assemblages from this period, provides for a high-resolution record of prevalent fish taxa in the Orcadian basin of North Scotland. In addition to their ability to serve as a lake-level and lake-chemistry proxy, the waxing and waning of dominant fish taxa exhibit a pronounced cyclicity, suggesting they respond to broader climate rhythms. Recent studies of mid-Devonian lacustrine sedimentary sequences have quantitatively demonstrated the presence of Milankovitch cyclicity in geochemical and gamma ray proxy records. Spectral analysis of gamma ray data show a strong obliquity peak usually associated with ice-house conditions; this obliquity signal is unexpected as tropical latitudes in the mid-Devonian are traditionally thought to have been in a greenhouse climate. Geochemical data include the measurement of bulk carbon and nitrogen stable isotopes, molecule-specific carbon isotopes of plant biomarkers, and depth ranks from eight sections of the Caithness Flagstone Group of the Orcadian Basin. Evidence for orbital forcing of climate change paired with the fossil fish record provides a unique opportunity to establish an astronomically calibrated timescale for the mid-Devonian, as well as to make a quantitative assessment of the validity of a greenhouse climate existing in the mid-Devonian.

470-Million-year-old black corals from China

NASA Astrophysics Data System (ADS)

Baliński, Andrzej; Sun, Yuanlin; Dzik, Jerzy

2012-08-01

Phosphatic (possibly secondarily phosphatised) remains of antipatharian coralla, previously unknown in the fossil record, occur abundantly in the early Ordovician Fenxiang Formation in the Hubei Province, southern China. Probably two species (and genera) are represented, which differ in spinosity of branches. The more spinose one, Sinopathes reptans, has its lateral spines bearing regular, longitudinally arranged costellae. The early Floian geological age of this finding, about 470 Ma, supports predictions on the timing of anthozoan phylogeny derived from the molecular phylogenetic evidence. Black corals (Antipatharia) are basal to the scleractinians in the Hexacorallia clade, being more derived than sea anemones and the Zoantharia. Based on calibration of the molecular clock with Mesozoic data, the first split of lineages within the scleractinian hexacorals was proposed to take place approximately 425 million years ago. This implies that the origin of Antipatharia should precede this date. They have not been known in the fossil record because of unmineralised skeleton composed primarily of laminar chitin complexed with a protein. Unlike all recent species, the encrusting basal part of the colony dominated in the Ordovician ones and only occasionally erect branches developed, rather chaotically ramified. This presumably plesiomorphic trait seems consistent with ancient geological age and suggests that some problematic fossils from the Late Cambrian may be their, even less-derived, relatives.

Multiple High-Frequency Carbon Isotope Excursions Across the Precambrian-Cambrian Boundary: Implications for Correlations and Environmental Change

NASA Astrophysics Data System (ADS)

Smith, E. F.; Macdonald, F. A.; Schrag, D. P.; Laakso, T.

2014-12-01

The GSSP Precambrian-Cambrian boundary in Newfoundland is defined by the first appearance datum (FAD) of Treptichnus pedum, which is considered to be roughly coincident with the FAD of small shelly fossils (SSFs) and a large negative carbon isotope excursion. An association between the FAD of T. pedum and a negative carbon isotope excursion has previously been documented in Northwest Canada (Narbonne et al., 1994) and Death Valley (Corsetti and Hagadorn, 2000), and since then has been used as an chronostratigraphic marker of the boundary, particularly in siliciclastic poor sections that do not preserve T. pedum. Here we present new high-resolution carbon isotope (δ13C ) chemostratigraphy from multiple sections in western Mongolia and the western United States that span the Ediacaran-Cambrian transition. High-resolution sampling (0.2-1 m) reveals that instead of one large negative excursion, there are multiple, high-frequency negative excursions with an overall negative trend during the latest Ediacaran. These data help to more precisely calibrate changes in the carbon cycle across the boundary as well as to highlight the potential problem of identifying the boundary with just a few negative δ13C values. We then use a simple carbon isotope box model to explore relationships between phosphorous delivery to the ocean, oxygenation, alkalinity, and turnovers in carbonate secreting organisms. Corsetti, F.A., and Hagadorn, J.W., 2000, Precambrian-Cambrian transition: Death Valley, United States: Geology, v. 28, no. 4, p. 299-302. Narbonne, G.M., Kaufman, A.J., and Knoll, A.H., 1994, Integrated chemostratigraphy and biostratigraphy of the Windermere Supergroup, northwestern Canada: Implications for Neoproterozoic correlations and the early evolution of animals: Geological Society of America Bulletin, v. 106, no. 10, p. 1281-1292.

Note: Improved calibration of atomic force microscope cantilevers using multiple reference cantilevers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sader, John E., E-mail: jsader@unimelb.edu.au; Friend, James R.

2015-05-15

Overall precision of the simplified calibration method in J. E. Sader et al., Rev. Sci. Instrum. 83, 103705 (2012), Sec. III D, is dominated by the spring constant of the reference cantilever. The question arises: How does one take measurements from multiple reference cantilevers, and combine these results, to improve uncertainty of the reference cantilever’s spring constant and hence the overall precision of the method? This question is addressed in this note. Its answer enables manufacturers to specify of a single set of data for the spring constant, resonant frequency, and quality factor, from measurements on multiple reference cantilevers. Withmore » this data set, users can trivially calibrate cantilevers of the same type.« less

Hydra multiple head star sensor and its in-flight self-calibration of optical heads alignment

NASA Astrophysics Data System (ADS)

Majewski, L.; Blarre, L.; Perrimon, N.; Kocher, Y.; Martinez, P. E.; Dussy, S.

2017-11-01

HYDRA is EADS SODERN new product line of APS-based autonomous star trackers. The baseline is a multiple head sensor made of three separated optical heads and one electronic unit. Actually the concept which was chosen offers more than three single-head star trackers working independently. Since HYDRA merges all fields of view the result is a more accurate, more robust and completely autonomous multiple-head sensor, releasing the AOCS from the need to manage the outputs of independent single-head star trackers. Specific to the multiple head architecture and the underlying data fusion, is the calibration of the relative alignments between the sensor optical heads. The performance of the sensor is related to its estimation of such alignments. HYDRA design is first reminded in this paper along with simplification it can bring at system level (AOCS). Then self-calibration of optical heads alignment is highlighted through descriptions and simulation results, thus demonstrating the performances of a key part of HYDRA multiple-head concept.

The Watinglo mandible: a second terminal Pleistocene Homo sapiens fossil from tropical Sahul with a test on existing models for the human settlement of the region.

PubMed

Bulbeck, D; O'Connor, S

2011-02-01

This paper analyses a fossil human mandible, dated to circa 10ka, from Watinglo rockshelter on the north coast of Papua New Guinea. The fossil is metrically and morphologically similar to male mandibles of recent Melanesians and Australian Aborigines. It is distinguished from Kow Swamp and Coobool Creek male mandibles (Murray Valley, terminal Pleistocene) by being smaller and having different shape characteristics, as well as smaller teeth and a slower rate of tooth wear. It pairs with the Liang Lemdubu female (Late Glacial Maximum, Aru Islands) in suggesting that the morphology of the terminal Pleistocene inhabitants of tropical Sahul was gracile compared to their contemporaries within the southern Murray drainage. An explanatory scenario for this morphological contrast is developed in the context of the Homo sapiens early fossil record, Australasian mtDNA evidence, terminal Pleistocene climatic variation, and the possibility of multiple entry points into Sahul. Copyright © 2010 Elsevier GmbH. All rights reserved.

Multiple prismatic calcium phosphate layers in the jaws of present-day sharks (Chondrichthyes; Selachii).

PubMed

Dingerkus, G; Séret, B; Guilbert, E

1991-01-15

Jaws of large individuals, over 2 m in total length, of the shark species Carcharodon carcharias (great white shark) and Isurus oxyrinchus (mako shark) of the family Lamnidae, and Galeocerdo cuvieri (tiger shark) and Carcharhinus leucas (bull shark) of the family Carcharhinidae were found to have multiple, up to five, layers of prismatic calcium phosphate surrounding the cartilages. Smaller individuals of these species and other known species of living chondrichthyans have only one layer of prismatic calcium phosphate surrounding the cartilages, as also do most species of fossil chondrichthyans. Two exceptions are the fossil shark genera Xenacanthus and Tamiobatis. Where it is found in living forms, this multiple layered calcification does not appear to be phylogenetic, as it appears to be lacking in other lamnid and carcharhinid genera and species. Rather it appears to be functional, only appearing in larger individuals and species of these two groups, and hence may be necessary to strengthen the jaw cartilages of such individuals for biting.

Common Calibration Source for Monitoring Long-term Ozone Trends

NASA Technical Reports Server (NTRS)

Kowalewski, Matthew

2004-01-01

Accurate long-term satellite measurements are crucial for monitoring the recovery of the ozone layer. The slow pace of the recovery and limited lifetimes of satellite monitoring instruments demands that datasets from multiple observation systems be combined to provide the long-term accuracy needed. A fundamental component of accurately monitoring long-term trends is the calibration of these various instruments. NASA s Radiometric Calibration and Development Facility at the Goddard Space Flight Center has provided resources to minimize calibration biases between multiple instruments through the use of a common calibration source and standardized procedures traceable to national standards. The Facility s 50 cm barium sulfate integrating sphere has been used as a common calibration source for both US and international satellite instruments, including the Total Ozone Mapping Spectrometer (TOMS), Solar Backscatter Ultraviolet 2 (SBUV/2) instruments, Shuttle SBUV (SSBUV), Ozone Mapping Instrument (OMI), Global Ozone Monitoring Experiment (GOME) (ESA), Scanning Imaging SpectroMeter for Atmospheric ChartographY (SCIAMACHY) (ESA), and others. We will discuss the advantages of using a common calibration source and its effects on long-term ozone data sets. In addition, sphere calibration results from various instruments will be presented to demonstrate the accuracy of the long-term characterization of the source itself.

Late Paleogene terrestrial fauna and paleoenvironments in Eastern Anatolia: New insights from the Kağızman-Tuzluca Basin

NASA Astrophysics Data System (ADS)

Métais, Grégoire; Sen, Sevket; Sözeri, Koray; Peigné, Stéphane; Varol, Baki

2015-08-01

In Eastern Turkey, relatively little work has been undertaken to characterize the sedimentologic and stratigraphical context of the Kağızman-Tuzluca Basin until now. Extending across the Turkey-Armenian border, this basin documents the syn- and post-collisional evolution of Eastern Anatolia, resulting from the closure of the Neotethyan Seaways and the final collision of the Afro-Arabian and Eurasian plates. From detailed sedimentological and paleontological studies, we propose an interpretation of the lithology and depositional environment of the Late Paleogene Alhan Formation located on the western bank of the Aras River. This sequence of terrestrial clastics rests directly and unconformably onto the ophiolitic mélange, and it documents several depositional sequences deposited in alluvial plain and lacustrine environments. At this stage, the age of the Alhan Formation can only be calibrated by fossil evidence. Several stratigraphic levels yielding fossil data along the section have been identified, but these poor assemblages of fauna and flora hamper extensive comparisons with roughly contemporaneous localities of Central and Southern Asia. Carnivorous and ruminant mammal remains are reported for the first time from the supposed Late Oligocene Güngörmez Formation. The identified fossil mammal taxa reveal biogeographic affinities between Central Anatolia and southern Asia, thus suggesting dispersal between these areas during the Oligocene or earlier. Further studies of the fossil assemblages from the Kağızman-Tuzluca Basin and other basins of Eastern Anatolia and lesser Caucasus regions are needed to better constrain the paleobiogeographic models.

O the Interpretation of Climatic Change from the Fossil Record: Climatic Change in Central and Eastern United States for the Past 2000 Years Estimated from Pollen Data.

NASA Astrophysics Data System (ADS)

Gajewski, Konrad J.

Pollen records from varved-lake sediments at seven locations in the northeastern United States record late Holocene climate changes over the past 1000-2000 years. Simplification of pollen diagrams by principal component analysis documents that climate changes affect vegetation at all sites, and not just at "sensitive" sites or ecotones. All seven pollen records show a long-term trend, medium frequency oscillations and higher frequency fluctuations. The between-site similarity of the trend and the coherency of the medium frequency oscillations demonstrates the importance of climate forcing to vegetation change at these scales. Response of vegetation to a climatic change is quite rapid, and depends not only on the nature of the climate fluctuation, but also on the pre-existing state of the vegetation. Multiple regression and canonical correlation techniques were used to calculate calibration functions from a spatial network of modern pollen and climate data. When analyzed at comparable scales, the spatial distribution of pollen assemblages in northeastern United States are related both to summer temperature and annual precipitation. Although summer temperature and annual precipitation are coupled, this coupling is not so strong as to negate the use of univariate calibration models. Over the 2000-year period of time, a gradual summer cooling of about 1.0(DEGREES)C/1000 years has occurred. Superimposed on the long-term trend are medium frequency temperature fluctuations of amplitude about 0.5(DEGREES)C that persist for several centuries. Annual precipitation is relatively constant, except for a period of increased rainfall from 600 years ago to the present in southern Maine.

Methods for Calibration of Prout-Tompkins Kinetics Parameters Using EZM Iteration and GLO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wemhoff, A P; Burnham, A K; de Supinski, B

2006-11-07

This document contains information regarding the standard procedures used to calibrate chemical kinetics parameters for the extended Prout-Tompkins model to match experimental data. Two methods for calibration are mentioned: EZM calibration and GLO calibration. EZM calibration matches kinetics parameters to three data points, while GLO calibration slightly adjusts kinetic parameters to match multiple points. Information is provided regarding the theoretical approach and application procedure for both of these calibration algorithms. It is recommended that for the calibration process, the user begin with EZM calibration to provide a good estimate, and then fine-tune the parameters using GLO. Two examples have beenmore » provided to guide the reader through a general calibrating process.« less

Miocene honey bees from the Randeck Maar of southwestern Germany (Hymenoptera, Apidae)

PubMed Central

Kotthoff, Ulrich; Wappler, Torsten; Engel, Michael S.

2011-01-01

Abstract The Miocene Randeck Maar (southwestern Germany) is one of the only sites with abundant material of fossil honey bees. The fauna has been the focus of much scrutiny by early authors who recognized multiple species or subspecies within the fauna. The history of work on the Randeck Maar is briefly reviewed and these fossils placed into context with other Tertiary and living species of the genus Apis Linnaeus (Apinae: Apini). Previously unrecorded specimens from Randeck Maar were compared with earlier series in an attempt to evaluate the observed variation. A morphometric analysis of forewing venation angles across representative Recent and Tertiary species of Apis as well as various non-Apini controls was undertaken to evaluate the distribution of variation in fossil honey bees. The resulting dendrogram shows considerable variation concerning the wing venation of Miocene Apini, but intergradation of other morphological characters reveals no clear pattern of separate species. This suggests that a single, highly variable species was present in Europe during the Miocene. The pattern also supports the notion that the multiple species and subspecies proposed by earlier authors for the Randeck Maar honey bee fauna are not valid, and all are accordingly recognized as Apis armbrusteri Zeuner. PMID:21594072

Automatic Camera Calibration Using Multiple Sets of Pairwise Correspondences.

PubMed

Vasconcelos, Francisco; Barreto, Joao P; Boyer, Edmond

2018-04-01

We propose a new method to add an uncalibrated node into a network of calibrated cameras using only pairwise point correspondences. While previous methods perform this task using triple correspondences, these are often difficult to establish when there is limited overlap between different views. In such challenging cases we must rely on pairwise correspondences and our solution becomes more advantageous. Our method includes an 11-point minimal solution for the intrinsic and extrinsic calibration of a camera from pairwise correspondences with other two calibrated cameras, and a new inlier selection framework that extends the traditional RANSAC family of algorithms to sampling across multiple datasets. Our method is validated on different application scenarios where a lack of triple correspondences might occur: addition of a new node to a camera network; calibration and motion estimation of a moving camera inside a camera network; and addition of views with limited overlap to a Structure-from-Motion model.

Magnetic polarity stratigraphy of Inchasi: a Pliocene mammal-bearing locality from the Bolivian Andes deposited just before the Great American Interchange

NASA Astrophysics Data System (ADS)

MacFadden, Bruce J.; Anaya, Federico; Argollo, Jaime

1993-01-01

The newly discovered section at Inchasi, located about 50 km southeast of Potosi, Bolivia, in the eastern Cordillera, consists of about 120 m of undeformed terrestrial sediments containing fossil mammals. Paleomagnetic analysis of 54 sites indicates a polarity pattern with an estimated duration of about 0.64 Ma. The rich Inchasi local fauna indicates a Montehermosan and/or Chapadmalalan land mammal age (Pliocene). Given these constraints, Inchasi correlates from the interval between the late Gilbert (within the Cochiti subchron) to the early Gauss (within the Mammoth subchron) chrons; that is, between about 4.0 and 3.3 Ma. The distinct lack of North American mammals in the Inchasi local fauna provides some of the first well-calibrated evidence that the Great American Interchange occurred after about 3.0 Ma, as has been previously stated based on other calibrations of the earliest immigrant (Uquian) faunas.

Gene transfers can date the tree of life.

PubMed

Davín, Adrián A; Tannier, Eric; Williams, Tom A; Boussau, Bastien; Daubin, Vincent; Szöllősi, Gergely J

2018-05-01

Biodiversity has always been predominantly microbial, and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life. Here, we show that patterns of lateral gene transfer deduced from an analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the history of life. We use state-of-the-art species tree-aware phylogenetic methods to reconstruct the history of thousands of gene families and demonstrate that dates implied by gene transfers are consistent with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukarya. We present the order of speciations according to lateral gene transfer data calibrated to geological time for three datasets comprising 40 genomes for Cyanobacteria, 60 genomes for Archaea and 60 genomes for Fungi. An inspection of discrepancies between transfers and clocks and a comparison with mammalian fossils show that gene transfer in microbes is potentially as informative for dating the tree of life as the geological record in macroorganisms.

Initial diversification of living amphibians predated the breakup of Pangaea.

PubMed

San Mauro, Diego; Vences, Miguel; Alcobendas, Marina; Zardoya, Rafael; Meyer, Axel

2005-05-01

The origin and divergence of the three living orders of amphibians (Anura, Caudata, Gymnophiona) and their main lineages are one of the most hotly debated topics in vertebrate evolution. Here, we present a robust molecular phylogeny based on the nuclear RAG1 gene as well as results from a variety of alternative independent molecular clock calibrations. Our analyses suggest that the origin and early divergence of the three living amphibian orders dates back to the Palaeozoic or early Mesozoic, before the breakup of Pangaea, and soon after the divergence from lobe-finned fishes. The resulting new biogeographic scenario, age estimate, and the inferred rapid divergence of the three lissamphibian orders may account for the lack of fossils that represent plausible ancestors or immediate sister taxa of all three orders and the heretofore paradoxical distribution of some amphibian fossil taxa. Furthermore, the ancient and rapid radiation of the three lissamphibian orders likely explains why branch lengths connecting their early nodes are particularly short, thus rendering phylogenetic inference of implicated relationships especially difficult.

Children are likely to suffer most from our fossil fuel addiction.

PubMed

Perera, Frederica P

2008-08-01

The periods of fetal and child development arguably represent the stages of greatest vulnerability to the dual impacts of fossil fuel combustion: the multiple toxic effects of emitted pollutants (polycyclic aromatic hydrocarbons, particles, sulfur oxides, nitrogen oxides, metals) and the broad health impacts of global climate change attributable in large part to carbon dioxide released by fossil fuel burning. In this commentary I highlight current scientific evidence indicating that the fetus and young child are at heightened risk of developmental impairment, asthma, and cancer from fossil fuel pollutants and from the predicted effects of climate disruption such as heat waves, flooding, infectious disease, malnutrition, and trauma. Increased risk during early development derives from the inherently greater biologic vulnerability of the developing fetus and child and from their long future lifetime, during which early insults can potentially manifest as adult as well as childhood disease. I cite recent reports concluding that reducing dependence on fossil fuel and promoting clean and sustainable energy is economically feasible. Although much has been written separately about the toxicity of fossil fuel burning emissions and the effects of climate change on health, these two faces of the problem have not been viewed together with a focus on the developing fetus and child. Adolescence and old age are also periods of vulnerability, but the potential for both immediate and long-term adverse effects is greatest when exposure occurs prenatally or in the early years. Consideration of the full spectrum of health risks to children from fossil fuel combustion underscores the urgent need for environmental and energy policies to reduce fossil fuel dependence and maximize the health benefits to this susceptible population. We do not have to leave our children a double legacy of ill health and ecologic disaster.

Children Are Likely to Suffer Most from Our Fossil Fuel Addiction

PubMed Central

Perera, Frederica P.

2008-01-01

Background The periods of fetal and child development arguably represent the stages of greatest vulnerability to the dual impacts of fossil fuel combustion: the multiple toxic effects of emitted pollutants (polycyclic aromatic hydrocarbons, particles, sulfur oxides, nitrogen oxides, metals) and the broad health impacts of global climate change attributable in large part to carbon dioxide released by fossil fuel burning. Objectives In this commentary I highlight current scientific evidence indicating that the fetus and young child are at heightened risk of developmental impairment, asthma, and cancer from fossil fuel pollutants and from the predicted effects of climate disruption such as heat waves, flooding, infectious disease, malnutrition, and trauma. Increased risk during early development derives from the inherently greater biologic vulnerability of the developing fetus and child and from their long future lifetime, during which early insults can potentially manifest as adult as well as childhood disease. I cite recent reports concluding that reducing dependence on fossil fuel and promoting clean and sustainable energy is economically feasible. Discussion Although much has been written separately about the toxicity of fossil fuel burning emissions and the effects of climate change on health, these two faces of the problem have not been viewed together with a focus on the developing fetus and child. Adolescence and old age are also periods of vulnerability, but the potential for both immediate and long-term adverse effects is greatest when exposure occurs prenatally or in the early years. Conclusions Consideration of the full spectrum of health risks to children from fossil fuel combustion underscores the urgent need for environmental and energy policies to reduce fossil fuel dependence and maximize the health benefits to this susceptible population. We do not have to leave our children a double legacy of ill health and ecologic disaster. PMID:18709169

Integrating fossils, phylogenies, and niche models into biogeography to reveal ancient evolutionary history: the case of Hypericum (hypericaceae).

PubMed

Meseguer, Andrea S; Lobo, Jorge M; Ree, Richard; Beerling, David J; Sanmartín, Isabel

2015-03-01

In disciplines such as macroevolution that are not amenable to experimentation, scientists usually rely on current observations to test hypotheses about historical events, assuming that "the present is the key to the past." Biogeographers, for example, used this assumption to reconstruct ancestral ranges from the distribution of extant species. Yet, under scenarios of high extinction rates, the biodiversity we observe today might not be representative of the historical diversity and this could result in incorrect biogeographic reconstructions. Here, we introduce a new approach to incorporate into biogeographic inference the temporal, spatial, and environmental information provided by the fossil record, as a direct evidence of the extinct biodiversity fraction. First, inferences of ancestral ranges for those nodes in the phylogeny calibrated with the fossil record are constrained to include the geographic distribution of the fossil. Second, we use fossil distribution and past climate data to reconstruct the climatic preferences and potential distribution of ancestral lineages over time, and use this information to build a biogeographic model that takes into account "ecological connectivity" through time. To show the power of this approach, we reconstruct the biogeographic history of the large angiosperm genus Hypericum, which has a fossil record extending back to the Early Cenozoic. Unlike previous reconstructions based on extant species distributions, our results reveal that Hypericum stem lineages were already distributed in the Holarctic before diversification of its crown-group, and that the geographic distribution of the genus has been relatively stable throughout the climatic oscillations of the Cenozoic. Geographical movement was mediated by the existence of climatic corridors, like Beringia, whereas the equatorial tropical belt acted as a climatic barrier, preventing Hypericum lineages to reach the southern temperate regions. Our study shows that an integrative approach to historical biogeography-that combines sources of evidence as diverse as paleontology, ecology, and phylogenetics-could help us obtain more accurate reconstructions of ancient evolutionary history. It also reveals the confounding effect different rates of extinction across regions have in biogeography, sometimes leading to ancestral areas being erroneously inferred as recent colonization events. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Integrating Fossils, Phylogenies, and Niche Models into Biogeography to Reveal Ancient Evolutionary History: The Case of Hypericum (Hypericaceae)

PubMed Central

Meseguer, Andrea S.; Lobo, Jorge M.; Ree, Richard; Beerling, David J.; Sanmartín, Isabel

2015-01-01

In disciplines such as macroevolution that are not amenable to experimentation, scientists usually rely on current observations to test hypotheses about historical events, assuming that “the present is the key to the past.” Biogeographers, for example, used this assumption to reconstruct ancestral ranges from the distribution of extant species. Yet, under scenarios of high extinction rates, the biodiversity we observe today might not be representative of the historical diversity and this could result in incorrect biogeographic reconstructions. Here, we introduce a new approach to incorporate into biogeographic inference the temporal, spatial, and environmental information provided by the fossil record, as a direct evidence of the extinct biodiversity fraction. First, inferences of ancestral ranges for those nodes in the phylogeny calibrated with the fossil record are constrained to include the geographic distribution of the fossil. Second, we use fossil distribution and past climate data to reconstruct the climatic preferences and potential distribution of ancestral lineages over time, and use this information to build a biogeographic model that takes into account “ecological connectivity” through time. To show the power of this approach, we reconstruct the biogeographic history of the large angiosperm genus Hypericum, which has a fossil record extending back to the Early Cenozoic. Unlike previous reconstructions based on extant species distributions, our results reveal that Hypericum stem lineages were already distributed in the Holarctic before diversification of its crown-group, and that the geographic distribution of the genus has been relatively stable throughout the climatic oscillations of the Cenozoic. Geographical movement was mediated by the existence of climatic corridors, like Beringia, whereas the equatorial tropical belt acted as a climatic barrier, preventing Hypericum lineages to reach the southern temperate regions. Our study shows that an integrative approach to historical biogeography—that combines sources of evidence as diverse as paleontology, ecology, and phylogenetics—could help us obtain more accurate reconstructions of ancient evolutionary history. It also reveals the confounding effect different rates of extinction across regions have in biogeography, sometimes leading to ancestral areas being erroneously inferred as recent colonization events. PMID:25398444

Search for the Evolution of Steroid Biosynthesis in the Geological Record

NASA Astrophysics Data System (ADS)

Brocks, J. J.

2004-12-01

To study the evolution of the structure of organisms we can directly examine fossilized shells, skeletons and petrified cells. In contrast, for the tentative reconstruction of the phylogeny of biosynthetic pathways, such as steroid anabolism, we rely entirely on the comparative molecular biology of living organisms. Thus, without fossil evidence, the times in geological history when successive steps of a metabolic pathway evolved remain particularly elusive. Molecular clocks of genes coding for the enzymes involved in a biosynthetic pathway might provide a rough guess when a natural product first appeared in geological time, but they are intrinsically unreliable without calibration points in the distant past. However, it might be possible to trace the evolutionary history of some biosynthetic pathways directly in the geological record by searching for hydrocarbon biomarkers of anabolic intermediates. Biomarkers are molecular fossils of natural products. They often retain the diagnostic carbon skeleton of their biological precursor and remain stable over hundreds of millions of years enclosed in organic-rich sedimentary rocks. Sterane hydrocarbons are particularly abundant biomarkers and potentially suitable for the search of biosynthetic intermediates. Steranes are the fossil equivalents of functionalized steroids found in eukaryotes and certain bacteria. The biosynthesis of typical eukaryotic steroids such as cholesterol (C27), ergosterol (C28) and sitosterol (C29) from the acyclic precursor squalene (C30) involves more than 20 enzymatic steps. The most crucial steps include modification of the carbon skeleton by removal of several methyl groups from the ring system and addition of alkyl groups to the steroid side chain. The evolution of this complex pathway must have occurred over geologically significant periods of time and likely involved several preadaptive intermediates that represented structurally less derived but fully functional lipids. Thus, if a molecular corollary of `ontogeny recapitulates phylogeny' applies, it might be possible to detect a sequence of increasingly modified fossil steroids in the geological record and to create a time frame for the evolution of this fundamental biosynthetic pathway. Here we present first results of an extensive search for the fossil remains of evolutionary intermediate steroids in sedimentary successions of Precambrian age.

A Comparative Study of Online Item Calibration Methods in Multidimensional Computerized Adaptive Testing

ERIC Educational Resources Information Center

Chen, Ping

2017-01-01

Calibration of new items online has been an important topic in item replenishment for multidimensional computerized adaptive testing (MCAT). Several online calibration methods have been proposed for MCAT, such as multidimensional "one expectation-maximization (EM) cycle" (M-OEM) and multidimensional "multiple EM cycles"…

Multiple cenozoic invasions of Africa by penguins (Aves, Sphenisciformes)

PubMed Central

Ksepka, Daniel T.; Thomas, Daniel B.

2012-01-01

Africa hosts a single breeding species of penguin today, yet the fossil record indicates that a diverse array of now-extinct taxa once inhabited southern African coastlines. Here, we show that the African penguin fauna had a complex history involving multiple dispersals and extinctions. Phylogenetic analyses and biogeographic reconstructions incorporating new fossil material indicate that, contrary to previous hypotheses, the four Early Pliocene African penguin species do not represent an endemic radiation or direct ancestors of the living Spheniscus demersus (blackfooted penguin). A minimum of three dispersals to Africa, probably assisted by the eastward-flowing Antarctic Circumpolar and South Atlantic currents, occurred during the Late Cenozoic. As regional sea-level fall eliminated islands and reduced offshore breeding areas during the Pliocene, all but one penguin lineage ended in extinction, resulting in today's depleted fauna. PMID:21900330

Calibrated birth-death phylogenetic time-tree priors for bayesian inference.

PubMed

Heled, Joseph; Drummond, Alexei J

2015-05-01

Here we introduce a general class of multiple calibration birth-death tree priors for use in Bayesian phylogenetic inference. All tree priors in this class separate ancestral node heights into a set of "calibrated nodes" and "uncalibrated nodes" such that the marginal distribution of the calibrated nodes is user-specified whereas the density ratio of the birth-death prior is retained for trees with equal values for the calibrated nodes. We describe two formulations, one in which the calibration information informs the prior on ranked tree topologies, through the (conditional) prior, and the other which factorizes the prior on divergence times and ranked topologies, thus allowing uniform, or any arbitrary prior distribution on ranked topologies. Although the first of these formulations has some attractive properties, the algorithm we present for computing its prior density is computationally intensive. However, the second formulation is always faster and computationally efficient for up to six calibrations. We demonstrate the utility of the new class of multiple-calibration tree priors using both small simulations and a real-world analysis and compare the results to existing schemes. The two new calibrated tree priors described in this article offer greater flexibility and control of prior specification in calibrated time-tree inference and divergence time dating, and will remove the need for indirect approaches to the assessment of the combined effect of calibration densities and tree priors in Bayesian phylogenetic inference. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Validation and calibration of structural models that combine information from multiple sources.

PubMed

Dahabreh, Issa J; Wong, John B; Trikalinos, Thomas A

2017-02-01

Mathematical models that attempt to capture structural relationships between their components and combine information from multiple sources are increasingly used in medicine. Areas covered: We provide an overview of methods for model validation and calibration and survey studies comparing alternative approaches. Expert commentary: Model validation entails a confrontation of models with data, background knowledge, and other models, and can inform judgments about model credibility. Calibration involves selecting parameter values to improve the agreement of model outputs with data. When the goal of modeling is quantitative inference on the effects of interventions or forecasting, calibration can be viewed as estimation. This view clarifies issues related to parameter identifiability and facilitates formal model validation and the examination of consistency among different sources of information. In contrast, when the goal of modeling is the generation of qualitative insights about the modeled phenomenon, calibration is a rather informal process for selecting inputs that result in model behavior that roughly reproduces select aspects of the modeled phenomenon and cannot be equated to an estimation procedure. Current empirical research on validation and calibration methods consists primarily of methodological appraisals or case-studies of alternative techniques and cannot address the numerous complex and multifaceted methodological decisions that modelers must make. Further research is needed on different approaches for developing and validating complex models that combine evidence from multiple sources.

Parallel computing for automated model calibration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burke, John S.; Danielson, Gary R.; Schulz, Douglas A.

2002-07-29

Natural resources model calibration is a significant burden on computing and staff resources in modeling efforts. Most assessments must consider multiple calibration objectives (for example magnitude and timing of stream flow peak). An automated calibration process that allows real time updating of data/models, allowing scientists to focus effort on improving models is needed. We are in the process of building a fully featured multi objective calibration tool capable of processing multiple models cheaply and efficiently using null cycle computing. Our parallel processing and calibration software routines have been generically, but our focus has been on natural resources model calibration. Somore » far, the natural resources models have been friendly to parallel calibration efforts in that they require no inter-process communication, only need a small amount of input data and only output a small amount of statistical information for each calibration run. A typical auto calibration run might involve running a model 10,000 times with a variety of input parameters and summary statistical output. In the past model calibration has been done against individual models for each data set. The individual model runs are relatively fast, ranging from seconds to minutes. The process was run on a single computer using a simple iterative process. We have completed two Auto Calibration prototypes and are currently designing a more feature rich tool. Our prototypes have focused on running the calibration in a distributed computing cross platform environment. They allow incorporation of?smart? calibration parameter generation (using artificial intelligence processing techniques). Null cycle computing similar to SETI@Home has also been a focus of our efforts. This paper details the design of the latest prototype and discusses our plans for the next revision of the software.« less

Using multiple calibration sets to improve the quantitative accuracy of partial least squares (PLS) regression on open-path fourier transform infrared (OP/FT-IR) spectra of ammonia over wide concentration ranges

USDA-ARS?s Scientific Manuscript database

A technique of using multiple calibration sets in partial least squares regression (PLS) was proposed to improve the quantitative determination of ammonia from open-path Fourier transform infrared spectra. The spectra were measured near animal farms, and the path-integrated concentration of ammonia...

Inflation of Molecular Clock Rates and Dates: Molecular Phylogenetics, Biogeography, and Diversification of a Global Cicada Radiation from Australasia (Hemiptera: Cicadidae: Cicadettini).

PubMed

Marshall, David C; Hill, Kathy B R; Moulds, Max; Vanderpool, Dan; Cooley, John R; Mohagan, Alma B; Simon, Chris

2016-01-01

Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1[Formula: see text] intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from: (i) an extrapolated EF-1[Formula: see text] exon clock derived from COI-calibrated analysis within the largest New Zealand subclade; (ii) post hoc scaling of the tribe-level chronogram using results from subclade analyses; and (iii) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non-Australasian genera belonging to two distal clades. Within Australia, we show that Cicadettini is more widely distributed than any other cicada tribe, diverse in temperate, arid and monsoonal habitats, and nearly absent from rainforests. We comment on the taxonomic implications of our findings for thirteen cicada genera. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Investigation of black and brown carbon multiple-wavelength-dependent light absorption from biomass and fossil fuel combustion source emissions

Treesearch

Michael R. Olson; Mercedes Victoria Garcia; Michael A. Robinson; Paul Van Rooy; Mark A. Dietenberger; Michael Bergin; James Jay Schauer

2015-01-01

Quantification of the black carbon (BC) and brown carbon (BrC) components of source emissions is critical to understanding the impact combustion aerosols have on atmospheric light absorption. Multiple-wavelength absorption was measured from fuels including wood, agricultural biomass, coals, plant matter, and petroleum distillates in controlled combustion settings....

A Consistent AVHRR Visible Calibration Record Based on Multiple Methods Applicable for the NOAA Degrading Orbits. Part 2 ; Validation

NASA Technical Reports Server (NTRS)

Doelling, David R.; Bhatt, Rajendra; Scarino, Benjamin R.; Gopalan, Arun; Haney, Conor O.; Minnis, Patrick; Bedka, Kristopher M.

2016-01-01

Consistent cross-sensor Advanced Very High Resolution Radiometer (AVHRR) calibration coefficients are determined using desert, polar ice, and deep convective cloud (DCC) invariant Earth targets. The greatest AVHRR calibration challenge is the slow orbit degradation of the host satellite, which precesses toward a terminator orbit. This issue is solved by characterizing the invariant targets with NOAA-16 AVHRR observed radiances that have been referenced to the Aqua Moderate Resolution Imaging Spectrometer (MODIS) calibration using simultaneous nadir overpass (SNO) observations. Another benefit of the NOAA-16 invariant target-modeled reflectance method is that, because of the similarities among the AVHRR spectral response functions, a smaller spectral band adjustment factor is required than when establishing calibrations relative to a non-AVHRR reference instrument. The sensor- and band-specific calibration uncertainties, with respect to the calibration reference, are, on average, 2 percent and 3 percent for channels 1 and 2, respectively. The uncertainties are smaller for sensors that are in afternoon orbits, have longer records, and spend less time in terminator conditions. The multiple invariant targets referenced to Aqua MODIS (MITRAM) AVHRR calibration coefficients are evaluated for individual target consistency, compared against Aqua MODIS/AVHRR SNOs, and selected published calibration gains. The MITRAM and SNO relative calibration biases mostly agree to within 1 percent for channels 1 and 2, respectively. The individual invariant target and MITRAM sensor relative calibration biases are mostly consistent to within 1 percent and 2 percent for channels 1 and 2, respectively. The differences between the MITRAM and other published calibrations are mostly attributed to the reference instrument calibration differences.

Validation and Calibration of Nuclear Thermal Hydraulics Multiscale Multiphysics Models - Subcooled Flow Boiling Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anh Bui; Nam Dinh; Brian Williams

In addition to validation data plan, development of advanced techniques for calibration and validation of complex multiscale, multiphysics nuclear reactor simulation codes are a main objective of the CASL VUQ plan. Advanced modeling of LWR systems normally involves a range of physico-chemical models describing multiple interacting phenomena, such as thermal hydraulics, reactor physics, coolant chemistry, etc., which occur over a wide range of spatial and temporal scales. To a large extent, the accuracy of (and uncertainty in) overall model predictions is determined by the correctness of various sub-models, which are not conservation-laws based, but empirically derived from measurement data. Suchmore » sub-models normally require extensive calibration before the models can be applied to analysis of real reactor problems. This work demonstrates a case study of calibration of a common model of subcooled flow boiling, which is an important multiscale, multiphysics phenomenon in LWR thermal hydraulics. The calibration process is based on a new strategy of model-data integration, in which, all sub-models are simultaneously analyzed and calibrated using multiple sets of data of different types. Specifically, both data on large-scale distributions of void fraction and fluid temperature and data on small-scale physics of wall evaporation were simultaneously used in this work’s calibration. In a departure from traditional (or common-sense) practice of tuning/calibrating complex models, a modern calibration technique based on statistical modeling and Bayesian inference was employed, which allowed simultaneous calibration of multiple sub-models (and related parameters) using different datasets. Quality of data (relevancy, scalability, and uncertainty) could be taken into consideration in the calibration process. This work presents a step forward in the development and realization of the “CIPS Validation Data Plan” at the Consortium for Advanced Simulation of LWRs to enable quantitative assessment of the CASL modeling of Crud-Induced Power Shift (CIPS) phenomenon, in particular, and the CASL advanced predictive capabilities, in general. This report is prepared for the Department of Energy’s Consortium for Advanced Simulation of LWRs program’s VUQ Focus Area.« less

Single Vector Calibration System for Multi-Axis Load Cells and Method for Calibrating a Multi-Axis Load Cell

NASA Technical Reports Server (NTRS)

Parker, Peter A. (Inventor)

2003-01-01

A single vector calibration system is provided which facilitates the calibration of multi-axis load cells, including wind tunnel force balances. The single vector system provides the capability to calibrate a multi-axis load cell using a single directional load, for example loading solely in the gravitational direction. The system manipulates the load cell in three-dimensional space, while keeping the uni-directional calibration load aligned. The use of a single vector calibration load reduces the set-up time for the multi-axis load combinations needed to generate a complete calibration mathematical model. The system also reduces load application inaccuracies caused by the conventional requirement to generate multiple force vectors. The simplicity of the system reduces calibration time and cost, while simultaneously increasing calibration accuracy.

4-D Imaging and Modeling of Eta Carinae's Inner Fossil Wind Structures

NASA Astrophysics Data System (ADS)

Madura, Thomas I.; Gull, Theodore; Teodoro, Mairan; Clementel, Nicola; Corcoran, Michael; Damineli, Augusto; Groh, Jose; Hamaguchi, Kenji; Hillier, D. John; Moffat, Anthony; Richardson, Noel; Weigelt, Gerd; Lindler, Don; Feggans, Keith

2017-11-01

Eta Carinae is the most massive active binary within 10,000 light-years and is famous for the largest non-terminal stellar explosion ever recorded. Observations reveal that the supermassive (~120 M⊙) binary, consisting of an LBV and either a WR or extreme O star, undergoes dramatic changes every 5.54 years due to the stars' very eccentric orbits (e ~ 0.9). Many of these changes are caused by a dynamic wind-wind collision region (WWCR) between the stars, plus expanding fossil WWCRs formed one, two, and three 5.54-year cycles ago. The fossil WWCRs can be spatially and spectrally resolved by the Hubble Space Telescope/Space Telescope Imaging Spectrograph (HST/STIS). Starting in June 2009, we used the HST/STIS to spatially map Eta Carinae's fossil WWCRs across one full orbit, following temporal changes in several forbidden emission lines (e.g. [Feiii] 4659 Å, [Feii] 4815 Å), creating detailed data cubes at multiple epochs. Multiple wind structures were imaged, revealing details about the binary's orbital motion, photoionization properties, and recent (~5 - 15 year) mass-loss history. These observations allow us to test 3-D hydrodynamical and radiative-transfer models of the interacting winds. Our observations and models strongly suggest that the wind and photoionization properties of Eta Carinae's binary have not changed substantially over the past several orbital cycles. They also provide a baseline for following future changes in Eta Carinae, essential for understanding the late-stage evolution of this nearby supernova progenitor. For more details, see Gull et al. (2016) and references therein.

Integrating ecosystems measurements from multiple eddy-covariance sites to a simple model of ecosystem process - Are there possibilities for a uniform model calibration?

NASA Astrophysics Data System (ADS)

Minunno, Francesco; Peltoniemi, Mikko; Launiainen, Samuli; Mäkelä, Annikki

2014-05-01

Biogeochemical models quantify the material and energy flux exchanges between biosphere, atmosphere and soil, however there is still considerable uncertainty underpinning model structure and parametrization. The increasing availability of data from of multiple sources provides useful information for model calibration and validation at different space and time scales. We calibrated a simplified ecosystem process model PRELES to data from multiple sites. In this work we had the following objective: to compare a multi-site calibration and site-specific calibrations, in order to test if PRELES is a model of general applicability, and to test how well one parameterization can predict ecosystem fluxes. Model calibration and evaluation were carried out by the means of the Bayesian method; Bayesian calibration (BC) and Bayesian model comparison (BMC) were used to quantify the uncertainty in model parameters and model structure. Evapotranspiration (ET) and gross primary production (GPP) measurements collected in 9 sites of Finland and Sweden were used in the study; half dataset was used for model calibrations and half for the comparative analyses. 10 BCs were performed; the model was independently calibrated for each of the nine sites (site-specific calibrations) and a multi-site calibration was achieved using the data from all the sites in one BC. Then 9 BMCs were carried out, one for each site, using output from the multi-site and the site-specific versions of PRELES. Similar estimates were obtained for the parameters at which model outputs are most sensitive. Not surprisingly, the joint posterior distribution achieved through the multi-site calibration was characterized by lower uncertainty, because more data were involved in the calibration process. No significant differences were encountered in the prediction of the multi-site and site-specific versions of PRELES, and after BMC, we concluded that the model can be reliably used at regional scale to simulate carbon and water fluxes of Boreal forests. Despite being a simple model, PRELES provided good estimates of GPP and ET; only for one site PRELES multi-site version underestimated water fluxes. Our study implies convergence of GPP and water processes in boreal zone to the extent that their plausible prediction is possible with a simple model using global parameterization.

Integrating the EMPD with an Alpine altitudinal training set to reconstruct climate variables in Holocene pollen records from high-altitude peat bogs

NASA Astrophysics Data System (ADS)

Furlanetto, Giulia; Badino, Federica; Brunetti, Michele; Champvillair, Elena; De Amicis, Mattia; Maggi, Valter; Pini, Roberta; Ravazzi, Cesare; Vallé, Francesca

2016-04-01

Temperatures and precipitation are the main environmental factors influencing vegetation and pollen production. Knowing the modern climate optima and tolerances of those plants represented in fossil assemblages and assuming that the relationships between plants and climate in the past are not dissimilar from the modern ones, fossil pollen records offer many descriptors to reconstruct past climate variables. The aim of our work is to investigate the potential of high-altitude pollen records from an Alpine peat bog (TBValter, close to the Ruitor Glacier, Western Italian Alps) for quantitative paleoclimate estimates. The idea behind is that high-altitude ecosystems are more sensitive to climate changes, especially to changes in July temperatures that severely affect the timberline ecotone. Meantime, we met with difficulties when considering the factors involved in pollen dispersal over a complex altitudinal mountain pattern, such as the Alps. We used the EMPD-European Modern Pollen Database (Davis et al., 2013) as modern training set to be compared with our high-altitude fossil site. The EMPD dataset is valuable in that it provides a large geographic coverage of main ecological and climate gradients (at sub-continental scale) but lacks in sampling of altitudinal gradients and high-altitude sites in the Alps. We therefore designed an independent altitudinal training set for the alpine valley hosting our fossil site. 27 sampling plots were selected along a 1700m-elevational transect. In a first step, each plot was provided with (i) 3 moss polsters collected following the guidelines provided by Cañellas-Boltà et al. (2009) and analyzed separately to account for differences in pollen deposition at small scale, (ii) morphometrical parameters obtained through a high-resolution DEM, and (iii) temperature and precipitation were estimated by means of weighted linear regression of the meteorological variable versus elevation, locally evaluated for each site (Brunetti et al., 2014), starting from a dense and quality-controlled observational dataset. In the most advanced step, we designed calibration functions using modern pollen and climate data stored in the EMPD and integrated with the 27 samples from the altitudinal training set. Regression and calibration method (LWWA) and MAT (Modern Analogue Technique) were used to reconstruct temperatures and precipitation. We applied the models to our fossil site to infer temperatures of the coldest (Tjan) and warmest (Tjul) months and the mean annual precipitation (Pann). Finally we compared our results with established climate proxy records (oxygen isotope records from ice cores, records of Alpine Glaciers fluctuations, stalagmites). This research is promoted by the CNR-DTA NextData Project. Brunetti et al., 2014. International Journal of Climatology 34, 1278-1296. Cañellas-Boltà et al., 2009. The Holocene 19(8), 1185-1200. Davis et al., 2013. Vegetation History and Archaeobotany 22, 521-530.

Phylogeography of the sand dollar genus Mellita: cryptic speciation along the coasts of the Americas.

PubMed

Coppard, Simon E; Zigler, Kirk S; Lessios, H A

2013-12-01

Sand dollars of the genus Mellita are members of the sandy shallow-water fauna. The genus ranges in tropical and subtropical regions on the two coasts of the Americas. To reconstruct the phylogeography of the genus we sequenced parts of the mitochondrial cytochrome oxidase I and of 16S rRNA as well as part of the nuclear 28S rRNA gene from a total of 185 specimens of all ten described morphospecies from 31 localities. Our analyses revealed the presence of eleven species, including six cryptic species. Sequences of five morphospecies do not constitute monophyletic molecular units and thus probably represent ecophenotypic variants. The fossil-calibrated phylogeny showed that the ancestor of Mellita diverged into a Pacific lineage and an Atlantic+Pacific lineage close to the Miocene/Pliocene boundary. Atlantic M. tenuis, M. quinquiesperforata and two undescribed species of Mellita have non-overlapping distributions. Pacific Mellita consist of two highly divergent lineages that became established at different times, resulting in sympatric M. longifissa and M. notabilis. Judged by modern day ranges, not all divergence in this genus conforms to an allopatric speciation model. Only the separation of M. quinquiesperforata from M. notabilis is clearly due to vicariance as the result of the completion of the Isthmus of Panama. The molecular phylogeny calibrated on fossil evidence estimated this event as having occurred ~3 Ma, thus providing evidence that, contrary to a recent proposal, the central American Isthmus was not completed until this date. Copyright © 2013 Elsevier Inc. All rights reserved.

Seawater 234U/238U recorded by modern and fossil corals

NASA Astrophysics Data System (ADS)

Chutcharavan, Peter M.; Dutton, Andrea; Ellwood, Michael J.

2018-03-01

U-series dating of corals is a crucial tool for generating absolute chronologies of Late Quaternary sea-level change and calibrating the radiocarbon timescale. Unfortunately, coralline aragonite is susceptible to post-depositional alteration of its primary geochemistry. One screening technique used to identify unaltered corals relies on the back-calculation of initial 234U/238U activity (δ234Ui) at the time of coral growth and implicitly assumes that seawater δ234U has remained constant during the Late Quaternary. Here, we test this assumption using the most comprehensive compilation to date of coral U-series measurements. Unlike previous compilations, this study normalizes U-series measurements to the same decay constants and corrects for offsets in interlaboratory calibrations, thus reducing systematic biases between reported δ234U values. Using this approach, we reassess (a) the value of modern seawater δ234U, and (b) the evolution of seawater δ234U over the last deglaciation. Modern coral δ234U values (145.0 ± 1.5‰) agree with previous measurements of seawater and modern corals only once the data have been normalized. Additionally, fossil corals in the surface ocean display δ234Ui values that are ∼5-7‰ lower during the last glacial maximum regardless of site, taxon, or diagenetic setting. We conclude that physical weathering of U-bearing minerals exposed during ice sheet retreat drives the increase in δ234U observed in the oceans, a mechanism that is consistent with the interpretation of the seawater Pb-isotope signal over the same timescale.

New Miocene Fossils and the History of Penguins in Australia.

PubMed

Park, Travis; Fitzgerald, Erich M G; Gallagher, Stephen J; Tomkins, Ellyn; Allan, Tony

2016-01-01

Australia has a fossil record of penguins reaching back to the Eocene, yet today is inhabited by just one breeding species, the little penguin Eudyptula minor. The description of recently collected penguin fossils from the re-dated upper Miocene Port Campbell Limestone of Portland (Victoria), in addition to reanalysis of previously described material, has allowed the Cenozoic history of penguins in Australia to be placed into a global context for the first time. Australian pre-Quaternary fossil penguins represent stem taxa phylogenetically disparate from each other and E. minor, implying multiple dispersals and extinctions. Late Eocene penguins from Australia are closest to contemporaneous taxa in Antarctica, New Zealand and South America. Given current material, the Miocene Australian fossil penguin fauna is apparently unique in harbouring 'giant penguins' after they went extinct elsewhere; and including stem taxa until at least 6 Ma, by which time crown penguins dominated elsewhere in the southern hemisphere. Separation of Australia from Antarctica during the Palaeogene, and its subsequent drift north, appears to have been a major event in Australian penguin biogeography. Increasing isolation through the Cenozoic may have limited penguin dispersal to Australia from outside the Australasian region, until intensification of the eastwards-flowing Antarctic Circumpolar Current in the mid-Miocene established a potential new dispersal vector to Australia.

New Miocene Fossils and the History of Penguins in Australia

PubMed Central

Park, Travis; Fitzgerald, Erich M. G.; Gallagher, Stephen J.; Tomkins, Ellyn; Allan, Tony

2016-01-01

Australia has a fossil record of penguins reaching back to the Eocene, yet today is inhabited by just one breeding species, the little penguin Eudyptula minor. The description of recently collected penguin fossils from the re-dated upper Miocene Port Campbell Limestone of Portland (Victoria), in addition to reanalysis of previously described material, has allowed the Cenozoic history of penguins in Australia to be placed into a global context for the first time. Australian pre-Quaternary fossil penguins represent stem taxa phylogenetically disparate from each other and E. minor, implying multiple dispersals and extinctions. Late Eocene penguins from Australia are closest to contemporaneous taxa in Antarctica, New Zealand and South America. Given current material, the Miocene Australian fossil penguin fauna is apparently unique in harbouring ‘giant penguins’ after they went extinct elsewhere; and including stem taxa until at least 6 Ma, by which time crown penguins dominated elsewhere in the southern hemisphere. Separation of Australia from Antarctica during the Palaeogene, and its subsequent drift north, appears to have been a major event in Australian penguin biogeography. Increasing isolation through the Cenozoic may have limited penguin dispersal to Australia from outside the Australasian region, until intensification of the eastwards-flowing Antarctic Circumpolar Current in the mid-Miocene established a potential new dispersal vector to Australia. PMID:27115739

Phylogenetic investigation of the complex evolutionary history of dispersal mode and diversification rates across living and fossil Fagales.

PubMed

Larson-Johnson, Kathryn

2016-01-01

As a primary determinant of spatial structure in angiosperm populations, fruit dispersal may impact large-scale ecological and evolutionary processes. Essential to understanding these mechanisms is an accurate reconstruction of dispersal mode over the entire history of an angiosperm lineage. A total-evidence phylogeny is presented for most fossil fruit and all extant genera in Fagales over its c. 95 million yr history. This phylogeny - the largest of its kind to include plant fossils - was used to reconstruct an evolutionary history directly informed by fossil morphologies and to assess relationships among dispersal mode, biogeographic range size, and diversification rate. Reconstructions indicate four transitions to wind dispersal and seven to biotic dispersal, with the phylogenetic integration of fossils crucial to understanding these patterns. Complexity further increased when more specialized behaviors were considered, with fluttering, gliding, autorotating, and scatter-hoarding evolving multiple times across the order. Preliminary biogeographic analyses suggest larger range sizes in biotically dispersed lineages, especially when pollination mode was held constant. Biotically dispersed lineages had significantly higher diversification rates than abiotically dispersed lineages, although transitions in dispersal mode alone cannot explain all detected diversification rate shifts across Fagales. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Putting scales into evolutionary time: the divergence of major scale insect lineages (Hemiptera) predates the radiation of modern angiosperm hosts

PubMed Central

Vea, Isabelle M.; Grimaldi, David A.

2016-01-01

The radiation of flowering plants in the mid-Cretaceous transformed landscapes and is widely believed to have fuelled the radiations of major groups of phytophagous insects. An excellent group to test this assertion is the scale insects (Coccomorpha: Hemiptera), with some 8,000 described Recent species and probably the most diverse fossil record of any phytophagous insect group preserved in amber. We used here a total-evidence approach (by tip-dating) employing 174 morphological characters of 73 Recent and 43 fossil taxa (48 families) and DNA sequences of three gene regions, to obtain divergence time estimates and compare the chronology of the most diverse lineage of scale insects, the neococcoid families, with the timing of the main angiosperm radiation. An estimated origin of the Coccomorpha occurred at the beginning of the Triassic, about 245 Ma [228–273], and of the neococcoids 60 million years later [210–165 Ma]. A total-evidence approach allows the integration of extinct scale insects into a phylogenetic framework, resulting in slightly younger median estimates than analyses using Recent taxa, calibrated with fossil ages only. From these estimates, we hypothesise that most major lineages of coccoids shifted from gymnosperms onto angiosperms when the latter became diverse and abundant in the mid- to Late Cretaceous. PMID:27000526

Target-based calibration method for multifields of view measurement using multiple stereo digital image correlation systems

NASA Astrophysics Data System (ADS)

Dong, Shuai; Yu, Shanshan; Huang, Zheng; Song, Shoutan; Shao, Xinxing; Kang, Xin; He, Xiaoyuan

2017-12-01

Multiple digital image correlation (DIC) systems can enlarge the measurement field without losing effective resolution in the area of interest (AOI). However, the results calculated in substereo DIC systems are located in its local coordinate system in most cases. To stitch the data obtained by each individual system, a data merging algorithm is presented in this paper for global measurement of multiple stereo DIC systems. A set of encoded targets is employed to assist the extrinsic calibration, of which the three-dimensional (3-D) coordinates are reconstructed via digital close range photogrammetry. Combining the 3-D targets with precalibrated intrinsic parameters of all cameras, the extrinsic calibration is significantly simplified. After calculating in substereo DIC systems, all data can be merged into a universal coordinate system based on the extrinsic calibration. Four stereo DIC systems are applied to a four point bending experiment of a steel reinforced concrete beam structure. Results demonstrate high accuracy for the displacement data merging in the overlapping field of views (FOVs) and show feasibility for the distributed FOVs measurement.

The fossil record of evolution: Data on diversification and extinction

NASA Technical Reports Server (NTRS)

Sepkoski, J. J., Jr.

1991-01-01

Understanding of the evolution of complex life, and of the roles that changing terrestrial and extraterrestrial environments played in life's history, is dependent upon synthetic knowledge of the fossil record. Paleontologists have been describing fossils for more that two centuries. However, much of this information is dispersed in monographs and journal articles published throughout the world. Over the past several years, this literature was surveyed, and a data base on times of origination and extinction of fossil genera was compiled. The data base, which now holds approximately 32,000 genera, covers all taxonomic groups of marine animals, incorporates the most recent taxonomic assignments, and uses a detailed global time framework that can resolve originations and extinctions to intervals averaging three million years in duration. These data can be used to compile patterns of global biodiversity, measure rates of taxic evolution, and test hypotheses concerning adaptive radiations, mass extinctions, etc. Thus far, considerable effort was devoted to using the data to test the hypothesis of periodicity of mass extinction. Rates of extinction measured from the data base have also been used to calibrate models of evolutionary radiations in marine environments. It was observed that new groups, or clades of animals (i.e., orders and classes) tend to reach appreciable diversity first in nearshore environments and then to radiate in more offshore environments; during decline, these clades may disappear from the nearshore while persisting in offshore, deep water habitats. These observations have led to suggestions that there is something special about stressful or perturbed environments that promotes the evolution of novel kinds of animals that can rapidly replace their predecessors. The numerical model that is being investigated to study this phenomenon treats environments along onshore-offshore gradients as if they were discrete habitats. Other aspects of this investigation are presented.

Architecture and morphology of coral reef sequences. Modeling and observations from uplifting islands of SE Sulawesi, Indonesia

NASA Astrophysics Data System (ADS)

Pastier, Anne-Morwenn; Husson, Laurent; Bezos, Antoine; Pedoja, Kevin; Elliot, Mary; Hafidz, Abdul; Imran, Muhammad; Lacroix, Pascal; Robert, Xavier

2016-04-01

During the Late Neogene, sea level oscillations have profoundly shaped the morphology of the coastlines of intertropical zones, wherein relative sea level simultaneously controlled reef expansion and erosion of earlier reef bodies. In uplifted domains like SE Sulawesi, the sequences of fossil reefs display a variety of fossil morphologies. Similarly, the morphologies of the modern reefs are highly variable, including cliff notches, narrow fringing reefs, wide flat terraces, and barriers reefs. In this region, where uplift rates vary rapidly laterally, the entire set of morphologies is displayed within short distances. We developed a numerical model that predicts the architecture of fossil reefs sequences and apply it to observations from SE Sulawesi, accounting -amongst other parameters- for reef growth, coastal erosion, and uplift rates. The observations that we use to calibrate our models are mostly the morphology of both the onshore (dGPS and high-resolution Pleiades DEM) and offshore (sonar) coast, as well as U-Th radiometrically dated coral samples. Our method allows unravelling the spatial and temporal evolution of large domains on map view. Our analysis indicates that the architecture and morphology of uplifting coastlines is almost systematically polyphased (as attested by samples of different ages within a unique terrace), which assigns a primordial role to erosion, comparable to reef growth. Our models also reproduce the variety of modern morphologies, which are chiefly dictated by the uplift rates of the pre-existing morphology of the substratum, itself responding to the joint effects of reef building and subsequent erosion. In turn, we find that fossil and modern morphologies can be returned to uplift rates rather precisely, as the parametric window of each specific morphology is often narrow.

Estimating the fossil disc mass during supermassive black hole mergers: the importance of torque implementation

NASA Astrophysics Data System (ADS)

Tazzari, M.; Lodato, G.

2015-05-01

In this paper, we revisit the issue of estimating the `fossil' disc mass in the circumprimary disc, during the merger of a supermassive black hole binary. As the binary orbital decay speeds up due to the emission of gravitational waves, the gas in the circumprimary disc might be forced to accrete rapidly and could in principle provide a significant electromagnetic counterpart to the gravitational wave emission. Since the luminosity of such flare is proportional to the gaseous mass in the circumprimary disc, estimating such mass accurately is important. Previous investigations of this issue have produced contradictory results, with some authors estimating super-Eddington flares and large disc mass, while others suggesting that the `fossil' disc mass is very low, even less than a Jupiter mass. Here, we perform simple 1D calculations to show that such very low estimates of the disc mass are an artefact of the specific implementation of the tidal torque in 1D models. In particular, for moderate mass ratios of the binary, the usual formula for the torque used in 1D models significantly overestimates the width of the gap induced by the secondary and this artificially leads to a very small leftover circumprimary disc. Using a modified torque, calibrated to reproduce the correct gap width as estimated by 3D models, leads to fossil disc masses of the order of one solar mass. The rapid accretion of the whole circumprimary disc would produce peak luminosities of the order of 1-20 times the Eddington luminosity. Even if a significant fraction of the gas escapes accretion by flowing out the secondary orbit during the merger (an effect not included in our calculations), we would still predict close to Eddington luminosities that might be easily detected.

The early Eocene birds of the Messel fossil site: a 48 million-year-old bird community adds a temporal perspective to the evolution of tropical avifaunas.

PubMed

Mayr, Gerald

2017-05-01

Birds play an important role in studies addressing the diversity and species richness of tropical ecosystems, but because of the poor avian fossil record in all extant tropical regions, a temporal perspective is mainly provided by divergence dates derived from calibrated molecular analyses. Tropical ecosystems were, however, widespread in the Northern Hemisphere during the early Cenozoic, and the early Eocene German fossil site Messel in particular has yielded a rich avian fossil record. The Messel avifauna is characterized by a considerable number of flightless birds, as well as a high diversity of aerial insectivores and the absence of large arboreal birds. With about 70 currently known species in 42 named genus-level and at least 39 family-level taxa, it approaches extant tropical biotas in terms of species richness and taxonomic diversity. With regard to its taxonomic composition and presumed ecological characteristics, the Messel avifauna is more similar to the Neotropics, Madagascar, and New Guinea than to tropical forests in continental Africa and Asia. Because the former regions were geographically isolated during most of the Cenozoic, their characteristics may be due to the absence of biotic factors, especially those related to the diversification of placental mammals, which impacted tropical avifaunas in Africa and Asia. The crown groups of most avian taxa that already existed in early Eocene forests are species-poor. This does not support the hypothesis that the antiquity of tropical ecosystems is key to the diversity of tropical avifaunas, and suggests that high diversification rates may be of greater significance. © 2016 Cambridge Philosophical Society.

Estimating Latest Cretaceous and Tertiary Atmospheric PCO2 from Stomatal Indices

NASA Astrophysics Data System (ADS)

Royer, D. L.; Wing, S. L.; Beerling, D. J.

2001-05-01

Most modern C3 seed plants show an inverse relationship between PCO2 and stomatal index (SI), where SI is the proportion of epidermal cells that are stomatal packages. This plant-atmosphere response therefore provides a reliable approach for estimating paleo-CO2 levels. Since stomatal responses to CO2 are generally species-specific, one is limited in paleo-reconstructions to species that exist both in the fossil record and living today. Fossils morphologically similar to living Ginkgo biloba and Metasequoia glyptostroboides extend back to the early and late Cretaceous, respectively, indicating that the fossil and living forms are very closely related. Measurements of SI made on fossil Ginkgo and Metasequoia were calibrated with historical collections of G. biloba and M. glyptostroboides leaves from sites that developed during the anthropogenically-driven CO2 increases of the past 145 years (288-369 ppmv) and with saplings of G. biloba and M. glyptostroboides grown in CO2 controlled growth chambers (350-800 ppmv). Both nonlinear regressions are highly significant (Ginkgo: n = 40, r2 = 0.91; Metasequoia: n = 18; r2 = 0.85). Results from a sequence of 23 latest Cretaceous to early Eocene-aged Ginkgo-bearing sites indicate that CO2 remained between 300 and 450 ppmv with the exception of one high estimate ( ~800 ppmv) near the Paleocene/Eocene boundary, and results from 4 middle Miocene-aged Ginkgo- and Metasequoia-bearing sites indicate that CO2 was between 320 and 400 ppmv. If correct, the CO2 values estimated here are too low to explain via the CO2 greenhouse effect alone the higher global mean temperatures (e.g., 3-4 ° C for the early Eocene) inferred from models and geological data for these two intervals.

A role for iron and oxygen chemistry in preserving soft tissues, cells and molecules from deep time.

PubMed

Schweitzer, Mary H; Zheng, Wenxia; Cleland, Timothy P; Goodwin, Mark B; Boatman, Elizabeth; Theil, Elizabeth; Marcus, Matthew A; Fakra, Sirine C

2014-01-22

The persistence of original soft tissues in Mesozoic fossil bone is not explained by current chemical degradation models. We identified iron particles (goethite-αFeO(OH)) associated with soft tissues recovered from two Mesozoic dinosaurs, using transmission electron microscopy, electron energy loss spectroscopy, micro-X-ray diffraction and Fe micro-X-ray absorption near-edge structure. Iron chelators increased fossil tissue immunoreactivity to multiple antibodies dramatically, suggesting a role for iron in both preserving and masking proteins in fossil tissues. Haemoglobin (HB) increased tissue stability more than 200-fold, from approximately 3 days to more than two years at room temperature (25°C) in an ostrich blood vessel model developed to test post-mortem 'tissue fixation' by cross-linking or peroxidation. HB-induced solution hypoxia coupled with iron chelation enhances preservation as follows: HB + O2 > HB - O2 > -O2 > +O2. The well-known O2/haeme interactions in the chemistry of life, such as respiration and bioenergetics, are complemented by O2/haeme interactions in the preservation of fossil soft tissues.

A role for iron and oxygen chemistry in preserving soft tissues, cells and molecules from deep time

PubMed Central

Schweitzer, Mary H.; Zheng, Wenxia; Cleland, Timothy P.; Goodwin, Mark B.; Boatman, Elizabeth; Theil, Elizabeth; Marcus, Matthew A.; Fakra, Sirine C.

2014-01-01

The persistence of original soft tissues in Mesozoic fossil bone is not explained by current chemical degradation models. We identified iron particles (goethite-αFeO(OH)) associated with soft tissues recovered from two Mesozoic dinosaurs, using transmission electron microscopy, electron energy loss spectroscopy, micro-X-ray diffraction and Fe micro-X-ray absorption near-edge structure. Iron chelators increased fossil tissue immunoreactivity to multiple antibodies dramatically, suggesting a role for iron in both preserving and masking proteins in fossil tissues. Haemoglobin (HB) increased tissue stability more than 200-fold, from approximately 3 days to more than two years at room temperature (25°C) in an ostrich blood vessel model developed to test post-mortem ‘tissue fixation’ by cross-linking or peroxidation. HB-induced solution hypoxia coupled with iron chelation enhances preservation as follows: HB + O2 > HB − O2 > −O2 ≫ +O2. The well-known O2/haeme interactions in the chemistry of life, such as respiration and bioenergetics, are complemented by O2/haeme interactions in the preservation of fossil soft tissues. PMID:24285202

The Ecological Rise of Whales Chronicled by the Fossil Record.

PubMed

Pyenson, Nicholas D

2017-06-05

The evolution of cetaceans is one of the best examples of macroevolution documented from the fossil record. While ecological transitions dominate each phase of cetacean history, this context is rarely stated explicitly. The first major ecological phase involves a transition from riverine and deltaic environments to marine ones, concomitant with dramatic evolutionary transformations documented in their early fossil record. The second major phase involves ecological shifts associated with evolutionary innovations: echolocation (facilitating hunting prey at depth) and filter-feeding (enhancing foraging efficiency on small prey). This latter phase involves body size shifts, attributable to changes in foraging depth and environmental forcing, as well as re-invasions of freshwater systems on continental basins by multiple lineages. Modern phenomena driving cetacean ecology, such as trophic dynamics and arms races, have an evolutionary basis that remains mostly unexamined. The fossil record of cetaceans provides an historical basis for understanding current ecological mechanisms and consequences, especially as global climate change rapidly alters ocean and river ecosystems at rates and scales comparable to those over geologic time. Published by Elsevier Ltd.

Case Studies of Two American Towns That Have Recently Developed Geotourism Venues: A Comparison of Steps Taken in Geoscience Education Program Development

NASA Astrophysics Data System (ADS)

Wandersee, J. H.; Clary, R. M.

2005-12-01

In June, 2003, CNN reported that there were three US public fossil parks (in OH, NY, and IA) that embraced educational missions and allowed the public to collect and actually keep the fossils they found. The new parks moved beyond exhibiting fossils to allowing the park visitor to have a direct, tangible, and authentic geobiological field experience, typically culminating in the visitor's identification and ownership of a small number of personally collected fossils. Our site-based, qualitative, comparative geoscience educational analysis of the strengths and weaknesses of the first three parks was presented at the 2004 International Geological Congress. We subsequently developed a fossil park design model for others contemplating the establishment or instructional use of such parks. Today there are five specially developed, public fossil parks in the US. All are owned and operated by city or county governments, or by non-profit organizations. Each considers its primary mission to be advancing geoscience education. In the current investigation, we conducted on-site, multiple case study research on the two newest US fossil parks. Both are located in small towns: Trammel Fossil Park in Sharonville, Ohio (population 13,000), and Fossil Beds Park in Fossil, Oregon (population 430). The former site is Ordovician in age, with four fossiliferous marine formations. The latter is an Oligocene lake bed and contains approximately 35 species of identified plant fossils. Our focus in both case studies was on identifying the steps of successful fossil park development that lead to a sound informal geoscience education program, based on principles of active, meaningful, and mindful learning (Langer, 1998; Michael and Modell, 2003; Mintzes, Wandersee, and Novak, 2000). We found that each town had developed a collaborative, community-driven, pedagogically innovative, field-based geotourism venue. Each was noteworthy in specific ways for its geoscience education potential as an outdoor teaching laboratory. We report on the results of actual fossil collecting and interpretation at each site, evaluating the opportunities we found to discover common fossils and to learn geobiology in the field. Our study's findings outline the steps of educational program development and support underlying each park. While one utilizes a very effective interpretive signage system that aims to be self-teaching, the other employs a helpful on-site geological interpreter. In one, following the collapse of the timber industry, the town's entire economic recovery plan is now predicated on geotourism and geoscience education activities centered around its fossil park. In the other, the fossil park has become the enticing geoscience jewel of the town's park system. We think the two different fossil park program development approaches we have elucidated (e.g., Wheeler County Oregon's Paleo Project and Sharonville's university-city-local developer collaboration) could be replicated at other appropriate fossil sites. We also correlated our findings with the new National Research Council study, America's Lab Report (2005), to show that fossil parks can offer scientific experiences to the public that contribute to the nation's scientific literacy.

Proposed low-energy absolute calibration of nuclear recoils in a dual-phase noble element TPC using D-D neutron scattering kinematics

NASA Astrophysics Data System (ADS)

Verbus, J. R.; Rhyne, C. A.; Malling, D. C.; Genecov, M.; Ghosh, S.; Moskowitz, A. G.; Chan, S.; Chapman, J. J.; de Viveiros, L.; Faham, C. H.; Fiorucci, S.; Huang, D. Q.; Pangilinan, M.; Taylor, W. C.; Gaitskell, R. J.

2017-04-01

We propose a new technique for the calibration of nuclear recoils in large noble element dual-phase time projection chambers used to search for WIMP dark matter in the local galactic halo. This technique provides an in situ measurement of the low-energy nuclear recoil response of the target media using the measured scattering angle between multiple neutron interactions within the detector volume. The low-energy reach and reduced systematics of this calibration have particular significance for the low-mass WIMP sensitivity of several leading dark matter experiments. Multiple strategies for improving this calibration technique are discussed, including the creation of a new type of quasi-monoenergetic neutron source with a minimum possible peak energy of 272 keV. We report results from a time-of-flight-based measurement of the neutron energy spectrum produced by an Adelphi Technology, Inc. DD108 neutron generator, confirming its suitability for the proposed nuclear recoil calibration.

In-flight radiometric calibration of the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS)

NASA Technical Reports Server (NTRS)

Conel, James E.; Green, Robert O.; Alley, Ronald E.; Bruegge, Carol J.; Carrere, Veronique; Margolis, Jack S.; Vane, Gregg; Chrien, Thomas G.; Slater, Philip N.; Biggard, Stuart F.

1988-01-01

A reflectance-based method was used to provide an analysis of the in-flight radiometric performance of AVIRIS. Field spectral reflectance measurements of the surface and extinction measurements of the atmosphere using solar radiation were used as input to atmospheric radiative transfer calculations. Five separate codes were used in the analysis. Four include multiple scattering, and the computed radiances from these for flight conditions were in good agreement. Code-generated radiances were compared with AVIRIS-predicted radiances based on two laboratory calibrations (pre- and post-season of flight) for a uniform highly reflecting natural dry lake target. For one spectrometer (C), the pre- and post-season calibration factors were found to give identical results, and to be in agreement with the atmospheric models that include multiple scattering. This positive result validates the field and laboratory calibration technique. Results for the other spectrometers (A, B and D) were widely at variance with the models no matter which calibration factors were used. Potential causes of these discrepancies are discussed.

Evolutionary History of Assassin Bugs (Insecta: Hemiptera: Reduviidae): Insights from Divergence Dating and Ancestral State Reconstruction

PubMed Central

Hwang, Wei Song; Weirauch, Christiane

2012-01-01

Assassin bugs are one of the most successful clades of predatory animals based on their species numbers (∼6,800 spp.) and wide distribution in terrestrial ecosystems. Various novel prey capture strategies and remarkable prey specializations contribute to their appeal as a model to study evolutionary pathways involved in predation. Here, we reconstruct the most comprehensive reduviid phylogeny (178 taxa, 18 subfamilies) to date based on molecular data (5 markers). This phylogeny tests current hypotheses on reduviid relationships emphasizing the polyphyletic Reduviinae and the blood-feeding, disease-vectoring Triatominae, and allows us, for the first time in assassin bugs, to reconstruct ancestral states of prey associations and microhabitats. Using a fossil-calibrated molecular tree, we estimated divergence times for key events in the evolutionary history of Reduviidae. Our results indicate that the polyphyletic Reduviinae fall into 11–14 separate clades. Triatominae are paraphyletic with respect to the reduviine genus Opisthacidius in the maximum likelihood analyses; this result is in contrast to prior hypotheses that found Triatominae to be monophyletic or polyphyletic and may be due to the more comprehensive taxon and character sampling in this study. The evolution of blood-feeding may thus have occurred once or twice independently among predatory assassin bugs. All prey specialists evolved from generalist ancestors, with multiple evolutionary origins of termite and ant specializations. A bark-associated life style on tree trunks is ancestral for most of the lineages of Higher Reduviidae; living on foliage has evolved at least six times independently. Reduviidae originated in the Middle Jurassic (178 Ma), but significant lineage diversification only began in the Late Cretaceous (97 Ma). The integration of molecular phylogenetics with fossil and life history data as presented in this paper provides insights into the evolutionary history of reduviids and clears the way for in-depth evolutionary hypothesis testing in one of the most speciose clades of predators. PMID:23029072

System stability and calibrations for hand-held electromagnetic frequency domain instruments

NASA Astrophysics Data System (ADS)

Saksa, Pauli J.; Sorsa, Joona

2017-05-01

There are a few multiple-frequency domain electromagnetic induction (EMI) hand-held rigid boom systems available for shallow geophysical resistivity investigations. They basically measure secondary field real and imaginary components after the system calibrations. One multiple-frequency system, the EMP-400 Profiler from Geophysical Survey Systems Inc., was tested for system calibrations, stability and various effects present in normal measurements like height variation, tilting, signal stacking and time stability. Results indicated that in test conditions, repeatable high-accuracy imaginary component values can be recorded for near-surface frequency soundings. In test conditions, real components are also stable but vary strongly in normal surveying measurements. However, certain calibration issues related to the combination of user influence and measurement system height were recognised as an important factor in reducing for data errors and for further processing like static offset corrections.

Tempo and mode of antibat ultrasound production and sonar jamming in the diverse hawkmoth radiation.

PubMed

Kawahara, Akito Y; Barber, Jesse R

2015-05-19

The bat-moth arms race has existed for over 60 million y, with moths evolving ultrasonically sensitive ears and ultrasound-producing organs to combat bat predation. The evolution of these defenses has never been thoroughly examined because of limitations in simultaneously conducting behavioral and phylogenetic analyses across an entire group. Hawkmoths include >1,500 species worldwide, some of which produce ultrasound using genital stridulatory structures. However, the function and evolution of this behavior remain largely unknown. We built a comprehensive behavioral dataset of hawkmoth hearing and ultrasonic reply to sonar attack using high-throughput field assays. Nearly half of the species tested (57 of 124 species) produced ultrasound to tactile stimulation or playback of bat echolocation attack. To test the function of ultrasound, we pitted big brown bats (Eptesicus fuscus) against hawkmoths over multiple nights and show that hawkmoths jam bat sonar. Ultrasound production was immediately and consistently effective at thwarting attack and bats regularly performed catching behavior without capturing moths. We also constructed a fossil-calibrated, multigene phylogeny to study the evolutionary history and divergence times of these antibat strategies across the entire family. We show that ultrasound production arose in multiple groups, starting in the late Oligocene (∼ 26 Ma) after the emergence of insectivorous bats. Sonar jamming and bat-detecting ears arose twice, independently, in the Miocene (18-14 Ma) either from earless hawkmoths that produced ultrasound in response to physical contact only, or from species that did not respond to touch or bat echolocation attack.

Development of a mobile and high-precision atmospheric CO2 monitoring station

NASA Astrophysics Data System (ADS)

Molnár, M.; Haszpra, L.; Major, I.; Svingor, É.; Veres, M.

2009-04-01

Nowadays one of the most burning questions for the science is the rate and the reasons of the recent climate change. Greenhouse gases (GHG), mainly CO2 and CH4 in the atmosphere could affect the climate of our planet. However, the relation between the amount of atmospheric GHG and the climate is complex, full with interactions and feedbacks partly poorly known even by now. The only way to understand the processes, to trace the changes, to develop and validate mathematical models for forecasts is the extensive, high precision, continuous monitoring of the atmosphere. Fossil fuel CO2 emissions are a major component of the European carbon budget. Separation of the fossil fuel signal from the natural biogenic one in the atmosphere is, therefore, a crucial task for quantifying exchange flux of the continental biosphere through atmospheric observations and inverse modelling. An independent method to estimate trace gas emissions is the top-down approach, using atmospheric CO2 concentration measurements combined with simultaneous radiocarbon (14C) observations. As adding fossil fuel CO2 to the atmosphere, therefore, leads not only to an increase in the CO2 content of the atmosphere but also to a decrease in the 14C/12C ratio in atmospheric CO2. The ATOMKI has more than two decade long experience in atmospheric 14CO2 monitoring. As a part of an ongoing research project being carried out in Hungary to investigate the amount and temporal and spatial variations of fossil fuel CO2 in the near surface atmosphere we developed a mobile and high-precision atmospheric CO2 monitoring station. We describe the layout and the operation of the measuring system which is designed for the continuous, unattended monitoring of CO2 mixing ratio in the near surface atmosphere based on an Ultramat 6F (Siemens) infrared gas analyser. In the station one atmospheric 14CO2 sampling unit is also installed which is developed and widely used since more than one decade by ATOMKI. Mixing ratio of CO2 is measured at 2 m above the ground by the monitoring station. Air is pumped through a 9.5-mm-diameter plastic tube (PFA, Swagelok) to a CO2 analyser located in a container box. Container box (Containex) is 1.5 m wide, 1.2 m deep and 2.2 m high, designed as a mobile measuring room which is field deployable, only electric power is required. A 15 micron pore size stainless steel Tee-Type (Swagelok) particle filter is located at the inlet of the sampler tube. Diaphragm pump (KNF) is used to draw air continuously through the sampling tube from monitoring level at flow rate of ~ 2 L/min. After leaving the pump, the air at 5 psig overpressure enters a glass trap for liquid water that is cooled in a regular household refrigerator, to dry the air to a dew point of 3°-4°C. Liquid water is forced out through an orifice at the bottom of the trap. The air sample inlet tube and the standard gases (Linde Hungary) are connected to miniature solenoid valves (S Series, ASCO Numatics) in a manifold which are normally closed and controlled by the CO2 analyser, which selects which gas is sampled. The air leaving the manifold through its common outlet is further dried to a dew point of about -25°C by passage through a 360-cm-long Nafion drier (Permapure), so that the water vapour interference and dilution effect are <0.1 ppm equivalent CO2. The Nafion drier is purged in a counter flow (300 cm3/min) arrangement using waste sample air that has been further dried by passage through anhydrous CaSO4 (Drierite). Analysis is carried out using an infrared gas analyser Ultramat 6F which is a specialised model for field applications by Siemens. A constant sample flow rate of 300 cm3/min is maintained by a mass flow controller (Aalborg). The reference cell of the CO2 analyzer is continuously flushed with a compressed reference gas of 350 ppm CO2 in synthetic air (Messer Hungarogáz). The basic calibration cycle is 2 hours, consisting of a zero-point calibration and a span calibration. Each calibration is consisting of 2 min flushing and 20 sec signal integration. The usual change of the response function is below 0.2 ppm after 2 hours following a previous calibration. The analyser measures the CO2 mixing ratio in the sample gas in every 3 seconds. Output data are registered by a data logger developed for this application (Special Control Devices). The overall uncertainty of our atmospheric CO2 mixing ratio measurements is < 0.5 ppm (< 0,2 %). This level of error is acceptable for fossil fuel CO2 calculations as the uncertainty of the other required parameter radiocarbon content of atmospheric CO2 is usually 0.3-0.5%. Using the developed mobile and high-precision atmospheric CO2 monitoring station we plan to determine the fossil fuel CO2 amount in the air of different cities and other average industrial regions in Hungary. This research project was supported by Hungarian NSF (Ref No. F69029).

Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar.

PubMed

Bacon, Christine D; Simmons, Mark P; Archer, Robert H; Zhao, Liang-Cheng; Andriantiana, Jacky

2016-01-01

Of the 97 currently recognized genera of Celastraceae, 19 are native to Madagascar, including six endemics. In this study we conducted the most thorough phylogenetic analysis of Celastraceae yet completed with respect to both character and taxon sampling, and include representatives of five new endemic genera. Fifty-one new accessions, together with 328 previously used accessions of Celastrales, were sampled for morphological characters, two rDNA gene regions, and two plastid gene regions. The endemic Malagasy genera are resolved in two separate lineages-Xenodrys by itself and all other endemic genera in a clade that also includes four lineages inferred to have dispersed from Madagascar: Brexia madagascariensis (Mascarene Islands, coastal Africa), Elaeodendron (West Indies, Africa to New Caledonia), and Pleurostylia (Africa to New Caledonia). Of the 12 extant Malagasy Celastraceae lineages identified, eight are clearly of African origin. The origins of the remaining four lineages are less clear, but reasonable possibilities include America, Eurasia, Africa, southern India, Malesia, and Australia. Based on 95% credible age intervals from fossil-calibrated molecular dating, all 12 extant Malagasy Celastraceae lineages appear to have arisen following dispersal after the separation of Madagascar from other landmasses within the last 70 million years. Copyright © 2015 Elsevier Inc. All rights reserved.

Rapid diversification of falcons (Aves: Falconidae) due to expansion of open habitats in the Late Miocene.

PubMed

Fuchs, Jérôme; Johnson, Jeff A; Mindell, David P

2015-01-01

Understanding how and why lineages diversify is central to understanding the origins of biological diversity. The avian family Falconidae (caracaras, forest-falcons, falcons) has an uneven distribution of species among multiple well-supported clades, and provides a useful system for testing hypotheses about diversification rate and correlation with environmental changes. We analyzed eight independent loci for 1-7 individuals from each of the 64 currently recognized Falconidae species, together with two fossil falconid temporal calibrations, to assess phylogeny, absolute divergence times and potential shifts in diversification rate. Our analyses supported similar diversification ages in the Early to Middle Miocene for the three traditional subfamilies, Herpetotherinae, Polyborinae and Falconinae. We estimated that divergences within the subfamily Falconinae began about 16mya and divergences within the most species-rich genus, Falco, including about 60% of all Falconidae species, began about 7.5mya. We found evidence for a significant increase in diversification rate at the basal phylogenetic node for the genus Falco, and the timing for this rate shift correlates generally with expansion of C4 grasslands beginning around the Miocene/Pliocene transition. Concomitantly, Falco lineages that are distributed primarily in grassland or savannah habitats, as opposed to woodlands, and exhibit migratory, as opposed to sedentary, behavior experienced a higher diversification rate. Published by Elsevier Inc.

A gas chromatograph for quantification of peroxycarboxylic nitric anhydrides calibrated by thermal dissociation cavity ring-down spectroscopy

NASA Astrophysics Data System (ADS)

Tokarek, T. W.; Huo, J. A.; Odame-Ankrah, C. A.; Hammoud, D.; Taha, Y. M.; Osthoff, H. D.

2014-06-01

The peroxycarboxylic nitric anhydrides (PANs, molecular formula RC(O)O2NO2) can readily be observed by gas chromatography coupled to electron capture detection (PAN-GC). Calibration of a PAN-GC remains a challenge because the response factors (RF's) differ for each of the PANs and because their synthesis in sufficiently high purity is non-trivial, in particular for PANs containing unsaturated side chains. In this manuscript, a PAN-GC and its calibration using diffusion standards, whose output was quantified by blue diode laser thermal dissociation cavity ring-down spectroscopy (TD-CRDS), are described. The PAN-GC peak areas correlated linearly with total peroxy nitrate (ΣPN) mixing ratios measured by TD-CRDS (r > 0.96). Accurate determination of RF's required the concentrations of PAN impurities in the synthetic standards to be subtracted from ΣPN. The PAN-GC and its TD-CRDS calibration method were deployed during ambient air measurement campaigns in Abbotsford, BC, from 20 July to 5 August, 2012, and during the Fort McMurray Oil Sands Strategic Investigation of Local Sources (FOSSILS) campaign at the AMS13 ground site in Fort McKay, AB, from 10 August to 5 September 2013. For the Abbotsford data set, the PAN-GC mixing ratios were compared and agreed with those determined in parallel by thermal dissociation chemical ionization mass spectrometry (TD-CIMS). Advantages and disadvantages of the PAN measurement techniques used in this work and the utility of TD-CRDS as a PAN-GC calibration method are discussed.

Multiple independent identification decisions: a method of calibrating eyewitness identifications.

PubMed

Pryke, Sean; Lindsay, R C L; Dysart, Jennifer E; Dupuis, Paul

2004-02-01

Two experiments (N = 147 and N = 90) explored the use of multiple independent lineups to identify a target seen live. In Experiment 1, simultaneous face, body, and sequential voice lineups were used. In Experiment 2, sequential face, body, voice, and clothing lineups were used. Both studies demonstrated that multiple identifications (by the same witness) from independent lineups of different features are highly diagnostic of suspect guilt (G. L. Wells & R. C. L. Lindsay, 1980). The number of suspect and foil selections from multiple independent lineups provides a powerful method of calibrating the accuracy of eyewitness identification. Implications for use of current methods are discussed. ((c) 2004 APA, all rights reserved)

Experimental Investigations of Non-Stationary Properties In Radiometer Receivers Using Measurements of Multiple Calibration References

NASA Technical Reports Server (NTRS)

Racette, Paul; Lang, Roger; Zhang, Zhao-Nan; Zacharias, David; Krebs, Carolyn A. (Technical Monitor)

2002-01-01

Radiometers must be periodically calibrated because the receiver response fluctuates. Many techniques exist to correct for the time varying response of a radiometer receiver. An analytical technique has been developed that uses generalized least squares regression (LSR) to predict the performance of a wide variety of calibration algorithms. The total measurement uncertainty including the uncertainty of the calibration can be computed using LSR. The uncertainties of the calibration samples used in the regression are based upon treating the receiver fluctuations as non-stationary processes. Signals originating from the different sources of emission are treated as simultaneously existing random processes. Thus, the radiometer output is a series of samples obtained from these random processes. The samples are treated as random variables but because the underlying processes are non-stationary the statistics of the samples are treated as non-stationary. The statistics of the calibration samples depend upon the time for which the samples are to be applied. The statistics of the random variables are equated to the mean statistics of the non-stationary processes over the interval defined by the time of calibration sample and when it is applied. This analysis opens the opportunity for experimental investigation into the underlying properties of receiver non stationarity through the use of multiple calibration references. In this presentation we will discuss the application of LSR to the analysis of various calibration algorithms, requirements for experimental verification of the theory, and preliminary results from analyzing experiment measurements.

Topology of magnetic flux ropes and formation of fossil flux transfer events and boundary layer plasmas

NASA Technical Reports Server (NTRS)

Lee, L. C.; Ma, Z. W.; Fu, Z. F.; Otto, A.

1993-01-01

A mechanism for the formation of fossil flux transfer events and the low-level boundary layer within the framework of multiple X-line reconnection is proposed. Attention is given to conditions for which the bulk of magnetic flux in a flux rope of finite extent has a simple magnetic topology, where the four possible connections of magnetic field lines are: IMF to MSP, MSP to IMF, IMF to IMF, and MSP to MSP. For a sufficient relative shift of the X lines, magnetic flux may enter a flux rope from the magnetosphere and exit into the magnetosphere. This process leads to the formation of magnetic flux ropes which contain a considerable amount of magnetosheath plasma on closed magnetospheric field lines. This process is discussed as a possible explanation for the formation of fossil flux transfer events in the magnetosphere and the formation of the low-latitude boundary layer.

Normalized Metadata Generation for Human Retrieval Using Multiple Video Surveillance Cameras.

PubMed

Jung, Jaehoon; Yoon, Inhye; Lee, Seungwon; Paik, Joonki

2016-06-24

Since it is impossible for surveillance personnel to keep monitoring videos from a multiple camera-based surveillance system, an efficient technique is needed to help recognize important situations by retrieving the metadata of an object-of-interest. In a multiple camera-based surveillance system, an object detected in a camera has a different shape in another camera, which is a critical issue of wide-range, real-time surveillance systems. In order to address the problem, this paper presents an object retrieval method by extracting the normalized metadata of an object-of-interest from multiple, heterogeneous cameras. The proposed metadata generation algorithm consists of three steps: (i) generation of a three-dimensional (3D) human model; (ii) human object-based automatic scene calibration; and (iii) metadata generation. More specifically, an appropriately-generated 3D human model provides the foot-to-head direction information that is used as the input of the automatic calibration of each camera. The normalized object information is used to retrieve an object-of-interest in a wide-range, multiple-camera surveillance system in the form of metadata. Experimental results show that the 3D human model matches the ground truth, and automatic calibration-based normalization of metadata enables a successful retrieval and tracking of a human object in the multiple-camera video surveillance system.

Normalized Metadata Generation for Human Retrieval Using Multiple Video Surveillance Cameras

PubMed Central

Jung, Jaehoon; Yoon, Inhye; Lee, Seungwon; Paik, Joonki

2016-01-01

Since it is impossible for surveillance personnel to keep monitoring videos from a multiple camera-based surveillance system, an efficient technique is needed to help recognize important situations by retrieving the metadata of an object-of-interest. In a multiple camera-based surveillance system, an object detected in a camera has a different shape in another camera, which is a critical issue of wide-range, real-time surveillance systems. In order to address the problem, this paper presents an object retrieval method by extracting the normalized metadata of an object-of-interest from multiple, heterogeneous cameras. The proposed metadata generation algorithm consists of three steps: (i) generation of a three-dimensional (3D) human model; (ii) human object-based automatic scene calibration; and (iii) metadata generation. More specifically, an appropriately-generated 3D human model provides the foot-to-head direction information that is used as the input of the automatic calibration of each camera. The normalized object information is used to retrieve an object-of-interest in a wide-range, multiple-camera surveillance system in the form of metadata. Experimental results show that the 3D human model matches the ground truth, and automatic calibration-based normalization of metadata enables a successful retrieval and tracking of a human object in the multiple-camera video surveillance system. PMID:27347961

Fast determination of total ginsenosides content in ginseng powder by near infrared reflectance spectroscopy

NASA Astrophysics Data System (ADS)

Chen, Hua-cai; Chen, Xing-dan; Lu, Yong-jun; Cao, Zhi-qiang

2006-01-01

Near infrared (NIR) reflectance spectroscopy was used to develop a fast determination method for total ginsenosides in Ginseng (Panax Ginseng) powder. The spectra were analyzed with multiplicative signal correction (MSC) correlation method. The best correlative spectra region with the total ginsenosides content was 1660 nm~1880 nm and 2230nm~2380 nm. The NIR calibration models of ginsenosides were built with multiple linear regression (MLR), principle component regression (PCR) and partial least squares (PLS) regression respectively. The results showed that the calibration model built with PLS combined with MSC and the optimal spectrum region was the best one. The correlation coefficient and the root mean square error of correction validation (RMSEC) of the best calibration model were 0.98 and 0.15% respectively. The optimal spectrum region for calibration was 1204nm~2014nm. The result suggested that using NIR to rapidly determinate the total ginsenosides content in ginseng powder were feasible.

Reduction and Analysis of GALFACTS Data in Search of Compact Variable Sources

NASA Astrophysics Data System (ADS)

Wenger, Trey; Barenfeld, S.; Ghosh, T.; Salter, C.

2012-01-01

The Galactic ALFA Continuum Transit Survey (GALFACTS) is an all-Arecibo sky, full-Stokes survey from 1225 to 1525 MHz using the multibeam Arecibo L-band Feed Array (ALFA). Using data from survey field N1, the first field covered by GALFACTS, we are searching for compact sources that vary in intensity and/or polarization. The multistep procedure for reducing the data includes radio frequency interference (RFI) removal, source detection, Gaussian fitting in multiple dimensions, polarization leakage calibration, and gain calibration. We have developed code to analyze and calculate the calibration parameters from the N1 calibration sources, and apply these to the data of the main run. For detected compact sources, our goal is to compare results from multiple passes over a source to search for rapid variability, as well as to compare our flux densities with those from the NRAO VLA Sky Survey (NVSS) to search for longer time-scale variations.

Bayesian Divergence-Time Estimation with Genome-Wide SNP Data of Sea Catfishes (Ariidae) Supports Miocene Closure of the Panamanian Isthmus.

PubMed

Stange, Madlen; Sánchez-Villagra, Marcelo R; Salzburger, Walter; Matschiner, Michael

2018-01-27

The closure of the Isthmus of Panama has long been considered to be one of the best defined biogeographic calibration points for molecular divergence-time estimation. However, geological and biological evidence has recently cast doubt on the presumed timing of the initial isthmus closure around 3 Ma but has instead suggested the existence of temporary land bridges as early as the Middle or Late Miocene. The biological evidence supporting these earlier land bridges was based either on only few molecular markers or on concatenation of genome-wide sequence data, an approach that is known to result in potentially misleading branch lengths and divergence times, which could compromise the reliability of this evidence. To allow divergence-time estimation with genomic data using the more appropriate multi-species coalescent model, we here develop a new method combining the SNP-based Bayesian species-tree inference of the software SNAPP with a molecular clock model that can be calibrated with fossil or biogeographic constraints. We validate our approach with simulations and use our method to reanalyze genomic data of Neotropical army ants (Dorylinae) that previously supported divergence times of Central and South American populations before the isthmus closure around 3 Ma. Our reanalysis with the multi-species coalescent model shifts all of these divergence times to ages younger than 3 Ma, suggesting that the older estimates supporting the earlier existence of temporary land bridges were artifacts resulting at least partially from the use of concatenation. We then apply our method to a new RAD-sequencing data set of Neotropical sea catfishes (Ariidae) and calibrate their species tree with extensive information from the fossil record. We identify a series of divergences between groups of Caribbean and Pacific sea catfishes around 10 Ma, indicating that processes related to the emergence of the isthmus led to vicariant speciation already in the Late Miocene, millions of years before the final isthmus closure. © The Author(s) 2018. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Intracalibration of particle detectors on a three-axis stabilized geostationary platform

NASA Astrophysics Data System (ADS)

Rowland, W.; Weigel, R. S.

2012-11-01

We describe an algorithm for intracalibration of measurements from plasma or energetic particle detectors on a three-axis stabilized platform. Modeling and forecasting of Earth's radiation belt environment requires data from particle instruments, and these data depend on measurements which have an inherent calibration uncertainty. Pre-launch calibration is typically performed, but on-orbit changes in the instrument often necessitate adjustment of calibration parameters to mitigate the effect of these changes on the measurements. On-orbit calibration practices for particle detectors aboard spin-stabilized spacecraft are well established. Three-axis stabilized platforms, however, pose unique challenges even when comparisons are being performed between multiple telescopes measuring the same energy ranges aboard the same satellite. This algorithm identifies time intervals when different telescopes are measuring particles with the same pitch angles. These measurements are used to compute scale factors which can be multiplied by the pre-launch geometric factor to correct any changes. The approach is first tested using measurements from GOES-13 MAGED particle detectors over a 5-month time period in 2010. We find statistically significant variations which are generally on the order of 5% or less. These results do not appear to be dependent on Poisson statistics nor upon whether a dead time correction was performed. When applied to data from a 5-month interval in 2011, one telescope shows a 10% shift from the 2010 scale factors. This technique has potential for operational use to help maintain relative calibration between multiple telescopes aboard a single satellite. It should also be extensible to inter-calibration between multiple satellites.

Intelligent emissions controller for substance injection in the post-primary combustion zone of fossil-fired boilers

DOEpatents

Reifman, Jaques; Feldman, Earl E.; Wei, Thomas Y. C.; Glickert, Roger W.

2003-01-01

The control of emissions from fossil-fired boilers wherein an injection of substances above the primary combustion zone employs multi-layer feedforward artificial neural networks for modeling static nonlinear relationships between the distribution of injected substances into the upper region of the furnace and the emissions exiting the furnace. Multivariable nonlinear constrained optimization algorithms use the mathematical expressions from the artificial neural networks to provide the optimal substance distribution that minimizes emission levels for a given total substance injection rate. Based upon the optimal operating conditions from the optimization algorithms, the incremental substance cost per unit of emissions reduction, and the open-market price per unit of emissions reduction, the intelligent emissions controller allows for the determination of whether it is more cost-effective to achieve additional increments in emission reduction through the injection of additional substance or through the purchase of emission credits on the open market. This is of particular interest to fossil-fired electrical power plant operators. The intelligent emission controller is particularly adapted for determining the economical control of such pollutants as oxides of nitrogen (NO.sub.x) and carbon monoxide (CO) emitted by fossil-fired boilers by the selective introduction of multiple inputs of substances (such as natural gas, ammonia, oil, water-oil emulsion, coal-water slurry and/or urea, and combinations of these substances) above the primary combustion zone of fossil-fired boilers.

Paleo-Antarctic rainforest into the modern Old World tropics: the rich past and threatened future of the "southern wet forest survivors".

PubMed

Kooyman, Robert M; Wilf, Peter; Barreda, Viviana D; Carpenter, Raymond J; Jordan, Gregory J; Sniderman, J M Kale; Allen, Andrew; Brodribb, Timothy J; Crayn, Darren; Feild, Taylor S; Laffan, Shawn W; Lusk, Christopher H; Rossetto, Maurizio; Weston, Peter H

2014-12-01

• Have Gondwanan rainforest floral associations survived? Where do they occur today? Have they survived continuously in particular locations? How significant is their living floristic signal? We revisit these classic questions in light of significant recent increases in relevant paleobotanical data.• We traced the extinction and persistence of lineages and associations through the past across four now separated regions-Australia, New Zealand, Patagonia, and Antarctica-using fossil occurrence data from 63 well-dated Gondwanan rainforest sites and 396 constituent taxa. Fossil sites were allocated to four age groups: Cretaceous, Paleocene-Eocene, Neogene plus Oligocene, and Pleistocene. We compared the modern and ancient distributions of lineages represented in the fossil record to see if dissimilarity increased with time. We quantified similarity-dissimilarity of composition and taxonomic structure among fossil assemblages, and between fossil and modern assemblages.• Strong similarities between ancient Patagonia and Australia confirmed shared Gondwanan rainforest history, but more of the lineages persisted in Australia. Samples of ancient Australia grouped with the extant floras of Australia, New Guinea, New Caledonia, Fiji, and Mt. Kinabalu. Decreasing similarity through time among the regional floras of Antarctica, Patagonia, New Zealand, and southern Australia reflects multiple extinction events.• Gondwanan rainforest lineages contribute significantly to modern rainforest community assembly and often co-occur in widely separated assemblages far from their early fossil records. Understanding how and where lineages from ancient Gondwanan assemblages co-occur today has implications for the conservation of global rainforest vegetation, including in the Old World tropics. © 2014 Botanical Society of America, Inc.

New geological and palaeontological age constraint for the gorilla-human lineage split.

PubMed

Katoh, Shigehiro; Beyene, Yonas; Itaya, Tetsumaru; Hyodo, Hironobu; Hyodo, Masayuki; Yagi, Koshi; Gouzu, Chitaro; WoldeGabriel, Giday; Hart, William K; Ambrose, Stanley H; Nakaya, Hideo; Bernor, Raymond L; Boisserie, Jean-Renaud; Bibi, Faysal; Saegusa, Haruo; Sasaki, Tomohiko; Sano, Katsuhiro; Asfaw, Berhane; Suwa, Gen

2016-02-11

The palaeobiological record of 12 million to 7 million years ago (Ma) is crucial to the elucidation of African ape and human origins, but few fossil assemblages of this period have been reported from sub-Saharan Africa. Since the 1970s, the Chorora Formation, Ethiopia, has been widely considered to contain ~10.5 million year (Myr) old mammalian fossils. More recently, Chororapithecus abyssinicus, a probable primitive member of the gorilla clade, was discovered from the formation. Here we report new field observations and geochemical, magnetostratigraphic and radioisotopic results that securely place the Chorora Formation sediments to between ~9 and ~7 Ma. The C. abyssinicus fossils are ~8.0 Myr old, forming a revised age constraint of the human-gorilla split. Other Chorora fossils range in age from ~8.5 to 7 Ma and comprise the first sub-Saharan mammalian assemblage that spans this period. These fossils suggest indigenous African evolution of multiple mammalian lineages/groups between 10 and 7 Ma, including a possible ancestral-descendent relationship between the ~9.8 Myr old Nakalipithecus nakayamai and C. abyssinicus. The new chronology and fossils suggest that faunal provinciality between eastern Africa and Eurasia had intensified by ~9 Ma, with decreased faunal interchange thereafter. The Chorora evidence supports the hypothesis of in situ African evolution of the Gorilla-Pan-human clade, and is concordant with the deeper divergence estimates of humans and great apes based on lower mutation rates of ~0.5 × 10(-9) per site per year (refs 13 - 15).

Pre-industrial baseline variation of upper midwestern forests in the United States

NASA Astrophysics Data System (ADS)

Dawson, A.; Paciorek, C. J.; Goring, S. J.; Williams, J. W.; Jackson, S. T.; McLachlan, J. S.

2016-12-01

Terrestrial ecosystems play an important role in Earth systems processes, yet we still do not understand how they respond to changes in climate. While it has been argued that terrestrial ecosystems were fairly stable (by Quaternary standards) in the millennia before major anthropogenic disruption, others have emphasized vegetation response to environmental variability during this time. These competing perspectives are not necessarily in conflict, but argue for a quantitative assessment of forest ecosystem variability over the last several millennia. Here we reconstruct maps of forest composition for the last two millenia, with uncertainty. To do this, we use a network of fossil pollen records - the most reliable paleoecological proxy for forest composition. We link the fossil pollen records to public land survey forest composition using a Bayesian hierarchical model which accounts for key processes including pollen production and dispersal. The model is calibrated using data from the pre-settlement time with the hope of minimizing anthropogenic impacts. Process parameters are estimated in the calibration phase, and are subsequently used in the prediction phase to generate spatially explicit maps of relative species composition across the upper Midwestern US over the last 2000 years, with robust uncertainty estimates. Estimates of forest composition and uncertainty show many previously noted vegetation shifts, three of which we discuss here. First, we see expansion of the hemlock range into western Wisconsin. Second, we see changes along the prairie-forest ecotone. Third, we see significant increases in elm at approximately 500 YBP in the region known as the Minnesota Big Woods. These changes are significant in both a statistical and ecological sense, but the scale of these changes is small relative to changes in the early holocene. Our novel spatio-temporal composition estimates will be used to improve the forecasting capabilities of ecosystem models.

Quaternary paleoecology of aquatic Diptera in tropical and Southern Hemisphere regions, with special reference to the Chironomidae

NASA Astrophysics Data System (ADS)

Verschuren, Dirk; Eggermont, Hilde

2006-08-01

Chironomid paleoecology in north-temperate regions has made tremendous progress over the past decade, but studies in tropical and Southern Hemisphere regions remain relatively scarce. Reasons for this imbalance are (1) incomplete taxonomic knowledge of chironomid faunas outside Europe and North America, (2) a scarcity of ecological data on local species and genera that might confer bio-indicator value to them, and (3) logistic difficulties hampering the lake surveying necessary to develop paleoenvironmental calibration data sets. Thus far, most chironomid paleoecology in tropical and Southern Hemisphere regions has relied on an indicator-species approach, combining autecological information on local species of which larval morphology is known with the traditional ecological typology of chironomid genera transferred from the Holarctic region. This paper reviews work accomplished to date in tropical and temperate South America, Australia, Africa, and New Zealand, including studies on various families of non-chironomid Diptera with diagnostic fossils. Research has focused mostly on late-Glacial and Holocene climate reconstruction, less on tracing past human disturbance of aquatic ecosystems and their drainage basins. Quantitative chironomid-based paleoenvironmental reconstruction has so far been done only in Australia and Africa. These studies compensated for the lack of traditional surface-sediment calibration data sets, nowadays often the main source of quantitative information on species ecological optima and tolerances, by maximally exploiting archival species-distribution data based on live collections of adult and/or larval midges. This stimulated efforts to achieve trustworthy species-level identification of fossil chironomid remains, and, as a result, the taxonomic resolution of paleoecological studies in Australia and Africa is higher on average than that achieved in European and North American studies.

The fossil trade: paying a price for human origins.

PubMed

Kjoergaard, Peter C

2012-06-01

Fossils have been traded for centuries. Over the past two hundred years the market has developed into an organized enterprise, with fossils serving multiple functions as objects of scientific study, collectors' items, and investments. Finding fossils, digging them up or purchasing them, transporting, studying, and conserving them, and putting them on display was and still is expensive. Since the early nineteenth century, funding bodies, academic institutions and museums, philanthropists, dealers, collectors, amateurs, and professional paleontologists have constituted elaborate networks driven by collaboration, necessity, ambition, accolades, and capital to generate knowledge and produce geological artifacts, increasing our understanding of the natural world, advancing careers and institutions, and contributing to personal fortunes. The emergence of paleoanthropology as a scientific discipline around 1900 generated a scientific focus on the human story that was easy to sell. The scarcity of ancient human remains made it close to impossible for a commercial market to evolve, yet finding them required serious funding. Elaborate schemes for financing expeditions and excavations went hand in hand with individual aspirations, patronage, philanthropy, networks, and alliance building, as concession rights and access to sponsors were objects of regular political intrigues and often bitter disputes.

Global patterns of insect diversification: towards a reconciliation of fossil and molecular evidence?

PubMed

Condamine, Fabien L; Clapham, Matthew E; Kergoat, Gael J

2016-01-18

Macroevolutionary studies of insects at diverse taxonomic scales often reveal dynamic evolutionary patterns, with multiple inferred diversification rate shifts. Responses to major past environmental changes, such as the Cretaceous Terrestrial Revolution, or the development of major key innovations, such as wings or complete metamorphosis are usually invoked as potential evolutionary triggers. However this view is partially contradicted by studies on the family-level fossil record showing that insect diversification was relatively constant through time. In an attempt to reconcile both views, we investigate large-scale insect diversification dynamics at family level using two distinct types of diversification analyses on a molecular timetree representing ca. 82% of the extant families, and reassess the insect fossil diversity using up-to-date records. Analyses focusing on the fossil record recovered an early burst of diversification, declining to low and steady rates through time, interrupted by extinction events. Phylogenetic analyses showed that major shifts of diversification rates only occurred in the four richest holometabolous orders. Both suggest that neither the development of flight or complete metamorphosis nor the Cretaceous Terrestrial Revolution environmental changes induced immediate changes in diversification regimes; instead clade-specific innovations likely promoted the diversification of major insect orders.

Global patterns of insect diversification: towards a reconciliation of fossil and molecular evidence?

PubMed Central

Condamine, Fabien L.; Clapham, Matthew E.; Kergoat, Gael J.

2016-01-01

Macroevolutionary studies of insects at diverse taxonomic scales often reveal dynamic evolutionary patterns, with multiple inferred diversification rate shifts. Responses to major past environmental changes, such as the Cretaceous Terrestrial Revolution, or the development of major key innovations, such as wings or complete metamorphosis are usually invoked as potential evolutionary triggers. However this view is partially contradicted by studies on the family-level fossil record showing that insect diversification was relatively constant through time. In an attempt to reconcile both views, we investigate large-scale insect diversification dynamics at family level using two distinct types of diversification analyses on a molecular timetree representing ca. 82% of the extant families, and reassess the insect fossil diversity using up-to-date records. Analyses focusing on the fossil record recovered an early burst of diversification, declining to low and steady rates through time, interrupted by extinction events. Phylogenetic analyses showed that major shifts of diversification rates only occurred in the four richest holometabolous orders. Both suggest that neither the development of flight or complete metamorphosis nor the Cretaceous Terrestrial Revolution environmental changes induced immediate changes in diversification regimes; instead clade-specific innovations likely promoted the diversification of major insect orders. PMID:26778170

Calibrating the Medical Council of Canada's Qualifying Examination Part I using an integrated item response theory framework: a comparison of models and designs.

PubMed

De Champlain, Andre F; Boulais, Andre-Philippe; Dallas, Andrew

2016-01-01

The aim of this research was to compare different methods of calibrating multiple choice question (MCQ) and clinical decision making (CDM) components for the Medical Council of Canada's Qualifying Examination Part I (MCCQEI) based on item response theory. Our data consisted of test results from 8,213 first time applicants to MCCQEI in spring and fall 2010 and 2011 test administrations. The data set contained several thousand multiple choice items and several hundred CDM cases. Four dichotomous calibrations were run using BILOG-MG 3.0. All 3 mixed item format (dichotomous MCQ responses and polytomous CDM case scores) calibrations were conducted using PARSCALE 4. The 2-PL model had identical numbers of items with chi-square values at or below a Type I error rate of 0.01 (83/3,499 or 0.02). In all 3 polytomous models, whether the MCQs were either anchored or concurrently run with the CDM cases, results suggest very poor fit. All IRT abilities estimated from dichotomous calibration designs correlated very highly with each other. IRT-based pass-fail rates were extremely similar, not only across calibration designs and methods, but also with regard to the actual reported decision to candidates. The largest difference noted in pass rates was 4.78%, which occurred between the mixed format concurrent 2-PL graded response model (pass rate= 80.43%) and the dichotomous anchored 1-PL calibrations (pass rate= 85.21%). Simpler calibration designs with dichotomized items should be implemented. The dichotomous calibrations provided better fit of the item response matrix than more complex, polytomous calibrations.

Molecules, morphology, and ecology indicate a recent, amphibious ancestry for echidnas.

PubMed

Phillips, Matthew J; Bennett, Thomas H; Lee, Michael S Y

2009-10-06

The semiaquatic platypus and terrestrial echidnas (spiny anteaters) are the only living egg-laying mammals (monotremes). The fossil record has provided few clues as to their origins and the evolution of their ecological specializations; however, recent reassignment of the Early Cretaceous Teinolophos and Steropodon to the platypus lineage implies that platypuses and echidnas diverged >112.5 million years ago, reinforcing the notion of monotremes as living fossils. This placement is based primarily on characters related to a single feature, the enlarged mandibular canal, which supplies blood vessels and dense electrosensory receptors to the platypus bill. Our reevaluation of the morphological data instead groups platypus and echidnas to the exclusion of Teinolophos and Steropodon and suggests that an enlarged mandibular canal is ancestral for monotremes (partly reversed in echidnas, in association with general mandibular reduction). A multigene evaluation of the echidna-platypus divergence using both a relaxed molecular clock and direct fossil calibrations reveals a recent split of 19-48 million years ago. Platypus-like monotremes (Monotrematum) predate this divergence, indicating that echidnas had aquatically foraging ancestors that reinvaded terrestrial ecosystems. This ecological shift and the associated radiation of echidnas represent a recent expansion of niche space despite potential competition from marsupials. Monotremes might have survived the invasion of marsupials into Australasia by exploiting ecological niches in which marsupials are restricted by their reproductive mode. Morphology, ecology, and molecular biology together indicate that Teinolophos and Steropodon are basal monotremes rather than platypus relatives, and that living monotremes are a relatively recent radiation.

Simple versus complex models of trait evolution and stasis as a response to environmental change

NASA Astrophysics Data System (ADS)

Hunt, Gene; Hopkins, Melanie J.; Lidgard, Scott

2015-04-01

Previous analyses of evolutionary patterns, or modes, in fossil lineages have focused overwhelmingly on three simple models: stasis, random walks, and directional evolution. Here we use likelihood methods to fit an expanded set of evolutionary models to a large compilation of ancestor-descendant series of populations from the fossil record. In addition to the standard three models, we assess more complex models with punctuations and shifts from one evolutionary mode to another. As in previous studies, we find that stasis is common in the fossil record, as is a strict version of stasis that entails no real evolutionary changes. Incidence of directional evolution is relatively low (13%), but higher than in previous studies because our analytical approach can more sensitively detect noisy trends. Complex evolutionary models are often favored, overwhelmingly so for sequences comprising many samples. This finding is consistent with evolutionary dynamics that are, in reality, more complex than any of the models we consider. Furthermore, the timing of shifts in evolutionary dynamics varies among traits measured from the same series. Finally, we use our empirical collection of evolutionary sequences and a long and highly resolved proxy for global climate to inform simulations in which traits adaptively track temperature changes over time. When realistically calibrated, we find that this simple model can reproduce important aspects of our paleontological results. We conclude that observed paleontological patterns, including the prevalence of stasis, need not be inconsistent with adaptive evolution, even in the face of unstable physical environments.

Calibration of weak-lensing shear in the Kilo-Degree Survey

NASA Astrophysics Data System (ADS)

Fenech Conti, I.; Herbonnet, R.; Hoekstra, H.; Merten, J.; Miller, L.; Viola, M.

2017-05-01

We describe and test the pipeline used to measure the weak-lensing shear signal from the Kilo-Degree Survey (KiDS). It includes a novel method of 'self-calibration' that partially corrects for the effect of noise bias. We also discuss the 'weight bias' that may arise in optimally weighted measurements, and present a scheme to mitigate that bias. To study the residual biases arising from both galaxy selection and shear measurement, and to derive an empirical correction to reduce the shear biases to ≲1 per cent, we create a suite of simulated images whose properties are close to those of the KiDS survey observations. We find that the use of 'self-calibration' reduces the additive and multiplicative shear biases significantly, although further correction via a calibration scheme is required, which also corrects for a dependence of the bias on galaxy properties. We find that the calibration relation itself is biased by the use of noisy, measured galaxy properties, which may limit the final accuracy that can be achieved. We assess the accuracy of the calibration in the tomographic bins used for the KiDS cosmic shear analysis, testing in particular the effect of possible variations in the uncertain distributions of galaxy size, magnitude and ellipticity, and conclude that the calibration procedure is accurate at the level of multiplicative bias ≲1 per cent required for the KiDS cosmic shear analysis.

Calibration of the Late Cretaceous to Paleocene geomagnetic polarity and astrochronological time scales: new results from high-precision U-Pb geochronology

NASA Astrophysics Data System (ADS)

Ramezani, Jahandar; Clyde, William; Wang, Tiantian; Johnson, Kirk; Bowring, Samuel

2016-04-01

Reversals in the Earth's magnetic polarity are geologically abrupt events of global magnitude that makes them ideal timelines for stratigraphic correlation across a variety of depositional environments, especially where diagnostic marine fossils are absent. Accurate and precise calibration of the Geomagnetic Polarity Timescale (GPTS) is thus essential to the reconstruction of Earth history and to resolving the mode and tempo of biotic and environmental change in deep time. The Late Cretaceous - Paleocene GPTS is of particular interest as it encompasses a critical period of Earth history marked by the Cretaceous greenhouse climate, the peak of dinosaur diversity, the end-Cretaceous mass extinction and its paleoecological aftermaths. Absolute calibration of the GPTS has been traditionally based on sea-floor spreading magnetic anomaly profiles combined with local magnetostratigraphic sequences for which a numerical age model could be established by interpolation between an often limited number of 40Ar/39Ar dates from intercalated volcanic ash deposits. Although the Neogene part of the GPTS has been adequately calibrated using cyclostratigraphy-based, astrochronological schemes, the application of these approaches to pre-Neogene parts of the timescale has been complicated given the uncertainties of the orbital models and the chaotic behavior of the solar system this far back in time. Here we present refined chronostratigraphic frameworks based on high-precision U-Pb geochronology of ash beds from the Western Interior Basin of North America and the Songliao Basin of Northeast China that places tight temporal constraints on the Late Cretaceous to Paleocene GPTS, either directly or by testing their astrochronological underpinnings. Further application of high-precision radioisotope geochronology and calibrated astrochronology promises a complete and robust Cretaceous-Paleogene GPTS, entirely independent of sea-floor magnetic anomaly profiles.

Photogrammetric Modeling and Image-Based Rendering for Rapid Virtual Environment Creation

DTIC Science & Technology

2004-12-01

area and different methods have been proposed. Pertinent methods include: Camera Calibration , Structure from Motion, Stereo Correspondence, and Image...Based Rendering 1.1.1 Camera Calibration Determining the 3D structure of a model from multiple views becomes simpler if the intrinsic (or internal...can introduce significant nonlinearities into the image. We have found that camera calibration is a straightforward process which can simplify the

Estimation of the quantification uncertainty from flow injection and liquid chromatography transient signals in inductively coupled plasma mass spectrometry

NASA Astrophysics Data System (ADS)

Laborda, Francisco; Medrano, Jesús; Castillo, Juan R.

2004-06-01

The quality of the quantitative results obtained from transient signals in high-performance liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICPMS) and flow injection-inductively coupled plasma mass spectrometry (FI-ICPMS) was investigated under multielement conditions. Quantification methods were based on multiple-point calibration by simple and weighted linear regression, and double-point calibration (measurement of the baseline and one standard). An uncertainty model, which includes the main sources of uncertainty from FI-ICPMS and HPLC-ICPMS (signal measurement, sample flow rate and injection volume), was developed to estimate peak area uncertainties and statistical weights used in weighted linear regression. The behaviour of the ICPMS instrument was characterized in order to be considered in the model, concluding that the instrument works as a concentration detector when it is used to monitorize transient signals from flow injection or chromatographic separations. Proper quantification by the three calibration methods was achieved when compared to reference materials, although the double-point calibration allowed to obtain results of the same quality as the multiple-point calibration, shortening the calibration time. Relative expanded uncertainties ranged from 10-20% for concentrations around the LOQ to 5% for concentrations higher than 100 times the LOQ.

A Paleocene penguin from New Zealand substantiates multiple origins of gigantism in fossil Sphenisciformes.

PubMed

Mayr, Gerald; Scofield, R Paul; De Pietri, Vanesa L; Tennyson, Alan J D

2017-12-12

One of the notable features of penguin evolution is the occurrence of very large species in the early Cenozoic, whose body size greatly exceeded that of the largest extant penguins. Here we describe a new giant species from the late Paleocene of New Zealand that documents the very early evolution of large body size in penguins. Kumimanu biceae, n. gen. et sp. is larger than all other fossil penguins that have substantial skeletal portions preserved. Several plesiomorphic features place the new species outside a clade including all post-Paleocene giant penguins. It is phylogenetically separated from giant Eocene and Oligocene penguin species by various smaller taxa, which indicates multiple origins of giant size in penguin evolution. That a penguin rivaling the largest previously known species existed in the Paleocene suggests that gigantism in penguins arose shortly after these birds became flightless divers. Our study therefore strengthens previous suggestions that the absence of very large penguins today is likely due to the Oligo-Miocene radiation of marine mammals.

Modeling Photo-multiplier Gain and Regenerating Pulse Height Data for Application Development

NASA Astrophysics Data System (ADS)

Aspinall, Michael D.; Jones, Ashley R.

2018-01-01

Systems that adopt organic scintillation detector arrays often require a calibration process prior to the intended measurement campaign to correct for significant performance variances between detectors within the array. These differences exist because of low tolerances associated with photo-multiplier tube technology and environmental influences. Differences in detector response can be corrected for by adjusting the supplied photo-multiplier tube voltage to control its gain and the effect that this has on the pulse height spectra from a gamma-only calibration source with a defined photo-peak. Automated methods that analyze these spectra and adjust the photo-multiplier tube bias accordingly are emerging for hardware that integrate acquisition electronics and high voltage control. However, development of such algorithms require access to the hardware, multiple detectors and calibration source for prolonged periods, all with associated constraints and risks. In this work, we report on a software function and related models developed to rescale and regenerate pulse height data acquired from a single scintillation detector. Such a function could be used to generate significant and varied pulse height data that can be used to integration-test algorithms that are capable of automatically response matching multiple detectors using pulse height spectra analysis. Furthermore, a function of this sort removes the dependence on multiple detectors, digital analyzers and calibration source. Results show a good match between the real and regenerated pulse height data. The function has also been used successfully to develop auto-calibration algorithms.

A New Approach for Checking and Complementing CALIPSO Lidar Calibration

NASA Technical Reports Server (NTRS)

Josset, Damien B.; Vaughan, Mark A.; Hu, Yongxiang; Avery, Melody A.; Powell, Kathleen A.; Hunt, William H.; Winker, David M.; Pelon, Jacques; Trepte, Charles R.; Lucker, Patricia L.;

Calibration and validation of toxicokinetic-toxicodynamic models for three neonicotinoids and some aquatic macroinvertebrates.

PubMed

Focks, Andreas; Belgers, Dick; Boerwinkel, Marie-Claire; Buijse, Laura; Roessink, Ivo; Van den Brink, Paul J

2018-05-01

Exposure patterns in ecotoxicological experiments often do not match the exposure profiles for which a risk assessment needs to be performed. This limitation can be overcome by using toxicokinetic-toxicodynamic (TKTD) models for the prediction of effects under time-variable exposure. For the use of TKTD models in the environmental risk assessment of chemicals, it is required to calibrate and validate the model for specific compound-species combinations. In this study, the survival of macroinvertebrates after exposure to the neonicotinoid insecticide was modelled using TKTD models from the General Unified Threshold models of Survival (GUTS) framework. The models were calibrated on existing survival data from acute or chronic tests under static exposure regime. Validation experiments were performed for two sets of species-compound combinations: one set focussed on multiple species sensitivity to a single compound: imidacloprid, and the other set on the effects of multiple compounds for a single species, i.e., the three neonicotinoid compounds imidacloprid, thiacloprid and thiamethoxam, on the survival of the mayfly Cloeon dipterum. The calibrated models were used to predict survival over time, including uncertainty ranges, for the different time-variable exposure profiles used in the validation experiments. From the comparison between observed and predicted survival, it appeared that the accuracy of the model predictions was acceptable for four of five tested species in the multiple species data set. For compounds such as neonicotinoids, which are known to have the potential to show increased toxicity under prolonged exposure, the calibration and validation of TKTD models for survival needs to be performed ideally by considering calibration data from both acute and chronic tests.

Iodine-Containing Mass-Defect-Tuned Dendrimers for Use as Internal Mass Spectrometry Calibrants

NASA Astrophysics Data System (ADS)

Giesen, Joseph A.; Diament, Benjamin J.; Grayson, Scott M.

2018-03-01

Calibrants based on synthetic dendrimers have been recently proposed as a versatile alternative to peptides and proteins for both MALDI and ESI mass spectrometry calibration. Because of their modular synthetic platform, dendrimer calibrants are particularly amenable to tailoring for specific applications. Utilizing this versatility, a set of dendrimers has been designed as an internal calibrant with a tailored mass defect to differentiate them from the majority of natural peptide analytes. This was achieved by incorporating a tris-iodinated aromatic core as an initiator for the dendrimer synthesis, thereby affording multiple calibration points ( m/z range 600-2300) with an optimized mass-defect offset relative to all peptides composed of the 20 most common proteinogenic amino acids. [Figure not available: see fulltext.

Learning a common dictionary for subject-transfer decoding with resting calibration.

PubMed

Morioka, Hiroshi; Kanemura, Atsunori; Hirayama, Jun-ichiro; Shikauchi, Manabu; Ogawa, Takeshi; Ikeda, Shigeyuki; Kawanabe, Motoaki; Ishii, Shin

2015-05-01

Brain signals measured over a series of experiments have inherent variability because of different physical and mental conditions among multiple subjects and sessions. Such variability complicates the analysis of data from multiple subjects and sessions in a consistent way, and degrades the performance of subject-transfer decoding in a brain-machine interface (BMI). To accommodate the variability in brain signals, we propose 1) a method for extracting spatial bases (or a dictionary) shared by multiple subjects, by employing a signal-processing technique of dictionary learning modified to compensate for variations between subjects and sessions, and 2) an approach to subject-transfer decoding that uses the resting-state activity of a previously unseen target subject as calibration data for compensating for variations, eliminating the need for a standard calibration based on task sessions. Applying our methodology to a dataset of electroencephalography (EEG) recordings during a selective visual-spatial attention task from multiple subjects and sessions, where the variability compensation was essential for reducing the redundancy of the dictionary, we found that the extracted common brain activities were reasonable in the light of neuroscience knowledge. The applicability to subject-transfer decoding was confirmed by improved performance over existing decoding methods. These results suggest that analyzing multisubject brain activities on common bases by the proposed method enables information sharing across subjects with low-burden resting calibration, and is effective for practical use of BMI in variable environments. Copyright © 2015 Elsevier Inc. All rights reserved.

Multi-objective vs. single-objective calibration of a hydrologic model using single- and multi-objective screening

NASA Astrophysics Data System (ADS)

Mai, Juliane; Cuntz, Matthias; Shafii, Mahyar; Zink, Matthias; Schäfer, David; Thober, Stephan; Samaniego, Luis; Tolson, Bryan

2016-04-01

Hydrologic models are traditionally calibrated against observed streamflow. Recent studies have shown however, that only a few global model parameters are constrained using this kind of integral signal. They can be identified using prior screening techniques. Since different objectives might constrain different parameters, it is advisable to use multiple information to calibrate those models. One common approach is to combine these multiple objectives (MO) into one single objective (SO) function and allow the use of a SO optimization algorithm. Another strategy is to consider the different objectives separately and apply a MO Pareto optimization algorithm. In this study, two major research questions will be addressed: 1) How do multi-objective calibrations compare with corresponding single-objective calibrations? 2) How much do calibration results deteriorate when the number of calibrated parameters is reduced by a prior screening technique? The hydrologic model employed in this study is a distributed hydrologic model (mHM) with 52 model parameters, i.e. transfer coefficients. The model uses grid cells as a primary hydrologic unit, and accounts for processes like snow accumulation and melting, soil moisture dynamics, infiltration, surface runoff, evapotranspiration, subsurface storage and discharge generation. The model is applied in three distinct catchments over Europe. The SO calibrations are performed using the Dynamically Dimensioned Search (DDS) algorithm with a fixed budget while the MO calibrations are achieved using the Pareto Dynamically Dimensioned Search (PA-DDS) algorithm allowing for the same budget. The two objectives used here are the Nash Sutcliffe Efficiency (NSE) of the simulated streamflow and the NSE of the logarithmic transformation. It is shown that the SO DDS results are located close to the edges of the Pareto fronts of the PA-DDS. The MO calibrations are hence preferable due to their supply of multiple equivalent solutions from which the user can choose at the end due to the specific needs. The sequential single-objective parameter screening was employed prior to the calibrations reducing the number of parameters by at least 50% in the different catchments and for the different single objectives. The single-objective calibrations led to a faster convergence of the objectives and are hence beneficial when using a DDS on single-objectives. The above mentioned parameter screening technique is generalized for multi-objectives and applied before calibration using the PA-DDS algorithm. Two different alternatives of this MO-screening are tested. The comparison of the calibration results using all parameters and using only screened parameters shows for both alternatives that the PA-DDS algorithm does not profit in terms of trade-off size and function evaluations required to achieve converged pareto fronts. This is because the PA-DDS algorithm automatically reduces search space with progress of the calibration run. This automatic reduction should be different for other search algorithms. It is therefore hypothesized that prior screening can but must not be beneficial for parameter estimation dependent on the chosen optimization algorithm.

Win–Win strategies to promote air pollutant control policies and non-fossil energy target regulation in China

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Lining; Patel, Pralit L.; Yu, Sha

The rapid growth of energy consumption in China has led to increased emissions of air pollutants. As a response, in its 12th Five Year Plan the Chinese government proposed mitigation targets for SO2 and NOx emissions. Herein we have investigated mitigation measures taken in different sectors and their corresponding impacts on the energy system. Additionally, as non-fossil energy development has gained traction in addressing energy and environmental challenges in China, we further investigated the impact of non-fossil energy development on air pollutant emissions, and then explored interactions and co-benefits between these two types of policies. An extended Global Change Assessmentmore » Model (GCAM) was used in this study, which includes an additional air pollutant emissions control module coupling multiple end-of-pipe (EOP) control technologies with energy technologies, as well as more detailed end-use sectors in China. We find that implementing EOP control technologies would reduce air pollution in the near future, but with little room left to implement these EOP technologies, other cleaner and more efficient technologies are also effective. These technologies would reduce final energy consumption, increase electricity’s share in final energy, and increase the share of non-fossil fuels in primary energy and electricity consumption. Increasing non-fossil energy usage at China’s proposed adoption rate would in turn also reduce SO2 and NOx emissions, however, the reductions from this policy alone still lag behind the targeted requirements of air pollutant reduction. Fortunately, a combination of air pollutant controls and non-fossil energy development could synergistically help realize the respective individual targets, and would result in lower costs than would addressing these issues separately.« less

High-precision 40Ar/39Ar age for the Jehol Biota

NASA Astrophysics Data System (ADS)

Chang, S.; Zhang, H.; Renne, P. R.; Fang, Y.

2008-12-01

Abundant fossils of the terrestrial Jehol Biota, including plants, insects, dinosaurs, birds, mammals and freshwater invertebrates, were discovered from the Yixian Formation and the overlying Jiufotang Formation in Inner Mongolia, Hebei Province and Liaoning Province, northeastern China. Because of the exceptional preservation of fossils, the Jehol Biota is one of the most important Mesozoic fossil outcrops and referred to as a "Mesozoic Pompeii". The Jehol Biota has provided a rare opportunity to address questions about the origin of birds, the evolution of feathers and flight, the early diversification of angiosperms and the timing of the radiation of placental mammals. The Tuchengzi Formation, which lies unconformably just below the Yixian Formation and consists mainly of variegated sandstones, is less fossiliferous than the two overlying formations. However, dinosaur tracks, silicified wood and compressed plants are found in this formation. A systematic 40Ar/39Ar dating of the Yixian and the Jiufotang formations was undertaken to provide a framework for understanding the timing and duration of the Jehol Biota and evolutionary events represented within it. Furthermore, determining the absolute age of the Tuchengzi Formation provides information to interpret abundant dinosaur tracks within and provide better age constrains for the beginning of the Jehol Biota. Here we present robust high-precision 40Ar/39Ar data for six tuff samples and two basalt samples collected from the Tuchengzi, the Yixian and the Jiufotang formations near the classic outcrops in western Liaoning, NE China. We obtain an age of 139.5 ± 1.0 Ma for the uppermost Tuchengzi Formation, an age of 129.7 ± 0.5 Ma for a basaltic lava from the bottom of the Yixian Formation and an age of 122.1 ± 0.3 Ma for a tuff from the base of the overlying Jiufotang Formation. Our data indicate that the Yixian Formation was deposited during the Early Cretaceous, the Barremian to early Aptian, within a time span of 7 Ma. Because of the systematic sampling and the high quality of our data, these results contribute the most accurate age calibration yet of the Jehol Biota within the Yixian Formation and the overlying Jiufotang Formation, providing significant calibration for the evolution of early angiosperms, primitive birds and feathered dinosaurs.

40 CFR 60.153 - Monitoring of operations.

Code of Federal Regulations, 2010 CFR

2010-07-01

...) The owner or operator of any multiple hearth, fluidized bed, or electric sludge incinerator subject to...) Install, calibrate, maintain and operate temperature measuring devices at every hearth in multiple hearth... zones of electric incinerators. For multiple hearth furnaces, a minimum of one temperature measuring...

Validity of Torque-Data Collection at Multiple Sites: A Framework for Collaboration on Clinical-Outcomes Research in Sports Medicine.

PubMed

Kuenze, Christopher; Eltouhky, Moataz; Thomas, Abbey; Sutherlin, Mark; Hart, Joseph

2016-05-01

Collecting torque data using a multimode dynamometer is common in sports-medicine research. The error in torque measurements across multiple sites and dynamometers has not been established. To assess the validity of 2 calibration protocols across 3 dynamometers and the error associated with torque measurement for each system. Observational study. 3 university laboratories at separate institutions. 2 Biodex System 3 dynamometers and 1 Biodex System 4 dynamometer. System calibration was completed using the manufacturer-recommended single-weight method and an experimental calibration method using a series of progressive weights. Both calibration methods were compared with a manually calculated theoretical torque across a range of applied weights. Relative error, absolute error, and percent error were calculated at each weight. Each outcome variable was compared between systems using 95% confidence intervals across low (0-65 Nm), moderate (66-110 Nm), and high (111-165 Nm) torque categorizations. Calibration coefficients were established for each system using both calibration protocols. However, within each system the calibration coefficients generated using the single-weight (System 4 = 2.42 [0.90], System 3a = 1.37 [1.11], System 3b = -0.96 [1.45]) and experimental calibration protocols (System 4 = 3.95 [1.08], System 3a = -0.79 [1.23], System 3b = 2.31 [1.66]) were similar and displayed acceptable mean relative error compared with calculated theoretical torque values. Overall, percent error was greatest for all 3 systems in low-torque conditions (System 4 = 11.66% [6.39], System 3a = 6.82% [11.98], System 3b = 4.35% [9.49]). The System 4 significantly overestimated torque across all 3 weight increments, and the System 3b overestimated torque over the moderate-torque increment. Conversion of raw voltage to torque values using the single-calibration-weight method is valid and comparable to a more complex multiweight calibration process; however, it is clear that calibration must be done for each individual system to ensure accurate data collection.

Parameter estimation uncertainty: Comparing apples and apples?

NASA Astrophysics Data System (ADS)

Hart, D.; Yoon, H.; McKenna, S. A.

2012-12-01

Given a highly parameterized ground water model in which the conceptual model of the heterogeneity is stochastic, an ensemble of inverse calibrations from multiple starting points (MSP) provides an ensemble of calibrated parameters and follow-on transport predictions. However, the multiple calibrations are computationally expensive. Parameter estimation uncertainty can also be modeled by decomposing the parameterization into a solution space and a null space. From a single calibration (single starting point) a single set of parameters defining the solution space can be extracted. The solution space is held constant while Monte Carlo sampling of the parameter set covering the null space creates an ensemble of the null space parameter set. A recently developed null-space Monte Carlo (NSMC) method combines the calibration solution space parameters with the ensemble of null space parameters, creating sets of calibration-constrained parameters for input to the follow-on transport predictions. Here, we examine the consistency between probabilistic ensembles of parameter estimates and predictions using the MSP calibration and the NSMC approaches. A highly parameterized model of the Culebra dolomite previously developed for the WIPP project in New Mexico is used as the test case. A total of 100 estimated fields are retained from the MSP approach and the ensemble of results defining the model fit to the data, the reproduction of the variogram model and prediction of an advective travel time are compared to the same results obtained using NSMC. We demonstrate that the NSMC fields based on a single calibration model can be significantly constrained by the calibrated solution space and the resulting distribution of advective travel times is biased toward the travel time from the single calibrated field. To overcome this, newly proposed strategies to employ a multiple calibration-constrained NSMC approach (M-NSMC) are evaluated. Comparison of the M-NSMC and MSP methods suggests that M-NSMC can provide a computationally efficient and practical solution for predictive uncertainty analysis in highly nonlinear and complex subsurface flow and transport models. This material is based upon work supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001114. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Dual carbon isotopes (14C and 13C) and optical properties of WSOC and HULIS-C during winter in Guangzhou, China.

PubMed

Liu, Junwen; Mo, Yangzhi; Ding, Ping; Li, Jun; Shen, Chengde; Zhang, Gan

2018-08-15

Water-soluble brown carbon (ws-BrC) exerts an important influence on climate change, but its emission sources and optical properties remain poorly understood. In this study, we isolated two ws-BrC proxies, water-soluble organic carbon (WSOC) and humic-like substance carbon (HULIS-C), from particulate matter collected in Guangzhou, China, during December 2012 for the measurement of dual carbon isotopes ( 14 C and 13 C) and light absorption. The mass absorption efficiencies of WSOC and HULIS-C at 365nm were 0.81±0.16 and 1.33±0.21m 2 g -1 C, respectively. The 14 C results showed that two-thirds of WSOC and HULIS-C were derived from non-fossil sources (e.g., biomass burning and biogenic emission), and the remaining third was derived from fossil sources. The δ 13 C values of WSOC and HULIS-C were -23.7±1.2‰ and -24.2±0.9‰, respectively, underlining the limited influences of C4 plants and natural gas on ws-BrC. Fitting the data to a multiple linear regression, we further concluded that approximately 80% and 10% of the light absorption at 365nm was due to non-fossil and fossil carbon, respectively. Non-fossil sources of ws-BrC, such as the burning of agricultural residue, were responsible for the light absorption recorded in Guangzhou. Copyright © 2018 Elsevier B.V. All rights reserved.

Comparing the accuracy and precision of three techniques used for estimating missing landmarks when reconstructing fossil hominin crania.

PubMed

Neeser, Rudolph; Ackermann, Rebecca Rogers; Gain, James

2009-09-01

Various methodological approaches have been used for reconstructing fossil hominin remains in order to increase sample sizes and to better understand morphological variation. Among these, morphometric quantitative techniques for reconstruction are increasingly common. Here we compare the accuracy of three approaches--mean substitution, thin plate splines, and multiple linear regression--for estimating missing landmarks of damaged fossil specimens. Comparisons are made varying the number of missing landmarks, sample sizes, and the reference species of the population used to perform the estimation. The testing is performed on landmark data from individuals of Homo sapiens, Pan troglodytes and Gorilla gorilla, and nine hominin fossil specimens. Results suggest that when a small, same-species fossil reference sample is available to guide reconstructions, thin plate spline approaches perform best. However, if no such sample is available (or if the species of the damaged individual is uncertain), estimates of missing morphology based on a single individual (or even a small sample) of close taxonomic affinity are less accurate than those based on a large sample of individuals drawn from more distantly related extant populations using a technique (such as a regression method) able to leverage the information (e.g., variation/covariation patterning) contained in this large sample. Thin plate splines also show an unexpectedly large amount of error in estimating landmarks, especially over large areas. Recommendations are made for estimating missing landmarks under various scenarios. Copyright 2009 Wiley-Liss, Inc.

Molecular evidence of keratin and melanosomes in feathers of the Early Cretaceous bird Eoconfuciusornis.

PubMed

Pan, Yanhong; Zheng, Wenxia; Moyer, Alison E; O'Connor, Jingmai K; Wang, Min; Zheng, Xiaoting; Wang, Xiaoli; Schroeter, Elena R; Zhou, Zhonghe; Schweitzer, Mary H

2016-12-06

Microbodies associated with feathers of both nonavian dinosaurs and early birds were first identified as bacteria but have been reinterpreted as melanosomes. Whereas melanosomes in modern feathers are always surrounded by and embedded in keratin, melanosomes embedded in keratin in fossils has not been demonstrated. Here we provide multiple independent molecular analyses of both microbodies and the associated matrix recovered from feathers of a new specimen of the basal bird Eoconfuciusornis from the Early Cretaceous Jehol Biota of China. Our work represents the oldest ultrastructural and immunological recognition of avian beta-keratin from an Early Cretaceous (∼130-Ma) bird. We apply immunogold to identify protein epitopes at high resolution, by localizing antibody-antigen complexes to specific fossil ultrastructures. Retention of original keratinous proteins in the matrix surrounding electron-opaque microbodies supports their assignment as melanosomes and adds to the criteria employable to distinguish melanosomes from microbial bodies. Our work sheds new light on molecular preservation within normally labile tissues preserved in fossils.

Variability in first Homo: Analysis of the ratio between the skulls KNM-ER 1470 and KNM-ER 1813 based on sexual dimorphism of Homo sapiens.

PubMed

Guimarães, S W Ferreira; Lorenzo, C

2015-10-01

The study of the skulls KNM-ER 1470 and KNM-ER 1813, considered the first members of the genus Homo, has raised some debates. While some of researchers maintain that there is only one species, another group argues that there are two species. On one hand these two fossils are still taxonomically undetermined, on the other hand they bring up another problem related to the existence of a genus with multiple species since its beginning, according to the last discoveries. In this paper, we have compared the size ratio between these fossils with ratios established in populations of Homo sapiens, in order to know if they fit into the human standard, considering intra-sexual and inter-sexual variation. Results help to establish whether these fossils correspond to different species or their differences could be related to sexual dimorphism within a single species. Copyright © 2015 Elsevier GmbH. All rights reserved.

Molecular evidence of keratin and melanosomes in feathers of the Early Cretaceous bird Eoconfuciusornis

PubMed Central

Pan, Yanhong; Zheng, Wenxia; Moyer, Alison E.; O’Connor, Jingmai K.; Zheng, Xiaoting; Wang, Xiaoli; Schroeter, Elena R.; Zhou, Zhonghe; Schweitzer, Mary H.

2016-01-01

Microbodies associated with feathers of both nonavian dinosaurs and early birds were first identified as bacteria but have been reinterpreted as melanosomes. Whereas melanosomes in modern feathers are always surrounded by and embedded in keratin, melanosomes embedded in keratin in fossils has not been demonstrated. Here we provide multiple independent molecular analyses of both microbodies and the associated matrix recovered from feathers of a new specimen of the basal bird Eoconfuciusornis from the Early Cretaceous Jehol Biota of China. Our work represents the oldest ultrastructural and immunological recognition of avian beta-keratin from an Early Cretaceous (∼130-Ma) bird. We apply immunogold to identify protein epitopes at high resolution, by localizing antibody–antigen complexes to specific fossil ultrastructures. Retention of original keratinous proteins in the matrix surrounding electron-opaque microbodies supports their assignment as melanosomes and adds to the criteria employable to distinguish melanosomes from microbial bodies. Our work sheds new light on molecular preservation within normally labile tissues preserved in fossils. PMID:27872291

Lattice Calibration with Turn-By-Turn BPM Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Xiaobiao; /SLAC; Sebek, James

2012-07-02

Turn-by-turn beam position monitor (BPM) data from multiple BPMs are fitted with a tracking code to calibrate magnet strengths in a manner similar to the well known LOCO code. Simulation shows that this turn-by-turn method can be a quick and efficient way for optics calibration. The method is applicable to both linacs and ring accelerators. Experimental results for a section of the SPEAR3 ring is also shown.

An Integrated Calibration Technique for Stereo Vision Systems (PREPRINT)

DTIC Science & Technology

2010-03-01

technique for stereo vision systems has been developed. To demonstrate and evaluate this calibration technique, multiple Wii Remotes (Wiimotes) from Nintendo ...from Nintendo were used to form stereo vision systems to perform 3D motion capture in real time. This integrated technique is a two-step process...Wiimotes) used in Nintendo Wii games. Many researchers have successfully dealt with the problem of camera calibration by taking images from a 2D

Multiple Use One-Sided Hypotheses Testing in Univariate Linear Calibration

NASA Technical Reports Server (NTRS)

Krishnamoorthy, K.; Kulkarni, Pandurang M.; Mathew, Thomas

1996-01-01

Consider a normally distributed response variable, related to an explanatory variable through the simple linear regression model. Data obtained on the response variable, corresponding to known values of the explanatory variable (i.e., calibration data), are to be used for testing hypotheses concerning unknown values of the explanatory variable. We consider the problem of testing an unlimited sequence of one sided hypotheses concerning the explanatory variable, using the corresponding sequence of values of the response variable and the same set of calibration data. This is the situation of multiple use of the calibration data. The tests derived in this context are characterized by two types of uncertainties: one uncertainty associated with the sequence of values of the response variable, and a second uncertainty associated with the calibration data. We derive tests based on a condition that incorporates both of these uncertainties. The solution has practical applications in the decision limit problem. We illustrate our results using an example dealing with the estimation of blood alcohol concentration based on breath estimates of the alcohol concentration. In the example, the problem is to test if the unknown blood alcohol concentration of an individual exceeds a threshold that is safe for driving.

Landsat-7 Enhanced Thematic Mapper plus radiometric calibration

USGS Publications Warehouse

Markham, B.L.; Boncyk, Wayne C.; Helder, D.L.; Barker, J.L.

1997-01-01

Landsat-7 is currently being built and tested for launch in 1998. The Enhanced Thematic Mapper Plus (ETM+) sensor for Landsat-7, a derivative of the highly successful Thematic Mapper (TM) sensors on Landsats 4 and 5, and the Landsat-7 ground system are being built to provide enhanced radiometric calibration performance. In addition, regular vicarious calibration campaigns are being planned to provide additional information for calibration of the ETM+ instrument. The primary upgrades to the instrument include the addition of two solar calibrators: the full aperture solar calibrator, a deployable diffuser, and the partial aperture solar calibrator, a passive device that allows the ETM+ to image the sun. The ground processing incorporates for the first time an off-line facility, the Image Assessment System (IAS), to perform calibration, evaluation and analysis. Within the IAS, processing capabilities include radiometric artifact characterization and correction, radiometric calibration from the multiple calibrator sources, inclusion of results from vicarious calibration and statistical trending of calibration data to improve calibration estimation. The Landsat Product Generation System, the portion of the ground system responsible for producing calibrated products, will incorporate the radiometric artifact correction algorithms and will use the calibration information generated by the IAS. This calibration information will also be supplied to ground processing systems throughout the world.

Soil specific re-calibration of water content sensors for a field-scale sensor network

NASA Astrophysics Data System (ADS)

Gasch, Caley K.; Brown, David J.; Anderson, Todd; Brooks, Erin S.; Yourek, Matt A.

2015-04-01

Obtaining accurate soil moisture data from a sensor network requires sensor calibration. Soil moisture sensors are factory calibrated, but multiple site specific factors may contribute to sensor inaccuracies. Thus, sensors should be calibrated for the specific soil type and conditions in which they will be installed. Lab calibration of a large number of sensors prior to installation in a heterogeneous setting may not be feasible, and it may not reflect the actual performance of the installed sensor. We investigated a multi-step approach to retroactively re-calibrate sensor water content data from the dielectric permittivity readings obtained by sensors in the field. We used water content data collected since 2009 from a sensor network installed at 42 locations and 5 depths (210 sensors total) within the 37-ha Cook Agronomy Farm with highly variable soils located in the Palouse region of the Northwest United States. First, volumetric water content was calculated from sensor dielectric readings using three equations: (1) a factory calibration using the Topp equation; (2) a custom calibration obtained empirically from an instrumented soil in the field; and (3) a hybrid equation that combines the Topp and custom equations. Second, we used soil physical properties (particle size and bulk density) and pedotransfer functions to estimate water content at saturation, field capacity, and wilting point for each installation location and depth. We also extracted the same reference points from the sensor readings, when available. Using these reference points, we re-scaled the sensor readings, such that water content was restricted to the range of values that we would expect given the physical properties of the soil. The re-calibration accuracy was assessed with volumetric water content measurements obtained from field-sampled cores taken on multiple dates. In general, the re-calibration was most accurate when all three reference points (saturation, field capacity, and wilting point) were represented in the sensor readings. We anticipate that obtaining water retention curves for field soils will improve the re-calibration accuracy by providing more precise estimates of saturation, field capacity, and wilting point. This approach may serve as an alternative method for sensor calibration in lieu of or to complement pre-installation calibration.

Toward improved calibration of watershed models: multisite many objective measures of information

USDA-ARS?s Scientific Manuscript database

This paper presents a computational framework for incorporation of disparate information from observed hydrologic responses at multiple locations into the calibration of watershed models. The framework consists of four components: (i) an a-priori characterization of system behavior; (ii) a formal an...

Geometric Characterization of Multi-Axis Multi-Pinhole SPECT

PubMed Central

DiFilippo, Frank P.

2008-01-01

A geometric model and calibration process are developed for SPECT imaging with multiple pinholes and multiple mechanical axes. Unlike the typical situation where pinhole collimators are mounted directly to rotating gamma ray detectors, this geometric model allows for independent rotation of the detectors and pinholes, for the case where the pinhole collimator is physically detached from the detectors. This geometric model is applied to a prototype small animal SPECT device with a total of 22 pinholes and which uses dual clinical SPECT detectors. All free parameters in the model are estimated from a calibration scan of point sources and without the need for a precision point source phantom. For a full calibration of this device, a scan of four point sources with 360° rotation is suitable for estimating all 95 free parameters of the geometric model. After a full calibration, a rapid calibration scan of two point sources with 180° rotation is suitable for estimating the subset of 22 parameters associated with repositioning the collimation device relative to the detectors. The high accuracy of the calibration process is validated experimentally. Residual differences between predicted and measured coordinates are normally distributed with 0.8 mm full width at half maximum and are estimated to contribute 0.12 mm root mean square to the reconstructed spatial resolution. Since this error is small compared to other contributions arising from the pinhole diameter and the detector, the accuracy of the calibration is sufficient for high resolution small animal SPECT imaging. PMID:18293574

Rigorous approaches to species delimitation have significant implications for African crocodilian systematics and conservation

PubMed Central

Shirley, Matthew H.; Vliet, Kent A.; Carr, Amanda N.; Austin, James D.

2014-01-01

Accurate species delimitation is a central assumption of biology that, in groups such as the Crocodylia, is often hindered by highly conserved morphology and frequent introgression. In Africa, crocodilian systematics has been hampered by complex regional biogeography and confounded taxonomic history. We used rigorous molecular and morphological species delimitation methods to test the hypothesis that the slender-snouted crocodile (Mecistops cataphractus) is composed of multiple species corresponding to the Congolian and Guinean biogeographic zones. Speciation probability was assessed by using 11 mitochondrial and nuclear genes, and cranial morphology for over 100 specimens, representing the full geographical extent of the species distribution. Molecular Bayesian and phylogenetic species delimitation showed unanimous support for two Mecistops species isolated to the Upper Guinean and Congo (including Lower Guinean) biomes that were supported by 13 cranial characters capable of unambiguously diagnosing each species. Fossil-calibrated phylogenetic reconstruction estimated that the species split ± 6.5–7.5 Ma, which is congruent with intraspecies divergence within the sympatric crocodile genus Osteolaemus and the formation of the Cameroon Volcanic Line. Our results underscore the necessity of comprehensive phylogeographic analyses within currently recognized taxa to detect cryptic species within the Crocodylia. We recommend that the community of crocodilian researchers reconsider the conceptualization of crocodilian species especially in the light of the conservation ramifications for this economically and ecologically important group. PMID:24335982

Renewable Energy used in State Renewable Portfolio Standards Yielded

Science.gov Websites

. Renewable Portfolio Standards also shows national water withdrawals and water consumption by fossil-fuel methodologies, while recognizing that states could perform their own more-detailed assessments," NREL's , respectively. Ranges are presented as the models and methodologies used are sensitive to multiple parameters

Wood Energy Production, Sustainable Farming Livelihood and Multifunctionality in Finland

ERIC Educational Resources Information Center

Huttunen, Suvi

2012-01-01

Climate change and the projected depletion of fossil energy resources pose multiple global challenges. Innovative technologies offer interesting possibilities to achieve more sustainable outcomes in the energy production sector. Local, decentralized alternatives have the potential to sustain livelihoods in rural areas. One example of such a…

Considerations in projecting energy-related emissions multiple decades into the future

EPA Science Inventory

Use of fossil fuels for energy is the primary source of anthropogenic emissions of many air pollutants. Thus, the evolution of the energy system into the future can influence future emissions, driving those emissions up or down as a function of shifts in energy demand and fuel us...

Advanced analysis techniques for uranium assay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geist, W. H.; Ensslin, Norbert; Carrillo, L. A.

2001-01-01

Uranium has a negligible passive neutron emission rate making its assay practicable only with an active interrogation method. The active interrogation uses external neutron sources to induce fission events in the uranium in order to determine the mass. This technique requires careful calibration with standards that are representative of the items to be assayed. The samples to be measured are not always well represented by the available standards which often leads to large biases. A technique of active multiplicity counting is being developed to reduce some of these assay difficulties. Active multiplicity counting uses the measured doubles and triples countmore » rates to determine the neutron multiplication (f4) and the product of the source-sample coupling ( C ) and the 235U mass (m). Since the 35U mass always appears in the multiplicity equations as the product of Cm, the coupling needs to be determined before the mass can be known. A relationship has been developed that relates the coupling to the neutron multiplication. The relationship is based on both an analytical derivation and also on empirical observations. To determine a scaling constant present in this relationship, known standards must be used. Evaluation of experimental data revealed an improvement over the traditional calibration curve analysis method of fitting the doubles count rate to the 235Um ass. Active multiplicity assay appears to relax the requirement that the calibration standards and unknown items have the same chemical form and geometry.« less

Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate.

PubMed

Cutter, Asher D

2008-04-01

Accurate inference of the dates of common ancestry among species forms a central problem in understanding the evolutionary history of organisms. Molecular estimates of divergence time rely on the molecular evolutionary prediction that neutral mutations and substitutions occur at the same constant rate in genomes of related species. This underlies the notion of a molecular clock. Most implementations of this idea depend on paleontological calibration to infer dates of common ancestry, but taxa with poor fossil records must rely on external, potentially inappropriate, calibration with distantly related species. The classic biological models Caenorhabditis and Drosophila are examples of such problem taxa. Here, I illustrate internal calibration in these groups with direct estimates of the mutation rate from contemporary populations that are corrected for interfering effects of selection on the assumption of neutrality of substitutions. Divergence times are inferred among 6 species each of Caenorhabditis and Drosophila, based on thousands of orthologous groups of genes. I propose that the 2 closest known species of Caenorhabditis shared a common ancestor <24 MYA (Caenorhabditis briggsae and Caenorhabditis sp. 5) and that Caenorhabditis elegans diverged from its closest known relatives <30 MYA, assuming that these species pass through at least 6 generations per year; these estimates are much more recent than reported previously with molecular clock calibrations from non-nematode phyla. Dates inferred for the common ancestor of Drosophila melanogaster and Drosophila simulans are roughly concordant with previous studies. These revised dates have important implications for rates of genome evolution and the origin of self-fertilization in Caenorhabditis.

Effect of pH Test-Strip Characteristics on Accuracy of Readings.

PubMed

Metheny, Norma A; Gunn, Emily M; Rubbelke, Cynthia S; Quillen, Terrilynn Fox; Ezekiel, Uthayashanker R; Meert, Kathleen L

2017-06-01

Little is known about characteristics of colorimetric pH test strips that are most likely to be associated with accurate interpretations in clinical situations. To compare the accuracy of 4 pH test strips with varying characteristics (ie, multiple vs single colorimetric squares per calibration, and differing calibration units [1.0 vs 0.5]). A convenience sample of 100 upper-level nursing students with normal color vision was recruited to evaluate the accuracy of the test strips. Six buffer solutions (pH range, 3.0 to 6.0) were used during the testing procedure. Each of the 100 participants performed 20 pH tests in random order, providing a total of 2000 readings. The sensitivity and specificity of each test strip was computed. In addition, the degree to which the test strips under- or overestimated the pH values was analyzed using descriptive statistics. Our criterion for correct readings was an exact match with the pH buffer solution being evaluated. Although none of the test strips evaluated in our study was 100% accurate at all of the measured pH values, those with multiple squares per pH calibration were clearly superior overall to those with a single test square. Test strips with multiple squares per calibration were associated with greater overall accuracy than test strips with a single square per calibration. However, because variable degrees of error were observed in all of the test strips, use of a pH meter is recommended when precise readings are crucial. ©2017 American Association of Critical-Care Nurses.

Uncertainty Analysis of Inertial Model Attitude Sensor Calibration and Application with a Recommended New Calibration Method

NASA Technical Reports Server (NTRS)

Tripp, John S.; Tcheng, Ping

1999-01-01

Statistical tools, previously developed for nonlinear least-squares estimation of multivariate sensor calibration parameters and the associated calibration uncertainty analysis, have been applied to single- and multiple-axis inertial model attitude sensors used in wind tunnel testing to measure angle of attack and roll angle. The analysis provides confidence and prediction intervals of calibrated sensor measurement uncertainty as functions of applied input pitch and roll angles. A comparative performance study of various experimental designs for inertial sensor calibration is presented along with corroborating experimental data. The importance of replicated calibrations over extended time periods has been emphasized; replication provides independent estimates of calibration precision and bias uncertainties, statistical tests for calibration or modeling bias uncertainty, and statistical tests for sensor parameter drift over time. A set of recommendations for a new standardized model attitude sensor calibration method and usage procedures is included. The statistical information provided by these procedures is necessary for the uncertainty analysis of aerospace test results now required by users of industrial wind tunnel test facilities.

Improvement of Gaofen-3 Absolute Positioning Accuracy Based on Cross-Calibration

PubMed Central

Deng, Mingjun; Li, Jiansong

2017-01-01

The Chinese Gaofen-3 (GF-3) mission was launched in August 2016, equipped with a full polarimetric synthetic aperture radar (SAR) sensor in the C-band, with a resolution of up to 1 m. The absolute positioning accuracy of GF-3 is of great importance, and in-orbit geometric calibration is a key technology for improving absolute positioning accuracy. Conventional geometric calibration is used to accurately calibrate the geometric calibration parameters of the image (internal delay and azimuth shifts) using high-precision ground control data, which are highly dependent on the control data of the calibration field, but it remains costly and labor-intensive to monitor changes in GF-3’s geometric calibration parameters. Based on the positioning consistency constraint of the conjugate points, this study presents a geometric cross-calibration method for the rapid and accurate calibration of GF-3. The proposed method can accurately calibrate geometric calibration parameters without using corner reflectors and high-precision digital elevation models, thus improving absolute positioning accuracy of the GF-3 image. GF-3 images from multiple regions were collected to verify the absolute positioning accuracy after cross-calibration. The results show that this method can achieve a calibration accuracy as high as that achieved by the conventional field calibration method. PMID:29240675

mtDNA from fossils reveals a radiation of Hawaiian geese recently derived from the Canada goose (Branta canadensis)

PubMed Central

Paxinos, Ellen E.; James, Helen F.; Olson, Storrs L.; Sorenson, Michael D.; Jackson, Jennifer; Fleischer, Robert C.

2002-01-01

Phylogenetic analysis of 1.35 kb of mtDNA sequence from fossils revealed a previously unknown radiation of Hawaiian geese, of which only one representative remains alive (the endangered Hawaiian goose or nene, Branta sandvicensis). This radiation is nested phylogenetically within a living species, the Canada goose (Branta canadensis) and is related most closely to the large-bodied lineage within that species. The barnacle goose (Branta leucopsis) is also nested within the Canada goose species and is related most closely to the small-bodied lineage of Canada geese. The peripheral isolation of the barnacle goose in the Palearctic apparently allowed the evolution of its distinctive plumage pattern, whereas the two Nearctic lineages of Canada geese share a primitive plumage pattern. The Hawaiian lineage of Canada geese diverged more dramatically, splitting into at least three species that differ in body size, body proportions, and flight ability. One fossil species, limited to the island of Hawaii, was related closely to the nene but was over four times larger, flightless, heavy-bodied and had a much more robust cranium. Application of a rate calibration to levels of DNA divergence suggests that this species evolved on the island of Hawaii in less than 500,000 years. This date is consistent with the potassium/argon-based age of the island of Hawaii of 430,000–500,000 years. The giant Hawaii goose resembles the moa-nalos, a group of massive, extinct, flightless ducks that lived on older Hawaiian Islands and thus is an example of convergent evolution of similar morphologies in island ecosystems. PMID:11818543

Assessing the evolutionary history of the class Synurophyceae (Heterokonta) using molecular, morphometric, and paleobiological approaches.

PubMed

Siver, Peter A; Jo, Bok Yeon; Kim, Jong Im; Shin, Woongghi; Lott, Anne Marie; Wolfe, Alexander P

2015-06-01

Heterokont algae of the class Synurophyceae, characterized by distinctive siliceous scales that cover the surface of the cell, are ecologically important in inland waters, yet their evolutionary history remains enigmatic. We explore phylogenetic relationships within this group of algae relative to geologic time, with a focus on evolution of siliceous components. We combined an expansive five-gene and time-calibrated molecular phylogeny of synurophyte algae with an extensive array of fossil specimens from the middle Eocene to infer evolutionary trends within the group. The group originated in the Jurassic approximately 157 million years ago (Ma), with the keystone genera Mallomonas and Synura diverging during the Early Cretaceous at 130 Ma. Mallomonas further splits into two major subclades, signaling the evolution of the V-rib believed to aid in the spacing and organization of scales on the cell covering. Synura also diverges into two primary subclades, separating taxa with forward-projecting spines on the scale from those with a keel positioned on the scale proper. Approximately one third of the fossil species are extinct, whereas the remaining taxa are linked to modern congeners. The taxonomy of synurophytes, which relies extensively on the morphology of the siliceous components, is largely congruent with molecular analyses. Scales of extinct synurophytes were significantly larger than those of modern taxa and may have played a role in their demise. In contrast, many fossil species linked to modern lineages were smaller in the middle Eocene, possibly reflecting growth in the greenhouse climatic state that characterized this geologic interval. © 2015 Botanical Society of America, Inc.

An Early Holocene Record of Cimex (Hemiptera: Cimicidae) From Western North America.

PubMed

Adams, Martin E; Jenkins, Dennis L

2017-07-01

The subfossil remains of 14 cimicids (Hemiptera: Cimicidae) were recovered during archaeological investigations of the Paisley Five Mile Point Cave site (35LK3400), an exceptionally well-dated (n = 229 radiocarbon dates) late Pleistocene-early Holocene rock shelter site in south-central Oregon. Nine of the specimens have been assigned to three modern species of Nearctic Cimicidae-Cimex antennatus Usinger & Ueshima, Cimex latipennis Usinger & Ueshima, and Cimex pilosellus (Horváth)-whereas the remaining five individuals were too fragmentary to positively identify. The chronology of the insect assemblage puts one specimen at circa 5,100 calibrated years before present (cal. yr BP), and the remaining 13 range in age from 9,400 to almost 11,000 cal. yr BP. Although fossil and subfossil cimicid remains have been recovered at other archaeological sites, the fossil record for bed bugs is largely undocumented. The Paisley Caves specimens thus far represent the oldest remains of the genus in probable contact with humans on record. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Probabilistic divergence time estimation without branch lengths: dating the origins of dinosaurs, avian flight and crown birds.

PubMed

Lloyd, G T; Bapst, D W; Friedman, M; Davis, K E

2016-11-01

Branch lengths-measured in character changes-are an essential requirement of clock-based divergence estimation, regardless of whether the fossil calibrations used represent nodes or tips. However, a separate set of divergence time approaches are typically used to date palaeontological trees, which may lack such branch lengths. Among these methods, sophisticated probabilistic approaches have recently emerged, in contrast with simpler algorithms relying on minimum node ages. Here, using a novel phylogenetic hypothesis for Mesozoic dinosaurs, we apply two such approaches to estimate divergence times for: (i) Dinosauria, (ii) Avialae (the earliest birds) and (iii) Neornithes (crown birds). We find: (i) the plausibility of a Permian origin for dinosaurs to be dependent on whether Nyasasaurus is the oldest dinosaur, (ii) a Middle to Late Jurassic origin of avian flight regardless of whether Archaeopteryx or Aurornis is considered the first bird and (iii) a Late Cretaceous origin for Neornithes that is broadly congruent with other node- and tip-dating estimates. Demonstrating the feasibility of probabilistic time-scaling further opens up divergence estimation to the rich histories of extinct biodiversity in the fossil record, even in the absence of detailed character data. © 2016 The Authors.

Influence of Past Changes in Atmospheric CO2 on Boron/Calcium of Planktic Fossil Foraminifera

NASA Astrophysics Data System (ADS)

Domeyko, R. A.; Allen, K. A.; deMenocal, P. B.

2014-12-01

Culture experiments have revealed that B/Ca of shells grown by the foraminiferal species Globigerinoides ruber increase with increasing seawater pH. Specifically, B/Ca responds to changes in the relative abundance of pH-sensitive dissolved carbon and boron species (Allen et al. 2011, 2012). Here, we present a high-resolution study on fossilized G. ruber from two sites in North Atlantic subtropical gyres (VM25-21 and ODP 1055B) through 20 ka BP to evaluate how B/Ca responds to past changes in atmospheric CO2. Forams were picked and crushed gently, then cleaned and dissolved using a variation of the Boyle and Keigwin (1985) and Barker et al. (2003) cleaning protocols prior to analysis. ODP 1055B (from Carolina Slope, West Atlantic) produced a high-resolution record with lower B/Ca values during the glacial period followed by a rapid shift to higher B/Ca values in the early deglaciation, with values remaining high through the Holocene. These results were not predicted by culture calibrations, but they are consistent with B/Ca records from the Caribbean (ODP 999, Foster et al. 2008), suggesting this pattern is characteristic of surface waters in the greater North Atlantic region.

Cretaceous origin of giant rhinoceros beetles (Dynastini; Coleoptera) and correlation of their evolution with the Pangean breakup.

PubMed

Jin, Haofei; Yonezawa, Takahiro; Zhong, Yang; Kishino, Hirohisa; Hasegawa, Masami

2017-03-17

The giant rhinoceros beetles (Dynastini, Scarabaeidae, Coleoptera) are distributed in tropical and temperate regions in Asia, America and Africa. Recent molecular phylogenetic studies have revealed that the giant rhinoceros beetles can be divided into three clades representing Asia, America and Africa. Although a correlation between their evolution and the continental drift during the Pangean breakup was suggested, there is no accurate divergence time estimation among the three clades based on molecular data. Moreover, there is a long chronological gap between the timing of the Pangean breakup (Cretaceous: 110-148 Ma) and the emergence of the oldest fossil record (Oligocene: 33 Ma). In this study, we estimated their divergence times based on molecular data, using several combinations of fossil calibration sets, and obtained robust estimates. The inter-continental divergence events among the clades were estimated to have occurred about 99 Ma (Asian clade and others) and 78 Ma (American clade and African clade), both of which are after the Pangean breakup. These estimates suggest their inter-continental divergences occurred by overseas sweepstakes dispersal, rather than by vicariances of the population caused by the Pangean breakup.

Inverse modeling of fossil fuel CO2 emissions at urban scale using OCO-2 retrievals of total column CO2

NASA Astrophysics Data System (ADS)

Ye, X.; Lauvaux, T.; Kort, E. A.; Lin, J. C.; Oda, T.; Yang, E.; Wu, D.

2016-12-01

Rapid economic development has given rise to a steady increase of global carbon emissions, which have accumulated in the atmosphere for the past 200 years. Urbanization has concentrated about 70% of the global fossil-fuel CO2 emissions in large metropolitan areas distributed around the world, which represents the most significant anthropogenic contribution to climate change. However, highly uncertain quantifications of urban CO2 emissions are commonplace for numerous cities because of poorly-documented inventories of energy consumption. Therefore, accurate estimates of carbon emissions from global observing systems are a necessity if mitigation strategies are meant to be implemented at global scales. Space-based observations of total column averaged CO2 concentration (XCO2) provide a very promising and powerful tool to quantify urban CO2 fluxes. For the first time, measurements from the Orbiting Carbon Observatory 2 (OCO-2) mission are assimilated in a high resolution inverse modeling system to quantify fossil-fuel CO2 emissions of multiple cities around the globe. The Open-source Data Inventory for Anthropogenic CO2 (ODIAC) emission inventory is employed as a first guess, while the atmospheric transport is simulated using the WRF-Chem model at 1-km resolution. Emission detection and quantification is performed with an Ensemble Kalman Filter method. We demonstrate here the potential of the inverse approach for assimilating thousands of OCO-2 retrievals along tracks near metropolitan areas. We present the detection potential of the system with real-case applications near power plants and present inverse emissions using actual OCO-2 measurements on various urban landscapes. Finally, we will discuss the potential of OCO-2-like satellite instruments for monitoring temporal variations of fossil-fuel CO2 emissions over multiple years, which can provide valuable insights for future satellite observation strategies.

On the absolute calibration of SO2 cameras

USGS Publications Warehouse

Lübcke, Peter; Bobrowski, Nicole; Illing, Sebastian; Kern, Christoph; Alvarez Nieves, Jose Manuel; Vogel, Leif; Zielcke, Johannes; Delgados Granados, Hugo; Platt, Ulrich

2013-01-01

This work investigates the uncertainty of results gained through the two commonly used, but quite different, calibration methods (DOAS and calibration cells). Measurements with three different instruments, an SO2 camera, a NFOVDOAS system and an Imaging DOAS (I-DOAS), are presented. We compare the calibration-cell approach with the calibration from the NFOV-DOAS system. The respective results are compared with measurements from an I-DOAS to verify the calibration curve over the spatial extent of the image. The results show that calibration cells, while working fine in some cases, can lead to an overestimation of the SO2 CD by up to 60% compared with CDs from the DOAS measurements. Besides these errors of calibration, radiative transfer effects (e.g. light dilution, multiple scattering) can significantly influence the results of both instrument types. The measurements presented in this work were taken at Popocatepetl, Mexico, between 1 March 2011 and 4 March 2011. Average SO2 emission rates between 4.00 and 14.34 kg s−1 were observed.

The Landsat Data Continuity Mission Operational Land Imager (OLI) Radiometric Calibration

NASA Technical Reports Server (NTRS)

Markham, Brian L.; Dabney, Philip W.; Murphy-Morris, Jeanine E.; Knight, Edward J.; Kvaran, Geir; Barsi, Julia A.

2010-01-01

The Operational Land Imager (OLI) on the Landsat Data Continuity Mission (LDCM) has a comprehensive radiometric characterization and calibration program beginning with the instrument design, and extending through integration and test, on-orbit operations and science data processing. Key instrument design features for radiometric calibration include dual solar diffusers and multi-lamped on-board calibrators. The radiometric calibration transfer procedure from NIST standards has multiple checks on the radiometric scale throughout the process and uses a heliostat as part of the transfer to orbit of the radiometric calibration. On-orbit lunar imaging will be used to track the instruments stability and side slither maneuvers will be used in addition to the solar diffuser to flat field across the thousands of detectors per band. A Calibration Validation Team is continuously involved in the process from design to operations. This team uses an Image Assessment System (IAS), part of the ground system to characterize and calibrate the on-orbit data.

Numerical dating of the Eckfeld maar fossil site, Eifel, Germany: a calibration mark for the Eocene time scale.

PubMed

Mertz, D F; Swisher, C C; Franzen, J L; Neuffer, F O; Lutz, H

2000-06-01

Sediments of the Eckfeld maar (Eifel, Germany) bear a well-preserved Eocene fauna and flora. Biostratigraphically, Eckfeld corresponds to the Middle Eocene mammal reference level MP (Mammals Paleogene) 13 of the ELMA (European Land Mammal Age) Geiseltalian. In the maar crater, basalt fragments were drilled, representing explosion crater eruption products. By 40Ar/39Ar dating of the basalt, for the first time a direct numerical calibration mark for an Eocene European mammal locality has been established. The Eckfeld basalt inverse isochron date of 44.3 +/- 0.4 Ma suggests an age for the Geiseltalian/Robiacian boundary at 44 Ma and, together with the 1995 time scale of Berggren et al., a time span ranging from 49 to 44 Ma for the Geiseltalian and from 44 to 37 Ma for the Robiacian, respectively. Additional 40Ar/39Ar dating on a genetically related basalt occurrence close to the maar confirms a period of volcanism of ca. 0.6 m.y. in the Eckfeld area, matching the oldest Eocene volcanic activity of the Hocheifel volcanic field.

Internal calibration on adjacent samples (InCAS) with Fourier transform mass spectrometry.

PubMed

O'Connor, P B; Costello, C E

2000-12-15

Using matrix-assisted laser desorption/ionization (MAL DI) on a trapped ion mass spectrometer such as a Fourier transform mass spectrometer (FTMS) allows accumulation of ions in the cell from multiple laser shots prior to detection. If ions from separate MALDI samples are accumulated simultaneously in the cell, ions from one sample can be used to calibrate ions from the other sample. Since the ions are detected simultaneously in the cell, this is, in effect, internal calibration, but there are no selective desorption effects in the MALDI source. This method of internal calibration with adjacent samples is demonstrated here on cesium iodide clusters, peptides, oligosaccharides, poly(propylene glycol), and fullerenes and provides typical FTMS internal calibration mass accuracy of < 1 ppm.

The OLI Radiometric Scale Realization Round Robin Measurement Campaign

NASA Technical Reports Server (NTRS)

Cutlip, Hansford; Cole,Jerold; Johnson, B. Carol; Maxwell, Stephen; Markham, Brian; Ong, Lawrence; Hom, Milton; Biggar, Stuart

2011-01-01

A round robin radiometric scale realization was performed at the Ball Aerospace Radiometric Calibration Laboratory in January/February 2011 in support of the Operational Land Imager (OLI) Program. Participants included Ball Aerospace, NIST, NASA Goddard Space Flight Center, and the University of Arizona. The eight day campaign included multiple observations of three integrating sphere sources by nine radiometers. The objective of the campaign was to validate the radiance calibration uncertainty ascribed to the integrating sphere used to calibrate the OLI instrument. The instrument level calibration source uncertainty was validated by quatnifying: (1) the long term stability of the NIST calibrated radiance artifact, (2) the responsivity scale of the Ball Aerospace transfer radiometer and (3) the operational characteristics of the large integrating sphere.

Indirect Correspondence-Based Robust Extrinsic Calibration of LiDAR and Camera

PubMed Central

Sim, Sungdae; Sock, Juil; Kwak, Kiho

2016-01-01

LiDAR and cameras have been broadly utilized in computer vision and autonomous vehicle applications. However, in order to convert data between the local coordinate systems, we must estimate the rigid body transformation between the sensors. In this paper, we propose a robust extrinsic calibration algorithm that can be implemented easily and has small calibration error. The extrinsic calibration parameters are estimated by minimizing the distance between corresponding features projected onto the image plane. The features are edge and centerline features on a v-shaped calibration target. The proposed algorithm contributes two ways to improve the calibration accuracy. First, we use different weights to distance between a point and a line feature according to the correspondence accuracy of the features. Second, we apply a penalizing function to exclude the influence of outliers in the calibration datasets. Additionally, based on our robust calibration approach for a single LiDAR-camera pair, we introduce a joint calibration that estimates the extrinsic parameters of multiple sensors at once by minimizing one objective function with loop closing constraints. We conduct several experiments to evaluate the performance of our extrinsic calibration algorithm. The experimental results show that our calibration method has better performance than the other approaches. PMID:27338416

Updated Astrometric Calibration of the Gemini Planet Imager: Application to the Theta1 Orionis B System

NASA Astrophysics Data System (ADS)

Tran, Debby; Konopacky, Quinn; GPIES Team

2018-01-01

The Gemini Planet Imager (GPI), housed on the 8-meter Gemini South telescope in Chile, is an instrument designed to detect Jupiter-like extrasolar planets by direct imaging. It relies on adaptive optics to correct the effects of atmospheric turbulence, along with an advanced coronagraph and calibration system. One of the scientific goals of GPI is to measure the orbital properties of the planets it discovers. Because these orbits have long periods, precise measurements of the relative position between the star and the planet (relative astrometry) are required. In this poster, I will present the astrometric calibration of GPI. We constrain the plate scale and orientation of the camera by observing different binary star systems with both GPI and another well-calibrated instrument, NIRC2, at the Keck telescope in Hawaii. We measure their separations with both instruments and use that information to calibrate the plate scale. By taking these calibration measurements over the course of three years, we have measured the plate scale to 0.05% and shown that it is stable across multiple epochs. One of the calibrators for GPI is Theta1 Orionis B, one of the star systems in the Trapezium Cluster in Orion. Using GPI and Keck measurements taken over the past several years combined with astrometry from the literature spanning two decades, we can place new constraints on the orbital properties of this massive multiple system. We will present the best fit orbital properties for these objects, including updated mass estimates for the components.

Determining geometric error model parameters of a terrestrial laser scanner through Two-face, Length-consistency, and Network methods

PubMed Central

Wang, Ling; Muralikrishnan, Bala; Rachakonda, Prem; Sawyer, Daniel

2017-01-01

Terrestrial laser scanners (TLS) are increasingly used in large-scale manufacturing and assembly where required measurement uncertainties are on the order of few tenths of a millimeter or smaller. In order to meet these stringent requirements, systematic errors within a TLS are compensated in-situ through self-calibration. In the Network method of self-calibration, numerous targets distributed in the work-volume are measured from multiple locations with the TLS to determine parameters of the TLS error model. In this paper, we propose two new self-calibration methods, the Two-face method and the Length-consistency method. The Length-consistency method is proposed as a more efficient way of realizing the Network method where the length between any pair of targets from multiple TLS positions are compared to determine TLS model parameters. The Two-face method is a two-step process. In the first step, many model parameters are determined directly from the difference between front-face and back-face measurements of targets distributed in the work volume. In the second step, all remaining model parameters are determined through the Length-consistency method. We compare the Two-face method, the Length-consistency method, and the Network method in terms of the uncertainties in the model parameters, and demonstrate the validity of our techniques using a calibrated scale bar and front-face back-face target measurements. The clear advantage of these self-calibration methods is that a reference instrument or calibrated artifacts are not required, thus significantly lowering the cost involved in the calibration process. PMID:28890607

Reassessment of Olduvai Bed I cercopithecoids: A new biochronological and biogeographical link to the South African fossil record.

PubMed

Gilbert, Christopher C; Frost, Stephen R; Delson, Eric

2016-03-01

Fossil monkeys have long been used as important faunal elements in studies of African Plio-Pleistocene biochronology, particularly in the case of the South African karst cave sites. Cercopithecoid fossils have been known from Tanzania's Olduvai Gorge for nearly a century, with multiple taxa documented including Theropithecus oswaldi and Cercopithecoides kimeui, along with papionins and colobines less clearly attributable to species. A small number of large papionin fossils, including a partial male cranium and partial female skull, have been previously identified as an early form of Papio, but noted as distinct from extant baboons as well as other fossil Papio species. In 2013 we reviewed the Olduvai cercopithecoid material at the National Museum of Tanzania, with a particular focus on the specimens from Beds I-IV. Quantitative and qualitative comparisons of the Olduvai papionins largely confirmed previous observations, with one notable exception. The large papionin taxon from Bed I previously recognized as Papio sp. is more properly recognized as Gorgopithecus major, a taxon previously known only from South Africa. Features shared between the Olduvai specimens and G. major include relatively short and concavo-convex tubular nasals, antero-posteriorly curved upper incisor roots, downwardly curved brow ridges in the midline, and robust zygomatic arches. The recognition of G. major at Olduvai Bed I, a well-known horizon with precise radiometric dates, provides an important biochronological and biogeographical link with South African localities Kromdraai A, Swartkrans Member 1 and possibly Swartkrans Members 2-3 and Cooper's A and D. Copyright © 2015 Elsevier Ltd. All rights reserved.

Sponge grade body fossil with cellular resolution dating 60 Myr before the Cambrian

PubMed Central

Yin, Zongjun; Zhu, Maoyan; Davidson, Eric H.; Bottjer, David J.; Zhao, Fangchen; Tafforeau, Paul

2015-01-01

An extraordinarily well preserved, 600-million-year (Myr)-old, three-dimensionally phosphatized fossil displaying multiple independent characters of modern adult sponges has been analyzed by SEM and synchrotron X-ray tomography. The fossilized animal (Eocyathispongia qiania gen. et sp. nov.) is slightly more than 1.2 mm wide and 1.1 mm tall, is composed of hundreds of thousands of cells, and has a gross structure consisting of three adjacent hollow tubes sharing a common base. The main tube is crowned with a large open funnel, and the others end in osculum-like openings to the exterior. The external surface is densely covered with flat tile-like cells closely resembling sponge pinacocytes, and this layer is punctuated with smaller pores. A dense patch of external structures that display the form of a lawn of sponge papillae has also survived. Within the main funnel, an area where features of the inner surface are preserved displays a regular pattern of uniform pits. Many of them are surrounded individually by distinct collars, mounted in a supporting reticulum. The possibility cannot be excluded that these pits are the remains of a field of choanocytes. The character set evinced by this specimen, ranging from general anatomy to cell type, uniquely indicates that this specimen is a fossil of probable poriferan affinity. So far, we have only this single specimen, and although its organized and complex cellular structure precludes any reasonable interpretation that its origin is abiogenic, confirmation that it is indeed a fossilized sponge will clearly require discovery of additional specimens. PMID:25775601

A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes).

PubMed

Kutschera, Verena E; Lecomte, Nicolas; Janke, Axel; Selva, Nuria; Sokolov, Alexander A; Haun, Timm; Steyer, Katharina; Nowak, Carsten; Hailer, Frank

2013-06-05

Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf, and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass. Here we provide the first mitochondrial DNA sequence data of red foxes from central Asia (Siberia), and new sequences from several European populations. In a range-wide synthesis of 729 red fox mitochondrial control region sequences, including 677 previously published and 52 newly obtained sequences, this manuscript describes the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. In a 335 bp alignment we found in total 175 unique haplotypes. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene. The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic. Both brown bears and red foxes colonized Japan's northern island Hokkaido at least three times, all lineages being most closely related to different mainland lineages. Red foxes, grey wolves, and brown bears thus represent an interesting case where species that occupy similar ecological niches also exhibit similar phylogeographic histories.

A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes)

PubMed Central

2013-01-01

Background Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf, and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass. Results Here we provide the first mitochondrial DNA sequence data of red foxes from central Asia (Siberia), and new sequences from several European populations. In a range-wide synthesis of 729 red fox mitochondrial control region sequences, including 677 previously published and 52 newly obtained sequences, this manuscript describes the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. In a 335 bp alignment we found in total 175 unique haplotypes. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene. Conclusions The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic. Both brown bears and red foxes colonized Japan’s northern island Hokkaido at least three times, all lineages being most closely related to different mainland lineages. Red foxes, grey wolves, and brown bears thus represent an interesting case where species that occupy similar ecological niches also exhibit similar phylogeographic histories. PMID:23738594

Biogeography of the Pistia clade (Araceae): based on chloroplast and mitochondrial DNA sequences and Bayesian divergence time inference.

PubMed

Renner, Susanne S; Zhang, Li-Bing

2004-06-01

Pistia stratiotes (water lettuce) and Lemna (duckweeds) are the only free-floating aquatic Araceae. The geographic origin and phylogenetic placement of these unrelated aroids present long-standing problems because of their highly modified reproductive structures and wide geographical distributions. We sampled chloroplast (trnL-trnF and rpl20-rps12 spacers, trnL intron) and mitochondrial sequences (nad1 b/c intron) for all genera implicated as close relatives of Pistia by morphological, restriction site, and sequencing data, and present a hypothesis about its geographic origin based on the consensus of trees obtained from the combined data, using Bayesian, maximum likelihood, parsimony, and distance analyses. Of the 14 genera closest to Pistia, only Alocasia, Arisaema, and Typhonium are species-rich, and the latter two were studied previously, facilitating the choice of representatives that span the roots of these genera. Results indicate that Pistia and the Seychelles endemic Protarum sechellarum are the basalmost branches in a grade comprising the tribes Colocasieae (Ariopsis, Steudnera, Remusatia, Alocasia, Colocasia), Arisaemateae (Arisaema, Pinellia), and Areae (Arum, Biarum, Dracunculus, Eminium, Helicodiceros, Theriophonum, Typhonium). Unexpectedly, all Areae genera are embedded in Typhonium, which throws new light on the geographic history of Areae. A Bayesian analysis of divergence times that explores the effects of multiple fossil and geological calibration points indicates that the Pistia lineage is 90 to 76 million years (my) old. The oldest fossils of the Pistia clade, though not Pistia itself, are 45-my-old leaves from Germany; the closest outgroup, Peltandreae (comprising a few species in Florida, the Mediterranean, and Madagascar), is known from 60-my-old leaves from Europe, Kazakhstan, North Dakota, and Tennessee. Based on the geographic ranges of close relatives, Pistia likely originated in the Tethys region, with Protarum then surviving on the Seychelles, which became isolated from Madagascar and India in the Late Cretaceous (85 my ago). Pistia and Protarum provide striking examples of ancient lineages that appear to have survived in unique or isolated habitats.

Assessing applicability of SWAT calibrated at multiple spatial scales from field to stream

USDA-ARS?s Scientific Manuscript database

The capability of SWAT for simulating long-term hydrology and water quality was evaluated using data collected in subwatershed K of the Little River Experimental watershed located in South Atlantic Coastal Plain of the USA. The SWAT model was calibrated to measurements made at various spatial scales...

Use of soft data for multi-criteria calibration and validation of APEX: Impact on model simulations

USDA-ARS?s Scientific Manuscript database

It is widely known that the use of soft data and multiple model performance criteria in model calibration and validation is critical to ensuring the model capture major hydrologic and water quality processes. The Agricultural Policy/Environmental eXtender (APEX) is a hydrologic and water quality mod...

Improving Multiple Surface Range Estimation of a 3-Dimensional FLASH LADAR in the Presence of Atmospheric Turbulence

DTIC Science & Technology

2013-06-01

during the design process. For instance, the detector could be calibrated with incoherent il- lumination and a separate calibration could be performed...Poisson dis- tribution is often employed as a statistical distribution for the detected images. How- ever, due to the highly coherent nature of laser

Operating Characteristics of the Multiple Critical Venturi System and Secondary Calibration Nozzles Used for Weight-Flow Measurements in the Langley 16-Foot Transonic Tunnel

NASA Technical Reports Server (NTRS)

Berrier, B. L.; Leavitt, L. D.; Bangert, L. S.

1985-01-01

An investigation has been conducted in the Langley 16 Foot Transonic Tunnel to determine the weight flow measurement characteristics of a multiple critical Venturi system and the nozzle discharge coefficient characteristics of a series of convergent calibration nozzles. The effects on model discharge coefficient of nozzle throat area, model choke plate open area, nozzle pressure ratio, jet total temperature, and number and combination of operating Venturis were investigated. Tests were conducted at static conditions (tunnel wind off) at nozzle pressure ratios from 1.3 to 7.0.

Optical detector calibrator system

NASA Technical Reports Server (NTRS)

Strobel, James P. (Inventor); Moerk, John S. (Inventor); Youngquist, Robert C. (Inventor)

1996-01-01

An optical detector calibrator system simulates a source of optical radiation to which a detector to be calibrated is responsive. A light source selected to emit radiation in a range of wavelengths corresponding to the spectral signature of the source is disposed within a housing containing a microprocessor for controlling the light source and other system elements. An adjustable iris and a multiple aperture filter wheel are provided for controlling the intensity of radiation emitted from the housing by the light source to adjust the simulated distance between the light source and the detector to be calibrated. The geared iris has an aperture whose size is adjustable by means of a first stepper motor controlled by the microprocessor. The multiple aperture filter wheel contains neutral density filters of different attenuation levels which are selectively positioned in the path of the emitted radiation by a second stepper motor that is also controlled by the microprocessor. An operator can select a number of detector tests including range, maximum and minimum sensitivity, and basic functionality. During the range test, the geared iris and filter wheel are repeatedly adjusted by the microprocessor as necessary to simulate an incrementally increasing simulated source distance. A light source calibration subsystem is incorporated in the system which insures that the intensity of the light source is maintained at a constant level over time.

Reducing DoD Fossil-Fuel Dependence

DTIC Science & Technology

2006-09-01

hour: the amount of energy available from one gigawatt in one hour. HFCS High - fructose corn syrup HHV High -heat value HICE Hydrogen internal combustion...63 Ethanol derived from corn .................................................... 63...particular, alternate fuels and energy sources are to be assessed in terms of multiple parameters, to include (but not limited to) stability, high & low

The Increase of Energy Consumption and Carbon Dioxide (CO2) Emission in Indonesia

NASA Astrophysics Data System (ADS)

Sasana, Hadi; Putri, Annisa Eka

2018-02-01

In the last decade, the increase of energy consumption that has multiplied carbondioxide emissions becomes world problems, especially in the developing countries undergoing industrialization to be developed ones like Indonesia. This aim of this study was to analyze the effect of fossil energy consumption, population growth, and consumption of renewable energy on carbon dioxide emission. The method used was multiple linear regression analysis with Ordinary Least Square approach using time series in the period of 1990 - 2014. The result showed that fossil energy consumption and population growth have a positive influence on carbon dioxide emission in Indonesia. Meanwhile, the consumption variable of renewable energy has a negative effect on the level of carbon dioxide emissions produced.

Anti-diabetic activity of a mineraloid isolate, in vitro and in genetically diabetic mice.

PubMed

Deneau, Joel; Ahmed, Taufeeq; Blotsky, Roger; Bojanowski, Krzysztof

2011-01-01

Type II diabetes is a metabolic disease mediated through multiple molecular pathways. Here, we report anti-diabetic effect of a standardized isolate from a fossil material - a mineraloid leonardite - in in vitro tests and in genetically diabetic mice. The mineraloid isolate stimulated mitochondrial metabolism in human fibroblasts and this stimulation correlated with enhanced expression of genes coding for mitochondrial proteins such as ATP synthases and ribosomal protein precursors, as measured by DNA microarrays. In the diabetic animal model, consumption of the Totala isolate resulted in decreased weight gain, blood glucose, and glycated hemoglobin. To our best knowledge, this is the first description ever of a fossil material having anti-diabetic activity in pre-clinical models.

Cloned plasmid DNA fragments as calibrators for controlling GMOs: different real-time duplex quantitative PCR methods.

PubMed

Taverniers, Isabel; Van Bockstaele, Erik; De Loose, Marc

2004-03-01

Analytical real-time PCR technology is a powerful tool for implementation of the GMO labeling regulations enforced in the EU. The quality of analytical measurement data obtained by quantitative real-time PCR depends on the correct use of calibrator and reference materials (RMs). For GMO methods of analysis, the choice of appropriate RMs is currently under debate. So far, genomic DNA solutions from certified reference materials (CRMs) are most often used as calibrators for GMO quantification by means of real-time PCR. However, due to some intrinsic features of these CRMs, errors may be expected in the estimations of DNA sequence quantities. In this paper, two new real-time PCR methods are presented for Roundup Ready soybean, in which two types of plasmid DNA fragments are used as calibrators. Single-target plasmids (STPs) diluted in a background of genomic DNA were used in the first method. Multiple-target plasmids (MTPs) containing both sequences in one molecule were used as calibrators for the second method. Both methods simultaneously detect a promoter 35S sequence as GMO-specific target and a lectin gene sequence as endogenous reference target in a duplex PCR. For the estimation of relative GMO percentages both "delta C(T)" and "standard curve" approaches are tested. Delta C(T) methods are based on direct comparison of measured C(T) values of both the GMO-specific target and the endogenous target. Standard curve methods measure absolute amounts of target copies or haploid genome equivalents. A duplex delta C(T) method with STP calibrators performed at least as well as a similar method with genomic DNA calibrators from commercial CRMs. Besides this, high quality results were obtained with a standard curve method using MTP calibrators. This paper demonstrates that plasmid DNA molecules containing either one or multiple target sequences form perfect alternative calibrators for GMO quantification and are especially suitable for duplex PCR reactions.

A spatial and vertical comparison of coral Sr/Ca variations and growth rates in Montastraea faveolata colonies in Veracruz, Mexico

NASA Astrophysics Data System (ADS)

Cobb, R. M.; DeLong, K. L.; Richey, J. N.; Flannery, J. A.; Kilbourne, K. H.; Smith, J. M.; Quinn, T. M.; Hudson, J. H.

2013-12-01

The massive coral genera Montastraea spp. is ubiquitous in modern and fossil coral reefs in the Gulf of Mexico and Caribbean Sea making this genus a potential archive for paleoclimate reconstructions. Interpretation of modern and fossil coral records requires understanding the origins of variability in coral geochemical variations on scales ranging from intracolony to regional as well as differing water depths. In 1991, the U.S. Geological Survey recovered cores from five Montastraea faveolata colonies offshore of Veracruz, Mexico (19.06°N, 96.93°W) in water depths from 2.7 m to 12.2 m. The average linear extension per year based on x-radiograph analysis is similar (8.1 and 8.6, ×1.9 mm/yr, 1σ; n=31) for colonies at water depths of 2.7 and 4.3 m, respectively, for the interval from 1963 to 1991. Progressively slower extension rates are observed for deeper colonies (7.6 × 1.8, 7.5 × 1.9, and 4.5 × 1.5 mm/yr, 1σ; n=31) for 5.8, 6.1 and 12.2 m, respectively. Correlation coefficients among annual linear extension records vary between 0.00 and 0.40 (n=31) with the lowest correlation between colonies in close proximity (~1 km) and highest between colonies furthest apart (~250 km). We analyzed coral Sr/Ca at approximately 18 samples per year (0.5 mm/sample) along corallite thecal walls parallel to the slab surface for the interval from 1982 to 1991. This geochemical proxy for SST reveals seasonal variations within the coral skeleton that correspond to the high- and low-density bands in the coral slab, which represent one year of growth. Our linear regression of coral Sr/Ca from a single core (5.8 m water depth) to the Optimum Interpolation sea surface temperature (OISST; Reynolds et al., 2002) results in a slope of -0.049 (×0.024 mmol/mol/°C, 1σ; n=100; r2=0.52), which is slightly greater than the slope of other published Montastraea calibrations, but less than those reported for Porites spp. An alternative calibration method is to examine mean coral Sr/Ca with mean SST for various locations from studies using the same analytical methods and reference standards. The mean Sr/Ca calibration for nine coral colonies from Veracruz, Puerto Rico, Florida Keys, and Dry Tortugas with OISST results in a slope similar to that observed for Porites spp. determined with the same method. Slope differences between calibration methods may be due to time averaging along the sample transect. Future work will examine coral Sr/Ca in the other four M. faveolata colonies from Veracruz to assess reproducibility.

Generic Raman-based calibration models enabling real-time monitoring of cell culture bioreactors.

PubMed

Mehdizadeh, Hamidreza; Lauri, David; Karry, Krizia M; Moshgbar, Mojgan; Procopio-Melino, Renee; Drapeau, Denis

2015-01-01

Raman-based multivariate calibration models have been developed for real-time in situ monitoring of multiple process parameters within cell culture bioreactors. Developed models are generic, in the sense that they are applicable to various products, media, and cell lines based on Chinese Hamster Ovarian (CHO) host cells, and are scalable to large pilot and manufacturing scales. Several batches using different CHO-based cell lines and corresponding proprietary media and process conditions have been used to generate calibration datasets, and models have been validated using independent datasets from separate batch runs. All models have been validated to be generic and capable of predicting process parameters with acceptable accuracy. The developed models allow monitoring multiple key bioprocess metabolic variables, and hence can be utilized as an important enabling tool for Quality by Design approaches which are strongly supported by the U.S. Food and Drug Administration. © 2015 American Institute of Chemical Engineers.

The self-calibration method for multiple systems at the CHARA Array

NASA Astrophysics Data System (ADS)

O'Brien, David

The self-calibration method, a new interferometric technique at the CHARA Array, has been used to derive orbits for several spectroscopic binaries. This method uses the wide component of a hierarchical triple system to calibrate visibility measurements of the triple's close binary system. At certain baselines and separations, the calibrator in one of these systems can be observed quasi-simultaneously with the target. Depending on the orientation of the CHARA observation baseline relative to the orientation of the wide orbit of the triple system, separated fringe packets may be observed. A sophisticated observing scheme must be put in place to ensure the existence of separated fringe packets on nights of observation. Prior to the onset of this project, the reduction of separated fringe packet data had never included the goal of deriving visibilities for both fringe packets, so new data reduction software has been written. Visibilities obtained with separated fringe packet data for the target close binary are run through both Monte Carlo simulations and grid search programs in order to determine the best-fit orbital elements of the close binary. Several targets have been observed in this fashion, and orbits have been derived for seven targets, including three new orbits. Derivation of the orbit of the close pair in a triple system allows for the calculation of the mutual inclination, which is the angle between the planes of the wide and close orbit. Knowledge of this quantity may give insight into the formation processes that create multiple star systems. INDEX WORDS: Long-baseline interferometry, Self calibration, Separated fringe packets, Triple systems, Close binaries, Multiple systems, Orbital parameters, Near-infrared interferometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buckley, L; Lambert, C; Nyiri, B

Purpose: To standardize the tube calibration for Elekta XVI cone beam CT (CBCT) systems in order to provide a meaningful estimate of the daily imaging dose and reduce the variation between units in a large centre with multiple treatment units. Methods: Initial measurements of the output from the CBCT systems were made using a Farmer chamber and standard CTDI phantom. The correlation between the measured CTDI and the tube current was confirmed using an Unfors Xi detector which was then used to perform a tube current calibration on each unit. Results: Initial measurements showed measured tube current variations of upmore » to 25% between units for scans with the same image settings. In order to reasonably estimate the imaging dose, a systematic approach to x-ray generator calibration was adopted to ensure that the imaging dose was consistent across all units at the centre and was adopted as part of the routine quality assurance program. Subsequent measurements show that the variation in measured dose across nine units is on the order of 5%. Conclusion: Increasingly, patients receiving radiation therapy have extended life expectancies and therefore the cumulative dose from daily imaging should not be ignored. In theory, an estimate of imaging dose can be made from the imaging parameters. However, measurements have shown that there are large differences in the x-ray generator calibration as installed at the clinic. Current protocols recommend routine checks of dose to ensure constancy. The present study suggests that in addition to constancy checks on a single machine, a tube current calibration should be performed on every unit to ensure agreement across multiple machines. This is crucial at a large centre with multiple units in order to provide physicians with a meaningful estimate of the daily imaging dose.« less

On using summary statistics from an external calibration sample to correct for covariate measurement error.

PubMed

Guo, Ying; Little, Roderick J; McConnell, Daniel S

2012-01-01

Covariate measurement error is common in epidemiologic studies. Current methods for correcting measurement error with information from external calibration samples are insufficient to provide valid adjusted inferences. We consider the problem of estimating the regression of an outcome Y on covariates X and Z, where Y and Z are observed, X is unobserved, but a variable W that measures X with error is observed. Information about measurement error is provided in an external calibration sample where data on X and W (but not Y and Z) are recorded. We describe a method that uses summary statistics from the calibration sample to create multiple imputations of the missing values of X in the regression sample, so that the regression coefficients of Y on X and Z and associated standard errors can be estimated using simple multiple imputation combining rules, yielding valid statistical inferences under the assumption of a multivariate normal distribution. The proposed method is shown by simulation to provide better inferences than existing methods, namely the naive method, classical calibration, and regression calibration, particularly for correction for bias and achieving nominal confidence levels. We also illustrate our method with an example using linear regression to examine the relation between serum reproductive hormone concentrations and bone mineral density loss in midlife women in the Michigan Bone Health and Metabolism Study. Existing methods fail to adjust appropriately for bias due to measurement error in the regression setting, particularly when measurement error is substantial. The proposed method corrects this deficiency.

Automatic multi-camera calibration for deployable positioning systems

NASA Astrophysics Data System (ADS)

Axelsson, Maria; Karlsson, Mikael; Rudner, Staffan

2012-06-01

Surveillance with automated positioning and tracking of subjects and vehicles in 3D is desired in many defence and security applications. Camera systems with stereo or multiple cameras are often used for 3D positioning. In such systems, accurate camera calibration is needed to obtain a reliable 3D position estimate. There is also a need for automated camera calibration to facilitate fast deployment of semi-mobile multi-camera 3D positioning systems. In this paper we investigate a method for automatic calibration of the extrinsic camera parameters (relative camera pose and orientation) of a multi-camera positioning system. It is based on estimation of the essential matrix between each camera pair using the 5-point method for intrinsically calibrated cameras. The method is compared to a manual calibration method using real HD video data from a field trial with a multicamera positioning system. The method is also evaluated on simulated data from a stereo camera model. The results show that the reprojection error of the automated camera calibration method is close to or smaller than the error for the manual calibration method and that the automated calibration method can replace the manual calibration.

Pyrite discs in coal: evidence for fossilized bacterial colonies

USGS Publications Warehouse

Southam, G.; Donald, R.; Rostad, A.; Brock, C.

2001-01-01

Discs of pyrite from 1 to 3 mm in diameter and ∼100 μm thick were observed within fracture planes in coal from the Black Mesa coal deposit in northeastern Arizona. The pyrite discs were composed of aggregates of crystals, which suggested that sulfide mineral diagenesis had initiated at multiple nucleation sites and occurred prior to the compaction forces occurring during coal formation. Stable sulfur isotope analysis of the discs (δ34S = −31.7‰) supports a bacterial origin resulting from dissimilatory sulfate reduction. Fossilized bacteria on the disc surfaces (average = 27/100 μm2) appeared as halos when viewed using reflected light microscopy, but were lenticular by scanning electron microscopy, each microfossil being 2–3 μm in length. A fossilized bacterial colony (pyrite disc), 1 mm in diameter, would contain ∼2.1 × 107 microfossils. These microfossils were not observed on hydrothermal pyrite. Coating and in-filling of sulfate-reducing bacteria with iron disulfide during in vitro sulfide mineral diagenesis provide mechanisms to explain the preservation of the three-dimensional lenticular microfossils observed on the pyrite discs.

Global Surface Temperature Anomalies and Attribution

NASA Astrophysics Data System (ADS)

Pietrafesa, L. J.

2017-12-01

We study Non-Stationary, Non-Linear time series of global surface temperatures from 1850 to 2016, and via an empirical, mathematical methodology, we reveal the buried, internal modes of variability of planetary temperatures over the past 167 years, and find periods of cooling and warming, both in the ocean and the atmosphere over land, with multiple modes of variability; seasonal, annual, inter-annual, multi-year, decadal, multi-decadal, centennial and overall warming trends in the ocean, atmosphere and the combination therein. The oceanic rate of warming is less than two thirds of that of the atmosphere. While our findings on overall trends of fossil fuel burning and planetary temperatures are only visually correlative, by employing a mathematical methodology well known in ergonomics, this study causally links the upward rise in planetary surface temperature from the latter part of the 19th Century and into the 21st Century, to the contemporaneous upward rise in fossil fuel burning and suggests that if present fossil fuel burning is not curtailed there will be continued warming of the planet in the future.

The first iguanian lizard from the Mesozoic of Africa

NASA Astrophysics Data System (ADS)

Apesteguía, Sebastián; Daza, Juan D.; Simões, Tiago R.; Rage, Jean Claude

2016-09-01

The fossil record shows that iguanian lizards were widely distributed during the Late Cretaceous. However, the biogeographic history and early evolution of one of its most diverse and peculiar clades (acrodontans) remain poorly known. Here, we present the first Mesozoic acrodontan from Africa, which also represents the oldest iguanian lizard from that continent. The new taxon comes from the Kem Kem Beds in Morocco (Cenomanian, Late Cretaceous) and is based on a partial lower jaw. The new taxon presents a number of features that are found only among acrodontan lizards and shares greatest similarities with uromastycines, specifically. In a combined evidence phylogenetic dataset comprehensive of all major acrodontan lineages using multiple tree inference methods (traditional and implied weighting maximum-parsimony, and Bayesian inference), we found support for the placement of the new species within uromastycines, along with Gueragama sulamericana (Late Cretaceous of Brazil). The new fossil supports the previously hypothesized widespread geographical distribution of acrodontans in Gondwana during the Mesozoic. Additionally, it provides the first fossil evidence of uromastycines in the Cretaceous, and the ancestry of acrodontan iguanians in Africa.

Remote sensing of salinity

NASA Technical Reports Server (NTRS)

Thomann, G. C.

1975-01-01

The complex dielectric constant of sea water is a function of salinity at 21 cm wavelength, and sea water salinity can be determined by a measurement of emissivity at 21 cm along with a measurement of thermodynamic temperature. Three aircraft and one helicopter experiments using two different 21 cm radiometers were conducted under different salinity and temperature conditions. Single or multiple ground truth measurements were used to calibrate the data in each experiment. It is inferred from these experiments that accuracies of 1 to 2%/OO are possible with a single surface calibration point necessary only every two hours if the following conditions are met--water temperatures above 20 C, salinities above 10%/OO, and level plane flight. More frequent calibration, constraint of the aircraft's orientation to the same as it was during calibration, and two point calibration (at a high and low salinity level) rather than single point calibration may give even better accuracies in some instances.

Fossil Signatures Using Elemental Abundance Distributions and Bayesian Probabilistic Classification

NASA Technical Reports Server (NTRS)

Hoover, Richard B.; Storrie-Lombardi, Michael C.

2004-01-01

Elemental abundances (C6, N7, O8, Na11, Mg12, Al3, P15, S16, Cl17, K19, Ca20, Ti22, Mn25, Fe26, and Ni28) were obtained for a set of terrestrial fossils and the rock matrix surrounding them. Principal Component Analysis extracted five factors accounting for the 92.5% of the data variance, i.e. information content, of the elemental abundance data. Hierarchical Cluster Analysis provided unsupervised sample classification distinguishing fossil from matrix samples on the basis of either raw abundances or PCA input that agreed strongly with visual classification. A stochastic, non-linear Artificial Neural Network produced a Bayesian probability of correct sample classification. The results provide a quantitative probabilistic methodology for discriminating terrestrial fossils from the surrounding rock matrix using chemical information. To demonstrate the applicability of these techniques to the assessment of meteoritic samples or in situ extraterrestrial exploration, we present preliminary data on samples of the Orgueil meteorite. In both systems an elemental signature produces target classification decisions remarkably consistent with morphological classification by a human expert using only structural (visual) information. We discuss the possibility of implementing a complexity analysis metric capable of automating certain image analysis and pattern recognition abilities of the human eye using low magnification optical microscopy images and discuss the extension of this technique across multiple scales.

Calibrating Item Families and Summarizing the Results Using Family Expected Response Functions

ERIC Educational Resources Information Center

Sinharay, Sandip; Johnson, Matthew S.; Williamson, David M.

2003-01-01

Item families, which are groups of related items, are becoming increasingly popular in complex educational assessments. For example, in automatic item generation (AIG) systems, a test may consist of multiple items generated from each of a number of item models. Item calibration or scoring for such an assessment requires fitting models that can…

NASA IKONOS Radiometric Characterization

NASA Technical Reports Server (NTRS)

Pagnutti, Mary; Frisbee, Troy; Zanoni, Vicki; Blonski, Slawek; Daehler, Erik; Grant, Brennan; Holekamp, Kara; Ryan, Robert; Sellers, Richard; Smith, Charles

2002-01-01

The objective of this program: Perform radiometric vicarious calibrations of IKQNOS imagery and compare with Space Imaging calibration coefficients The approach taken: utilize multiple well-characterized sites which are widely used by the NASA science community for radiometric characterization of airborne and spaceborne sensors; and to Perform independent characterizations with independent teams. Each team has slightly different measurement techniques and data processing methods.

New postcranial fossils of Australopithecus afarensis from Hadar, Ethiopia (1990-2007).

PubMed

Ward, Carol V; Kimbel, William H; Harmon, Elizabeth H; Johanson, Donald C

2012-07-01

Renewed fieldwork at Hadar, Ethiopia, from 1990 to 2007, by a team based at the Institute of Human Origins, Arizona State University, resulted in the recovery of 49 new postcranial fossils attributed to Australopithecus afarensis. These fossils include elements from both the upper and lower limbs as well as the axial skeleton, and increase the sample size of previously known elements for A. afarensis. The expanded Hadar sample provides evidence of multiple new individuals that are intermediate in size between the smallest and largest individuals previously documented, and so support the hypothesis that a single dimorphic species is represented. Consideration of the functional anatomy of the new fossils supports the hypothesis that no functional or behavioral differences need to be invoked to explain the morphological variation between large and small A. afarensis individuals. Several specimens provide important new data about this species, including new vertebrae supporting the hypothesis that A. afarensis may have had a more human-like thoracic form than previously appreciated, with an invaginated thoracic vertebral column. A distal pollical phalanx confirms the presence of a human-like flexor pollicis longus muscle in A. afarensis. The new fossils include the first complete fourth metatarsal known for A. afarensis. This specimen exhibits the dorsoplantarly expanded base, axial torsion and domed head typical of humans, revealing the presence of human-like permanent longitudinal and transverse arches and extension of the metatarsophalangeal joints as in human-like heel-off during gait. The new Hadar postcranial fossils provide a more complete picture of postcranial functional anatomy, and individual and temporal variation within this sample. They provide the basis for further in-depth analyses of the behavioral and evolutionary significance of A. afarensis anatomy, and greater insight into the biology and evolution of these early hominins. Copyright © 2011 Elsevier Ltd. All rights reserved.

Daytime sky polarization calibration limitations

NASA Astrophysics Data System (ADS)

Harrington, David M.; Kuhn, Jeffrey R.; Ariste, Arturo López

2017-01-01

The daytime sky has recently been demonstrated as a useful calibration tool for deriving polarization cross-talk properties of large astronomical telescopes. The Daniel K. Inouye Solar Telescope and other large telescopes under construction can benefit from precise polarimetric calibration of large mirrors. Several atmospheric phenomena and instrumental errors potentially limit the technique's accuracy. At the 3.67-m AEOS telescope on Haleakala, we performed a large observing campaign with the HiVIS spectropolarimeter to identify limitations and develop algorithms for extracting consistent calibrations. Effective sampling of the telescope optical configurations and filtering of data for several derived parameters provide robustness to the derived Mueller matrix calibrations. Second-order scattering models of the sky show that this method is relatively insensitive to multiple-scattering in the sky, provided calibration observations are done in regions of high polarization degree. The technique is also insensitive to assumptions about telescope-induced polarization, provided the mirror coatings are highly reflective. Zemax-derived polarization models show agreement between the functional dependence of polarization predictions and the corresponding on-sky calibrations.

High-resolution global fossil fuel CO2 emissions for 1992 to 2010 using integrated in-situ and remotely sensed data in a fossil fuel data assimilation system

NASA Astrophysics Data System (ADS)

Asefi-Najafabady, S.; Gurney, K. R.; Rayner, P.; Huang, J.; Song, Y.

2012-12-01

The largest single net source of CO2 into the Earth's atmosphere is due to the combustion of fossil fuel and an accurate quantification of the fossil fuel flux is needed to better address the concern of rising atmospheric greenhouse gas concentrations. In the last decade, there has been a growing need, from both the science and policymaking communities for quantification of global fossil fuel CO2 emissions at finer space and time scales. Motivated by this concern, we have built a global fossil fuel CO2 emission inventory at 0.25° and 0.1° resolutions for the years of 1992 - 2010 using a combination of in situ and remotely sensed data in a fossil fuel data assimilation system (FFDAS). A suite of observations which include nightlights, population, sectoral national emissions and power plant stations are used to constrain the FFDAS model. FFDAS is based on a modified Kaya identity which expresses emissions as the product of areal population density, per capita economic activity, energy intensity of economic activity, and carbon intensity of energy consumption. Nightlights has been shown to correlate well with national and regional GDP and its relationship with population has been used as an initial means of downscaling fossil fuel emissions. However nightlights data are subject to instrumental saturation, causing areas of bright nightlights, such as urban cores, to be truncated. To address the saturation problem during several time periods, the National Geophysical Data Center (NGDC) has requested and received data collected at multiple fixed gain settings to observe the bright areas with no saturation. However, this dataset is limited to only four years (1999, 2002, 2006 and 2010). We have applied a numerical technique to these four years of data to estimate the unsaturated values for all years from 1992 to 2010. The corrected nightlights time series is then used in FFDAS to generate a multiyear fossil fuel CO2 emissions data product. Nightlights and population provide an approximate location and magnitude for fossil fuel CO2 emissions. Some emitting sectors, such as power plant emissions and heavy industry, are not coincident with where people live or lights are on. Therefore, for better accuracy, we used direct emissions information from power stations as a constraint to the FFDAS estimation. We present this new high resolution, multiyear emissions data product with analysis of the space/time patterns, trends and posterior uncertainty. We also compare the FFDAS results to the "bottom-up" high resolution fossil fuel CO2 emissions estimation generated by the Vulcan Project in the United States. Finally, we examine the sensitivity of the results to differences in the procedures used to generate the improved multiyear nightlights time series.

Inflight Radiometric Calibration of New Horizons' Multispectral Visible Imaging Camera (MVIC)

NASA Technical Reports Server (NTRS)

Howett, C. J. A.; Parker, A. H.; Olkin, C. B.; Reuter, D. C.; Ennico, K.; Grundy, W. M.; Graps, A. L.; Harrison, K. P.; Throop, H. B.; Buie, M. W.;

Testing Astronomical and 40Ar/39Ar Timescales for the K/Pg Boundary Interval Using High-Resolution Magnetostratigraphy and U-Pb Geochronology in the Denver Basin of Colorado

NASA Astrophysics Data System (ADS)

Clyde, W.; Bowring, S. A.; Johnson, K. R.; Ramezani, J.; Jones, M. M.

2015-12-01

Accurate and precise calibration of the Geomagnetic Polarity Timescale (GPTS) in absolute time is critical for resolving rates of geological and biological processes which in turn help constrain the underlying causes of those processes. Numerical calibration of the GPTS was traditionally carried out by interpolation between a limited number of 40Ar/39Ar dated volcanic ash deposits from superpositional sequences with well-defined magnetostratigraphies. More recently, the Neogene part of the GPTS has been calibrated using high-resolution astrochronological methods, however the application of these approaches to pre-Neogene parts of the timescale is controversial given the uncertainties in relevant orbital parameters this far back in time and differing interpretations of local cyclostratigraphic records. The Cretaceous-Paleogene (K/Pg) boundary interval is a good example, where various astronomical and 40Ar/39Ar calibrations have been proposed with varying degrees of agreement. The Denver Basin (Colorado, USA) contains one of the most complete stratigraphic sequences across the K/Pg boundary in the world, preserving evidence of bolide impact as well as biotic extinction and recovery in a thick stratigraphic package that is accessible by both core and outcrop. We present a series of high-precision U-Pb age determinations from interbedded volcanic ash deposits within a tightly constrained magnetobiostratigraphic framework across the K/Pg boundary in the Denver Basin. This new timeline provides a precise absolute age for the K/Pg boundary, constrains the ages of magnetic polarity Chrons C28 to C30, and provides a direct and independent test of early Paleogene astronomical and 40Ar/39Ar based timescales. Temporal calibration of fossil pollen evidence of the "fern spike" in the Denver Basin shows that plant extinctions peaked within ~50-500 years of the bolide impact and primary productivity recovered ~500-5000 years after the impact.

Determining the Cause of the Late Triassic Adamanian-Revueltian Vertebrate Faunal Turnover in Western North America: Climate Change, Bolide Impact, or no Extinction at All?

NASA Astrophysics Data System (ADS)

Martz, J. W.

2016-12-01

The Triassic was one of the most critical intervals in terrestrial vertebrate history, during which both adaptive radiation and extinction played roles in shaping the future of Mesozoic ecosystems. In recent years, it has become increasingly clear that the transition from the globally diverse ecosystems of the Triassic to the more uniformly dinosaur-dominated ecosystems of the later Mesozoic was complex, involving a variety of environmental changes on both local and global levels. The Adamanian-Revueltian faunal turnover is a putative faunal turnover event identified in the Upper Triassic Chinle Formation of the western United States which involved a decline in diversity among crocodylian-line archosaurs and the extinction of several taxa coincident with the appearance or increase in abundance of other taxa. Careful lithostratigraphic and biostratigraphic work in Petrified Forest National Park in northern Arizona has identified the stratigraphic horizon at which this turnover is likely to have occurred, and sedimentology and improved radioisotopic calibration indicates that the turnover was early Alaunian (middle Norian) and at least roughly coincident with both the Manicouagan bolide impact and an abrupt shift towards a more arid climate in the western United States. However, testing the reality of the turnover and its coincidence with particular environmental changes requires the application of statistical methods highly dependent on the sample sizes and stratigraphic distribution of vertebrate fossils. The problem is exacerbated by the fact that for some vertebrates, the turnover is characterized by changes in abundance rather than range termination, which is more difficult to evaluate statistically, and that some fossils can only be assigned to higher taxa. Moreover, radioisotopic calibration of the putative turnover horizon is coarse, suggesting that correlating faunal turnovers to distant events is more difficult than correlating them to local environmental changes when the former requires both stratigraphic and radioisotopic precision.

Comparable Ages for the Independent Origins of Electrogenesis in African and South American Weakly Electric Fishes

PubMed Central

Lavoué, Sébastien; Miya, Masaki; Arnegard, Matthew E.; Sullivan, John P.; Hopkins, Carl D.; Nishida, Mutsumi

2012-01-01

One of the most remarkable examples of convergent evolution among vertebrates is illustrated by the independent origins of an active electric sense in South American and African weakly electric fishes, the Gymnotiformes and Mormyroidea, respectively. These groups independently evolved similar complex systems for object localization and communication via the generation and reception of weak electric fields. While good estimates of divergence times are critical to understanding the temporal context for the evolution and diversification of these two groups, their respective ages have been difficult to estimate due to the absence of an informative fossil record, use of strict molecular clock models in previous studies, and/or incomplete taxonomic sampling. Here, we examine the timing of the origins of the Gymnotiformes and the Mormyroidea using complete mitogenome sequences and a parametric Bayesian method for divergence time reconstruction. Under two different fossil-based calibration methods, we estimated similar ages for the independent origins of the Mormyroidea and Gymnotiformes. Our absolute estimates for the origins of these groups either slightly postdate, or just predate, the final separation of Africa and South America by continental drift. The most recent common ancestor of the Mormyroidea and Gymnotiformes was found to be a non-electrogenic basal teleost living more than 85 millions years earlier. For both electric fish lineages, we also estimated similar intervals (16–19 or 22–26 million years, depending on calibration method) between the appearance of electroreception and the origin of myogenic electric organs, providing rough upper estimates for the time periods during which these complex electric organs evolved de novo from skeletal muscle precursors. The fact that the Gymnotiformes and Mormyroidea are of similar age enhances the comparative value of the weakly electric fish system for investigating pathways to evolutionary novelty, as well as the influences of key innovations in communication on the process of species radiation. PMID:22606250

Fossil energy technical manpower: forecasts of supply and demand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Friedman, B.S.

1975-10-01

The nation's overall need for engineers and physical scientists will continue to grow but is not expected to outpace the production of new graduates in these fields. Technical manpower shortages that might hinder the nation's fossil and other energy programs are not likely to occur. If a shortage does become a real threat, it could be countered by corrective actions: intensify efforts to sign up or retrieve the thousands of engineers and physical scientists who leave their technical field soon after graduation; recruit graduates, now working in other fields, who have potential for retraining in the critical area; increase themore » productivity of professionals through greater use of para-professionals or technicians; shorten the education pipeline by encouraging students to shift mid-stream from related disciplines to those in short supply; and as a last resort, admit the requisite number of non-quota immigrants with the desired training. Government agencies and industry are advised not to engage in campaigns to stimulate enrollment in specific technical fields. Such recruiting is usually a ''too-much, too-late'' measure. Forecasts of job opportunities are self-defeating and very often misleading. It is, therefore, unethical to use them as a basis for persuading high school students to enroll in specific disciplines. Certain kinds of student recruiting are, however, recommended: selective recruiting to attract more of the high-calibre students; and selective recruiting and use of stipends to attract more female, minority and/or low-income students with high potential. If universities recruit, it should be on the basis of intrinsic interest in a particular discipline, rather than on job outlook. As always, there is a need to improve the calibre and competence of the university ''end-product.'' Several programs and actions designed to do this are recommended for universities, ERDA and other governmental agencies, professional societies and industry.« less

Polyphyly of the extinct family Oviparosiphidae and its implications for inferring aphid evolution (Hemiptera, Sternorrhyncha)

PubMed Central

Żyła, Dagmara; Homan, Agnieszka; Wegierek, Piotr

2017-01-01

Aphidoidea, the so-called "true aphids" are one of the most challenging groups in terms of solving the phylogenetic relationships. Morphology-based analyses were strongly affected by widespread homoplasy, while the molecular-based attempts struggled with the lack of sufficient phylogenetic signal. Despite significant improvements, the higher classification still remains unresolved and rather controversial. However, the use of the fossil record, one of the most valuable sources of information, was mainly limited to calibration of a phylogenetic tree, without a direct inclusion into the analysis. The extinct family Oviparosiphidae has long been considered as the common ancestor of all recent Aphidoidea and it was used as a calibration point in several analyses, but it has been never analyzed in a phylogenetic context. The family has been treated as a monophyletic group purely based on the simultaneous presence of two abdominal structures, ovipositor and siphunculi. However, it has been shown recently that at least one more extinct lineage, present at the same time, was characterized by the same features. For these reasons, we performed a maximum parsimony analysis using morphological data for extinct aphid taxa to prove the monophyly of Oviparosiphidae. Our analysis shows that the presumed ancestor lineage of recent aphids is a polyphyletic group. Our results support the hypothesis of an early Mesozoic rapid radiation of aphids, which led to several different lineages characterized by both ovipositor and siphunculi. The results indicate the necessity of examining the other extinct families, and shows that the diversity of aphids before the Cretaceous Terrestrial Revolution (KTR) was higher than expected. Even though there is not enough data to perform a formal analysis, fossils seem to suggest a significant impact of the KTR on aphid diversification. Additionally, we have made a redescription of two genera and description of a new species, Vitimaphis subridens sp. nov. PMID:28445493

Environmental determinants of radiolarian assemblages in the western Pacific since the last deglaciation

NASA Astrophysics Data System (ADS)

Hernández-Almeida, I.; Cortese, G.; Yu, P.-S.; Chen, M.-T.; Kucera, M.

2017-08-01

Radiolarians are a very diverse microzooplanktonic group, often distributed in regionally restricted assemblages and responding to specific environmental factors. These properties of radiolarian assemblages make the group more conducive for the development and application of basin-wide ecological models. Here we use a new surface sediment data set from the western Pacific to demonstrate that ecological patterns derived from basin-wide open-ocean data sets cannot be transferred on semirestricted marginal seas. The data set consists of 160 surface sediment samples from three tropical-subtropical regions (East China Sea, South China Sea, and western Pacific), combining 54 new assemblage counts with taxonomically harmonized data from previous studies. Multivariate statistical analyses indicate that winter sea surface temperature at 10 m depth (SSTw) was the most significant environmental variable affecting the composition of radiolarian assemblages, allowing the development of an optimal calibration model (Locally Weighted-Weighted Averaging regression inverse deshrinking, R2cv = 0.88, root-mean-square error of prediction = 1.6°C). The dominant effect of SSTw on radiolarian assemblage composition in the western Pacific is attributed to the East Asian Winter Monsoon (EAWM), which is particularly strong in the marginal seas. To test the applicability of the calibration model on fossil radiolarian assemblages from the marginal seas, the calibration model was applied to two downcore records from the Okinawa Trough, covering the last 18 ka. We observe that these assemblages find most appropriate analogs among modern samples from the marginal basins (East China Sea and South China Sea). Downcore temperature reconstructions at both sites show similarities to known regional SST reconstructions, providing proof of concept for the new radiolarian-based SSTw calibration model.

An efficient multistage algorithm for full calibration of the hemodynamic model from BOLD signal responses.

PubMed

Zambri, Brian; Djellouli, Rabia; Laleg-Kirati, Taous-Meriem

2017-11-01

We propose a computational strategy that falls into the category of prediction/correction iterative-type approaches, for calibrating the hemodynamic model. The proposed method is used to estimate consecutively the values of the two sets of model parameters. Numerical results corresponding to both synthetic and real functional magnetic resonance imaging measurements for a single stimulus as well as for multiple stimuli are reported to highlight the capability of this computational methodology to fully calibrate the considered hemodynamic model. Copyright © 2017 John Wiley & Sons, Ltd.

Least-Squares Self-Calibration of Imaging Array Data

NASA Technical Reports Server (NTRS)

Arendt, R. G.; Moseley, S. H.; Fixsen, D. J.

2004-01-01

When arrays are used to collect multiple appropriately-dithered images of the same region of sky, the resulting data set can be calibrated using a least-squares minimization procedure that determines the optimal fit between the data and a model of that data. The model parameters include the desired sky intensities as well as instrument parameters such as pixel-to-pixel gains and offsets. The least-squares solution simultaneously provides the formal error estimates for the model parameters. With a suitable observing strategy, the need for separate calibration observations is reduced or eliminated. We show examples of this calibration technique applied to HST NICMOS observations of the Hubble Deep Fields and simulated SIRTF IRAC observations.

Reduction of interferences in graphite furnace atomic absorption spectrometry by multiple linear regression modelling

NASA Astrophysics Data System (ADS)

Grotti, Marco; Abelmoschi, Maria Luisa; Soggia, Francesco; Tiberiade, Christian; Frache, Roberto

2000-12-01

The multivariate effects of Na, K, Mg and Ca as nitrates on the electrothermal atomisation of manganese, cadmium and iron were studied by multiple linear regression modelling. Since the models proved to efficiently predict the effects of the considered matrix elements in a wide range of concentrations, they were applied to correct the interferences occurring in the determination of trace elements in seawater after pre-concentration of the analytes. In order to obtain a statistically significant number of samples, a large volume of the certified seawater reference materials CASS-3 and NASS-3 was treated with Chelex-100 resin; then, the chelating resin was separated from the solution, divided into several sub-samples, each of them was eluted with nitric acid and analysed by electrothermal atomic absorption spectrometry (for trace element determinations) and inductively coupled plasma optical emission spectrometry (for matrix element determinations). To minimise any other systematic error besides that due to matrix effects, accuracy of the pre-concentration step and contamination levels of the procedure were checked by inductively coupled plasma mass spectrometric measurements. Analytical results obtained by applying the multiple linear regression models were compared with those obtained with other calibration methods, such as external calibration using acid-based standards, external calibration using matrix-matched standards and the analyte addition technique. Empirical models proved to efficiently reduce interferences occurring in the analysis of real samples, allowing an improvement of accuracy better than for other calibration methods.

Calibration of amino acid racemization (AAR) kinetics in United States mid-Atlantic Coastal Plain Quaternary mollusks using 87Sr/ 86Sr analyses: Evaluation of kinetic models and estimation of regional Late Pleistocene temperature history

USGS Publications Warehouse

Wehmiller, J.F.; Harris, W.B.; Boutin, B.S.; Farrell, K.M.

2012-01-01

The use of amino acid racemization (AAR) for estimating ages of Quaternary fossils usually requires a combination of kinetic and effective temperature modeling or independent age calibration of analyzed samples. Because of limited availability of calibration samples, age estimates are often based on model extrapolations from single calibration points over wide ranges of D/L values. Here we present paired AAR and 87Sr/ 86Sr results for Pleistocene mollusks from the North Carolina Coastal Plain, USA. 87Sr/ 86Sr age estimates, derived from the lookup table of McArthur et al. [McArthur, J.M., Howarth, R.J., Bailey, T.R., 2001. Strontium isotopic stratigraphy: LOWESS version 3: best fit to the marine Sr-isotopic curve for 0-509 Ma and accompanying Look-up table for deriving numerical age. Journal of Geology 109, 155-169], provide independent age calibration over the full range of amino acid D/L values, thereby allowing comparisons of alternative kinetic models for seven amino acids. The often-used parabolic kinetic model is found to be insufficient to explain the pattern of racemization, although the kinetic pathways for valine racemization and isoleucine epimerization can be closely approximated with this function. Logarithmic and power law regressions more accurately represent the racemization pathways for all amino acids. The reliability of a non-linear model for leucine racemization, developed and refined over the past 20 years, is confirmed by the 87Sr/ 86Sr age results. This age model indicates that the subsurface record (up to 80m thick) of the North Carolina Coastal Plain spans the entire Quaternary, back to ???2.5Ma. The calibrated kinetics derived from this age model yield an estimate of the effective temperature for the study region of 11??2??C., from which we estimate full glacial (Last Glacial Maximum - LGM) temperatures for the region on the order of 7-10??C cooler than present. These temperatures compare favorably with independent paleoclimate information for the region. ?? 2011 Elsevier B.V.

VizieR Online Data Catalog: GRB 160509A VLA monitoring campain results (Laskar+, 2016)

NASA Astrophysics Data System (ADS)

Laskar, T.; Alexander, K. D.; Berger, E.; Fong, W.-F.; Margutti, R.; Shivvers, I.; Williams, P. K. G.; Kopac, D.; Kobayashi, S.; Mundell, C.; Gomboc, A.; Zheng, W.; Menten, K. M.; Graham, M. L.; Filippenko, A. V.

2017-04-01

GRB 160509A was discovered by the Fermi LAT on 2016 May 09 at 08:59:04.36 UTC (Longo+ 2016GCN..19403...1L). We observed the afterglow with the VLA starting at 0.36 days. We tracked the flux density of the afterglow over multiple epochs spanning 1.2-33.5GHz, using 3C48, 3C286, and 3C147 as flux and bandpass calibrators, and J2005+7752 as the gain calibrator. Our VLA observations spanning 0.36-20 days after the burst clearly reveal the presence of multiple spectral components in the radio afterglow. (1 data file).

Parts-Per-Billion Mass Measurement Accuracy Achieved through the Combination of Multiple Linear Regression and Automatic Gain Control in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

PubMed Central

Williams, D. Keith; Muddiman, David C.

2008-01-01

Fourier transform ion cyclotron resonance mass spectrometry has the ability to achieve unprecedented mass measurement accuracy (MMA); MMA is one of the most significant attributes of mass spectrometric measurements as it affords extraordinary molecular specificity. However, due to space-charge effects, the achievable MMA significantly depends on the total number of ions trapped in the ICR cell for a particular measurement. Even through the use of automatic gain control (AGC), the total ion population is not constant between spectra. Multiple linear regression calibration in conjunction with AGC is utilized in these experiments to formally account for the differences in total ion population in the ICR cell between the external calibration spectra and experimental spectra. This ability allows for the extension of dynamic range of the instrument while allowing mean MMA values to remain less than 1 ppm. In addition, multiple linear regression calibration is used to account for both differences in total ion population in the ICR cell as well as relative ion abundance of a given species, which also affords mean MMA values at the parts-per-billion level. PMID:17539605

A Novel Sensor System for Measuring Wheel Loads of Vehicles on Highways

PubMed Central

Zhang, Wenbin; Suo, Chunguang; Wang, Qi

2008-01-01

With the development of the highway transportation and business trade, vehicle Weigh-In-Motion (WIM) technology has become a key technology for measuring traffic loads. In this paper a novel WIM system based on monitoring of pavement strain responses in rigid pavement was investigated. In this WIM system multiple low cost, light weight, small volume and high accuracy embedded concrete strain sensors were used as WIM sensors to measure rigid pavement strain responses. In order to verify the feasibility of the method, a system prototype based on multiple sensors was designed and deployed on a relatively busy freeway. Field calibration and tests were performed with known two-axle truck wheel loads and the measurement errors were calculated based on the static weights measured with a static weighbridge. This enables the weights of other vehicles to be calculated from the calibration constant. Calibration and test results for individual sensors or three-sensor fusions are both provided. Repeatability, sources of error, and weight accuracy are discussed. Successful results showed that the proposed method was feasible and proven to have a high accuracy. Furthermore, a sample mean approach using multiple fused individual sensors could provide better performance compared to individual sensors. PMID:27873952

Self-adaptive calibration for staring infrared sensors

NASA Astrophysics Data System (ADS)

Kendall, William B.; Stocker, Alan D.

1993-10-01

This paper presents a new, self-adaptive technique for the correlation of non-uniformities (fixed-pattern noise) in high-density infrared focal-plane detector arrays. We have developed a new approach to non-uniformity correction in which we use multiple image frames of the scene itself, and take advantage of the aim-point wander caused by jitter, residual tracking errors, or deliberately induced motion. Such wander causes each detector in the array to view multiple scene elements, and each scene element to be viewed by multiple detectors. It is therefore possible to formulate (and solve) a set of simultaneous equations from which correction parameters can be computed for the detectors. We have tested our approach with actual images collected by the ARPA-sponsored MUSIC infrared sensor. For these tests we employed a 60-frame (0.75-second) sequence of terrain images for which an out-of-date calibration was deliberately used. The sensor was aimed at a point on the ground via an operator-assisted tracking system having a maximum aim point wander on the order of ten pixels. With these data, we were able to improve the calibration accuracy by a factor of approximately 100.

The Tule Springs local fauna: Rancholabrean vertebrates from the Las Vegas Formation, Nevada

USGS Publications Warehouse

Scott, Eric; Springer, Kathleen; Sagebiel, James C.

2017-01-01

A middle to late Pleistocene sedimentary sequence in the upper Las Vegas Wash, north of Las Vegas, Nevada, has yielded the largest open-site Rancholabrean vertebrate fossil assemblage in the southern Great Basin and Mojave Deserts. Recent paleontologic field studies have led to the discovery of hundreds of fossil localities and specimens, greatly extending the geographic and temporal footprint of original investigations in the early 1960s. The significance of the deposits and their entombed fossils led to the preservation of 22,650 acres of the upper Las Vegas Wash as Tule Springs Fossil Beds National Monument. These discoveries also warrant designation of the assemblage as a local fauna, named for the site of the original paleontologic studies at Tule Springs.The large mammal component of the Tule Springs local fauna is dominated by remains of Mammuthus columbi as well as Camelops hesternus, along with less common remains of Equus (including E. scotti) and Bison. Large carnivorans including Canis dirus, Smilodon fatalis, and Panthera atrox are also recorded. Micromammals, amphibians, lizards, snakes, birds, invertebrates, plant macrofossils, and pollen also occur in the deposits and provide important and complementary paleoenvironmental information. The fauna occurs within the Las Vegas Formation, an extensive and stratigraphically complex sequence of groundwater discharge deposits that represent a mosaic of desert wetland environments. Radiometric and luminescence dating indicates the sequence spans the last ∼570 ka, and records hydrologic changes in a dynamic and temporally congruent response to northern hemispheric abrupt climatic oscillations. The vertebrate fauna occurs in multiple stratigraphic horizons in this sequence, with ages of the fossils spanning from ∼100 to ∼12.5 ka.

Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

PubMed Central

Springer, Mark S.; Meredith, Robert W.; Gatesy, John; Emerling, Christopher A.; Park, Jong; Rabosky, Daniel L.; Stadler, Tanja; Steiner, Cynthia; Ryder, Oliver A.; Janečka, Jan E.; Fisher, Colleen A.; Murphy, William J.

2012-01-01

Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71–63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event (“Grande Coupure”) at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts. PMID:23166696

Chemotaxonomy in some Mediterranean plants and implications for fossil biomarker records

NASA Astrophysics Data System (ADS)

Norström, Elin; Katrantsiotis, Christos; Smittenberg, Rienk H.; Kouli, Katerina

2017-12-01

The increasing utilization of n-alkanes as plant-derived paleo-environmental proxies calls for improved chemotaxonomic control of the modern flora in order to calibrate fossil sediment records to modern analogues. Several recent studies have investigated long-chain n-alkane concentrations and chain-length distributions in species from various vegetation biomes, but up to date, the Mediterranean flora is relatively unexplored in this respect. Here, we analyse the n-alkane concentrations and chain-length distributions in some of the most common species of the modern macchia and phrygana vegetation in south western Peloponnese, Greece. We show that the drought adapted phrygana herbs and shrubs, as well as some of the sclerophyll and gymnosperm macchia components, produce high concentrations of n-alkanes, on average more than double n-alkane production in local wetland reed vegetation. Furthermore, the chain-length distribution in the analysed plants is related to plant functionality, with longer chain lengths associated with higher drought adaptive capacities, probably as a response to long-term evolutionary processes in a moisture limited environment. Furthermore, species with relatively higher average chain lengths (ACL) showed more enriched carbon isotope composition in their tissues (δ13Cplant), suggesting a dual imprint from both physiological and biochemical drought adaptation. The findings have bearings on interpretation of fossil sedimentary biomarker records in the Mediterranean region, which is discussed in relation to a case study from Agios Floros fen, Messenian plain, Peloponnese. The 6000 year long n-alkane record from Agios Floros (ACL, δ13Cwax) is linked to the modern analogue and then evaluated through a comparison with other regional-wide as well as local climate and vegetation proxy-data. The high concentration of long chain n-alkanes in phrygana vegetation suggests a dominating imprint from this vegetation type in sedimentary archives from this ecotone.

GPR as a Low Impact Paleontogical Survey Technique

NASA Astrophysics Data System (ADS)

Sturdevant, G. C.; Leverence, R.; Stewart, R.

2013-12-01

The Deweyville Formation, a Pleistocene fluvial sandstone, is a prolific source of megafaunal fossils from periods of low stand environmental conditions. GPR was employed in an environmentally sensitive area in close proximity to a salt dome in Northwest Harris County, Texas as a method of evaluating the probable paleo-depositional environment and to prospect for potential further site development of two distinct fossiliferous zones. The primary zone of interest is a lag gravel bounded sand responsible for producing a regionally unique fossil assemblage including South American megafauna (Lundelius et al, 2013). The secondary zone of interest contains undisturbed mammoth remains housed in coarse white sand emplaced on top of a clay drape which has been hypothesized to represent an oxbow lake formed by the meandering paleo-Brazos river. With an accurate map of the paleo-channel planning future activity can focus on maximizing fossil recovery and minimizing site impact. Pulse EKKO 250 MHz, 400MHz, and 1GHz system was employed in a prospect area proximal to the secondary site to calibrate and evaluate these systems for their resolution and penetration depth in the modern sediments. The data was processed using EKKO Mapper and EKKO View Deluxe software packages, 3d volumes were produced and sliced. Preliminary results from the 250 MHz demonstrate successful imaging of the sand-clay interface. After these surveys were run a small portion of the site was excavated to confirm the estimated velocities, the observed anomalies, and refine our modeling and interpretation, and improve grid design for further surveys. It was confirmed that the sand-clay interface was easily observable using GPR, however the grid spacing proved to be too wide, leading to artifacts in the 3d volume produced.

Revised age of late Neanderthal occupation and the end of the Middle Paleolithic in the northern Caucasus

PubMed Central

Pinhasi, Ron; Higham, Thomas F. G.; Golovanova, Liubov V.; Doronichev, Vladimir B.

2011-01-01

Advances in direct radiocarbon dating of Neanderthal and anatomically modern human (AMH) fossils and the development of archaeostratigraphic chronologies now allow refined regional models for Neanderthal–AMH coexistence. In addition, they allow us to explore the issue of late Neanderthal survival in regions of Western Eurasia located within early routes of AMH expansion such as the Caucasus. Here we report the direct radiocarbon (14C) dating of a late Neanderthal specimen from a Late Middle Paleolithic (LMP) layer in Mezmaiskaya Cave, northern Caucasus. Additionally, we provide a more accurate chronology for the timing of Neanderthal extinction in the region through a robust series of 16 ultrafiltered bone collagen radiocarbon dates from LMP layers and using Bayesian modeling to produce a boundary probability distribution function corresponding to the end of the LMP at Mezmaiskaya. The direct date of the fossil (39,700 ± 1,100 14C BP) is in good agreement with the probability distribution function, indicating at a high level of probability that Neanderthals did not survive at Mezmaiskaya Cave after 39 ka cal BP ("calendrical" age in kiloannum before present, based on IntCal09 calibration curve). This challenges previous claims for late Neanderthal survival in the northern Caucasus. We see striking and largely synchronous chronometric similarities between the Bayesian age modeling for the end of the LMP at Mezmaiskaya and chronometric data from Ortvale Klde for the end of the LMP in the southern Caucasus. Our results confirm the lack of reliably dated Neanderthal fossils younger than ∼40 ka cal BP in any other region of Western Eurasia, including the Caucasus. PMID:21555570

A calibration method based on virtual large planar target for cameras with large FOV

NASA Astrophysics Data System (ADS)

Yu, Lei; Han, Yangyang; Nie, Hong; Ou, Qiaofeng; Xiong, Bangshu

2018-02-01

In order to obtain high precision in camera calibration, a target should be large enough to cover the whole field of view (FOV). For cameras with large FOV, using a small target will seriously reduce the precision of calibration. However, using a large target causes many difficulties in making, carrying and employing the large target. In order to solve this problem, a calibration method based on the virtual large planar target (VLPT), which is virtually constructed with multiple small targets (STs), is proposed for cameras with large FOV. In the VLPT-based calibration method, first, the positions and directions of STs are changed several times to obtain a number of calibration images. Secondly, the VLPT of each calibration image is created by finding the virtual point corresponding to the feature points of the STs. Finally, intrinsic and extrinsic parameters of the camera are calculated by using the VLPTs. Experiment results show that the proposed method can not only achieve the similar calibration precision as those employing a large target, but also have good stability in the whole measurement area. Thus, the difficulties to accurately calibrate cameras with large FOV can be perfectly tackled by the proposed method with good operability.

Multiple Source DF (Direction Finding) Signal Processing: An Experimental System,

DTIC Science & Technology

The MUltiple SIgnal Characterization ( MUSIC ) algorithm is an implementation of the Signal Subspace Approach to provide parameter estimates of...the signal subspace (obtained from the received data) and the array manifold (obtained via array calibration). The MUSIC algorithm has been

A Review of Calibration Transfer Practices and Instrument Differences in Spectroscopy.

PubMed

Workman, Jerome J

2018-03-01

Calibration transfer for use with spectroscopic instruments, particularly for near-infrared, infrared, and Raman analysis, has been the subject of multiple articles, research papers, book chapters, and technical reviews. There has been a myriad of approaches published and claims made for resolving the problems associated with transferring calibrations; however, the capability of attaining identical results over time from two or more instruments using an identical calibration still eludes technologists. Calibration transfer, in a precise definition, refers to a series of analytical approaches or chemometric techniques used to attempt to apply a single spectral database, and the calibration model developed using that database, for two or more instruments, with statistically retained accuracy and precision. Ideally, one would develop a single calibration for any particular application, and move it indiscriminately across instruments and achieve identical analysis or prediction results. There are many technical aspects involved in such precision calibration transfer, related to the measuring instrument reproducibility and repeatability, the reference chemical values used for the calibration, the multivariate mathematics used for calibration, and sample presentation repeatability and reproducibility. Ideally, a multivariate model developed on a single instrument would provide a statistically identical analysis when used on other instruments following transfer. This paper reviews common calibration transfer techniques, mostly related to instrument differences, and the mathematics of the uncertainty between instruments when making spectroscopic measurements of identical samples. It does not specifically address calibration maintenance or reference laboratory differences.

An internally consistent pressure calibration of geobarometers applicable to the Earth’s upper mantle using in situ XRD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beyer, Christopher; Rosenthal, Anja; Myhill, Robert

We have performed an experimental cross calibration of a suite of mineral equilibria within mantle rock bulk compositions that are commonly used in geobarometry to determine the equilibration depths of upper mantle assemblages. Multiple barometers were compared simultaneously in experimental runs, where the pressure was determined using in-situ measurements of the unit cell volumes of MgO, NaCl, Re and h-BN between 3.6 and 10.4 GPa, and 1250 and 1500 °C. The experiments were performed in a large volume press (LVPs) in combination with synchrotron X-ray diffraction. Noble metal capsules drilled with multiple sample chambers were loaded with a range ofmore » bulk compositions representative of peridotite, eclogite and pyroxenite lithologies. By this approach, we simultaneously calibrated the geobarometers applicable to different mantle lithologies under identical and well determined pressure and temperature conditions. We identified discrepancies between the calculated and experimental pressures for which we propose simple linear or constant correction factors to some of the previously published barometric equations. As a result, we establish internally-consistent cross-calibrations for a number of garnet-orthopyroxene, garnet-clinopyroxene, Ca-Tschermaks-in-clinopyroxene and majorite geobarometers.« less

An application of synchrotron based x-ray tomography in palaeontology: Investigating small, three-dimensional, exceptionally preserved fossil arthropods

NASA Astrophysics Data System (ADS)

Braiden, A. K.; Orr, P. J.; Tafforeau, P.; Kearns, S. L.

2009-04-01

The fossil record is biased towards biomineralised elements (for example bones, shells and teeth) that usually retain their original three-dimensional shape. Non-biomineralised arthropods, often comprising only exoskeletal tissues such as cuticle, are comparatively rare and are usually preserved in two-dimensions (including examples inside early diagenetic concretions). Rarer still are exceptionally preserved fossils that contain replicated soft tissues; although tissues that are replicated during the initial stages of decay are usually three- dimensional and often preserved in detail, the fossil as a whole is almost invariably two dimensional. Fossil shrimp recovered from Upper Triassic (Rhaetian) unconsolidated clays at Frome, Somerset, England represent a low diversity, three-dimensionally preserved fauna, in which certain labile tissues and organs are routinely preserved in three dimensions in life position. Initial SEM analysis of exposed, internal structures in unprepared specimens confirmed the presence of musculature (replicated in calcium phosphate) and a clay infilled gut. Due to the rarity of the material, and small size of the specimens (maximum length 12mm), non-destructive synchrotron radiation, x-ray microtomography was used to determine the extent, and fidelity, of preservation of the internal anatomy. Medium resolution (voxel size of 5.3μm) and high resolution (voxel size 0.7μm) imaging was carried out on selected specimens. This confirmed high fidelity replication of the following: limited volumes of abdominal, and more rarely, cephalothoracic musculature; the hepatopancreas; gonads and, in rare cases, blood vessels and antennal glands. Notably, these are all preserved in situ enveloped by structureless, fine-grained, authigenic carbonate. This carbonate precipitated inside the cuticle, but only at the periphery of the carcass and after, or during, the initial stages of decay; it infills voids created by the initial shrinkage of abdominal musculature (possibly due to dehydration) but not those created by its subsequent decay. The digestive tract is infilled with ingested clay material. X-ray microtomographic imaging also revealed the presence of pyrite as framboids and polyhedra. The spatial distribution of framboidal pyrite, and tissue replicating calcium phosphate, indicates their precipitation is likely to be related to the original composition of the biological tissues. For example, although the pyrite framboids do not replicate tissues, they are found in association with the hepatopancreas. It is probably not coincidental that iron is especially abundant in this area in vivo. Notably, subtle differences in greyscale tone in the x-ray images are shown to correspond to authigenic phases of different composition. When calibrated against phases for which accurate compositions can be determined using other criteria (e.g. SEM-EDX), it is possible to identify the presence of particular authigenic mineral phases in such fossils.

Sensor fusion V; Proceedings of the Meeting, Boston, MA, Nov. 15-17, 1992

NASA Technical Reports Server (NTRS)

Schenker, Paul S. (Editor)

1992-01-01

Topics addressed include 3D object perception, human-machine interface in multisensor systems, sensor fusion architecture, fusion of multiple and distributed sensors, interface and decision models for sensor fusion, computational networks, simple sensing for complex action, multisensor-based control, and metrology and calibration of multisensor systems. Particular attention is given to controlling 3D objects by sketching 2D views, the graphical simulation and animation environment for flexible structure robots, designing robotic systems from sensorimotor modules, cylindrical object reconstruction from a sequence of images, an accurate estimation of surface properties by integrating information using Bayesian networks, an adaptive fusion model for a distributed detection system, multiple concurrent object descriptions in support of autonomous navigation, robot control with multiple sensors and heuristic knowledge, and optical array detectors for image sensors calibration. (No individual items are abstracted in this volume)

A multimethod Global Sensitivity Analysis to aid the calibration of geomechanical models via time-lapse seismic data

NASA Astrophysics Data System (ADS)

Price, D. C.; Angus, D. A.; Garcia, A.; Fisher, Q. J.; Parsons, S.; Kato, J.

2018-03-01

Time-lapse seismic attributes are used extensively in the history matching of production simulator models. However, although proven to contain information regarding production induced stress change, it is typically only loosely (i.e. qualitatively) used to calibrate geomechanical models. In this study we conduct a multimethod Global Sensitivity Analysis (GSA) to assess the feasibility and aid the quantitative calibration of geomechanical models via near-offset time-lapse seismic data. Specifically, the calibration of mechanical properties of the overburden. Via the GSA, we analyse the near-offset overburden seismic traveltimes from over 4000 perturbations of a Finite Element (FE) geomechanical model of a typical High Pressure High Temperature (HPHT) reservoir in the North Sea. We find that, out of an initially large set of material properties, the near-offset overburden traveltimes are primarily affected by Young's modulus and the effective stress (i.e. Biot) coefficient. The unexpected significance of the Biot coefficient highlights the importance of modelling fluid flow and pore pressure outside of the reservoir. The FE model is complex and highly nonlinear. Multiple combinations of model parameters can yield equally possible model realizations. Consequently, numerical calibration via a large number of random model perturbations is unfeasible. However, the significant differences in traveltime results suggest that more sophisticated calibration methods could potentially be feasible for finding numerous suitable solutions. The results of the time-varying GSA demonstrate how acquiring multiple vintages of time-lapse seismic data can be advantageous. However, they also suggest that significant overburden near-offset seismic time-shifts, useful for model calibration, may take up to 3 yrs after the start of production to manifest. Due to the nonlinearity of the model behaviour, similar uncertainty in the reservoir mechanical properties appears to influence overburden traveltime to a much greater extent. Therefore, reservoir properties must be known to a suitable degree of accuracy before the calibration of the overburden can be considered.

Use of the moon to support on-orbit sensor calibration for climate change measurements

USGS Publications Warehouse

Stone, T.C.; Kieffer, H.H.

2006-01-01

Production of reliable climate datasets from multiple observational measurements acquired by remote sensing satellite systems available now and in the future places stringent requirements on the stability of sensors and consistency among the instruments and platforms. Detecting trends in environmental parameters measured at solar reflectance wavelengths (0.3 to 2.5 microns) requires on-orbit instrument stability at a level of 1% over a decade. This benchmark can be attained using the Moon as a radiometric reference. The lunar calibration program at the U.S. Geological Survey has an operational model to predict the lunar spectral irradiance with precision ???1%, explicitly accounting for the effects of phase, lunar librations, and the lunar surface photometric function. A system for utilization of the Moon by on-orbit instruments has been established. With multiple lunar views taken by a spacecraft instrument, sensor response characterization with sub-percent precision over several years has been achieved. Meteorological satellites in geostationary orbit (GEO) capture the Moon in operational images; applying lunar calibration to GEO visible-channel image archives has the potential to develop a climate record extending decades into the past. The USGS model and system can provide reliable transfer of calibration among instruments that have viewed the Moon as a common source. This capability will be enhanced with improvements to the USGS model absolute scale. Lunar calibration may prove essential to the critical calibration needs to cover a potential gap in observational capabilities prior to deployment of NPP/NPOESS. A key requirement is that current and future instruments observe the Moon.

Refugial isolation and divergence in the Narrowheaded Gartersnake species complex (Thamnophis rufipunctatus) as revealed by multilocus DNA sequence data

USGS Publications Warehouse

Wood, Dustin A.; Vandergast, A.G.; Espinal, A. Lemos; Fisher, R.N.; Holycross, A.T.

2011-01-01

Glacial–interglacial cycles of the Pleistocene are hypothesized as one of the foremost contributors to biological diversification. This is especially true for cold-adapted montane species, where range shifts have had a pronounced effect on population-level divergence. Gartersnakes of the Thamnophis rufipunctatus species complex are restricted to cold headwater streams in the highlands of the Sierra Madre Occidental and southwestern USA. We used coalescent and multilocus phylogenetic approaches to test whether genetic diversification of this montane-restricted species complex is consistent with two prevailing models of range fluctuation for species affected by Pleistocene climate changes. Our concatenated nuDNA and multilocus species analyses recovered evidence for the persistence of multiple lineages that are restricted geographically, despite a mtDNA signature consistent with either more recent connectivity (and introgression) or recent expansion (and incomplete lineage sorting). Divergence times estimated using a relaxed molecular clock and fossil calibrations fall within the Late Pleistocene, and zero gene flow scenarios among current geographically isolated lineages could not be rejected. These results suggest that increased climate shifts in the Late Pleistocene have driven diversification and current range retraction patterns and that the differences between markers reflect the stochasticity of gene lineages (i.e. ancestral polymorphism) rather than gene flow and introgression. These results have important implications for the conservation of T. rufipunctatus (sensu novo), which is restricted to two drainage systems in the southwestern US and has undergone a recent and dramatic decline.

Phylogenetics, biogeography, and staminal evolution in the tribe Mentheae (Lamiaceae).

PubMed

Drew, Bryan T; Sytsma, Kenneth J

2012-05-01

The mint family (Lamiaceae) is the sixth largest family of flowering plants, with the tribe Mentheae containing about a third of the species. We present a detailed perspective on the evolution of the tribe Mentheae based on a phylogenetic analysis of cpDNA and nrDNA that is the most comprehensive to date, a biogeographic set of analyses using a fossil-calibrated chronogram, and an examination of staminal evolution. Data from four cpDNA and two nrDNA markers representing all extant genera within the tribe Mentheae were analyzed using the programs BEAST, Lagrange, S-DIVA, and BayesTraits. BEAST was used to simultaneously estimate phylogeny and divergence times, Lagrange and S-DIVA were used for biogeographical reconstruction, and BayesTraits was used to infer staminal evolution within the tribe. Currently accepted subtribal delimitations are shown to be invalid and are updated. The Mentheae and all five of its subtribes have a Mediterranean origin and have dispersed to the New World multiple times. The vast majority of New World species of subtribe Menthinae are the product of a single dispersal event in the mid-late Miocene. At least four transitions from four stamens to two stamens have occurred within Mentheae, once in the subtribe Salviinae, once in the subtribe Lycopinae, and at least twice in the subtribe Menthinae. Worldwide cooling trends probably played a large role in the diversification and present day distribution of the tribe Mentheae. Additional work is needed to ascertain relationships within some Mentheae genera, especially in the subtribe Menthinae.

Orchid phylogenomics and multiple drivers of their extraordinary diversification

PubMed Central

Givnish, Thomas J.; Spalink, Daniel; Ames, Mercedes; Lyon, Stephanie P.; Hunter, Steven J.; Zuluaga, Alejandro; Iles, William J. D.; Clements, Mark A.; Arroyo, Mary T. K.; Leebens-Mack, James; Endara, Lorena; Kriebel, Ricardo; Neubig, Kurt M.; Whitten, W. Mark; Williams, Norris H.; Cameron, Kenneth M.

2015-01-01

Orchids are the most diverse family of angiosperms, with over 25 000 species, more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here, we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. A supermatrix analysis places an additional 144 species based on three plastid genes. Orchids appear to have arisen roughly 112 million years ago (Mya); the subfamilies Orchidoideae and Epidendroideae diverged from each other at the end of the Cretaceous; and the eight tribes and three previously unplaced subtribes of the upper epidendroids diverged rapidly from each other between 37.9 and 30.8 Mya. Orchids appear to have undergone one significant acceleration of net species diversification in the orchidoids, and two accelerations and one deceleration in the upper epidendroids. Consistent with theory, such accelerations were correlated with the evolution of pollinia, the epiphytic habit, CAM photosynthesis, tropical distribution (especially in extensive cordilleras), and pollination via Lepidoptera or euglossine bees. Deceit pollination appears to have elevated the number of orchid species by one-half but not via acceleration of the rate of net diversification. The highest rate of net species diversification within the orchids (0.382 sp sp−1 My−1) is 6.8 times that at the Asparagales crown. PMID:26311671

When did decapods invade hydrothermal vents? Clues from the Western Pacific and Indian Oceans.

PubMed

Yang, Jin-Shu; Lu, Bo; Chen, Dian-Fu; Yu, Yan-Qin; Yang, Fan; Nagasawa, Hiromichi; Tsuchida, Shinji; Fujiwara, Yoshihiro; Yang, Wei-Jun

2013-02-01

Hydrothermal vents are typically located in midocean ridges and back-arc basins and are usually generated by the movement of tectonic plates. Life thrives in these environments despite the extreme conditions. In addition to chemoautotrophic bacteria, decapod crustaceans are dominant in many of the hydrothermal vents discovered to date. Contrary to the hypothesis that these species are remnants of relic fauna, increasing evidence supports the notion that hydrothermal vent decapods have diversified in more recent times with previous research attributing the origin of alvinocarid shrimps to the Miocene. This study investigated seven representative decapod species from four hydrothermal vents throughout the Western Pacific and Indian Oceans. A partitioned mix-model phylogenomic analysis of mitochondrial DNA produced a consistent phylogenetic topology of these vent-endemic species. Additionally, molecular dating analysis calibrated using multiple fossils suggested that both bythograeid crabs and alvinocarid shrimps originated in the late Mesozoic and early Cenozoic. Although of limited sampling, our estimates support the extinction/repopulation hypothesis, which postulates recent diversification times for most hydrothermal vent species due to their mass extinction by global deep-water anoxic/dysoxic events during the Late Cretaceous and Early Tertiary. The continental-derived property of the West Pacific province is compatible with the possibility that vent decapods diversified from ancestors from shallow-water regions such as cold seeps. Our results move us a step closer toward understanding the evolutionary origin of hydrothermal vent species and their distribution in the Western Pacific-Indian Ocean Region.

Novel quantitative calibration approach for multi-configuration electromagnetic induction (EMI) systems using data acquired at multiple elevations

NASA Astrophysics Data System (ADS)

Tan, Xihe; Mester, Achim; von Hebel, Christian; van der Kruk, Jan; Zimmermann, Egon; Vereecken, Harry; van Waasen, Stefan

2017-04-01

Electromagnetic induction (EMI) systems offer a great potential to obtain highly resolved layered electrical conductivity models of the shallow subsurface. State-of-the-art inversion procedures require quantitative calibration of EMI data, especially for short-offset EMI systems where significant data shifts are often observed. These shifts are caused by external influences such as the presence of the operator, zero-leveling procedures, the field setup used to move the EMI system and/or cables close by. Calibrations can be performed by using collocated electrical resistivity measurements or taking soil samples, however, these two methods take a lot of time in the field. To improve the calibration in a fast and concise way, we introduce a novel on-site calibration method using a series of apparent electrical conductivity (ECa) values acquired at multiple elevations for a multi-configuration EMI system. No additional instrument or pre-knowledge of the subsurface is needed to acquire quantitative ECa data. By using this calibration method, we correct each coil configuration, i.e., transmitter and receiver coil separation and the horizontal or vertical coplanar (HCP or VCP) coil orientation with a unique set of calibration parameters. A multi-layer soil structure at the corresponding measurement location is inverted together with the calibration parameters using full-solution Maxwell equations for the forward modelling within the shuffled complex evolution (SCE) algorithm to find the optimum solution under a user-defined parameter space. Synthetic data verified the feasibility for calibrating HCP and VCP measurements of a custom made six-coil EMI system with coil offsets between 0.35 m and 1.8 m for quantitative data inversions. As a next step, we applied the calibration approach on acquired experimental data from a bare soil test field (Selhausen, Germany) for the considered EMI system. The obtained calibration parameters were applied to measurements over a 30 m transect line that covers a range of conductivities between 5 and 40 mS/m. Inverted calibrated EMI data of the transect line showed very similar electrical conductivity distributions and layer interfaces of the subsurface compared to reference data obtained from vertical electrical sounding (VES) measurements. These results show that a combined calibration and inversion of multi-configuration EMI data is possible when including measurements at different elevations, which will speed up the measurement process to obtain quantitative EMI data since the labor intensive electrical resistivity measurement or soil coring is not necessary anymore.

Stable carbon isotopes to monitor the CO2 source mix in the urban environment

NASA Astrophysics Data System (ADS)

Vogel, F. R.; Wu, L.; Ramonet, M.; Broquet, G.; Worthy, D. E. J.

2014-12-01

Urban areas are said to be responsible for approximately 71% of fossil fuel CO2 emissions while comprising only two percent of the land area [IEA, 2008]. This limited spatial expansion could facility a monitoring of anthropogenic GHGs from atmospheric observations. As major sources of emissions, cities also have a huge potential to drive emissions reductions. To effectively manage emissions, cities must however, first establish techniques to validate their reported emission statistics. A pilot study which includes continues 13CO2 data from calibrated cavity ring-down spectrometers [Vogel et al. 2013] of two "sister sites" in the vicinity of Toronto, Canada is contrasted to recent observations of 13CO2 observations in Paris during significant pollution events. Using Miller-Tans plots [Miller and Tans, 2003] for our multi-season observations reveals significant changes of the source signatures of night time CO2 emissions which reflect the importance of natural gas burning in Megacities (up to 80% of fossil fuel sources) and show-case the potential of future isotope studies to determine source sectors. Especially the winter data this approach seems suitable to determine the source contribution of different fuel types (natural gas, liquid fuels and coal) which can inform the interpretation of other Greenhouse Gases and air pollution levels.

Associated terrestrial and marine fossils in the late-glacial Presumpscot Formation, southern Maine, USA, and the marine reservoir effect on radiocarbon ages

USGS Publications Warehouse

Thompson, W.B.; Griggs, C.B.; Miller, N.G.; Nelson, R.E.; Weddle, T.K.; Kilian, T.M.

2011-01-01

Excavations in the late-glacial Presumpscot Formation at Portland, Maine, uncovered tree remains and other terrestrial organics associated with marine invertebrate shells in a landslide deposit. Buds of Populus balsamifera (balsam poplar) occurred with twigs of Picea glauca (white spruce) in the Presumpscot clay. Tree rings in Picea logs indicate that the trees all died during winter dormancy in the same year. Ring widths show patterns of variation indicating responses to environmental changes. Fossil mosses and insects represent a variety of species and wet to dry microsites. The late-glacial environment at the site was similar to that of today's Maine coast. Radiocarbon ages of 14 tree samples are 11,907??31 to 11,650??5014C yr BP. Wiggle matching of dated tree-ring segments to radiocarbon calibration data sets dates the landslide occurrence at ca. 13,520+95/??20calyr BP. Ages of shells juxtaposed with the logs are 12,850??6514C yr BP (Mytilus edulis) and 12,800??5514C yr BP (Balanus sp.), indicating a marine reservoir age of about 1000yr. Using this value to correct previously published radiocarbon ages reduces the discrepancy between the Maine deglaciation chronology and the varve-based chronology elsewhere in New England. ?? 2011 University of Washington.

Contribution of collagen stable isotope biogeochemistry to the paleobiology of extinct endemic vertebrates from Tenerife (Canary Islands, Spain).

PubMed

Bocherens, H; Michaux, J; Billiou, D; Castanet, J; Garcìa-Talavera, F

2003-09-01

The paleodiet and paleoenvironmental context of two extinct species from Tenerife island, one giant rat Canariomys bravoi and one giant lizard Gallotia goliath, have been investigated using carbon and nitrogen isotopic compositions of fossil bone collagen. Preliminary to this study, a calibration of the isotopic variations of bone collagen from modern Rat Rattus rattus, Rabbit Oryctolagus cuniculus and Lizard Gallotia galotti relative to environmental conditions on Tenerife Islands has been attempted. No clear relationship could be found between collagen delta13C and delta15N values and aridity; the only relevant factors seem to be seashore proximity for rat, and the relative amount of C3 and CAM plants. It seems that anthropic activities have interfered with the expected relationships between collagen isotopic compositions and environmental conditions. Most fossil specimens yielded well preserved collagen. The isotopic composition of giant rat and giant lizard collagen suggest a purely C3 environment, possibly more humid than today on Tenerife. Large ranges of nitrogen isotopic compositions, especially within giant rats, may be due to local environmental conditions. Further work is needed in order to provide more valuable paleobiological information in order to better understand the role of environmental factors in the evolution and extinction of insular endemic species on Tenerife.

Low atmospheric CO(2) levels during the Permo- Carboniferous glaciation inferred from fossil lycopsids.

PubMed

Beerling, D J

2002-10-01

Earth history was punctuated during the Permo-Carboniferous [300-250 million years (Myr) ago] by the longest and most severe glaciation of the entire Phanerozoic Eon. But significant uncertainty surrounds the concentration of CO(2) in the atmosphere through this time interval and therefore its role in the evolution of this major prePleistocene glaciation. Here, I derive 24 Late Paleozoic CO(2) estimates from the fossil cuticle record of arborsecent lycopsids of the equatorial Carboniferous and Permian swamp communities. Quantitative calibration of Late Carboniferous (330-300 Myr ago) and Permian (270-260 Myr ago) lycopsid stomatal indices yield average atmospheric CO(2) concentrations of 344 ppm and 313 ppm, respectively. The reconstructions show a high degree of self-consistency and a degree of precision an order of magnitude greater than other approaches. Low CO(2) levels during the Permo-Carboniferous glaciation are in agreement with glaciological evidence for the presence of continental ice and coupled models of climate and ice-sheet growth on Pangea. Moreover, the Permian data indicate atmospheric CO(2) levels were low 260 Myr ago, by which time continental deglaciation was already underway. Positive biotic feedbacks on climate, and geotectonic events, therefore are implicated as mechanisms underlying deglaciation.

Low atmospheric CO2 levels during the Permo- Carboniferous glaciation inferred from fossil lycopsids

PubMed Central

Beerling, D. J.

2002-01-01

Earth history was punctuated during the Permo-Carboniferous [300–250 million years (Myr) ago] by the longest and most severe glaciation of the entire Phanerozoic Eon. But significant uncertainty surrounds the concentration of CO2 in the atmosphere through this time interval and therefore its role in the evolution of this major prePleistocene glaciation. Here, I derive 24 Late Paleozoic CO2 estimates from the fossil cuticle record of arborsecent lycopsids of the equatorial Carboniferous and Permian swamp communities. Quantitative calibration of Late Carboniferous (330–300 Myr ago) and Permian (270–260 Myr ago) lycopsid stomatal indices yield average atmospheric CO2 concentrations of 344 ppm and 313 ppm, respectively. The reconstructions show a high degree of self-consistency and a degree of precision an order of magnitude greater than other approaches. Low CO2 levels during the Permo-Carboniferous glaciation are in agreement with glaciological evidence for the presence of continental ice and coupled models of climate and ice-sheet growth on Pangea. Moreover, the Permian data indicate atmospheric CO2 levels were low 260 Myr ago, by which time continental deglaciation was already underway. Positive biotic feedbacks on climate, and geotectonic events, therefore are implicated as mechanisms underlying deglaciation. PMID:12235372

Assessing The Effects of Within-lake Variability of Fossil Assemblages On Quantitative Chironomid-inferred Temperature Reconstruction

NASA Astrophysics Data System (ADS)

Heiri, O.; Birks, H. J. B.; Brooks, S. J.; Velle, G.; Willassen, E.

An important aspect when applying organism-based palaeolimnological methods to sediment cores is the inherent variability of fossil assemblages within a lake basin. Subfossil chironomids in lake sediments have been used extensively to quantify past summer air and water temperatures. However, little is known on how heterogeneous fossil distribution affects these estimates. In an effort to assess this variability we took a total of 20 surface sediment samples each in three small and shallow (7-9 m wa- ter depth) Norwegian lakes. In every lake two transects of seven samples were taken from the centre of the lake towards the littoral and six samples in the deepest part of the lake basin. Although the fossil assemblages were generally very similar within a lake basin, there was - in all three lakes - a distinct shift in the abundances of chi- ronomid taxa towards the littoral (water depth explaining 10-18% of the total variance in the percentage data as assessed by a Detrended Canonical Correspondence Anal- ysis). When we applied to our data a quantitative chironomid-July air temperature transfer-function based on surface sediments from the deepest parts of 153 Norwegian lakes, the variability of reconstructed temperatures in our three study lakes was only slightly smaller in the 6 deep-water samples (standard deviations (SD) of 0.48, 0.52 and 0.58C) than in all the 20 samples (SD of 0.55, 0.56 and 0.59 C). Our results suggest that within-lake variability of subfossil chironomid assemblages can account for a significant part of the overall prediction error of the chironomid-July air tempera- ture model of 1.03C. Furthermore, the lack of a clear trend in inferred values towards the littoral and the similar standard deviation of the total samples as compared to the deep-water samples suggest that the Norwegian transfer-function, though calibrated on samples from the deepest part of the lake, may also be applicable to sediment cores from closer to the lake shore. It remains to be tested, however, if this holds true in deeper lakes than the ones sampled in our study.

The Snowmastodon Project

USGS Publications Warehouse

Johnson, Kirk R.; Miller, Ian M.; Pigati, Jeffery S.

2014-01-01

Studies of terrestrial biotic and environmental dynamics of the last interglacial period, Marine Oxygen Isotope Stage (MIS) 5, provide insight into the effects of long-term climate change on Pleistocene ecosystems. In North America, however, there are relatively few fossil sites that definitively date to MIS 5. Even fewer contain multiple ecosystem components (vertebrates, invertebrates, plants) that have been studied in detail, and none are located at high elevation. Thus, our view of North American ecosystems during MIS 5 is, at best, an incomplete composite view, and alpine ecosystems are entirely undocumented. The Ziegler Reservoir fossil site allows us to begin filling these gaps. Discovered on October 14, 2010 by a construction crew while enlarging a small reservoir near Snowmass Village, Colorado (USA), the site is situated high in the Rocky Mountains at an elevation of ~ 2705 m. Initial excavations exposed a series of stacked fossil ecosystems, including abundant faunal and floral components. Subsequent work revealed an exceptionally diverse biota composed of nearly 6000 large bones of late Pleistocene megafauna, including mastodons, mammoths, ground sloths, horses, camels, deer, bison, black bear, coyotes, and big horn sheep. This collection is complemented by more than 200 bones from at least 40 species of small animals including otters, muskrats, minks, rabbits, beavers, frogs, lizards, snakes, fish, and birds, and more than 20,000 salamander bones. Geomorphic evidence and multiple dating techniques show that the small, ridge-top basin containing the site was formed by a lateral lobe of a valley glacier that filled, and ultimately overtopped, the Snowmass Creek drainage during the Bull Lake glaciation (MIS 6). When the glacier receded, a lake that occupied the basin began to fill slowly with what is hypothesized to be eolian sediment and occasional input from slope failures of the impounding moraine. As sedimentation continued, the lake transformed first into a shallow pond, then a marsh, and later an alpine meadow. In all, the Ziegler Reservoir sedimentary record spans the time encompassed by the end of MIS 6, all of MIS 5 and MIS 4, and the earliest part of MIS 3. MIS 5e, which is considered to be the peak warmth of the last interglacial period, is especially well represented. Preservation of organic material at the Ziegler Reservoir fossil site is exceptional. Even after more than 100,000 years of burial, sedge and willow leaves were still green, mollusks and gastropods showed color, beetle parts remained iridescent, fossil conifer cones were intact, and an entire beach of 20-meter-long driftwood logs was found intact. The exquisite preservation allowed for detailed analysis of pollen, plant macrofossils, conifer cones, and fossil wood, as well as insects, chironomids, mollusks, ostracodes, and other invertebrates — all in addition to the spectacular faunal remains. This special volume of Quaternary Research represents a comprehensive scientific report of “The Snowmastodon Project,” as the investigations at the Ziegler Reservoir fossil site came to be known. Summarizing the work of scientists from more than 20 institutions, the volume details the environments in which the animals lived, provides insight into how they died, and forms the foundation of our understanding of alpine ecosystem dynamics during the last interglacial period in the Rocky Mountains.

Estimation of primate speciation dates using local molecular clocks.

PubMed

Yoder, A D; Yang, Z

2000-07-01

Protein-coding genes of the mitochondrial genomes from 31 mammalian species were analyzed to estimate the speciation dates within primates and also between rats and mice. Three calibration points were used based on paleontological data: one at 20-25 MYA for the hominoid/cercopithecoid divergence, one at 53-57 MYA for the cetacean/artiodactyl divergence, and the third at 110-130 MYA for the metatherian/eutherian divergence. Both the nucleotide and the amino acid sequences were analyzed, producing conflicting results. The global molecular clock was clearly violated for both the nucleotide and the amino acid data. Models of local clocks were implemented using maximum likelihood, allowing different evolutionary rates for some lineages while assuming rate constancy in others. Surprisingly, the highly divergent third codon positions appeared to contain phylogenetic information and produced more sensible estimates of primate divergence dates than did the amino acid sequences. Estimated dates varied considerably depending on the data type, the calibration point, and the substitution model but differed little among the four tree topologies used. We conclude that the calibration derived from the primate fossil record is too recent to be reliable; we also point out a number of problems in date estimation when the molecular clock does not hold. Despite these obstacles, we derived estimates of primate divergence dates that were well supported by the data and were generally consistent with the paleontological record. Estimation of the mouse-rat divergence date, however, was problematic.

The Paleontology Portal: An online resource meeting the needs a spectrum of learners

NASA Astrophysics Data System (ADS)

Lindberg, D.; Scotchmoor, J. G.

2005-12-01

The Paleontology Portal website provides a central, interactive entry point to high-quality North American paleontology resources on the Internet for multiple audiences: the research community, government and industry, K-16 students, and the general public. The Portal successfully blends research and education, pulling together information with reviewed and annotated website links for a wide variety of informal learners. Using web-based technology and relational databases, users can explore an interactive map and associated stratigraphic column to access information about particular geographic regions, geologic time periods, depositional environments, and representative taxa. Users are also able to search multiple museum collection databases using a single query form of their own design. Other features include highlights of famous fossil sites and assemblages and a fossil image gallery. Throughout the site, users find images and links to information specific to each time period or geographic region, including current research projects and publications, websites, on-line exhibits and educational materials, and information on collecting fossils. The next phase of development will target the development of resource modules on topics such as collection management and fossil preparation, appropriate for users ranging from the general public to professional paleontologists. Another initiative includes developing methods of personalizing the Portal to support exhibits at museums and other venues on geological history and paleontology. The Paleontology Portal, built by the UC Museum of Paleontology, is a joint project of the Society of Vertebrate Paleontology, the Paleontological Society, and the US Geological Survey, in collaboration with the Paleontological Research Institution, the Fort Worth Museum of Science and History, and the Denver Museum of Nature and Science, which serve as hubs for the project. Paleoportal serves as an effective model in two aspects: (1) providing access to a spectrum of reviewed resources from a single starting interface that enables users from novice to professional to access background-appropriate information, and (2) involvement of a wide range of stakeholders (professional societies, universities and museums, and individuals) in both concept development and management. The project is funded by the National Science Foundation under award no. 0234594

Camera calibration for multidirectional flame chemiluminescence tomography

NASA Astrophysics Data System (ADS)

Wang, Jia; Zhang, Weiguang; Zhang, Yuhong; Yu, Xun

2017-04-01

Flame chemiluminescence tomography (FCT), which combines computerized tomography theory and multidirectional chemiluminescence emission measurements, can realize instantaneous three-dimensional (3-D) diagnostics for flames with high spatial and temporal resolutions. One critical step of FCT is to record the projections by multiple cameras from different view angles. For high accuracy reconstructions, it requires that extrinsic parameters (the positions and orientations) and intrinsic parameters (especially the image distances) of cameras be accurately calibrated first. Taking the focus effect of the camera into account, a modified camera calibration method was presented for FCT, and a 3-D calibration pattern was designed to solve the parameters. The precision of the method was evaluated by reprojections of feature points to cameras with the calibration results. The maximum root mean square error of the feature points' position is 1.42 pixels and 0.0064 mm for the image distance. An FCT system with 12 cameras was calibrated by the proposed method and the 3-D CH* intensity of a propane flame was measured. The results showed that the FCT system provides reasonable reconstruction accuracy using the camera's calibration results.

Precision Spectrophotometric Calibration System for Dark Energy Instruments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schubnell, Michael S.

2015-06-30

For this research we build a precision calibration system and carried out measurements to demonstrate the precision that can be achieved with a high precision spectrometric calibration system. It was shown that the system is capable of providing a complete spectrophotometric calibration at the sub-pixel level. The calibration system uses a fast, high precision monochromator that can quickly and efficiently scan over an instrument’s entire spectral range with a spectral line width of less than 0.01 nm corresponding to a fraction of a pixel on the CCD. The system was extensively evaluated in the laboratory. Our research showed that amore » complete spectrophotometric calibration standard for spectroscopic survey instruments such as DESI is possible. The monochromator precision and repeatability to a small fraction of the DESI spectrograph LSF was demonstrated with re-initialization on every scan and thermal drift compensation by locking to multiple external line sources. A projector system that mimics telescope aperture for point source at infinity was demonstrated.« less

Heterogeneity in preferences for woody biomass energy in the US Mountain West

Treesearch

Robert M. Campbell; Tyron J. Venn; Nathaniel M. Anderson

2018-01-01

The United States has passed legislation aimed at reducing greenhouse gas emissions (United States Congress, 2005; United States Congress, 2007; EPA, 2015). In order to achieve the goals set by these commitments, significant amounts of fossil fuel energy will need to be replaced with renewable energy. There are multiple renewable technologies from which to choose, and...

The Effect of Amplifier Bias Drift on Differential Magnitude Estimation in Multiple-Star Systems

NASA Astrophysics Data System (ADS)

Tyler, David W.; Muralimanohar, Hariharan; Borelli, Kathy J.

2007-02-01

We show how the temporal drift of CCD amplifier bias can cause significant relative magnitude estimation error in speckle interferometric observations of multiple-star systems. When amplifier bias varies over time, the estimation error arises if the time between acquisition of dark-frame calibration data and science data is long relative to the timescale over which the bias changes. Using analysis, we show that while detector-temperature drift over time causes a variation in accumulated dark current and a residual bias in calibrated imagery, only amplifier bias variations cause a residual bias in the estimated energy spectrum. We then use telescope data taken specifically to investigate this phenomenon to show that for the detector used, temporal bias drift can cause residual energy spectrum bias as large or larger than the mean value of the noise energy spectrum. Finally, we use a computer simulation to demonstrate the effect of residual bias on differential magnitude estimation. A supplemental calibration technique is described in the appendices.

Calibration of a DSSSD detector with radioactive sources

NASA Astrophysics Data System (ADS)

Guadilla, V.; Taín, J. L.; Agramunt, J.; Algora, A.; Domingo-Pardo, C.; Rubio, B.

2013-06-01

The energy calibration of a DSSSD is carried out with the spectra produced by a 207Bi conversion electron source, a 137Cs gamma source and a 239Pu/241Am/244Cm triple alpha source, as well as employing a precision pulse generator in the whole dynamic range. Multiplicity and coincidence of signals in different strips for the same event are also studied.

Incorporating plant fossil data into species distribution models is not straightforward: Pitfalls and possible solutions

NASA Astrophysics Data System (ADS)

Moreno-Amat, Elena; Rubiales, Juan Manuel; Morales-Molino, César; García-Amorena, Ignacio

2017-08-01

The increasing development of species distribution models (SDMs) using palaeodata has created new prospects to address questions of evolution, ecology and biogeography from wider perspectives. Palaeobotanical data provide information on the past distribution of taxa at a given time and place and its incorporation on modelling has contributed to advancing the SDM field. This has allowed, for example, to calibrate models under past climate conditions or to validate projected models calibrated on current species distributions. However, these data also bear certain shortcomings when used in SDMs that may hinder the resulting ecological outcomes and eventually lead to misleading conclusions. Palaeodata may not be equivalent to present data, but instead frequently exhibit limitations and biases regarding species representation, taxonomy and chronological control, and their inclusion in SDMs should be carefully assessed. The limitations of palaeobotanical data applied to SDM studies are infrequently discussed and often neglected in the modelling literature; thus, we argue for the more careful selection and control of these data. We encourage authors to use palaeobotanical data in their SDMs studies and for doing so, we propose some recommendations to improve the robustness, reliability and significance of palaeo-SDM analyses.

Calibrating the Cryogenian

NASA Astrophysics Data System (ADS)

MacDonald, F. A.; Schmitz, M. D.; Crowley, J. L.; Haam, E.; Huybers, P.; Cohen, P. A.; Johnston, D. T.

2009-12-01

The IGCP 512 sub-commission on the Neoproterozoic is currently discussing criteria for the definition of the Cryogenian period. Herein we provide new U/Pb ID-TIMS ages and carbon and oxygen isotope data from Fifteenmile and Mt. Harper Groups in the Yukon Territory that inform the basis for the placement of the basal Cryogenian “golden spike”. Our U/Pb ages are from volcanic tuffs interbedded within glaciogenic, fossiliferous, and carbonate strata. With the current lack of Neoproterozoic index fossils and the paucity of radiogenic age constraints, chemo-stratigraphic correlations are particularly important for tuning the Neoproterozoic timescale. In an effort to move beyond conventional 'wiggle matching', chemostratigraphic correlations are determined using a new statistical method1, which indicates that the resulting chemo-stratigraphic correlations are statistically significant. These results permit us to refine and integrate Neoproterozoic climate, microfossil, and geochemical proxy records both regionally and globally. The newly calibrated microfossil record points to a eukaryotic radiation roughly coincident with the Bitter Springs isotopic stage and a barren interval between the Sturtian and Marinoan glaciations. 1 Haam, E. & Huybers, P., 2009, A test for the presence of covariance between time-uncertain series of data with applications to the Dongge Cave speleothem and atmospheric radiocarbon records, Paleoceanography, in press.

On the Origin and Trigger of the Notothenioid Adaptive Radiation

PubMed Central

Matschiner, Michael; Hanel, Reinhold; Salzburger, Walter

2011-01-01

Adaptive radiation is usually triggered by ecological opportunity, arising through (i) the colonization of a new habitat by its progenitor; (ii) the extinction of competitors; or (iii) the emergence of an evolutionary key innovation in the ancestral lineage. Support for the key innovation hypothesis is scarce, however, even in textbook examples of adaptive radiation. Antifreeze glycoproteins (AFGPs) have been proposed as putative key innovation for the adaptive radiation of notothenioid fishes in the ice-cold waters of Antarctica. A crucial prerequisite for this assumption is the concurrence of the notothenioid radiation with the onset of Antarctic sea ice conditions. Here, we use a fossil-calibrated multi-marker phylogeny of nothothenioid and related acanthomorph fishes to date AFGP emergence and the notothenioid radiation. All time-constraints are cross-validated to assess their reliability resulting in six powerful calibration points. We find that the notothenioid radiation began near the Oligocene-Miocene transition, which coincides with the increasing presence of Antarctic sea ice. Divergence dates of notothenioids are thus consistent with the key innovation hypothesis of AFGP. Early notothenioid divergences are furthermore congruent with vicariant speciation and the breakup of Gondwana. PMID:21533117

Acropora interbranch skeleton Sr/Ca ratios: Evaluation of a potential new high-resolution paleothermometer

NASA Astrophysics Data System (ADS)

Sadler, James; Nguyen, Ai D.; Leonard, Nicole D.; Webb, Gregory E.; Nothdurft, Luke D.

2016-04-01

The majority of coral geochemistry-based paleoclimate reconstructions in the Indo-Pacific are conducted on selectively cored colonies of massive Porites. This restriction to a single genus may make it difficult to amass the required paleoclimate data for studies that require deep reef coring techniques. Acropora, however, is a highly abundant coral genus in both modern and fossil reef systems and displays potential as a novel climate archive. Here we present a calibration study for Sr/Ca ratios recovered from interbranch skeleton in corymbose Acropora colonies from Heron Reef, southern Great Barrier Reef. Significant intercolony differences in absolute Sr/Ca ratios were normalized by producing anomaly plots of both coral geochemistry and instrumental water temperature records. Weighted linear regression of these anomalies from the lagoon and fore-reef slope provide a sensitivity of -0.05 mmol/mol °C-1, with a correlation coefficient (r2 = 0.65) comparable to those of genera currently used in paleoclimate reconstructions. Reconstructions of lagoon and reef slope mean seasonality in water temperature accurately identify the greater seasonal amplitude observed in the lagoon of Heron Reef. A longer calibration period is, however, required for reliable reconstructions of annual mean water temperatures.

SU-G-BRB-15: Verifications of Absolute and Relative Dosimetry of a Novel Stereotactic Breast Device: GammaPodTM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Becker, S; Mossahebi, S; Yi, B

Purpose: A dedicated stereotactic breast radiotherapy device, GammaPod, was developed to treat early stage breast cancer. The first clinical unit was installed and commissioned at University of Maryland. We report our methodology of absolute dosimetry in multiple calibration conditions and dosimetric verifications of treatment plans produced by the system. Methods: GammaPod unit is comprised of a rotating hemi-spherical source carrier containing 36 Co-60 sources and a concentric tungsten collimator providing beams of 15 and 25 mm. Absolute dose calibration formalism was developed with modifications to AAPM protocols for unique geometry and different calibration medium (acrylic, polyethylene or liquid water). Breastmore » cup-size specific and collimator output factors were measured and verified with respect to Monte-Carlo simulations for single isocenter plans. Multiple isocenter plans were generated for various target size, location and cup-sizes in phantoms and 20 breast cancer patients images. Stereotactic mini-farmer chamber, OSL and TLD detectors as well as radio-chromic films were used for dosimetric measurements. Results: At the time of calibration (1/14/2016), absolute dose rate of the GammaPod was established to be 2.10 Gy/min in acrylic for 25 mm for sources installed in March 2011. Output factor for 15 mm collimator was measured to be 0.950. Absolute dose calibration was independently verified by IROC-Houston with a TLD/Institution ratio of 0.99. Cup size specific output measurements in liquid water for single isocenter were found to be within 3.0% of MC simulations. Point-dose measurements of multiple isocenter treatment plans were found to be within −1.0 ± 1.2 % of treatment planning system while 2-dimensional gamma analysis yielded a pass rate of 97.9 ± 2.2 % using gamma criteria of 3% and 2mm. Conclusion: The first GammaPod treatment unit for breast stereotactic radiotherapy was successfully installed, calibrated and commissioned for patient treatments. An absolute dosimetry and dosimetric verification protocols were successfully created.« less

Investigation of Martian Aqueous Processes Using Multiple Alpha Particle X-ray Spectrometer (APXS) Datasets

NASA Technical Reports Server (NTRS)

Yen, A. S.; Ming, D. W.; Gellert, R.; Vaniman, D.; Clark, B.; Morris, R. V.; Mittlefehldt, D. W.; Arvidson, R. E.

2014-01-01

The APXS instruments flown on the Mars Exploration Rovers (MER) Spirit and Opportunity and the Mars Science Laboratory (MSL) Curiosity were based on the same fundamental design. The calibration effort of the MSL APXS used the same reference standards analyzed in the MER calibration which ensures that data produced by all three instruments provide the same compositional results for the same sample. This cross-calibration effort is unprecedented and allows direct comparisons and contrasts of samples analyzed at Gusev Crater by Spirit, Meridiani Planum by Opportunity, and Gale Crater by Curiosity.

Spectral Analysis of the Primary Flight Focal Plane Arrays for the Thermal Infrared Sensor

NASA Technical Reports Server (NTRS)

Montanaro, Matthew; Reuter, Dennis C.; Markham, Brian L.; Thome, Kurtis J.; Lunsford, Allen W.; Jhabvala, Murzy D.; Rohrbach, Scott O.; Gerace, Aaron D.

2011-01-01

Thermal Infrared Sensor (TIRS) is a (1) New longwave infrared (10 - 12 micron) sensor for the Landsat Data Continuity Mission, (2) 185 km ground swath; 100 meter pixel size on ground, (3) Pushbroom sensor configuration. Issue of Calibration are: (1) Single detector -- only one calibration, (2) Multiple detectors - unique calibration for each detector -- leads to pixel-to-pixel artifacts. Objectives are: (1) Predict extent of residual striping when viewing a uniform blackbody target through various atmospheres, (2) Determine how different spectral shapes affect the derived surface temperature in a realistic synthetic scene.

Investigating the stratigraphy and palaeoenvironments for a suite of newly discovered mid-Cretaceous vertebrate fossil-localities in the Winton Formation, Queensland, Australia

NASA Astrophysics Data System (ADS)

Tucker, Ryan T.; Roberts, Eric M.; Darlington, Vikie; Salisbury, Steven W.

2017-08-01

The Winton Formation of central Queensland is recognized as a quintessential source of mid-Cretaceous terrestrial faunas and floras in Australia. However, sedimentological investigations linking fossil assemblages and palaeoenvironments across this unit remain limited. The intent of this study was to interpret depositional environments and improve stratigraphic correlations between multiple fossil localities within the preserved Winton Formation in the Eromanga Basin, including Isisford, Lark Quarry, and Bladensburg National Park. Twenty-three facies and six repeated facies associations were documented, indicating a mosaic of marginal marine to inland alluvial depositional environments. These developed synchronously with the final regression of the Eromanga Seaway from central Australia during the late Albian-early Turonian. Investigations of regional- and local-scale structural features and outcrop, core and well analysis were combined with detrital zircon provenance signatures to help correlate stratigraphy and vertebrate faunas across the basin. Significant palaeoenvironmental differences exist between the lower and upper portions of the preserved Winton Formation, warranting informal subdivisions; a lower tidally influenced fluvial-deltaic member and an upper inland alluvial member. This work further demonstrates that the Isisford fauna is part of the lower member of the preserved Winton Formation; whereas, fossil localities around Winton, including Lark Quarry and Bladensburg National Park, are part of the upper member of the Winton Formation. These results permit a more meaningful framework for both regional and global comparisons of the Winton flora and fauna.

Self-calibration method for rotating laser positioning system using interscanning technology and ultrasonic ranging.

PubMed

Wu, Jun; Yu, Zhijing; Zhuge, Jingchang

2016-04-01

A rotating laser positioning system (RLPS) is an efficient measurement method for large-scale metrology. Due to multiple transmitter stations, which consist of a measurement network, the position relationship of these stations must be first calibrated. However, with such auxiliary devices such as a laser tracker, scale bar, and complex calibration process, the traditional calibration methods greatly reduce the measurement efficiency. This paper proposes a self-calibration method for RLPS, which can automatically obtain the position relationship. The method is implemented through interscanning technology by using a calibration bar mounted on the transmitter station. Each bar is composed of three RLPS receivers and one ultrasonic sensor whose coordinates are known in advance. The calibration algorithm is mainly based on multiplane and distance constraints and is introduced in detail through a two-station mathematical model. The repeated experiments demonstrate that the coordinate measurement uncertainty of spatial points by using this method is about 0.1 mm, and the accuracy experiments show that the average coordinate measurement deviation is about 0.3 mm compared with a laser tracker. The accuracy can meet the requirements of most applications, while the calibration efficiency is significantly improved.

Tracked ultrasound calibration studies with a phantom made of LEGO bricks

NASA Astrophysics Data System (ADS)

Soehl, Marie; Walsh, Ryan; Rankin, Adam; Lasso, Andras; Fichtinger, Gabor

2014-03-01

In this study, spatial calibration of tracked ultrasound was compared by using a calibration phantom made of LEGO® bricks and two 3-D printed N-wire phantoms. METHODS: The accuracy and variance of calibrations were compared under a variety of operating conditions. Twenty trials were performed using an electromagnetic tracking device with a linear probe and three trials were performed using varied probes, varied tracking devices and the three aforementioned phantoms. The accuracy and variance of spatial calibrations found through the standard deviation and error of the 3-D image reprojection were used to compare the calibrations produced from the phantoms. RESULTS: This study found no significant difference between the measured variables of the calibrations. The average standard deviation of multiple 3-D image reprojections with the highest performing printed phantom and those from the phantom made of LEGO® bricks differed by 0.05 mm and the error of the reprojections differed by 0.13 mm. CONCLUSION: Given that the phantom made of LEGO® bricks is significantly less expensive, more readily available, and more easily modified than precision-machined N-wire phantoms, it prompts to be a viable calibration tool especially for quick laboratory research and proof of concept implementations of tracked ultrasound navigation.

Phase stable RF transport system

DOEpatents

Curtin, Michael T.; Natter, Eckard F.; Denney, Peter M.

1992-01-01

An RF transport system delivers a phase-stable RF signal to a load, such as an RF cavity of a charged particle accelerator. A circuit generates a calibration signal at an odd multiple frequency of the RF signal where the calibration signal is superimposed with the RF signal on a common cable that connects the RF signal with the load. Signal isolating diplexers are located at both the RF signal source end and load end of the common cable to enable the calibration to be inserted and extracted from the cable signals without any affect on the RF signal. Any phase shift in the calibration signal during traverse of the common cable is then functionally related to the phase shift in the RF signal. The calibration phase shift is used to control a phase shifter for the RF signal to maintain a stable RF signal at the load.

MT3DMS: Model use, calibration, and validation

USGS Publications Warehouse

Zheng, C.; Hill, Mary C.; Cao, G.; Ma, R.

2012-01-01

MT3DMS is a three-dimensional multi-species solute transport model for solving advection, dispersion, and chemical reactions of contaminants in saturated groundwater flow systems. MT3DMS interfaces directly with the U.S. Geological Survey finite-difference groundwater flow model MODFLOW for the flow solution and supports the hydrologic and discretization features of MODFLOW. MT3DMS contains multiple transport solution techniques in one code, which can often be important, including in model calibration. Since its first release in 1990 as MT3D for single-species mass transport modeling, MT3DMS has been widely used in research projects and practical field applications. This article provides a brief introduction to MT3DMS and presents recommendations about calibration and validation procedures for field applications of MT3DMS. The examples presented suggest the need to consider alternative processes as models are calibrated and suggest opportunities and difficulties associated with using groundwater age in transport model calibration.

Quantification of Methane and Ethane Emissions from the San Juan Basin

NASA Astrophysics Data System (ADS)

Smith, M. L.; Kort, E. A.; Karion, A.; Sweeney, C.; Gvakharia, A.

2015-12-01

Methane (CH4), a potent greenhouse gas, and the primary component of natural gas, is emitted from areas of high fossil fuel production and processing. Recently, persistent and large methane emissions (~0.59 Tg yr-1) from the four corners area of the United States have been identified using satellite (SCIAMACHY) observations taken over the years 2003 to 2009. These emissions appear to be the largest CH4 anomaly (positive deviation above background values) in the contiguous U.S., and exceed bottom-up inventory estimates for the area by 1.8 to 3.5 times. The majority of emissions sources expected to contribute to this anomalous CH4 signal are located in the San Juan basin of New Mexico, and include harvesting and processing of natural gas, coal, and coalbed CH4. The magnitude of CH4 emissions from the San Juan basin have not yet been directly quantified using airborne measurements. Additionally, changing fossil fuel-related activities in the basin may have altered the magnitude of CH4 emissions compared to estimates derived from 2003-2009 satellite measurements. Here, we present in-situ airborne observations of CH4 over the San Juan basin, which allow tight quantification of CH4 fluxes using the mass balance method. Observations over the basin were taken for multiple wind directions on multiple days in April, 2015 to obtain a robust estimate of CH4 emissions. The flux of ethane (C2H6), the second most abundant component of natural gas and a tracer species indicative of fossil-derived CH4, was also quantified. Substantial C2H6 emissions may affect regional air quality and chemistry through its influence on tropospheric ozone production.

Bandicoot fossils and DNA elucidate lineage antiquity amongst xeric-adapted Australasian marsupials

NASA Astrophysics Data System (ADS)

Kear, Benjamin P.; Aplin, Ken P.; Westerman, Michael

2016-11-01

Bandicoots (Peramelemorphia) are a unique order of Australasian marsupials whose sparse fossil record has been used as prima facie evidence for climate change coincident faunal turnover. In particular, the hypothesized replacement of ancient rainforest-dwelling extinct lineages by antecedents of xeric-tolerant extant taxa during the late Miocene (~10 Ma) has been advocated as a broader pattern evident amongst other marsupial clades. Problematically, however, this is in persistent conflict with DNA phylogenies. We therefore determine the pattern and timing of bandicoot evolution using the first combined morphological + DNA sequence dataset of Peramelemorphia. In addition, we document a remarkably archaic new fossil peramelemorphian taxon that inhabited a latest Quaternary mosaic savannah-riparian forest ecosystem on the Aru Islands of Eastern Indonesia. Our phylogenetic analyses reveal that unsuspected dental homoplasy and the detrimental effects of missing data collectively obscure stem bandicoot relationships. Nevertheless, recalibrated molecular clocks and multiple ancestral area optimizations unanimously infer an early diversification of modern xeric-adapted forms. These probably originated during the late Palaeogene (30-40 Ma) alongside progenitors of other desert marsupials, and thus occupied seasonally dry heterogenous habitats long before the onset of late Neogene aridity.

Bandicoot fossils and DNA elucidate lineage antiquity amongst xeric-adapted Australasian marsupials.

PubMed

Kear, Benjamin P; Aplin, Ken P; Westerman, Michael

2016-11-24

Bandicoots (Peramelemorphia) are a unique order of Australasian marsupials whose sparse fossil record has been used as prima facie evidence for climate change coincident faunal turnover. In particular, the hypothesized replacement of ancient rainforest-dwelling extinct lineages by antecedents of xeric-tolerant extant taxa during the late Miocene (~10 Ma) has been advocated as a broader pattern evident amongst other marsupial clades. Problematically, however, this is in persistent conflict with DNA phylogenies. We therefore determine the pattern and timing of bandicoot evolution using the first combined morphological + DNA sequence dataset of Peramelemorphia. In addition, we document a remarkably archaic new fossil peramelemorphian taxon that inhabited a latest Quaternary mosaic savannah-riparian forest ecosystem on the Aru Islands of Eastern Indonesia. Our phylogenetic analyses reveal that unsuspected dental homoplasy and the detrimental effects of missing data collectively obscure stem bandicoot relationships. Nevertheless, recalibrated molecular clocks and multiple ancestral area optimizations unanimously infer an early diversification of modern xeric-adapted forms. These probably originated during the late Palaeogene (30-40 Ma) alongside progenitors of other desert marsupials, and thus occupied seasonally dry heterogenous habitats long before the onset of late Neogene aridity.

Waveguide Calibrator for Multi-Element Probe Calibration

NASA Technical Reports Server (NTRS)

Sommerfeldt, Scott D.; Blotter, Jonathan D.

2007-01-01

A calibrator, referred to as the spider design, can be used to calibrate probes incorporating multiple acoustic sensing elements. The application is an acoustic energy density probe, although the calibrator can be used for other types of acoustic probes. The calibrator relies on the use of acoustic waveguide technology to produce the same acoustic field at each of the sensing elements. As a result, the sensing elements can be separated from each other, but still calibrated through use of the acoustic waveguides. Standard calibration techniques involve placement of an individual microphone into a small cavity with a known, uniform pressure to perform the calibration. If a cavity is manufactured with sufficient size to insert the energy density probe, it has been found that a uniform pressure field can only be created at very low frequencies, due to the size of the probe. The size of the energy density probe prevents one from having the same pressure at each microphone in a cavity, due to the wave effects. The "spider" design probe is effective in calibrating multiple microphones separated from each other. The spider design ensures that the same wave effects exist for each microphone, each with an indivdual sound path. The calibrator s speaker is mounted at one end of a 14-cm-long and 4.1-cm diameter small plane-wave tube. This length was chosen so that the first evanescent cross mode of the plane-wave tube would be attenuated by about 90 dB, thus leaving just the plane wave at the termination plane of the tube. The tube terminates with a small, acrylic plate with five holes placed symmetrically about the axis of the speaker. Four ports are included for the four microphones on the probe. The fifth port is included for the pre-calibrated reference microphone. The ports in the acrylic plate are in turn connected to the probe sensing elements via flexible PVC tubes. These five tubes are the same length, so the acoustic wave effects are the same in each tube. The flexible nature of the tubes allows them to be positioned so that each tube terminates at one of the microphones of the energy density probe, which is mounted in the acrylic structure, or the calibrated reference microphone. Tests performed verify that the pressure did not vary due to bends in the tubes. The results of these tests indicate that the average sound pressure level in the tubes varied by only 0.03 dB as the tubes were bent to various angles. The current calibrator design is effective up to a frequency of approximately 4.5 kHz. This upper design frequency is largely due to the diameter of the plane-wave tubes.

Development of a calibration for the B isotope paleo-pH proxy in the deep sea coral Desmophyllum dianthus

NASA Astrophysics Data System (ADS)

Anagnostou, E.; Huang, K.; You, C.; Sherrell, R. M.

2011-12-01

The boron isotope ratio (δ11B) of foraminifera and coral carbonate has been proposed to record seawater pH. Here we test this pH proxy in the deep sea coral Desmophyllum dianthus (D. dianthus ). This coral species is cosmopolitan in geographic distribution and tolerates a wide temperature and depth range. Previous studies have shown that fossil D. dianthus skeletons can be dated precisely with U/Th measurements. Additionally, skeletal mass is sufficient for multiple elemental, isotopic, and radiocarbon measurements per sample making it a powerful candidate for paleoceanographic reconstructions. Ten modern corals from a depth range of 274-1470m in the Atlantic, Pacific, and Southern Oceans were analyzed using the sublimation method and multi-collector ICP-MS (Neptune), and the measured δ11B was regressed against ambient pH taken from hydrographic data sets (range pH 7.6 to 8.1). Replicate skeletal subsamples from a single coral agree within 0.35% (2SD). The array of δ11B values for these corals plots above the seawater borate δ11B vs. pH curve (Klochko et al., 2006) by an apparently constant value of 11.7 ± 1.2%, well above the range of values seen in foraminifera and surface corals. This offset is attributed to either partial incorporation of boric acid from seawater or, more likely, to physiological manipulation of the calcifying fluid to pH 8.7-9.0. The uncertainty in calculation of seawater pH from δ11B, dominated by the uncertainty in the offset value, currently limits the precision of absolute pH reconstructions to ±0.09pH units. However, the empirical calibration could be used to examine relative pH changes, thereby overcoming contributions to the uncertainty in the offset that result from the calculation of the empirical fractionation factor α and from sampling bias and variable vital effects among individuals, reducing the reconstruction error envelope. This study provides the first evidence that δ11B in D. dianthus has the potential to record ambient seawater pH.

Using multiple IMUs in a stacked filter configuration for calibration and fine alignment

NASA Astrophysics Data System (ADS)

El-Osery, Aly; Bruder, Stephen; Wedeward, Kevin

2018-05-01

Determination of a vehicle or person's position and/or orientation is a critical task for a multitude of applications ranging from automated cars and first responders to missiles and fighter jets. Most of these applications rely primarily on global navigation satellite systems, e.g., GPS, which are highly vulnerable to degradation whether by environmental factors or malicious actions. The use of inertial navigation techniques has been shown to provide increased reliability of navigation systems in these situations. Due to advances in MEMS technology and processing capabilities, the use of small and low-cost inertial measurement units (IMUs) are becoming increasingly feasible, which results in small size, weight and power (SWaP) solutions. A known limitation of MEMS IMUs are errors that causes the navigation solution to drift; furthermore, calibration and initialization are challenging tasks. In this paper, we investigate the use of multiple IMUs to aid in calibrating the navigation system and obtaining accurate initialization by performing fine alignment. By using a centralized filter, physical constraints between the multiple IMUs on a rigid body are leveraged to provide relative updates, which in turn aids in the estimation of the individual biases and scale-factors. Developed algorithms will be validated through simulation and actual measurements using low-cost IMUs.

Calibration of Multiple In Silico Tools for Predicting Pathogenicity of Mismatch Repair Gene Missense Substitutions

PubMed Central

Thompson, Bryony A.; Greenblatt, Marc S.; Vallee, Maxime P.; Herkert, Johanna C.; Tessereau, Chloe; Young, Erin L.; Adzhubey, Ivan A.; Li, Biao; Bell, Russell; Feng, Bingjian; Mooney, Sean D.; Radivojac, Predrag; Sunyaev, Shamil R.; Frebourg, Thierry; Hofstra, Robert M.W.; Sijmons, Rolf H.; Boucher, Ken; Thomas, Alun; Goldgar, David E.; Spurdle, Amanda B.; Tavtigian, Sean V.

2015-01-01

Classification of rare missense substitutions observed during genetic testing for patient management is a considerable problem in clinical genetics. The Bayesian integrated evaluation of unclassified variants is a solution originally developed for BRCA1/2. Here, we take a step toward an analogous system for the mismatch repair (MMR) genes (MLH1, MSH2, MSH6, and PMS2) that confer colon cancer susceptibility in Lynch syndrome by calibrating in silico tools to estimate prior probabilities of pathogenicity for MMR gene missense substitutions. A qualitative five-class classification system was developed and applied to 143 MMR missense variants. This identified 74 missense substitutions suitable for calibration. These substitutions were scored using six different in silico tools (Align-Grantham Variation Grantham Deviation, multivariate analysis of protein polymorphisms [MAPP], Mut-Pred, PolyPhen-2.1, Sorting Intolerant From Tolerant, and Xvar), using curated MMR multiple sequence alignments where possible. The output from each tool was calibrated by regression against the classifications of the 74 missense substitutions; these calibrated outputs are interpretable as prior probabilities of pathogenicity. MAPP was the most accurate tool and MAPP + PolyPhen-2.1 provided the best-combined model (R2 = 0.62 and area under receiver operating characteristic = 0.93). The MAPP + PolyPhen-2.1 output is sufficiently predictive to feed as a continuous variable into the quantitative Bayesian integrated evaluation for clinical classification of MMR gene missense substitutions. PMID:22949387

Molecular composition and ultrastructure of Jurassic paravian feathers

PubMed Central

Lindgren, Johan; Sjövall, Peter; Carney, Ryan M.; Cincotta, Aude; Uvdal, Per; Hutcheson, Steven W.; Gustafsson, Ola; Lefèvre, Ulysse; Escuillié, François; Heimdal, Jimmy; Engdahl, Anders; Gren, Johan A.; Kear, Benjamin P.; Wakamatsu, Kazumasa; Yans, Johan; Godefroit, Pascal

2015-01-01

Feathers are amongst the most complex epidermal structures known, and they have a well-documented evolutionary trajectory across non-avian dinosaurs and basal birds. Moreover, melanosome-like microbodies preserved in association with fossil plumage have been used to reconstruct original colour, behaviour and physiology. However, these putative ancient melanosomes might alternatively represent microorganismal residues, a conflicting interpretation compounded by a lack of unambiguous chemical data. We therefore used sensitive molecular imaging, supported by multiple independent analytical tests, to demonstrate that the filamentous epidermal appendages in a new specimen of the Jurassic paravian Anchiornis comprise remnant eumelanosomes and fibril-like microstructures, preserved as endogenous eumelanin and authigenic calcium phosphate. These results provide novel insights into the early evolution of feathers at the sub-cellular level, and unequivocally determine that melanosomes can be preserved in fossil feathers. PMID:26311035

An automated calibration method for non-see-through head mounted displays.

PubMed

Gilson, Stuart J; Fitzgibbon, Andrew W; Glennerster, Andrew

2011-08-15

Accurate calibration of a head mounted display (HMD) is essential both for research on the visual system and for realistic interaction with virtual objects. Yet, existing calibration methods are time consuming and depend on human judgements, making them error prone, and are often limited to optical see-through HMDs. Building on our existing approach to HMD calibration Gilson et al. (2008), we show here how it is possible to calibrate a non-see-through HMD. A camera is placed inside a HMD displaying an image of a regular grid, which is captured by the camera. The HMD is then removed and the camera, which remains fixed in position, is used to capture images of a tracked calibration object in multiple positions. The centroids of the markers on the calibration object are recovered and their locations re-expressed in relation to the HMD grid. This allows established camera calibration techniques to be used to recover estimates of the HMD display's intrinsic parameters (width, height, focal length) and extrinsic parameters (optic centre and orientation of the principal ray). We calibrated a HMD in this manner and report the magnitude of the errors between real image features and reprojected features. Our calibration method produces low reprojection errors without the need for error-prone human judgements. Copyright © 2011 Elsevier B.V. All rights reserved.

Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants

PubMed Central

Wolski, Witold E; Lalowski, Maciej; Jungblut, Peter; Reinert, Knut

2005-01-01

Background Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra. The PMF process requires calibration, usually performed with external or internal calibrants of known molecular masses. Results We have introduced two novel MS calibration methods. The first method utilises the local similarity of peptide maps generated after separation of complex protein samples by two-dimensional gel electrophoresis. It computes a multiple peak-list alignment of the data set using a modified Minimum Spanning Tree (MST) algorithm. The second method exploits the idea that hundreds of MS samples are measured in parallel on one sample support. It improves the calibration coefficients by applying a two-dimensional Thin Plate Splines (TPS) smoothing algorithm. We studied the novel calibration methods utilising data generated by three different MALDI-TOF-MS instruments. We demonstrate that a PMF data set can be calibrated without resorting to external or relying on widely occurring internal calibrants. The methods developed here were implemented in R and are part of the BioConductor package mscalib available from . Conclusion The MST calibration algorithm is well suited to calibrate MS spectra of protein samples resulting from two-dimensional gel electrophoretic separation. The TPS based calibration algorithm might be used to correct systematic mass measurement errors observed for large MS sample supports. As compared to other methods, our combined MS spectra calibration strategy increases the peptide/protein identification rate by an additional 5 – 15%. PMID:16102175

Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations

PubMed Central

Kang, Hongzhang; Sun, Xiao; Yin, Shan; Du, Hongmei; Yamanaka, Norikazu; Gapare, Washington; Wu, Harry X.; Liu, Chunjiang

2012-01-01

The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis) is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands) was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (N ST = 0.751> G ST = 0.690, P<0.05). Q. variabilis displayed high interpopulation and low intrapopulation genetic diversity across the distribution range. Both unimodal mismatch distribution and significant negative Fu’s FS indicated a demographic expansion of Q. variabilis populations in East Asia. A fossil calibrated phylogenetic tree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s), a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia. PMID:23115642

Node-to-node field calibration of wireless distributed air pollution sensor network.

PubMed

Kizel, Fadi; Etzion, Yael; Shafran-Nathan, Rakefet; Levy, Ilan; Fishbain, Barak; Bartonova, Alena; Broday, David M

2018-02-01

Low-cost air quality sensors offer high-resolution spatiotemporal measurements that can be used for air resources management and exposure estimation. Yet, such sensors require frequent calibration to provide reliable data, since even after a laboratory calibration they might not report correct values when they are deployed in the field, due to interference with other pollutants, as a result of sensitivity to environmental conditions and due to sensor aging and drift. Field calibration has been suggested as a means for overcoming these limitations, with the common strategy involving periodical collocations of the sensors at an air quality monitoring station. However, the cost and complexity involved in relocating numerous sensor nodes back and forth, and the loss of data during the repeated calibration periods make this strategy inefficient. This work examines an alternative approach, a node-to-node (N2N) calibration, where only one sensor in each chain is directly calibrated against the reference measurements and the rest of the sensors are calibrated sequentially one against the other while they are deployed and collocated in pairs. The calibration can be performed multiple times as a routine procedure. This procedure minimizes the total number of sensor relocations, and enables calibration while simultaneously collecting data at the deployment sites. We studied N2N chain calibration and the propagation of the calibration error analytically, computationally and experimentally. The in-situ N2N calibration is shown to be generic and applicable for different pollutants, sensing technologies, sensor platforms, chain lengths, and sensor order within the chain. In particular, we show that chain calibration of three nodes, each calibrated for a week, propagate calibration errors that are similar to those found in direct field calibration. Hence, N2N calibration is shown to be suitable for calibration of distributed sensor networks. Copyright © 2017 Elsevier Ltd. All rights reserved.

Use of Numerical Groundwater Model and Analytical Empirical Orthogonal Function for Calibrating Spatiotemporal pattern of Pumpage, Recharge and Parameter

NASA Astrophysics Data System (ADS)

Huang, C. L.; Hsu, N. S.; Hsu, F. C.; Liu, H. J.

2016-12-01

This study develops a novel methodology for the spatiotemporal groundwater calibration of mega-quantitative recharge and parameters by coupling a specialized numerical model and analytical empirical orthogonal function (EOF). The actual spatiotemporal patterns of groundwater pumpage are estimated by an originally developed back propagation neural network-based response matrix with the electrical consumption analysis. The spatiotemporal patterns of the recharge from surface water and hydrogeological parameters (i.e. horizontal hydraulic conductivity and vertical leakance) are calibrated by EOF with the simulated error hydrograph of groundwater storage, in order to qualify the multiple error sources and quantify the revised volume. The objective function of the optimization model is minimizing the root mean square error of the simulated storage error percentage across multiple aquifers, meanwhile subject to mass balance of groundwater budget and the governing equation in transient state. The established method was applied on the groundwater system of Chou-Shui River Alluvial Fan. The simulated period is from January 2012 to December 2014. The total numbers of hydraulic conductivity, vertical leakance and recharge from surface water among four aquifers are 126, 96 and 1080, respectively. Results showed that the RMSE during the calibration process was decreased dramatically and can quickly converse within 6th iteration, because of efficient filtration of the transmission induced by the estimated error and recharge across the boundary. Moreover, the average simulated error percentage according to groundwater level corresponding to the calibrated budget variables and parameters of aquifer one is as small as 0.11%. It represent that the developed methodology not only can effectively detect the flow tendency and error source in all aquifers to achieve accurately spatiotemporal calibration, but also can capture the peak and fluctuation of groundwater level in shallow aquifer.

SU-E-J-47: Development of a High-Precision, Image-Guided Radiotherapy, Multi- Purpose Radiation Isocenter Quality-Assurance Calibration and Checking System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, C; Yan, G; Helmig, R

2014-06-01

Purpose: To develop a system that can define the radiation isocenter and correlate this information with couch coordinates, laser alignment, optical distance indicator (ODI) settings, optical tracking system (OTS) calibrations, and mechanical isocenter walkout. Methods: Our team developed a multi-adapter, multi-purpose quality assurance (QA) and calibration device that uses an electronic portal imaging device (EPID) and in-house image-processing software to define the radiation isocenter, thereby allowing linear accelerator (Linac) components to be verified and calibrated. Motivated by the concept that each Linac component related to patient setup for image-guided radiotherapy based on cone-beam CT should be calibrated with respect tomore » the radiation isocenter, we designed multiple concentric adapters of various materials and shapes to meet the needs of MV and KV radiation isocenter definition, laser alignment, and OTS calibration. The phantom's ability to accurately define the radiation isocenter was validated on 4 Elekta Linacs using a commercial ball bearing (BB) phantom as a reference. Radiation isocenter walkout and the accuracy of couch coordinates, ODI, and OTS were then quantified with the device. Results: The device was able to define the radiation isocenter within 0.3 mm. Radiation isocenter walkout was within ±1 mm at 4 cardinal angles. By switching adapters, we identified that the accuracy of the couch position digital readout, ODI, OTS, and mechanical isocenter walkout was within sub-mm. Conclusion: This multi-adapter, multi-purpose isocenter phantom can be used to accurately define the radiation isocenter and represents a potential paradigm shift in Linac QA. Moreover, multiple concentric adapters allowed for sub-mm accuracy for the other relevant components. This intuitive and user-friendly design is currently patent pending.« less

On the ages of resonant, eroded and fossil asteroid families

NASA Astrophysics Data System (ADS)

Milani, Andrea; Knežević, Zoran; Spoto, Federica; Cellino, Alberto; Novaković, Bojan; Tsirvoulis, Georgios

2017-05-01

In this work we have estimated 10 collisional ages of 9 families for which for different reasons our previous attempts failed. In general, these are difficult cases that required dedicated effort, such as a new family classifications for asteroids in mean motion resonances, in particular the 1/1 and 2/1 with Jupiter, as well as a revision of the classification inside the 3/2 resonance. Of the families locked in mean motion resonances, by employing a numerical calibration to estimate the Yarkovsky effect in proper eccentricity, we succeeded in determining ages of the families of (1911) Schubart and of the "super-Hilda" family, assuming this is actually a severely eroded original family of (153) Hilda. In the Trojan region we found families with almost no Yarkovsky evolution, for which we could compute only physically implausible ages. Hence, we interpreted their modest dispersions of proper elements as implying that the Trojan asteroid families are fossil families, frozen at their proper elements determined by the original ejection velocity field. We have found a new family, among the Griquas locked in the 2/1 resonance with Jupiter, the family of (11097) 1994 UD1. We have estimated the ages of 6 families affected by secular resonances: families of (5) Astraea, (25) Phocaea, (283) Emma, (363) Padua, (686) Gersuind, and (945) Barcelona. By using in all these cases a numerical calibration method, we have shown that the secular resonances do not affect significantly the secular change of proper a. We have confirmed the existence of the family resulting from cratering on (5) Astraea by computing a new set of resonant proper elements adapted to the resonance g +g5 - 2g6 : this new family has a much larger membership and has a shape compatible with simple collisional models. For the family of (145) Adeona we could estimate the age only after removal of a number of assumed interlopers. With the present paper we have concluded the series dedicated to the determination of asteroid ages with a uniform method. Overall we computed 53 ages for a total of 49 families. For the future work there remain families too small at present to provide reliable estimates, as well as some complex families (221, 135, 298) which may have more ages than we could currently estimate. Future improvement of some already determined family ages is also possible by increasing family membership, revising the calibrations, and using more reliable physical data.

Preliminary calibration of the ACP safeguards neutron counter

NASA Astrophysics Data System (ADS)

Lee, T. H.; Kim, H. D.; Yoon, J. S.; Lee, S. Y.; Swinhoe, M.; Menlove, H. O.

2007-10-01

The Advanced Spent Fuel Conditioning Process (ACP), a kind of pyroprocess, has been developed at the Korea Atomic Energy Research Institute (KAERI). Since there is no IAEA safeguards criteria for this process, KAERI has developed a neutron coincidence counter to make it possible to perform a material control and accounting (MC&A) for its ACP materials for the purpose of a transparency in the peaceful uses of nuclear materials at KAERI. The test results of the ACP Safeguards Neutron Counter (ASNC) show a satisfactory performance for the Doubles count measurement with a low measurement error for its cylindrical sample cavity. The neutron detection efficiency is about 21% with an error of ±1.32% along the axial direction of the cavity. Using two 252Cf neutron sources, we obtained various parameters for the Singles and Doubles rates for the ASNC. The Singles, Doubles, and Triples rates for a 252Cf point source were obtained by using the MCNPX code and the results for the ft8 cap multiplicity tally option with the values of ɛ, fd, and ft measured with a strong source most closely match the measurement results to within a 1% error. A preliminary calibration curve for the ASNC was generated by using the point model equation relationship between 244Cm and 252Cf and the calibration coefficient for the non-multiplying sample is 2.78×10 5 (Doubles counts/s/g 244Cm). The preliminary calibration curves for the ACP samples were also obtained by using an MCNPX simulation. A neutron multiplication influence on an increase of the Doubles rate for a metal ingot and UO2 powder is clearly observed. These calibration curves will be modified and complemented, when hot calibration samples become available. To verify the validity of this calibration curve, a measurement of spent fuel standards for a known 244Cm mass will be performed in the near future.

Environmental accounting of natural capital and ecosystem services for the US National Forest System

Treesearch

Elliot T. Campbell; Mark T. Brown; NO-VALUE

2012-01-01

The National Forests of the United States encompass 192.7 million acres (78 million hectares) of land, which is nearly five percent of the total land area of the nation. These lands are managed by the US Forest Service (USFS) for multiple uses, including extraction of timber, production of fossil fuels and minerals, public recreation, and the preservation of...

Using Multiple Outcomes of Sexual Behavior to Provide Insights Into Chlamydia Transmission and the Effectiveness of Prevention Interventions in Adolescents.

PubMed

Enns, Eva Andrea; Kao, Szu-Yu; Kozhimannil, Katy Backes; Kahn, Judith; Farris, Jill; Kulasingam, Shalini L

2017-10-01

Mathematical models are important tools for assessing prevention and management strategies for sexually transmitted infections. These models are usually developed for a single infection and require calibration to observed epidemiological trends in the infection of interest. Incorporating other outcomes of sexual behavior into the model, such as pregnancy, may better inform the calibration process. We developed a mathematical model of chlamydia transmission and pregnancy in Minnesota adolescents aged 15 to 19 years. We calibrated the model to statewide rates of reported chlamydia cases alone (chlamydia calibration) and in combination with pregnancy rates (dual calibration). We evaluated the impact of calibrating to different outcomes of sexual behavior on estimated input parameter values, predicted epidemiological outcomes, and predicted impact of chlamydia prevention interventions. The two calibration scenarios produced different estimates of the probability of condom use, the probability of chlamydia transmission per sex act, the proportion of asymptomatic infections, and the screening rate among men. These differences resulted in the dual calibration scenario predicting lower prevalence and incidence of chlamydia compared with calibrating to chlamydia cases alone. When evaluating the impact of a 10% increase in condom use, the dual calibration scenario predicted fewer infections averted over 5 years compared with chlamydia calibration alone [111 (6.8%) vs 158 (8.5%)]. While pregnancy and chlamydia in adolescents are often considered separately, both are outcomes of unprotected sexual activity. Incorporating both as calibration targets in a model of chlamydia transmission resulted in different parameter estimates, potentially impacting the intervention effectiveness predicted by the model.

Integrated calibration of multiview phase-measuring profilometry

NASA Astrophysics Data System (ADS)

Lee, Yeong Beum; Kim, Min H.

2017-11-01

Phase-measuring profilometry (PMP) measures per-pixel height information of a surface with high accuracy. Height information captured by a camera in PMP relies on its screen coordinates. Therefore, a PMP measurement from a view cannot be integrated directly to other measurements from different views due to the intrinsic difference of the screen coordinates. In order to integrate multiple PMP scans, an auxiliary calibration of each camera's intrinsic and extrinsic properties is required, in addition to principal PMP calibration. This is cumbersome and often requires physical constraints in the system setup, and multiview PMP is consequently rarely practiced. In this work, we present a novel multiview PMP method that yields three-dimensional global coordinates directly so that three-dimensional measurements can be integrated easily. Our PMP calibration parameterizes intrinsic and extrinsic properties of the configuration of both a camera and a projector simultaneously. It also does not require any geometric constraints on the setup. In addition, we propose a novel calibration target that can remain static without requiring any mechanical operation while conducting multiview calibrations, whereas existing calibration methods require manually changing the target's position and orientation. Our results validate the accuracy of measurements and demonstrate the advantages on our multiview PMP.

Clinical results from a noninvasive blood glucose monitor

NASA Astrophysics Data System (ADS)

Blank, Thomas B.; Ruchti, Timothy L.; Lorenz, Alex D.; Monfre, Stephen L.; Makarewicz, M. R.; Mattu, Mutua; Hazen, Kevin

2002-05-01

Non-invasive blood glucose monitoring has long been proposed as a means for advancing the management of diabetes through increased measurement and control. The use of a near-infrared, NIR, spectroscopy based methodology for noninvasive monitoring has been pursued by a number of groups. The accuracy of the NIR measurement technology is limited by challenges related to the instrumentation, the heterogeneity and time-variant nature of skin tissue, and the complexity of the calibration methodology. In this work, we discuss results from a clinical study that targeted the evaluation of individual calibrations for each subject based on a series of controlled calibration visits. While the customization of the calibrations to individuals was intended to reduce model complexity, the extensive requirements for each individual set of calibration data were difficult to achieve and required several days of measurement. Through the careful selection of a small subset of data from all samples collected on the 138 study participants in a previous study, we have developed a methodology for applying a single standard calibration to multiple persons. The standard calibrations have been applied to a plurality of individuals and shown to be persistent over periods greater than 24 weeks.

Phaeodarian radiolarians as potential indicators of thermal maturation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Casey, R.E.

1986-04-01

Phaeodarian radiolarian skeletons contain large amounts of organic matter, and discolored phaeodarian skeletons are observed in the fossil record, which suggests that the skeletons may be useful as thermal maturation indicators. Such a maturation index would be useful in Monterey-type rocks that are difficult to interpret with conventional thermal maturation indexes. Phaeodarians extracted from plankton samples, Holocene Santa Barbara and Orca basin sediments, and Neogene Monterey rocks with siliceous facies were subjected to different temperatures of varying duration in pyrolysis experiments. To calibrate the observed phaeodarian color changes with a known standard, Holocene pine pollen were subjected to the samemore » treatment. These phaeodarian go through the same color change spectrum as do the pollen, but they appear to lag slightly behind the pollen color changes.« less

Paleontological baselines for evaluating extinction risk in the modern oceans

NASA Astrophysics Data System (ADS)

Finnegan, Seth; Anderson, Sean C.; Harnik, Paul G.; Simpson, Carl; Tittensor, Derek P.; Byrnes, Jarrett E.; Finkel, Zoe V.; Lindberg, David R.; Liow, Lee Hsiang; Lockwood, Rowan; Lotze, Heike K.; McClain, Craig R.; McGuire, Jenny L.; O'Dea, Aaron; Pandolfi, John M.

2015-05-01

Marine taxa are threatened by anthropogenic impacts, but knowledge of their extinction vulnerabilities is limited. The fossil record provides rich information on past extinctions that can help predict biotic responses. We show that over 23 million years, taxonomic membership and geographic range size consistently explain a large proportion of extinction risk variation in six major taxonomic groups. We assess intrinsic risk—extinction risk predicted by paleontologically calibrated models—for modern genera in these groups. Mapping the geographic distribution of these genera identifies coastal biogeographic provinces where fauna with high intrinsic risk are strongly affected by human activity or climate change. Such regions are disproportionately in the tropics, raising the possibility that these ecosystems may be particularly vulnerable to future extinctions. Intrinsic risk provides a prehuman baseline for considering current threats to marine biodiversity.

Remote sensing of evapotranspiration using automated calibration: Development and testing in the state of Florida

NASA Astrophysics Data System (ADS)

Evans, Aaron H.

Thermal remote sensing is a powerful tool for measuring the spatial variability of evapotranspiration due to the cooling effect of vaporization. The residual method is a popular technique which calculates evapotranspiration by subtracting sensible heat from available energy. Estimating sensible heat requires aerodynamic surface temperature which is difficult to retrieve accurately. Methods such as SEBAL/METRIC correct for this problem by calibrating the relationship between sensible heat and retrieved surface temperature. Disadvantage of these calibrations are 1) user must manually identify extremely dry and wet pixels in image 2) each calibration is only applicable over limited spatial extent. Producing larger maps is operationally limited due to time required to manually calibrate multiple spatial extents over multiple days. This dissertation develops techniques which automatically detect dry and wet pixels. LANDSAT imagery is used because it resolves dry pixels. Calibrations using 1) only dry pixels and 2) including wet pixels are developed. Snapshots of retrieved evaporative fraction and actual evapotranspiration are compared to eddy covariance measurements for five study areas in Florida: 1) Big Cypress 2) Disney Wilderness 3) Everglades 4) near Gainesville, FL. 5) Kennedy Space Center. The sensitivity of evaporative fraction to temperature, available energy, roughness length and wind speed is tested. A technique for temporally interpolating evapotranspiration by fusing LANDSAT and MODIS is developed and tested. The automated algorithm is successful at detecting wet and dry pixels (if they exist). Including wet pixels in calibration and assuming constant atmospheric conductance significantly improved results for all but Big Cypress and Gainesville. Evaporative fraction is not very sensitive to instantaneous available energy but it is sensitive to temperature when wet pixels are included because temperature is required for estimating wet pixel evapotranspiration. Data fusion techniques only slightly outperformed linear interpolation. Eddy covariance comparison and temporal interpolation produced acceptable bias error for most cases suggesting automated calibration and interpolation could be used to predict monthly or annual ET. Maps demonstrating spatial patterns of evapotranspiration at field scale were successfully produced, but only for limited spatial extents. A framework has been established for producing larger maps by creating a mosaic of smaller individual maps.

Dry calibration of electromagnetic flowmeters based on numerical models combining multiple physical phenomena (multiphysics)

NASA Astrophysics Data System (ADS)

Fu, X.; Hu, L.; Lee, K. M.; Zou, J.; Ruan, X. D.; Yang, H. Y.

2010-10-01

This paper presents a method for dry calibration of an electromagnetic flowmeter (EMF). This method, which determines the voltage induced in the EMF as conductive liquid flows through a magnetic field, numerically solves a coupled set of multiphysical equations with measured boundary conditions for the magnetic, electric, and flow fields in the measuring pipe of the flowmeter. Specifically, this paper details the formulation of dry calibration and an efficient algorithm (that adaptively minimizes the number of measurements and requires only the normal component of the magnetic flux density as boundary conditions on the pipe surface to reconstruct the magnetic field involved) for computing the sensitivity of EMF. Along with an in-depth discussion on factors that could significantly affect the final precision of a dry calibrated EMF, the effects of flow disturbance on measuring errors have been experimentally studied by installing a baffle at the inflow port of the EMF. Results of the dry calibration on an actual EMF were compared against flow-rig calibration; excellent agreements (within 0.3%) between dry calibration and flow-rig tests verify the multiphysical computation of the fields and the robustness of the method. As requiring no actual flow, the dry calibration is particularly useful for calibrating large-diameter EMFs where conventional flow-rig methods are often costly and difficult to implement.

Cenozoic extinction and recolonization in the New Zealand flora: the case of the fleshy-fruited epacrids (Styphelieae, Styphelioideae, Ericaceae).

PubMed

Puente-Lelièvre, Caroline; Harrington, Mark G; Brown, Elizabeth A; Kuzmina, Maria; Crayn, Darren M

2013-01-01

The origins and evolutionary history of the New Zealand flora has been the subject of much debate. The recent description of Cyathodophyllum novaezelandieae from early Miocene sediments in New Zealand provides possible evidence for the antiquity of the fleshy fruited epacrids (tribe Styphelieae, Ericaceae) in New Zealand. Yet the extant species in this tribe are thought to be very closely related to or conspecific with Australian taxa, suggesting recent trans-Tasman origins. In order to investigate the origins and evolution of the extant New Zealand Styphelieae we produced molecular phylogenetic trees based on sequences of three plastid regions that include representatives of all the genera of the tribe and eight of the ten New Zealand species. We estimated the range of minimum ages of the New Zealand lineages with Bayesian relaxed-clock analyses using different calibration methods and relative dating. We found strong support for each of the eight extant species of New Zealand Styphelieae being a distinct lineage that is nested within an Australian clade. In all except one case the sister is from Tasmania and/or the east coast of mainland Australia; for Acrothamnus colensoi the sister is in New Guinea. Estimated dates indicate that all of the New Zealand lineages diverged from their non-New Zealand sisters within the last 7 Ma. Time discontinuity between the fossil C.novae-zelandiae (20-23 Ma) and the origins of the extant New Zealand lineages (none older than 5 Ma) indicates that the fossil and extant Styphelieae in New Zealand are not related. The relative dating analysis showed that to accept this relationship, it would be necessary to accept that the Styphelieae arose in the early-mid Mesozoic (210-120 Ma), which is starkly at odds with multiple lines of evidence on the age of Ericales and indeed the angiosperms. Therefore, our results do not support the hypothesis that Styphelieae have been continuously present in New Zealand since the early Miocene. Instead they suggest a historical biogeographical scenario in which the lineage to which C. novae-zelandiae belongs went extinct in New Zealand, and the extant New Zealand Styphelieae are derived from Australian lineages that recolonised (presumably by long distance dispersal) no earlier than the late Miocene to Pliocene. Copyright © 2012 Elsevier Inc. All rights reserved.

Alnus subgenus Alnus in the Eocene of western North America based on leaves, associated catkins, pollen, and fruits.

PubMed

Liu, Xiaoyan; Manchester, Steven R; Jin, Jianhua

2014-11-01

The fossil record of alder (Alnus) is well known in the Cenozoic deposits throughout the northern hemisphere, based on numerous reports of the distinctive pollen, cone-like infructescences, staminate inflorescences, and leaves. However, our understanding of the systematic position of these fossils relative to the modern phylogeny of the genus has been limited because most fossils were described from only one organ. We examined well-preserved leaves and associated fruiting and staminate catkins from the middle Eocene, Clarno Formation, Oregon, USA by stereomicroscopy. In situ and dispersed pollen were cleaned with HF and acetolized for light and scanning electron microscopy. We reconstructed a new extinct species based on multiple organs and discuss significant phytogeographic and phylogenetic implications for Alnus. Alnus clarnoensis sp. nov. is described based on serrate leaves with 1-4 small teeth between each primary tooth, associated cone-like fruiting catkins with fruits in situ, and associated slender pollen catkins bearing in situ 3- to 6-pored pollen with arci between the pores. Combined investigations of each organ indicate that they probably derive from the same species and can be confidently attributed to subgenus Alnus Furlow based on leaf architecture and pollen pore number frequency. The Clarno fossils are most similar to the extant North American species of subgenus Alnus rather than to those from Asia and Europe, indicating that this modern subgenus was already distinct by the middle Eocene and that the intercontinental migration likely occurred earlier. © 2014 Botanical Society of America, Inc.

Virtual reconstruction of modern and fossil hominoid crania: consequences of reference sample choice.

PubMed

Senck, Sascha; Bookstein, Fred L; Benazzi, Stefano; Kastner, Johann; Weber, Gerhard W

2015-05-01

Most hominin cranial fossils are incomplete and require reconstruction prior to subsequent analyses. Missing data can be estimated by geometric morphometrics using information from complete specimens, for example, by using thin-plate splines. In this study, we estimate missing data in several virtually fragmented models of hominoid crania (Homo, Pan, Pongo) and fossil hominins (e.g., Australopithecus africanus, Homo heidelbergensis). The aim is to investigate in which way different references influence estimations of cranial shape and how this information can be employed in the reconstruction of fossils. We used a sample of 64 three-dimensional digital models of complete human, chimpanzee, and orangutan crania and a set of 758 landmarks and semilandmarks. The virtually knocked out neurocranial and facial areas that were reconstructed corresponded to those of a real case found in A.L. 444-2 (A. afarensis) cranium. Accuracy of multiple intraspecies and interspecies reconstructions was computed as the maximum square root of the mean squared difference between the original and the reconstruction (root mean square). The results show that the uncertainty in reconstructions is a function of both the geometry of the knockout area and the dissimilarity between the reference sample and the specimen(s) undergoing reconstruction. We suggest that it is possible to estimate large missing cranial areas if the shape of the reference is similar enough to the shape of the specimen reconstructed, though caution must be exercised when employing these reconstructions in subsequent analyses. We provide a potential guide for the choice of the reference by means of bending energy. © 2015 Wiley Periodicals, Inc.

Hominin track assemblages from Okote Member deposits near Ileret, Kenya, and their implications for understanding fossil hominin paleobiology at 1.5 Ma.

PubMed

Hatala, Kevin G; Roach, Neil T; Ostrofsky, Kelly R; Wunderlich, Roshna E; Dingwall, Heather L; Villmoare, Brian A; Green, David J; Braun, David R; Harris, John W K; Behrensmeyer, Anna K; Richmond, Brian G

2017-11-01

Tracks can provide unique, direct records of behaviors of fossil organisms moving across their landscapes millions of years ago. While track discoveries have been rare in the human fossil record, over the last decade our team has uncovered multiple sediment surfaces within the Okote Member of the Koobi Fora Formation near Ileret, Kenya that contain large assemblages of ∼1.5 Ma fossil hominin tracks. Here, we provide detailed information on the context and nature of each of these discoveries, and we outline the specific data that are preserved on the Ileret hominin track surfaces. We analyze previously unpublished data to refine and expand upon earlier hypotheses regarding implications for hominin anatomy and social behavior. While each of the track surfaces discovered at Ileret preserves a different amount of data that must be handled in particular ways, general patterns are evident. Overall, the analyses presented here support earlier interpretations of the ∼1.5 Ma Ileret track assemblages, providing further evidence of large, human-like body sizes and possibly evidence of a group composition that could support the emergence of certain human-like patterns of social behavior. These data, used in concert with other forms of paleontological and archaeological evidence that are deposited on different temporal scales, offer unique windows through which we can broaden our understanding of the paleobiology of hominins living in East Africa at ∼1.5 Ma. Copyright © 2017 Elsevier Ltd. All rights reserved.

Introducing global peat-specific temperature and pH calibrations based on brGDGT bacterial lipids

NASA Astrophysics Data System (ADS)

Naafs, B. D. A.; Inglis, G. N.; Zheng, Y.; Amesbury, M. J.; Biester, H.; Bindler, R.; Blewett, J.; Burrows, M. A.; del Castillo Torres, D.; Chambers, F. M.; Cohen, A. D.; Evershed, R. P.; Feakins, S. J.; Gałka, M.; Gallego-Sala, A.; Gandois, L.; Gray, D. M.; Hatcher, P. G.; Honorio Coronado, E. N.; Hughes, P. D. M.; Huguet, A.; Könönen, M.; Laggoun-Défarge, F.; Lähteenoja, O.; Lamentowicz, M.; Marchant, R.; McClymont, E.; Pontevedra-Pombal, X.; Ponton, C.; Pourmand, A.; Rizzuti, A. M.; Rochefort, L.; Schellekens, J.; De Vleeschouwer, F.; Pancost, R. D.

2017-07-01

Glycerol dialkyl glycerol tetraethers (GDGTs) are membrane-spanning lipids from Bacteria and Archaea that are ubiquitous in a range of natural archives and especially abundant in peat. Previous work demonstrated that the distribution of bacterial branched GDGTs (brGDGTs) in mineral soils is correlated to environmental factors such as mean annual air temperature (MAAT) and soil pH. However, the influence of these parameters on brGDGT distributions in peat is largely unknown. Here we investigate the distribution of brGDGTs in 470 samples from 96 peatlands around the world with a broad mean annual air temperature (-8 to 27 °C) and pH (3-8) range and present the first peat-specific brGDGT-based temperature and pH calibrations. Our results demonstrate that the degree of cyclisation of brGDGTs in peat is positively correlated with pH, pH = 2.49 × CBTpeat + 8.07 (n = 51, R2 = 0.58, RMSE = 0.8) and the degree of methylation of brGDGTs is positively correlated with MAAT, MAATpeat (°C) = 52.18 × MBT5me‧ - 23.05 (n = 96, R2 = 0.76, RMSE = 4.7 °C). These peat-specific calibrations are distinct from the available mineral soil calibrations. In light of the error in the temperature calibration (∼4.7 °C), we urge caution in any application to reconstruct late Holocene climate variability, where the climatic signals are relatively small, and the duration of excursions could be brief. Instead, these proxies are well-suited to reconstruct large amplitude, longer-term shifts in climate such as deglacial transitions. Indeed, when applied to a peat deposit spanning the late glacial period (∼15.2 kyr), we demonstrate that MAATpeat yields absolute temperatures and relative temperature changes that are consistent with those from other proxies. In addition, the application of MAATpeat to fossil peat (i.e. lignites) has the potential to reconstruct terrestrial climate during the Cenozoic. We conclude that there is clear potential to use brGDGTs in peats and lignites to reconstruct past terrestrial climate.

Is a 'one size fits all' taphonomic model appropriate for the Mazon Creek Lagerstätte?

NASA Astrophysics Data System (ADS)

Clements, Thomas; Purnell, Mark; Gabbott, Sarah

2017-04-01

The Late Carboniferous Mazon Creek Lagerstätte (Illinois, USA) is a world renowned fossil deposit with a huge diversity of preserved flora and fauna. It is widely considered to represent the most complete Late Carboniferous river delta ecosystem because researchers have identified that the deposit preserves organisms from multiple habitats including coastal swamps, brackish lagoons and oceanic environments. Often these fossils have exquisite soft tissue preservation yielding far more information that the 'normal' skeletal fossil record, while some soft bodied animals, such as the notorious Tully Monster (Tullimonstrum gregarium), are only known from this locality. However, constraining a 'one-size fits all' taphonomic model for the Mazon Creek is difficult because of our poor understanding of sideritic concretionary formation or preservation (i.e. the presence of large numbers of unfossiliferous concretions), the large geographical area, the influences of fresh, brackish and saline waters during burial and the subsequent complicated diagenetic processes. To determine the preservational pathways of Mazon Creek fossils, we have compiled data of the mode of preservation of morphological characters for all major groups of fossil organisms found in this Lagerstätte. This data can be used to test for variance in mode of preservation between taxa and also between specific tissue types. Furthermore, experimental decay data is used to constrain the impact of decay prior to fossilisation. Our analysis indicates that there are variations in preservation potential of specific characters shared by taxa. Modes of preservation, however, seem to be consistent across the majority of taxa dependant on locality. This quantitative approach is being utilised as part of a larger ongoing investigation which combines taphonomy with geochemical analysis of siderite concretions from across the vast geographical area of the Mazon Creek. Together this approach will allow us to elucidate the preservation pathways of organisms and will lead to better understanding of taphonomic biases operating in this Lagerstätte.

Calibration and error analysis of metal-oxide-semiconductor field-effect transistor dosimeters for computed tomography radiation dosimetry.

PubMed

Trattner, Sigal; Prinsen, Peter; Wiegert, Jens; Gerland, Elazar-Lars; Shefer, Efrat; Morton, Tom; Thompson, Carla M; Yagil, Yoad; Cheng, Bin; Jambawalikar, Sachin; Al-Senan, Rani; Amurao, Maxwell; Halliburton, Sandra S; Einstein, Andrew J

2017-12-01

Metal-oxide-semiconductor field-effect transistors (MOSFETs) serve as a helpful tool for organ radiation dosimetry and their use has grown in computed tomography (CT). While different approaches have been used for MOSFET calibration, those using the commonly available 100 mm pencil ionization chamber have not incorporated measurements performed throughout its length, and moreover, no previous work has rigorously evaluated the multiple sources of error involved in MOSFET calibration. In this paper, we propose a new MOSFET calibration approach to translate MOSFET voltage measurements into absorbed dose from CT, based on serial measurements performed throughout the length of a 100-mm ionization chamber, and perform an analysis of the errors of MOSFET voltage measurements and four sources of error in calibration. MOSFET calibration was performed at two sites, to determine single calibration factors for tube potentials of 80, 100, and 120 kVp, using a 100-mm-long pencil ion chamber and a cylindrical computed tomography dose index (CTDI) phantom of 32 cm diameter. The dose profile along the 100-mm ion chamber axis was sampled in 5 mm intervals by nine MOSFETs in the nine holes of the CTDI phantom. Variance of the absorbed dose was modeled as a sum of the MOSFET voltage measurement variance and the calibration factor variance, the latter being comprised of three main subcomponents: ionization chamber reading variance, MOSFET-to-MOSFET variation and a contribution related to the fact that the average calibration factor of a few MOSFETs was used as an estimate for the average value of all MOSFETs. MOSFET voltage measurement error was estimated based on sets of repeated measurements. The calibration factor overall voltage measurement error was calculated from the above analysis. Calibration factors determined were close to those reported in the literature and by the manufacturer (~3 mV/mGy), ranging from 2.87 to 3.13 mV/mGy. The error σ V of a MOSFET voltage measurement was shown to be proportional to the square root of the voltage V: σV=cV where c = 0.11 mV. A main contributor to the error in the calibration factor was the ionization chamber reading error with 5% error. The usage of a single calibration factor for all MOSFETs introduced an additional error of about 5-7%, depending on the number of MOSFETs that were used to determine the single calibration factor. The expected overall error in a high-dose region (~30 mGy) was estimated to be about 8%, compared to 6% when an individual MOSFET calibration was performed. For a low-dose region (~3 mGy), these values were 13% and 12%. A MOSFET calibration method was developed using a 100-mm pencil ion chamber and a CTDI phantom, accompanied by an absorbed dose error analysis reflecting multiple sources of measurement error. When using a single calibration factor, per tube potential, for different MOSFETs, only a small error was introduced into absorbed dose determinations, thus supporting the use of a single calibration factor for experiments involving many MOSFETs, such as those required to accurately estimate radiation effective dose. © 2017 American Association of Physicists in Medicine.

Improving Planck calibration by including frequency-dependent relativistic corrections

NASA Astrophysics Data System (ADS)

Quartin, Miguel; Notari, Alessio

2015-09-01

The Planck satellite detectors are calibrated in the 2015 release using the "orbital dipole", which is the time-dependent dipole generated by the Doppler effect due to the motion of the satellite around the Sun. Such an effect has also relativistic time-dependent corrections of relative magnitude 10-3, due to coupling with the "solar dipole" (the motion of the Sun compared to the CMB rest frame), which are included in the data calibration by the Planck collaboration. We point out that such corrections are subject to a frequency-dependent multiplicative factor. This factor differs from unity especially at the highest frequencies, relevant for the HFI instrument. Since currently Planck calibration errors are dominated by systematics, to the point that polarization data is currently unreliable at large scales, such a correction can in principle be highly relevant for future data releases.

Exceptional fossil preservation demonstrates a new mode of axial skeleton elongation in early ray-finned fishes.

PubMed

Maxwell, Erin E; Furrer, Heinz; Sánchez-Villagra, Marcelo R

2013-01-01

Elongate body plans have evolved independently multiple times in vertebrates, and involve either an increase in the number or in the length of the vertebrae. Here, we describe a new mechanism of body elongation in saurichthyids, an extinct group of elongate early ray-finned fishes. The rare preservation of soft tissue in a specimen of Saurichthys curionii from the Middle Triassic (Ladinian) of Switzerland provides significant new information on the relationship between the musculature and the skeleton. This new fossil material shows that elongation in these fishes results from doubling the number of neural arch-like elements per myomeric segment. This unique way of generating an elongate body plan demonstrates the evolutionary lability of the vertebral column in non-teleostean fishes. The shape and arrangement of preserved myosepta suggest that S. curionii was not a highly flexible fish, in spite of the increase in the number of neural arch-like elements.

Perimortem fractures in Lucy suggest mortality from fall out of tall tree.

PubMed

Kappelman, John; Ketcham, Richard A; Pearce, Stephen; Todd, Lawrence; Akins, Wiley; Colbert, Matthew W; Feseha, Mulugeta; Maisano, Jessica A; Witzel, Adrienne

2016-09-22

The Pliocene fossil 'Lucy' (Australopithecus afarensis) was discovered in the Afar region of Ethiopia in 1974 and is among the oldest and most complete fossil hominin skeletons discovered. Here we propose, on the basis of close study of her skeleton, that her cause of death was a vertical deceleration event or impact following a fall from considerable height that produced compressive and hinge (greenstick) fractures in multiple skeletal elements. Impacts that are so severe as to cause concomitant fractures usually also damage internal organs; together, these injuries are hypothesized to have caused her death. Lucy has been at the centre of a vigorous debate about the role, if any, of arboreal locomotion in early human evolution. It is therefore ironic that her death can be attributed to injuries resulting from a fall, probably out of a tall tree, thus offering unusual evidence for the presence of arborealism in this species.

Daughters inherit colonies from mothers in the 'living-fossil' ant Nothomyrmecia macrops

NASA Astrophysics Data System (ADS)

Sanetra, Matthias; Crozier, Ross H.

2002-02-01

Newly mated queens of monogynous (single queen) ants usually found their colonies independently, without the assistance of workers. In polygynous (multiple queen) species queens are often adopted back into their natal nest and new colonies are established by budding. We report that the Australian 'living-fossil' ant, Nothomyrmecia macrops, is exceptional in that its single queen can be replaced by one of the colony's daughters. This type of colony founding is an interesting alternative reproductive strategy in monogynous ants, which maximizes fitness under kin selection. Successive queen replacement results in a series of reproductives over time (serial polygyny), making these colonies potentially immortal. Workers raise nieces and nephews (relatedness ≤ 0.375) the year after queen replacement. Although N. macrops is 'primitive' in many other respects, colony inheritance is likely to be a derived specialization resulting from ecological constraints on solitary founding.

Unusual anal fin in a Devonian jawless vertebrate reveals complex origins of paired appendages

PubMed Central

Sansom, Robert S.; Gabbott, Sarah E.; Purnell, M. A.

2013-01-01

Jawed vertebrates (gnathostomes) have undergone radical anatomical and developmental changes in comparison with their jawless cousins (cyclostomes). Key among these is paired appendages (fins, legs and wings), which first evolved at some point on the gnathostome stem. The anatomy of fossil stem gnathostomes is, therefore, fundamental to our understanding of the nature and timing of the origin of this complex innovation. Here, we show that Euphanerops, a fossil jawless fish from the Devonian, possessed paired anal-fin radials, but no pectoral or pelvic fins. This unique condition occurs at an early stage on the stem-gnathostome lineage. This condition, and comparison with the varied condition of paired fins in other ostracoderms, indicates that there was a large amount of developmental plasticity during this episode—rather than a gradual evolution of this complex feature. Apparently, a number of different clades were exploring morphospace or undergoing multiple losses. PMID:23576777

Life in changing fluids: A critical appraisal of swimming animals before the Cambrian.

PubMed

Gold, David

2018-05-03

Molecular and fossil data place the initial diversification of animals in the Neoproterozoic, though there remains too much enough uncertainty to produce an exact chronology. This is unfortunate, as the Neoproterozoic represents a period of intense climate change, including multiple global glaciation events as well changes to ocean chemistry and oxygen content. Several authors have suggested that the coevolution of animals and their environment was tightly coupled, but such hypotheses rest on the presence of swimming (pelagic) species. In this paper, I review the evidence for pelagic animals during the Neoproterozoic. I conclude that there are very few groups of planktotrophic swimming animals that were likely to have existed at this time, with the possible exception of medusozoan cnidarians (jellyfish). Ultimately, hypotheses connecting Earth and animal evolution in the Neoproterozoic need to be tested with more geochemical work, fossil discoveries, and refinement of molecular clocks targeted on the relevant groups.

Isotopic fingerprints of bacterial chemosymbiosis in the bivalve Loripes lacteus

NASA Astrophysics Data System (ADS)

Dreier, A.; Stannek, L.; Blumenberg, M.; Taviani, M.; Sigovini, M.; Wrede, C.; Thiel, V.; Hoppert, M.

2012-04-01

Metazoans with chemosynthetic bacterial endosymbionts are widespread in marine habitats and respective endosymbioses are known from seven recent animal phyla. However, little is known about endosymbioses in fossil settings and, hence, ecological significance in earth history. In the presented project, we investigate the ancient and recent bivalve fauna living at marine sedimentary oxic/anoxic interfaces. Two bivalve species collected from the same benthic environment - a Mediterranean lagoon - were studied in detail. The diet of Loripes lacteus is based on thiotrophic gill symbionts whereas Venerupis aureus is a filter feeding bivalve without symbionts. The presence of three key enzymes from sulfur oxidation (APS-reductase), carbon fixation (RubisCO) and assimilation of nitrogen (glutamine synthetase [GS]) were detected by immunofluorescence in symbionts of Loripes and/or by activity tests in living specimens. In search of biosignatures associated with thiotrophic chemosymbionts that might be suitable for detection of chemosymbiotic diets in recent and fossil bivalve shells, we analyzed the isotopic composition of shell lipids (δ13C) and the bulk organic matrix of the shell (δ13C, δ15N, δ34S). We could show that the combined δ15N and δ13C values from shell extracts are stable in subfossil (Pleistocene) bivalve specimens, as long as the isotopic data is "calibrated" with respective signatures from a filter feeding bivalve sampled from the same site or lithostratigraphic bed.

Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution

PubMed Central

Broughton, Richard E.; Betancur-R., Ricardo; Li, Chenhong; Arratia, Gloria; Ortí, Guillermo

2013-01-01

Over half of all vertebrates are “fishes”, which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a full sample of all bony fishes. Here we conducted a comprehensive phylogenetic study on a broad taxonomic sample of 61 actinopterygian and sarcopterygian lineages (with a chondrichthyan outgroup) using a molecular data set of 21 independent loci. These data yielded a resolved phylogenetic hypothesis for extant Osteichthyes, including 1) reciprocally monophyletic Sarcopterygii and Actinopterygii, as currently understood, with polypteriforms as the first diverging lineage within Actinopterygii; 2) a monophyletic group containing gars and bowfin (= Holostei) as sister group to teleosts; and 3) the earliest diverging lineage among teleosts being Elopomorpha, rather than Osteoglossomorpha. Relaxed-clock dating analysis employing a set of 24 newly applied fossil calibrations reveals divergence times that are more consistent with paleontological estimates than previous studies. Establishing a new phylogenetic pattern with accurate divergence dates for bony fishes illustrates several areas where the fossil record is incomplete and provides critical new insights on diversification of this important vertebrate group. PMID:23788273

Associated terrestrial and marine fossils in the late-glacial Presumpscot Formation, southern Maine, USA, and the marine reservoir effect on radiocarbon ages

NASA Astrophysics Data System (ADS)

Thompson, Woodrow B.; Griggs, Carol B.; Miller, Norton G.; Nelson, Robert E.; Weddle, Thomas K.; Kilian, Taylor M.

2011-05-01

Excavations in the late-glacial Presumpscot Formation at Portland, Maine, uncovered tree remains and other terrestrial organics associated with marine invertebrate shells in a landslide deposit. Buds of Populus balsamifera (balsam poplar) occurred with twigs of Picea glauca (white spruce) in the Presumpscot clay. Tree rings in Picea logs indicate that the trees all died during winter dormancy in the same year. Ring widths show patterns of variation indicating responses to environmental changes. Fossil mosses and insects represent a variety of species and wet to dry microsites. The late-glacial environment at the site was similar to that of today's Maine coast. Radiocarbon ages of 14 tree samples are 11,907 ± 31 to 11,650 ± 50 14C yr BP. Wiggle matching of dated tree-ring segments to radiocarbon calibration data sets dates the landslide occurrence at ca. 13,520 + 95/-20 cal yr BP. Ages of shells juxtaposed with the logs are 12,850 ± 65 14C yr BP ( Mytilus edulis) and 12,800 ± 55 14C yr BP ( Balanus sp.), indicating a marine reservoir age of about 1000 yr. Using this value to correct previously published radiocarbon ages reduces the discrepancy between the Maine deglaciation chronology and the varve-based chronology elsewhere in New England.

Origin of the Eumetazoa: testing ecological predictions of molecular clocks against the Proterozoic fossil record

NASA Technical Reports Server (NTRS)

Peterson, Kevin J.; Butterfield, Nicholas J.

2005-01-01

Molecular clocks have the potential to shed light on the timing of early metazoan divergences, but differing algorithms and calibration points yield conspicuously discordant results. We argue here that competing molecular clock hypotheses should be testable in the fossil record, on the principle that fundamentally new grades of animal organization will have ecosystem-wide impacts. Using a set of seven nuclear-encoded protein sequences, we demonstrate the paraphyly of Porifera and calculate sponge/eumetazoan and cnidarian/bilaterian divergence times by using both distance [minimum evolution (ME)] and maximum likelihood (ML) molecular clocks; ME brackets the appearance of Eumetazoa between 634 and 604 Ma, whereas ML suggests it was between 867 and 748 Ma. Significantly, the ME, but not the ML, estimate is coincident with a major regime change in the Proterozoic acritarch record, including: (i) disappearance of low-diversity, evolutionarily static, pre-Ediacaran acanthomorphs; (ii) radiation of the high-diversity, short-lived Doushantuo-Pertatataka microbiota; and (iii) an order-of-magnitude increase in evolutionary turnover rate. We interpret this turnover as a consequence of the novel ecological challenges accompanying the evolution of the eumetazoan nervous system and gut. Thus, the more readily preserved microfossil record provides positive evidence for the absence of pre-Ediacaran eumetazoans and strongly supports the veracity, and therefore more general application, of the ME molecular clock.

Radiation of extant cetaceans driven by restructuring of the oceans.

PubMed

Steeman, Mette E; Hebsgaard, Martin B; Fordyce, R Ewan; Ho, Simon Y W; Rabosky, Daniel L; Nielsen, Rasmus; Rahbek, Carsten; Glenner, Henrik; Sørensen, Martin V; Willerslev, Eske

2009-12-01

The remarkable fossil record of whales and dolphins (Cetacea) has made them an exemplar of macroevolution. Although their overall adaptive transition from terrestrial to fully aquatic organisms is well known, this is not true for the radiation of modern whales. Here, we explore the diversification of extant cetaceans by constructing a robust molecular phylogeny that includes 87 of 89 extant species. The phylogeny and divergence times are derived from nuclear and mitochondrial markers, calibrated with fossils. We find that the toothed whales are monophyletic, suggesting that echolocation evolved only once early in that lineage some 36-34 Ma. The rorqual family (Balaenopteridae) is restored with the exclusion of the gray whale, suggesting that gulp feeding evolved 18-16 Ma. Delphinida, comprising all living dolphins and porpoises other than the Ganges/Indus dolphins, originated about 26 Ma; it contains the taxonomically rich delphinids, which began diversifying less than 11 Ma. We tested 2 hypothesized drivers of the extant cetacean radiation by assessing the tempo of lineage accumulation through time. We find no support for a rapid burst of speciation early in the history of extant whales, contrasting with expectations of an adaptive radiation model. However, we do find support for increased diversification rates during periods of pronounced physical restructuring of the oceans. The results imply that paleogeographic and paleoceanographic changes, such as closure of major seaways, have influenced the dynamics of radiation in extant cetaceans.

CEOS visualization environment (COVE) tool for intercalibration of satellite instruments

USGS Publications Warehouse

Kessler, P.D.; Killough, B.D.; Gowda, S.; Williams, B.R.; Chander, G.; Qu, Min

2013-01-01

Increasingly, data from multiple instruments are used to gain a more complete understanding of land surface processes at a variety of scales. Intercalibration, comparison, and coordination of satellite instrument coverage areas is a critical effort of international and domestic space agencies and organizations. The Committee on Earth Observation Satellites Visualization Environment (COVE) is a suite of browser-based applications that leverage Google Earth to display past, present, and future satellite instrument coverage areas and coincident calibration opportunities. This forecasting and ground coverage analysis and visualization capability greatly benefits the remote sensing calibration community in preparation for multisatellite ground calibration campaigns or individual satellite calibration studies. COVE has been developed for use by a broad international community to improve the efficiency and efficacy of such calibration planning efforts, whether those efforts require past, present, or future predictions. This paper provides a brief overview of the COVE tool, its validation, accuracies, and limitations with emphasis on the applicability of this visualization tool for supporting ground field campaigns and intercalibration of satellite instruments.

An overview of sensor calibration inter-comparison and applications

USGS Publications Warehouse

Xiong, Xiaoxiong; Cao, Changyong; Chander, Gyanesh

2010-01-01

Long-term climate data records (CDR) are often constructed using observations made by multiple Earth observing sensors over a broad range of spectra and a large scale in both time and space. These sensors can be of the same or different types operated on the same or different platforms. They can be developed and built with different technologies and are likely operated over different time spans. It has been known that the uncertainty of climate models and data records depends not only on the calibration quality (accuracy and stability) of individual sensors, but also on their calibration consistency across instruments and platforms. Therefore, sensor calibration inter-comparison and validation have become increasingly demanding and will continue to play an important role for a better understanding of the science product quality. This paper provides an overview of different methodologies, which have been successfully applied for sensor calibration inter-comparison. Specific examples using different sensors, including MODIS, AVHRR, and ETM+, are presented to illustrate the implementation of these methodologies.

Genetic algorithms for the application of Activated Sludge Model No. 1.

PubMed

Kim, S; Lee, H; Kim, J; Kim, C; Ko, J; Woo, H; Kim, S

2002-01-01

The genetic algorithm (GA) has been integrated into the IWA ASM No. 1 to calibrate important stoichiometric and kinetic parameters. The evolutionary feature of GA was used to configure the multiple local optima as well as the global optimum. The objective function of optimization was designed to minimize the difference between estimated and measured effluent concentrations at the activated sludge system. Both steady state and dynamic data of the simulation benchmark were used for calibration using denitrification layout. Depending upon the confidence intervals and objective functions, the proposed method provided distributions of parameter space. Field data have been collected and applied to validate calibration capacity of GA. Dynamic calibration was suggested to capture periodic variations of inflow concentrations. Also, in order to verify this proposed method in real wastewater treatment plant, measured data sets for substrate concentrations were obtained from Haeundae wastewater treatment plant and used to estimate parameters in the dynamic system. The simulation results with calibrated parameters matched well with the observed concentrations of effluent COD.

CEOS Visualization Environment (COVE) Tool for Intercalibration of Satellite Instruments

NASA Technical Reports Server (NTRS)

Kessler, Paul D.; Killough, Brian D.; Gowda, Sanjay; Williams, Brian R.; Chander, Gyanesh; Qu, Min

2013-01-01

Increasingly, data from multiple instruments are used to gain a more complete understanding of land surface processes at a variety of scales. Intercalibration, comparison, and coordination of satellite instrument coverage areas is a critical effort of space agencies and of international and domestic organizations. The Committee on Earth Observation Satellites Visualization Environment (COVE) is a suite of browser-based applications that leverage Google Earth to display past, present, and future satellite instrument coverage areas and coincident calibration opportunities. This forecasting and ground coverage analysis and visualization capability greatly benefits the remote sensing calibration community in preparation for multisatellite ground calibration campaigns or individual satellite calibration studies. COVE has been developed for use by a broad international community to improve the efficiency and efficacy of such calibration efforts. This paper provides a brief overview of the COVE tool, its validation, accuracies and limitations with emphasis on the applicability of this visualization tool for supporting ground field campaigns and intercalibration of satellite instruments.

["Human races": history of a dangerous illusion].

PubMed

Louryan, S

2014-01-01

The multiplication of offences prompted by racism and the increase of complaints for racism leads us to consider the illusory concept of "human races". This idea crossed the history, and was reinforced by the discovery of remote tribes and human fossils, and by the development of sociobiology and quantitative psychology. Deprived of scientific base, the theory of the "races" must bow before the notions of genetic variation and unicity of mankind.

Multiple Regression Redshift Calibration for Clusters of Galaxies

NASA Astrophysics Data System (ADS)

Kalinkov, M.; Kuneva, I.; Valtchanov, I.

A new procedure for calibration of distances to ACO (Abell et al.1989) clusters of galaxies has been developed. In the previous version of the Reference Catalog of ACO Clusters of Galaxies (Kalinkov & Kuneva 1992) an attempt has been made to compare various calibration schemes. For the Version 93 we have made some refinements. Many improvements from the early days of the photometric calibration have been made --- from Rowan-Robinson (1972), Corwin (1974), Kalinkov & Kuneva (1975), Mills Hoskins (1977) to more complicated --- Leir & van den Bergh (1977), Postman et al.(1985), Kalinkov Kuneva (1985, 1986, 1990), Scaramella et al.(1991), Zucca et al. (1993). It was shown that it is impossible to use the same calibration relation for northern (A) and southern (ACO) clusters of galaxies. Therefore the calibration have to be made separately for both catalogs. Moreover it is better if one could find relations for the 274 A-clusters, studied by the authors of ACO. We use the luminosity distance for H0=100km/s/Mpc and q0 = 0.5 and we have 1200 clusters with measured redshifts. The first step is to fit log(z) on m10 (magnitude of the tenth rank galaxy) for A-clusters and on m1, m3 and m10 for ACO clusters. The second step is to take into account the K-correction and the Scott effect (Postman et al.1985) with iterative process. To avoid the initial errors of the redshift estimates in A- and ACO catalogs we adopt Hubble's law for the apparent radial distribution of galaxies in clusters. This enable us to calculate a new cluster richness from preliminary redshift estimate. This is the third step. Further continues the study of the correlation matrix between log(z) and prospective predictors --- new richness groups, BM, RS and A types, radio and X-ray fluxes, apparent separations between the first three brightest galaxies, mean population (gal/sq.deg), Multiple linear as well as nonlinear regression estimators are found. Many clusters that deviate by more than 2.5 sigmas are rejected. Each case is examined for observational errors, substructuring, foreground and background. Some of the clusters are doubtful --- most probably they have to be excluded from the catalogs. The multiple regressions allow us to estimate redshift in the range 0.02 to 0.2 with an error of 7 percent.

The Continuing Debate on Deep Molluscan Phylogeny: Evidence for Serialia (Mollusca, Monoplacophora + Polyplacophora)

PubMed Central

Stöger, I.; Sigwart, J. D.; Kano, Y.; Knebelsberger, T.; Marshall, B. A.; Schwabe, E.; Schrödl, M.

2013-01-01

Molluscs are a diverse animal phylum with a formidable fossil record. Although there is little doubt about the monophyly of the eight extant classes, relationships between these groups are controversial. We analysed a comprehensive multilocus molecular data set for molluscs, the first to include multiple species from all classes, including five monoplacophorans in both extant families. Our analyses of five markers resolve two major clades: the first includes gastropods and bivalves sister to Serialia (monoplacophorans and chitons), and the second comprises scaphopods sister to aplacophorans and cephalopods. Traditional groupings such as Testaria, Aculifera, and Conchifera are rejected by our data with significant Approximately Unbiased (AU) test values. A new molecular clock indicates that molluscs had a terminal Precambrian origin with rapid divergence of all eight extant classes in the Cambrian. The recovery of Serialia as a derived, Late Cambrian clade is potentially in line with the stratigraphic chronology of morphologically heterogeneous early mollusc fossils. Serialia is in conflict with traditional molluscan classifications and recent phylogenomic data. Yet our hypothesis, as others from molecular data, implies frequent molluscan shell and body transformations by heterochronic shifts in development and multiple convergent adaptations, leading to the variable shells and body plans in extant lineages. PMID:24350268

Dispersals of Hyoscyameae and Mandragoreae (Solanaceae) from the New World to Eurasia in the early Miocene and their biogeographic diversification within Eurasia.

PubMed

Tu, Tieyao; Volis, Sergei; Dillon, Michael O; Sun, Hang; Wen, Jun

2010-12-01

The cosmopolitan Solanaceae contains 21 tribes and has the greatest diversity in South America. Hyoscyameae and Mandragoreae are the only tribes of this family distributed exclusively in Eurasia with two centers of diversity: the Mediterranean-Turanian (MT) region and the Tibetan Plateau (TP). In this study, we examined the origins and biogeographical diversifications of the two tribes based on the phylogenetic framework and chronogram inferred from a combined data set of six plastid DNA regions (the atpB gene, the ndhF gene, the rps16-trnK intergenic spacer, the rbcL gene, the trnC-psbM region and the psbA-trnH intergenic spacer) with two fossil calibration points. Our data suggest that Hyoscyameae and Mandragoreae each forms a monophyletic group independently derived from different New World lineages in the early Miocene. Phylogenetic relationships within both tribes are generally well resolved. All genera of Hyoscyameae are found to be monophyletic and they diversified in middle to late Miocene. At nearly the same time, Mandragoreae split into two clades, corresponding to the MT region and the TP region, respectively. Both the phylogenetic relationships and the estimated ages of Hyoscyameae and Mandragoreae support two independent dispersal events of their ancestors from the New World into Eurasia. After their arrivals in Eurasia, the two tribes diversified primarily in the MT region and in the TP region via multiple biogeographic processes including vicariance, dispersal, recolonization or being preserved as relicts, from the mid Miocene to the late Quaternary. Published by Elsevier Inc.

Search for Martian fossil communities: Science strategies, sediment sites, and sample handling

NASA Technical Reports Server (NTRS)

Desmarais, David J.

1988-01-01

The strategy for locating and sampling possible fossilized Martian organisms benefits from our experience with fossil microbial ecosystems on Earth. Evidence of early life is typically preserved as stromatolites in carbonates and cherts, and as microfossils in cherts, carbonates and shales. Stromatolites, which are laminated flat or domal structures built by microbial communities, are very likely the oldest and most widespread relics of early life. These communities flourished in supratidal to subtidal coastal benthic environments, wherever sunlight was available and where incoming sediments were insufficient to bury the communities before they became established. A logical site for such communities on Mars might be those areas in an ancient lake bed which were furthest from sediment input, but were still sufficiently shallow to have received sunlight. Therefore, although some sites within Valles Marineris might have contained ponded water, the possibly abundant sediment inputs might have overwhelmed stromatolite-like communities. Localized depressions which acted as catchment basins for ancient branched valley systems might be superior sites. Perhaps such depressions received drainage which, because of the relatively modest water discharges implied for these streams, was relatively low in transported sediment. Multiple streams converging on a single basin might have been able to maintain a shallow water environment for extended periods of time.

Fire impacts on the cryosphere

NASA Astrophysics Data System (ADS)

Kehrwald, N. M.; Zennaro, P.; Skiles, M.; Barbante, C.

2015-12-01

Continental-scale smog clouds and massive boreal smoke plumes deposit dark particles on glaciers, darkening their surfaces and altering surface albedo. These atmospheric brown clouds are primarily comprised of both fossil fuel and biomass burning combustion products. Here, we examine the biomass burning contribution to aerosols trapped in the cryosphere through investigating the specific molecular marker levoglucosan (1,6-anhydro-β-D-glucopyranose) in ice cores. Levoglucosan is only produced by cellulose combustion, and therefore is an ideal comparison for multi-proxy investigations incorporating other markers with multiple sources. Wildfire combustion products are a major component of dark aerosols deposited on the Greenland ice sheet during the 2012 melt event. Levoglucosan concentrations that demonstrate the biomass burning contribution are similar to black carbon concentrations that record both fossil fuel and biomass burning during this same event. This similarity is especially important as levoglucosan and black carbon trends differ during the industrial era in the NEEM, Greenland ice core, demonstrating different contributions of fossil fuel and biomass burning to the Greenland ice sheet. These differences are also present in the EPICA Dome C Antarctic ice core. Low-latitude ice cores such as Kilimanjaro, Tanzania and Muztag, Tibet demonstrate that climate is still the primary control over fire activity in these regions, even with increased modern biomass burning and the possible impacts of atmospheric brown clouds.

U-series ages of solitary corals from the California coast by mass spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stein, M.; Wasserburg, G.J.; Chen, J.H.

1991-12-01

The purpose of this study is to evaluate the feasibility of dating fossil solitary corals from Pleistocene marine strandlines outside tropical latitudes using the recently developed high sensitivity, high-precision U-series technique based on thermal-ionization mass-spectrometry (TIMS). The TIMS technique is much more efficient than conventional {alpha} spectrometry and, as a result, multiple samples of an individual coral skeleton, or different specimens from the same bed can be analyzed. Detached and well-rounded fossil specimens of the solitary coral Balanophyllia elegans were collected from relict littoral deposits on emergent marine terraces along the California coast at Cayucos terrace, Shell Beach terrace, Nestormore » terrace, San Diego, Bird Rock terrace, San Diego. Attached living specimens were collected from the intertidal zone on the modern terrace at Moss Beach. The calculated initial {sup 234}U activities in the fossil specimens of Balanophyllia elegans are higher than the {sup 234}U activity in modern seawater or in the modern specimen. The higher initial activities could possibly reflect the influx of {sup 234}U-enriched continental water into Pleistocene coastal waters, or it could reflect the influx of {sup 234}U-enriched continental water into Pleistocene coastal waters, or it could reflect minor diagenetic alteration, a persistent and fundamental problem in dating all corals.« less

Biohydrogen Production: Strategies to Improve Process Efficiency through Microbial Routes

PubMed Central

Chandrasekhar, Kuppam; Lee, Yong-Jik; Lee, Dong-Woo

2015-01-01

The current fossil fuel-based generation of energy has led to large-scale industrial development. However, the reliance on fossil fuels leads to the significant depletion of natural resources of buried combustible geologic deposits and to negative effects on the global climate with emissions of greenhouse gases. Accordingly, enormous efforts are directed to transition from fossil fuels to nonpolluting and renewable energy sources. One potential alternative is biohydrogen (H2), a clean energy carrier with high-energy yields; upon the combustion of H2, H2O is the only major by-product. In recent decades, the attractive and renewable characteristics of H2 led us to develop a variety of biological routes for the production of H2. Based on the mode of H2 generation, the biological routes for H2 production are categorized into four groups: photobiological fermentation, anaerobic fermentation, enzymatic and microbial electrolysis, and a combination of these processes. Thus, this review primarily focuses on the evaluation of the biological routes for the production of H2. In particular, we assess the efficiency and feasibility of these bioprocesses with respect to the factors that affect operations, and we delineate the limitations. Additionally, alternative options such as bioaugmentation, multiple process integration, and microbial electrolysis to improve process efficiency are discussed to address industrial-level applications. PMID:25874756

Biohydrogen production: strategies to improve process efficiency through microbial routes.

PubMed

Chandrasekhar, Kuppam; Lee, Yong-Jik; Lee, Dong-Woo

2015-04-14

The current fossil fuel-based generation of energy has led to large-scale industrial development. However, the reliance on fossil fuels leads to the significant depletion of natural resources of buried combustible geologic deposits and to negative effects on the global climate with emissions of greenhouse gases. Accordingly, enormous efforts are directed to transition from fossil fuels to nonpolluting and renewable energy sources. One potential alternative is biohydrogen (H2), a clean energy carrier with high-energy yields; upon the combustion of H2, H2O is the only major by-product. In recent decades, the attractive and renewable characteristics of H2 led us to develop a variety of biological routes for the production of H2. Based on the mode of H2 generation, the biological routes for H2 production are categorized into four groups: photobiological fermentation, anaerobic fermentation, enzymatic and microbial electrolysis, and a combination of these processes. Thus, this review primarily focuses on the evaluation of the biological routes for the production of H2. In particular, we assess the efficiency and feasibility of these bioprocesses with respect to the factors that affect operations, and we delineate the limitations. Additionally, alternative options such as bioaugmentation, multiple process integration, and microbial electrolysis to improve process efficiency are discussed to address industrial-level applications.

Oxygen isotope analysis of phosphate: improved precision using TC/EA CF-IRMS.

PubMed

LaPorte, D F; Holmden, C; Patterson, W P; Prokopiuk, T; Eglington, B M

2009-06-01

Oxygen isotope values of biogenic apatite have long demonstrated considerable promise for paleothermometry potential because of the abundance of material in the fossil record and greater resistance of apatite to diagenesis compared to carbonate. Unfortunately, this promise has not been fully realized because of relatively poor precision of isotopic measurements, and exceedingly small size of some substrates for analysis. Building on previous work, we demonstrate that it is possible to improve precision of delta18O(PO4) measurements using a 'reverse-plumbed' thermal conversion elemental analyzer (TC/EA) coupled to a continuous flow isotope ratio mass spectrometer (CF-IRMS) via a helium stream [Correction made here after initial online publication]. This modification to the flow of helium through the TC/EA, and careful location of the packing of glassy carbon fragments relative to the hot spot in the reactor, leads to narrower, more symmetrically distributed CO elution peaks with diminished tailing. In addition, we describe our apatite purification chemistry that uses nitric acid and cation exchange resin. Purification chemistry is optimized for processing small samples, minimizing isotopic fractionation of PO4(-3) and permitting Ca, Sr and Nd to be eluted and purified further for the measurement of delta44Ca and 87Sr/86Sr in modern biogenic apatite and 143Nd/144Nd in fossil apatite. Our methodology yields an external precision of +/- 0.15 per thousand (1sigma) for delta18O(PO4). The uncertainty is related to the preparation of the Ag3PO4 salt, conversion to CO gas in a reversed-plumbed TC/EA, analysis of oxygen isotopes using a CF-IRMS, and uncertainty in constructing calibration lines that convert raw delta18O data to the VSMOW scale. Matrix matching of samples and standards for the purpose of calibration to the VSMOW scale was determined to be unnecessary. Our method requires only slightly modified equipment that is widely available. This fact, and the demonstrated improvement in precision, should help to make apatite paleothermometry far more accessible to paleoclimate researchers. Copyright 2009 John Wiley & Sons, Ltd.

Waking the undead: Implications of a soft explosive model for the timing of placental mammal diversification.

PubMed

Springer, Mark S; Emerling, Christopher A; Meredith, Robert W; Janečka, Jan E; Eizirik, Eduardo; Murphy, William J

2017-01-01

The explosive, long fuse, and short fuse models represent competing hypotheses for the timing of placental mammal diversification. Support for the explosive model, which posits both interordinal and intraordinal diversification after the KPg mass extinction, derives from morphological cladistic studies that place Cretaceous eutherians outside of crown Placentalia. By contrast, most molecular studies favor the long fuse model wherein interordinal cladogenesis occurred in the Cretaceous followed by intraordinal cladogenesis after the KPg boundary. Phillips (2016) proposed a soft explosive model that allows for the emergence of a few lineages (Xenarthra, Afrotheria, Euarchontoglires, Laurasiatheria) in the Cretaceous, but otherwise agrees with the explosive model in positing the majority of interordinal diversification after the KPg mass extinction. Phillips (2016) argues that rate transference errors associated with large body size and long lifespan have inflated previous estimates of interordinal divergence times, and further suggests that most interordinal divergences are positioned after the KPg boundary when rate transference errors are avoided through the elimination of calibrations in large-bodied and/or long lifespan clades. Here, we show that rate transference errors can also occur in the opposite direction and drag forward estimated divergence dates when calibrations in large-bodied/long lifespan clades are omitted. This dragging forward effect results in the occurrence of more than half a billion years of 'zombie lineages' on Phillips' preferred timetree. By contrast with ghost lineages, which are a logical byproduct of an incomplete fossil record, zombie lineages occur when estimated divergence dates are younger than the minimum age of the oldest crown fossils. We also present the results of new timetree analyses that address the rate transference problem highlighted by Phillips (2016) by deleting taxa that exceed thresholds for body size and lifespan. These analyses recover all interordinal divergence times in the Cretaceous and are consistent with the long fuse model of placental diversification. Finally, we outline potential problems with morphological cladistic analyses of higher-level relationships among placental mammals that may account for the perceived discrepancies between molecular and paleontological estimates of placental divergence times. Copyright © 2016 Elsevier Inc. All rights reserved.

Oxygen and Carbon Isotope Variations in a Modern Rodent Community – Implications for Palaeoenvironmental Reconstructions

PubMed Central

Gehler, Alexander; Tütken, Thomas; Pack, Andreas

2012-01-01

Background The oxygen (δ18O) and carbon (δ13C) isotope compositions of bioapatite from skeletal remains of fossil mammals are well-established proxies for the reconstruction of palaeoenvironmental and palaeoclimatic conditions. Stable isotope studies of modern analogues are an important prerequisite for such reconstructions from fossil mammal remains. While numerous studies have investigated modern large- and medium-sized mammals, comparable studies are rare for small mammals. Due to their high abundance in terrestrial ecosystems, short life spans and small habitat size, small mammals are good recorders of local environments. Methodology/Findings The δ18O and δ13C values of teeth and bones of seven sympatric modern rodent species collected from owl pellets at a single locality were measured, and the inter-specific, intra-specific and intra-individual variations were evaluated. Minimum sample sizes to obtain reproducible population δ18O means within one standard deviation were determined. These parameters are comparable to existing data from large mammals. Additionally, the fractionation between coexisting carbonate (δ18OCO3) and phosphate (δ18OPO4) in rodent bioapatite was determined, and δ18O values were compared to existing calibration equations between the δ18O of rodent bioapatite and local surface water (δ18OLW). Specific calibration equations between δ18OPO4 and δ18OLW may be applicable on a taxonomic level higher than the species. However, a significant bias can occur when bone-based equations are applied to tooth-data and vice versa, which is due to differences in skeletal tissue formation times. δ13C values reflect the rodents’ diet and agree well with field observations of their nutritional behaviour. Conclusions/Significance Rodents have a high potential for the reconstruction of palaeoenvironmental conditions by means of bioapatite δ18O and δ13C analysis. No significant disadvantages compared to larger mammals were observed. However, for refined palaeoenvironmental reconstructions a better understanding of stable isotope signatures in modern analogous communities and potential biases due to seasonality effects, population dynamics and tissue formation rates is necessary. PMID:23226212

Low Cost and Efficient 3d Indoor Mapping Using Multiple Consumer Rgb-D Cameras

NASA Astrophysics Data System (ADS)

Chen, C.; Yang, B. S.; Song, S.

2016-06-01

Driven by the miniaturization, lightweight of positioning and remote sensing sensors as well as the urgent needs for fusing indoor and outdoor maps for next generation navigation, 3D indoor mapping from mobile scanning is a hot research and application topic. The point clouds with auxiliary data such as colour, infrared images derived from 3D indoor mobile mapping suite can be used in a variety of novel applications, including indoor scene visualization, automated floorplan generation, gaming, reverse engineering, navigation, simulation and etc. State-of-the-art 3D indoor mapping systems equipped with multiple laser scanners product accurate point clouds of building interiors containing billions of points. However, these laser scanner based systems are mostly expensive and not portable. Low cost consumer RGB-D Cameras provides an alternative way to solve the core challenge of indoor mapping that is capturing detailed underlying geometry of the building interiors. Nevertheless, RGB-D Cameras have a very limited field of view resulting in low efficiency in the data collecting stage and incomplete dataset that missing major building structures (e.g. ceilings, walls). Endeavour to collect a complete scene without data blanks using single RGB-D Camera is not technic sound because of the large amount of human labour and position parameters need to be solved. To find an efficient and low cost way to solve the 3D indoor mapping, in this paper, we present an indoor mapping suite prototype that is built upon a novel calibration method which calibrates internal parameters and external parameters of multiple RGB-D Cameras. Three Kinect sensors are mounted on a rig with different view direction to form a large field of view. The calibration procedure is three folds: 1, the internal parameters of the colour and infrared camera inside each Kinect are calibrated using a chess board pattern, respectively; 2, the external parameters between the colour and infrared camera inside each Kinect are calibrated using a chess board pattern; 3, the external parameters between every Kinect are firstly calculated using a pre-set calibration field and further refined by an iterative closet point algorithm. Experiments are carried out to validate the proposed method upon RGB-D datasets collected by the indoor mapping suite prototype. The effectiveness and accuracy of the proposed method is evaluated by comparing the point clouds derived from the prototype with ground truth data collected by commercial terrestrial laser scanner at ultra-high density. The overall analysis of the results shows that the proposed method achieves seamless integration of multiple point clouds form different RGB-D cameras collected at 30 frame per second.

Observations of the orbital debris complex by the Midcourse Space Experiment (MSX) satellite

NASA Technical Reports Server (NTRS)

Vilas, Faith; Anz-Meador, Phillip; Talent, Dave

1997-01-01

The midcourse space experiment (MSX) provides the opportunity to observe debris at multiple, simultaneous wavelengths, or in conjunction with other sensors and prior data sets. The instruments onboard MSX include an infrared telescope, an infrared interferometer, a visible telescope, an ultraviolet telescope and a spectroscopic imager. The spacecraft carries calibration spheres for instrument calibration and atmospheric drag studies. The experimental program, the implementation aspects, the data reduction techniques and the preliminary results are described.

Recent Research on the Automated Mass Measuring System

NASA Astrophysics Data System (ADS)

Yao, Hong; Ren, Xiao-Ping; Wang, Jian; Zhong, Rui-Lin; Ding, Jing-An

The research development of robotic measurement system as well as the representative automatic system were introduced in the paper, and then discussed a sub-multiple calibration scheme adopted on a fully-automatic CCR10 system effectively. Automatic robot system can be able to perform the dissemination of the mass scale without any manual intervention as well as the fast speed calibration of weight samples against a reference weight. At the last, evaluation of the expanded uncertainty was given out.

A Multi-Band Body-Worn Distributed Radio-Frequency Exposure Meter: Design, On-Body Calibration and Study of Body Morphology

PubMed Central

Thielens, Arno; Agneessens, Sam; Van Torre, Patrick; Van den Bossche, Matthias; Eeftens, Marloes; Huss, Anke; Vermeulen, Roel; de Seze, René; Mazet, Paul; Cardis, Elisabeth; Röösli, Martin; Martens, Luc; Joseph, Wout

2018-01-01

A multi-band Body-Worn Distributed exposure Meter (BWDM) calibrated for simultaneous measurement of the incident power density in 11 telecommunication frequency bands, is proposed. The BDWM consists of 22 textile antennas integrated in a garment and is calibrated on six human subjects in an anechoic chamber to assess its measurement uncertainty in terms of 68% confidence interval of the on-body antenna aperture. It is shown that by using multiple antennas in each frequency band, the uncertainty of the BWDM is 22 dB improved with respect to single nodes on the front and back of the torso and variations are decreased to maximum 8.8 dB. Moreover, deploying single antennas for different body morphologies results in a variation up to 9.3 dB, which is reduced to 3.6 dB using multiple antennas for six subjects with various body mass index values. The designed BWDM, has an improved uncertainty of up to 9.6 dB in comparison to commercially available personal exposure meters calibrated on body. As an application, an average incident power density in the range of 26.7–90.8 μW·m−2 is measured in Ghent, Belgium. The measurements show that commercial personal exposure meters underestimate the actual exposure by a factor of up to 20.6. PMID:29346280

Calibrated imaging reveals altered grey matter metabolism related to white matter microstructure and symptom severity in multiple sclerosis.

PubMed

Hubbard, Nicholas A; Turner, Monroe P; Ouyang, Minhui; Himes, Lyndahl; Thomas, Binu P; Hutchison, Joanna L; Faghihahmadabadi, Shawheen; Davis, Scott L; Strain, Jeremy F; Spence, Jeffrey; Krawczyk, Daniel C; Huang, Hao; Lu, Hanzhang; Hart, John; Frohman, Teresa C; Frohman, Elliot M; Okuda, Darin T; Rypma, Bart

2017-11-01

Multiple sclerosis (MS) involves damage to white matter microstructures. This damage has been related to grey matter function as measured by standard, physiologically-nonspecific neuroimaging indices (i.e., blood-oxygen-level dependent signal [BOLD]). Here, we used calibrated functional magnetic resonance imaging and diffusion tensor imaging to examine the extent to which specific, evoked grey matter physiological processes were associated with white matter diffusion in MS. Evoked changes in BOLD, cerebral blood flow (CBF), and oxygen metabolism (CMRO 2 ) were measured in visual cortex. Individual differences in the diffusion tensor measure, radial diffusivity, within occipital tracts were strongly associated with MS patients' BOLD and CMRO 2 . However, these relationships were in opposite directions, complicating the interpretation of the relationship between BOLD and white matter microstructural damage in MS. CMRO 2 was strongly associated with individual differences in patients' fatigue and neurological disability, suggesting that alterations to evoked oxygen metabolic processes may be taken as a marker for primary symptoms of MS. This work demonstrates the first application of calibrated and diffusion imaging together and details the first application of calibrated functional MRI in a neurological population. Results lend support for neuroenergetic hypotheses of MS pathophysiology and provide an initial demonstration of the utility of evoked oxygen metabolism signals for neurology research. Hum Brain Mapp 38:5375-5390, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The Calibration Target for the Mars 2020 SHERLOC Instrument: Multiple Science Roles for Future Manned and Unmanned Mars Exploration

NASA Technical Reports Server (NTRS)

Fries, M.; Bhartia, R.; Beegle, L.; Burton, A.; Ross, A.; Shahar, A.

2014-01-01

The Scanning Habitable Environments with Raman & Luminescence for Organics & Chemicals (SHERLOC) instrument is a deep ultraviolet (UV) Raman/fluorescence instrument selected as part of the Mars 2020 rover instrument suite. SHERLOC will be mounted on the rover arm and its primary role is to identify carbonaceous species in martian samples, which may be selected for inclusion into a returnable sample cache. The SHERLOC instrument will require the use of a calibration target, and by design, multiple science roles will be addressed in the design of the target. Samples of materials used in NASA Extravehicular Mobility unit (EMU, or "space suit") manufacture have been included in the target to serve as both solid polymer calibration targets for SHERLOC instrument function, as well as for testing the resiliency of those materials under martian ambient conditions. A martian meteorite will also be included in the target to serve as a well-characterized example of a martian rock that contains trace carbonaceous material. This rock will be the first rock that we know of that has completed a round trip between planets and will therefore serve an EPO role to attract public attention to science and planetary exploration. The SHERLOC calibration target will address a wide range of NASA goals to include basic science of interest to both the Science Mission Directorate (SMD) and Human Exploration and Operations Mission Directorate (HEOMD).

Multivariate meta-analysis of individual participant data helped externally validate the performance and implementation of a prediction model.

PubMed

Snell, Kym I E; Hua, Harry; Debray, Thomas P A; Ensor, Joie; Look, Maxime P; Moons, Karel G M; Riley, Richard D

2016-01-01

Our aim was to improve meta-analysis methods for summarizing a prediction model's performance when individual participant data are available from multiple studies for external validation. We suggest multivariate meta-analysis for jointly synthesizing calibration and discrimination performance, while accounting for their correlation. The approach estimates a prediction model's average performance, the heterogeneity in performance across populations, and the probability of "good" performance in new populations. This allows different implementation strategies (e.g., recalibration) to be compared. Application is made to a diagnostic model for deep vein thrombosis (DVT) and a prognostic model for breast cancer mortality. In both examples, multivariate meta-analysis reveals that calibration performance is excellent on average but highly heterogeneous across populations unless the model's intercept (baseline hazard) is recalibrated. For the cancer model, the probability of "good" performance (defined by C statistic ≥0.7 and calibration slope between 0.9 and 1.1) in a new population was 0.67 with recalibration but 0.22 without recalibration. For the DVT model, even with recalibration, there was only a 0.03 probability of "good" performance. Multivariate meta-analysis can be used to externally validate a prediction model's calibration and discrimination performance across multiple populations and to evaluate different implementation strategies. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

Calibration of NOAA-7 AVHRR, GOES-5 and GOES-6 VISSR/VAS solar channels

NASA Technical Reports Server (NTRS)

Frouin, R.; Gautier, C.

1986-01-01

The NOAA-7, GOES-5 and GOES-6 Visible Infrared Spin Scan Radiometer/Vertical Atmospheric Sounder (VISSR/VAS) solar channels were calibrated. The White Sands Monument area in New Mexico, whose reflectance properties are well known, and space are used as calibration targets. The shortwave reflected terrestrial irradiance that is measured at satellite altitude is computed using a fairly accurate radiative transfer model which accounts for multiple scattering and bidirectional effects. The ground target reflectance and relevant characteristics of the overlying atmosphere are estimated from climatological data and observation at the nearest meteorological sites. The approach is believed to produce accuracies of 8 to 13% depending on the channel considered.

Reconstructing Tropical Southwest Pacific Climate Variability and Mean State Changes at Vanuatu during the Medieval Climate Anomaly using Geochemical Proxies from Corals

NASA Astrophysics Data System (ADS)

Lawman, A. E.; Quinn, T. M.; Partin, J. W.; Taylor, F. W.; Thirumalai, K.; WU, C. C.; Shen, C. C.

2017-12-01

The Medieval Climate Anomaly (MCA: 950-1250 CE) is identified as a period during the last 2 millennia with Northern Hemisphere surface temperatures similar to the present. However, our understanding of tropical climate variability during the MCA is poorly constrained due to a lack of sub-annually resolved proxy records. We investigate seasonal and interannual variability during the MCA using geochemical records developed from two well preserved Porites lutea fossilized corals from the tropical southwest Pacific (Tasmaloum, Vanuatu; 15.6°S, 166.9°E). Absolute U/Th dates of 1127.1 ± 2.7 CE and 1105.1 ± 3.0 CE indicate that the selected fossil corals lived during the MCA. We use paired coral Sr/Ca and δ18O measurements to reconstruct sea surface temperature (SST) and the δ18O of seawater (a proxy for salinity). To provide context for the fossil coral records and test whether the mean state and climate variability at Vanuatu during the MCA is similar to the modern climate, our analysis also incorporates two modern coral records from Sabine Bank (15.9°S, 166.0°E) and Malo Channel (15.7°S, 167.2°E), Vanuatu for comparison. We quantify the uncertainty in our modern and fossil coral SST estimates via replication with multiple, overlapping coral records. Both the modern and fossil corals reproduce their respective mean SST value over their common period of overlap, which is 25 years in both cases. Based on over 100 years of monthly Sr/Ca data from each time period, we find that SSTs at Vanuatu during the MCA are 1.3 ± 0.7°C cooler relative to the modern. We also find that the median amplitude of the annual cycle is 0.8 ± 0.3°C larger during the MCA relative to the modern. Multiple data analysis techniques, including the standard deviation and the difference between the 95th and 5th percentiles of the annual SST cycle estimates, also show that the MCA has greater annual SST variability relative to the modern. Stable isotope data acquisition is ongoing, and when complete we will have a suite of records of paired coral Sr/Ca and δ18O measurements. We will apply similar statistical techniques developed for the Sr/Ca-SST record to also investigate variability in the δ18O of seawater (salinity). Modern salinity variability at Vanuatu arises due to hydrological anomalies associated with the El Niño-Southern Oscillation in the tropical Pacific.

Fossil Groups in the Local Universe

NASA Technical Reports Server (NTRS)

OSullivan, Ewan

2005-01-01

The two galaxies observed as part of this project were originally selected as fossil group candidates because of their isolation from other galaxies and their apparent high X-ray luminosity and extended X-ray emission. However, the X-ray data available was minimal, being drawn from the ROSAT All-Sky Survey. We have performed an initial analysis of the XMM data from both galaxies and found that their gaseous halos are smaller, cooler, and less luminous than expected. In the case of NGC 57, the RASS estimate of extent and luminosity was biased because of a previously unidentified background group which is visible in the XMM data to one side of the galaxy. In the case of IC 153 1, the contribution from background point sources near the galaxy appears to be to blame. This suggests that both galaxies should be reclassified as isolated ellipticals. Such systems are very rare, and currently poorly understood; for comparison, there are now 6-10 known fossil groups, but only one isolated elliptical with useful X-ray data. We are currently re-analyzing the data for the two galaxies to take advantage of the calibration improvements of SAS 6.1, and to include calculations of the mass profiles of the two systems. A paper is currently in preparation dealing with the X-ray properties and environment of the galaxies, and we expect to submit this to the Astrophysical Journal within the next two months. Multi-band optical imaging of the field surrounding NGC 57 has been acquired to confirm its isolated status and provide more information on the background group. IC 1531 was accepted as a target in Chandra cycle 6 as part of a related proposal, and we intend to add this new observation to our XMM data when it becomes available. A second paper is planned to include the results of this combined analysis.

An extinct Eocene taxon of the daisy family (Asteraceae): evolutionary, ecological and biogeographical implications.

PubMed

Barreda, Viviana D; Palazzesi, Luis; Katinas, Liliana; Crisci, Jorge V; Tellería, María C; Bremer, Kåre; Passalia, Mauro G; Passala, Mauro G; Bechis, Florencia; Corsolini, Rodolfo

2012-01-01

Morphological, molecular and biogeographical information bearing on early evolution of the sunflower alliance of families suggests that the clade containing the extant daisy family (Asteraceae) differentiated in South America during the Eocene, although palaeontological studies on this continent failed to reveal conclusive support for this hypothesis. Here we describe in detail Raiguenrayun cura gen. & sp. nov., an exceptionally well preserved capitulescence of Asteraceae recovered from Eocene deposits of northwestern Patagonia, Argentina. The fossil was collected from the 47·5 million-year-old Huitrera Formation at the Estancia Don Hipólito locality, Río Negro Province, Argentina. The arrangement of the capitula in a cymose capitulescence, the many-flowered capitula with multiseriate-imbricate involucral bracts and the pappus-like structures indicate a close morphological relationship with Asteraceae. Raiguenrayun cura and the associated pollen Mutisiapollis telleriae do not match exactly any living member of the family, and clearly represent extinct taxa. They share a mosaic of morphological features today recognized in taxa phylogenetically close to the root of Asteraceae, such as Stifftieae, Wunderlichioideae and Gochnatieae (Mutisioideae sensu lato) and Dicomeae and Oldenburgieae (Carduoideae), today endemic to or mainly distributed in South America and Africa, respectively. This is the first fossil genus of Asteraceae based on an outstandingly preserved capitulescence that might represent the ancestor of Mutisioideae-Carduoideae. It might have evolved in southern South America some time during the early Palaeogene and subsequently entered Africa, before the biogeographical isolation of these continents became much more pronounced. The new fossil represents the first reliable point for calibration, favouring an earlier date to the split between Barnadesioideae and the rest of Asteraceae than previously thought, which can be traced back at least 47·5 million years. This is the oldest well dated member of Asteraceae and perhaps the earliest indirect evidence for bird pollination in the family.

An extinct Eocene taxon of the daisy family (Asteraceae): evolutionary, ecological and biogeographical implications

PubMed Central

Barreda, Viviana D.; Palazzesi, Luis; Katinas, Liliana; Crisci, Jorge V.; Tellería, María C.; Bremer, Kåre; Passala, Mauro G.; Bechis, Florencia; Corsolini, Rodolfo

2012-01-01

Background and Aims Morphological, molecular and biogeographical information bearing on early evolution of the sunflower alliance of families suggests that the clade containing the extant daisy family (Asteraceae) differentiated in South America during the Eocene, although palaeontological studies on this continent failed to reveal conclusive support for this hypothesis. Here we describe in detail Raiguenrayun cura gen. & sp. nov., an exceptionally well preserved capitulescence of Asteraceae recovered from Eocene deposits of northwestern Patagonia, Argentina. Methods The fossil was collected from the 47·5 million-year-old Huitrera Formation at the Estancia Don Hipólito locality, Río Negro Province, Argentina. Key Results The arrangement of the capitula in a cymose capitulescence, the many-flowered capitula with multiseriate–imbricate involucral bracts and the pappus-like structures indicate a close morphological relationship with Asteraceae. Raiguenrayun cura and the associated pollen Mutisiapollis telleriae do not match exactly any living member of the family, and clearly represent extinct taxa. They share a mosaic of morphological features today recognized in taxa phylogenetically close to the root of Asteraceae, such as Stifftieae, Wunderlichioideae and Gochnatieae (Mutisioideae sensu lato) and Dicomeae and Oldenburgieae (Carduoideae), today endemic to or mainly distributed in South America and Africa, respectively. Conclusions This is the first fossil genus of Asteraceae based on an outstandingly preserved capitulescence that might represent the ancestor of Mutisioideae–Carduoideae. It might have evolved in southern South America some time during the early Palaeogene and subsequently entered Africa, before the biogeographical isolation of these continents became much more pronounced. The new fossil represents the first reliable point for calibration, favouring an earlier date to the split between Barnadesioideae and the rest of Asteraceae than previously thought, which can be traced back at least 47·5 million years. This is the oldest well dated member of Asteraceae and perhaps the earliest indirect evidence for bird pollination in the family. PMID:22179952

Systematic vertical and lateral changes in quality and time resolution of the macrofossil record: insights from Holocene transgressive deposits, Po coastal plain, Italy

NASA Astrophysics Data System (ADS)

Azzarone, Michele; Scarponi, Daniele; Kusnerik, Kristopher; Amorosi, Alessandro; Bohacs, Kevin M.; Drexler, Tina M.; Kowalewski, Michał

2017-04-01

In siliciclastic marine settings, skeletal concentrations are a characteristic feature of transgressive intervals that provide insights into paleobiology and sequence stratigraphy. To investigate taphonomic signatures of transgressive intervals, we analyzed three cores from a Holocene depositional profile of the Po coastal plain, in northern Italy. Coupled multivariate taphonomic and bathymetric trends delineate spatial and temporal gradients in sediment starvation/bypassing, suggesting that quality and resolution of the fossil record vary predictably along the studied depositional profile. Moreover, joint consideration of taphonomic, bathymetric, and fossil density trends across the study area reveals distinctive signatures that are useful in characterizing facies associations and recognizing surfaces and intervals of sequence stratigraphic significance. Within the southern Po plain succession, taphonomic degradation of macroskeletal remains increases from proximal—nearshore to distal—offshore locations. This trend is discernible for both biologically-driven (bioerosion) and chemically/physically-driven (e.g., dissolution, abrasion) shell alterations. Compared to the up-dip (most proximal) core, the down-dip core is distinguished by shell-rich lithosomes affected by ecological condensation (co-occurrence of environmentally non-overlapping taxa) and by higher taphonomic alteration. The onshore-offshore taphonomic trend likely reflects variation in sediment-supply along the depositional profile of the Holocene Northern Adriatic shelf, with surface/near-surface residence-time of macroskeletal remains increasing down dip due to lower accumulation rates. These results indicate that, during transgressive phases, changes in sea-level (base level) are likely to produce down-dip taphonomic gradients across shelves, where the quality and resolution of the fossil record both deteriorate distally. The amino acid radiometrically calibrated dates on bivalves and the chronostratigraphic framework for this profile suggest that the high levels of taphonomic degradation observed distally developed over millennial time scales ( 8ky). The patterns documented here may be characteristic of siliciclastic-dominated depositional systems that experience high-frequency, base-level fluctuations.

The Middle Triassic insect radiation revealed by isotopic age and iconic fossils from NW China

NASA Astrophysics Data System (ADS)

Zheng, Daran; Chang, Su-Chin; Wang, He; Fang, Yan; Wang, Jun; Feng, Chongqing; Xie, Guwei; Jarzembowski, Edmund A.; Zhang, Haichun; Wang, Bo

2017-04-01

Following the end-Permian mass extinction, the Triassic represented an important period witnessing the recovery and radiation of marine and terrestrial ecosystems. Terrestrial plants and vertebrates have been widely investigated; however the insects, the most diverse organisms on earth, remain enigmatic due to the rarity of Early-Middle Triassic fossils. Here we report new fossils from a Ladinian deposit dated at 238-237 Ma and a Carnian deposit in northwestern China, including the earliest definite caddisfly cases (Trichoptera) and water boatmen (Hemiptera), diverse polyphagan beetles (Coleoptera) and scorpionflies (Mecoptera). Our findings suggest that the Holometabola, comprising the majority of modern-day insect species, experienced an extraordinary diversification in the Middle Triassic and was already been dominant in some Middle and Late Triassic insect faunas, after the extinction of several ecologically dominant, Paleozoic insect groups in the latest Permian and earliest Triassic. This turnover is perhaps related to notable episodes of extreme warming and drying, leading to the eventual demise of coal-swamp ecosystems, evidenced by floral turnover during this interval. The forest revival during the Middle Triassic probably stimulated the rapid radiation and evolution of insects including some key aquatic lineages which built new associations that persist to the present day. Our results provide not only new insights into the early evolution of insect diversity and ecology, but also robust evidence for the view that the Triassic is the "Dawn of the Modern World". Besides, LA-ICP-MS U-Pb dating initially gave a late Ladinian age for the Tongchuan entomnfauna after the results: 237.41 ± 0.91 Ma and 238 ± 0.97 Ma. The age is in agreement with that of the marine Ladinian-Carnian boundary, representing a novel age constraint for the terrestrial strata near this boundary. This age can provide a calibration for marine and terrestrial correlation near Ladinian-Carnian boundary, and also for the correlation of the contemporaneous biotas.

Re-calibration of coronary risk prediction: an example of the Seven Countries Study.

PubMed

Puddu, Paolo Emilio; Piras, Paolo; Kromhout, Daan; Tolonen, Hanna; Kafatos, Anthony; Menotti, Alessandro

2017-12-14

We aimed at performing a calibration and re-calibration process using six standard risk factors from Northern (NE, N = 2360) or Southern European (SE, N = 2789) middle-aged men of the Seven Countries Study, whose parameters and data were fully known, to establish whether re-calibration gave the right answer. Greenwood-Nam-D'Agostino technique as modified by Demler (GNDD) in 2015 produced chi-squared statistics using 10 deciles of observed/expected CHD mortality risk, corresponding to Hosmer-Lemeshaw chi-squared employed for multiple logistic equations whereby binary data are used. Instead of the number of events, the GNDD test uses survival probabilities of observed and predicted events. The exercise applied, in five different ways, the parameters of the NE-predictive model to SE (and vice-versa) and compared the outcome of the simulated re-calibration with the real data. Good re-calibration could be obtained only when risk factor coefficients were substituted, being similar in magnitude and not significantly different between NE-SE. In all other ways, a good re-calibration could not be obtained. This is enough to praise for an overall need of re-evaluation of most investigations that, without GNDD or another proper technique for statistically assessing the potential differences, concluded that re-calibration is a fair method and might therefore be used, with no specific caution.

Global calibration of multi-cameras with non-overlapping fields of view based on photogrammetry and reconfigurable target

NASA Astrophysics Data System (ADS)

Xia, Renbo; Hu, Maobang; Zhao, Jibin; Chen, Songlin; Chen, Yueling

2018-06-01

Multi-camera vision systems are often needed to achieve large-scale and high-precision measurement because these systems have larger fields of view (FOV) than a single camera. Multiple cameras may have no or narrow overlapping FOVs in many applications, which pose a huge challenge to global calibration. This paper presents a global calibration method for multi-cameras without overlapping FOVs based on photogrammetry technology and a reconfigurable target. Firstly, two planar targets are fixed together and made into a long target according to the distance between the two cameras to be calibrated. The relative positions of the two planar targets can be obtained by photogrammetric methods and used as invariant constraints in global calibration. Then, the reprojection errors of target feature points in the two cameras’ coordinate systems are calculated at the same time and optimized by the Levenberg–Marquardt algorithm to find the optimal solution of the transformation matrix between the two cameras. Finally, all the camera coordinate systems are converted to the reference coordinate system in order to achieve global calibration. Experiments show that the proposed method has the advantages of high accuracy (the RMS error is 0.04 mm) and low cost and is especially suitable for on-site calibration.

A Synthesis of Star Calibration Techniques for Ground-Based Narrowband Electron-Multiplying Charge-Coupled Device Imagers Used in Auroral Photometry

NASA Technical Reports Server (NTRS)

Grubbs, Guy II; Michell, Robert; Samara, Marilia; Hampton, Don; Jahn, Jorg-Micha

2016-01-01

A technique is presented for the periodic and systematic calibration of ground-based optical imagers. It is important to have a common system of units (Rayleighs or photon flux) for cross comparison as well as self-comparison over time. With the advancement in technology, the sensitivity of these imagers has improved so that stars can be used for more precise calibration. Background subtraction, flat fielding, star mapping, and other common techniques are combined in deriving a calibration technique appropriate for a variety of ground-based imager installations. Spectral (4278, 5577, and 8446 A ) ground-based imager data with multiple fields of view (19, 47, and 180 deg) are processed and calibrated using the techniques developed. The calibration techniques applied result in intensity measurements in agreement between different imagers using identical spectral filtering, and the intensity at each wavelength observed is within the expected range of auroral measurements. The application of these star calibration techniques, which convert raw imager counts into units of photon flux, makes it possible to do quantitative photometry. The computed photon fluxes, in units of Rayleighs, can be used for the absolute photometry between instruments or as input parameters for auroral electron transport models.

Direct Reading Particle Counters: Calibration Verification and Multiple Instrument Agreement via Bump Testing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jankovic, John; Zontek, Tracy L.; Ogle, Burton R.

We examined the calibration records of two direct reading instruments designated as condensation particle counters in order to determine the number of times they were found to be out of tolerance at annual manufacturer's recalibration. For both instruments were found to be out of tolerance more times than within tolerance. And, it was concluded that annual calibration alone was insufficient to provide operational confidence in an instrument's response. Thus, a method based on subsequent agreement with data gathered from a newly calibrated instrument was developed to confirm operational readiness between annual calibrations, hereafter referred to as bump testing. The methodmore » consists of measuring source particles produced by a gas grille spark igniter in a gallon-size jar. Sampling from this chamber with a newly calibrated instrument to determine the calibrated response over the particle concentration range of interest serves as a reference. Agreement between this reference response and subsequent responses at later dates implies that the instrument is performing as it was at the time of calibration. Side-by-side sampling allows the level of agreement between two or more instruments to be determined. This is useful when simultaneously collected data are compared for differences, i.e., background with process aerosol concentrations. A reference set of data was obtained using the spark igniter. The generation system was found to be reproducible and suitable to form the basis of calibration verification. Finally, the bump test is simple enough to be performed periodically throughout the calibration year or prior to field monitoring.« less

Direct Reading Particle Counters: Calibration Verification and Multiple Instrument Agreement via Bump Testing

DOE PAGES

Jankovic, John; Zontek, Tracy L.; Ogle, Burton R.; ...

2015-01-27

We examined the calibration records of two direct reading instruments designated as condensation particle counters in order to determine the number of times they were found to be out of tolerance at annual manufacturer's recalibration. For both instruments were found to be out of tolerance more times than within tolerance. And, it was concluded that annual calibration alone was insufficient to provide operational confidence in an instrument's response. Thus, a method based on subsequent agreement with data gathered from a newly calibrated instrument was developed to confirm operational readiness between annual calibrations, hereafter referred to as bump testing. The methodmore » consists of measuring source particles produced by a gas grille spark igniter in a gallon-size jar. Sampling from this chamber with a newly calibrated instrument to determine the calibrated response over the particle concentration range of interest serves as a reference. Agreement between this reference response and subsequent responses at later dates implies that the instrument is performing as it was at the time of calibration. Side-by-side sampling allows the level of agreement between two or more instruments to be determined. This is useful when simultaneously collected data are compared for differences, i.e., background with process aerosol concentrations. A reference set of data was obtained using the spark igniter. The generation system was found to be reproducible and suitable to form the basis of calibration verification. Finally, the bump test is simple enough to be performed periodically throughout the calibration year or prior to field monitoring.« less

Application of single-image camera calibration for ultrasound augmented laparoscopic visualization

NASA Astrophysics Data System (ADS)

Liu, Xinyang; Su, He; Kang, Sukryool; Kane, Timothy D.; Shekhar, Raj

2015-03-01

Accurate calibration of laparoscopic cameras is essential for enabling many surgical visualization and navigation technologies such as the ultrasound-augmented visualization system that we have developed for laparoscopic surgery. In addition to accuracy and robustness, there is a practical need for a fast and easy camera calibration method that can be performed on demand in the operating room (OR). Conventional camera calibration methods are not suitable for the OR use because they are lengthy and tedious. They require acquisition of multiple images of a target pattern in its entirety to produce satisfactory result. In this work, we evaluated the performance of a single-image camera calibration tool (rdCalib; Percieve3D, Coimbra, Portugal) featuring automatic detection of corner points in the image, whether partial or complete, of a custom target pattern. Intrinsic camera parameters of a 5-mm and a 10-mm standard Stryker® laparoscopes obtained using rdCalib and the well-accepted OpenCV camera calibration method were compared. Target registration error (TRE) as a measure of camera calibration accuracy for our optical tracking-based AR system was also compared between the two calibration methods. Based on our experiments, the single-image camera calibration yields consistent and accurate results (mean TRE = 1.18 ± 0.35 mm for the 5-mm scope and mean TRE = 1.13 ± 0.32 mm for the 10-mm scope), which are comparable to the results obtained using the OpenCV method with 30 images. The new single-image camera calibration method is promising to be applied to our augmented reality visualization system for laparoscopic surgery.

Application of single-image camera calibration for ultrasound augmented laparoscopic visualization

PubMed Central

Liu, Xinyang; Su, He; Kang, Sukryool; Kane, Timothy D.; Shekhar, Raj

2017-01-01

Accurate calibration of laparoscopic cameras is essential for enabling many surgical visualization and navigation technologies such as the ultrasound-augmented visualization system that we have developed for laparoscopic surgery. In addition to accuracy and robustness, there is a practical need for a fast and easy camera calibration method that can be performed on demand in the operating room (OR). Conventional camera calibration methods are not suitable for the OR use because they are lengthy and tedious. They require acquisition of multiple images of a target pattern in its entirety to produce satisfactory result. In this work, we evaluated the performance of a single-image camera calibration tool (rdCalib; Percieve3D, Coimbra, Portugal) featuring automatic detection of corner points in the image, whether partial or complete, of a custom target pattern. Intrinsic camera parameters of a 5-mm and a 10-mm standard Stryker® laparoscopes obtained using rdCalib and the well-accepted OpenCV camera calibration method were compared. Target registration error (TRE) as a measure of camera calibration accuracy for our optical tracking-based AR system was also compared between the two calibration methods. Based on our experiments, the single-image camera calibration yields consistent and accurate results (mean TRE = 1.18 ± 0.35 mm for the 5-mm scope and mean TRE = 1.13 ± 0.32 mm for the 10-mm scope), which are comparable to the results obtained using the OpenCV method with 30 images. The new single-image camera calibration method is promising to be applied to our augmented reality visualization system for laparoscopic surgery. PMID:28943703

Application of single-image camera calibration for ultrasound augmented laparoscopic visualization.

PubMed

Liu, Xinyang; Su, He; Kang, Sukryool; Kane, Timothy D; Shekhar, Raj

2015-03-01

Accurate calibration of laparoscopic cameras is essential for enabling many surgical visualization and navigation technologies such as the ultrasound-augmented visualization system that we have developed for laparoscopic surgery. In addition to accuracy and robustness, there is a practical need for a fast and easy camera calibration method that can be performed on demand in the operating room (OR). Conventional camera calibration methods are not suitable for the OR use because they are lengthy and tedious. They require acquisition of multiple images of a target pattern in its entirety to produce satisfactory result. In this work, we evaluated the performance of a single-image camera calibration tool ( rdCalib ; Percieve3D, Coimbra, Portugal) featuring automatic detection of corner points in the image, whether partial or complete, of a custom target pattern. Intrinsic camera parameters of a 5-mm and a 10-mm standard Stryker ® laparoscopes obtained using rdCalib and the well-accepted OpenCV camera calibration method were compared. Target registration error (TRE) as a measure of camera calibration accuracy for our optical tracking-based AR system was also compared between the two calibration methods. Based on our experiments, the single-image camera calibration yields consistent and accurate results (mean TRE = 1.18 ± 0.35 mm for the 5-mm scope and mean TRE = 1.13 ± 0.32 mm for the 10-mm scope), which are comparable to the results obtained using the OpenCV method with 30 images. The new single-image camera calibration method is promising to be applied to our augmented reality visualization system for laparoscopic surgery.

Long Term Uncertainty Investigations of 1 MN Force Calibration Machine at NPL, India (NPLI)

NASA Astrophysics Data System (ADS)

Kumar, Rajesh; Kumar, Harish; Kumar, Anil; Vikram

2012-01-01

The present paper is an attempt to study the long term uncertainty of 1 MN hydraulic multiplication system (HMS) force calibration machine (FCM) at the National Physical Laboratory, India (NPLI), which is used for calibration of the force measuring instruments in the range of 100 kN - 1 MN. The 1 MN HMS FCM was installed at NPLI in 1993 and was built on the principle of hydraulic amplifications of dead weights. The best measurement capability (BMC) of the machine is ± 0.025% (k = 2) and it is traceable to national standards by means of precision force transfer standards (FTS). The present study discusses the uncertainty variations of the 1 MN HMS FCM over the years and describes the other parameters in detail, too. The 1 MN HMS FCM was calibrated in the years 2004, 2006, 2007, 2008, 2009 and 2010 and the results have been reported.

Improving Planck calibration by including frequency-dependent relativistic corrections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quartin, Miguel; Notari, Alessio, E-mail: mquartin@if.ufrj.br, E-mail: notari@ffn.ub.es

2015-09-01

The Planck satellite detectors are calibrated in the 2015 release using the 'orbital dipole', which is the time-dependent dipole generated by the Doppler effect due to the motion of the satellite around the Sun. Such an effect has also relativistic time-dependent corrections of relative magnitude 10{sup −3}, due to coupling with the 'solar dipole' (the motion of the Sun compared to the CMB rest frame), which are included in the data calibration by the Planck collaboration. We point out that such corrections are subject to a frequency-dependent multiplicative factor. This factor differs from unity especially at the highest frequencies, relevantmore » for the HFI instrument. Since currently Planck calibration errors are dominated by systematics, to the point that polarization data is currently unreliable at large scales, such a correction can in principle be highly relevant for future data releases.« less

Coupling HYDRUS-1D Code with PA-DDS Algorithms for Inverse Calibration

NASA Astrophysics Data System (ADS)

Wang, Xiang; Asadzadeh, Masoud; Holländer, Hartmut

2017-04-01

Numerical modelling requires calibration to predict future stages. A standard method for calibration is inverse calibration where generally multi-objective optimization algorithms are used to find a solution, e.g. to find an optimal solution of the van Genuchten Mualem (VGM) parameters to predict water fluxes in the vadose zone. We coupled HYDRUS-1D with PA-DDS to add a new, robust function for inverse calibration to the model. The PA-DDS method is a recently developed multi-objective optimization algorithm, which combines Dynamically Dimensioned Search (DDS) and Pareto Archived Evolution Strategy (PAES). The results were compared to a standard method (Marquardt-Levenberg method) implemented in HYDRUS-1D. Calibration performance is evaluated using observed and simulated soil moisture at two soil layers in the Southern Abbotsford, British Columbia, Canada in the terms of the root mean squared error (RMSE) and the Nash-Sutcliffe Efficiency (NSE). Results showed low RMSE values of 0.014 and 0.017 and strong NSE values of 0.961 and 0.939. Compared to the results by the Marquardt-Levenberg method, we received better calibration results for deeper located soil sensors. However, VGM parameters were similar comparing with previous studies. Both methods are equally computational efficient. We claim that a direct implementation of PA-DDS into HYDRUS-1D should reduce the computation effort further. This, the PA-DDS method is efficient for calibrating recharge for complex vadose zone modelling with multiple soil layer and can be a potential tool for calibration of heat and solute transport. Future work should focus on the effectiveness of PA-DDS for calibrating more complex versions of the model with complex vadose zone settings, with more soil layers, and against measured heat and solute transport. Keywords: Recharge, Calibration, HYDRUS-1D, Multi-objective Optimization

Landsat 8 operational land imager on-orbit geometric calibration and performance

USGS Publications Warehouse

Storey, James C.; Choate, Michael J.; Lee, Kenton

2014-01-01

The Landsat 8 spacecraft was launched on 11 February 2013 carrying the Operational Land Imager (OLI) payload for moderate resolution imaging in the visible, near infrared (NIR), and short-wave infrared (SWIR) spectral bands. During the 90-day commissioning period following launch, several on-orbit geometric calibration activities were performed to refine the prelaunch calibration parameters. The results of these calibration activities were subsequently used to measure geometric performance characteristics in order to verify the OLI geometric requirements. Three types of geometric calibrations were performed including: (1) updating the OLI-to-spacecraft alignment knowledge; (2) refining the alignment of the sub-images from the multiple OLI sensor chips; and (3) refining the alignment of the OLI spectral bands. The aspects of geometric performance that were measured and verified included: (1) geolocation accuracy with terrain correction, but without ground control (L1Gt); (2) Level 1 product accuracy with terrain correction and ground control (L1T); (3) band-to-band registration accuracy; and (4) multi-temporal image-to-image registration accuracy. Using the results of the on-orbit calibration update, all aspects of geometric performance were shown to meet or exceed system requirements.

Application of a hybrid MPI/OpenMP approach for parallel groundwater model calibration using multi-core computers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Guoping; D'Azevedo, Ed F; Zhang, Fan

2010-01-01

Calibration of groundwater models involves hundreds to thousands of forward solutions, each of which may solve many transient coupled nonlinear partial differential equations, resulting in a computationally intensive problem. We describe a hybrid MPI/OpenMP approach to exploit two levels of parallelisms in software and hardware to reduce calibration time on multi-core computers. HydroGeoChem 5.0 (HGC5) is parallelized using OpenMP for direct solutions for a reactive transport model application, and a field-scale coupled flow and transport model application. In the reactive transport model, a single parallelizable loop is identified to account for over 97% of the total computational time using GPROF.more » Addition of a few lines of OpenMP compiler directives to the loop yields a speedup of about 10 on a 16-core compute node. For the field-scale model, parallelizable loops in 14 of 174 HGC5 subroutines that require 99% of the execution time are identified. As these loops are parallelized incrementally, the scalability is found to be limited by a loop where Cray PAT detects over 90% cache missing rates. With this loop rewritten, similar speedup as the first application is achieved. The OpenMP-parallelized code can be run efficiently on multiple workstations in a network or multiple compute nodes on a cluster as slaves using parallel PEST to speedup model calibration. To run calibration on clusters as a single task, the Levenberg Marquardt algorithm is added to HGC5 with the Jacobian calculation and lambda search parallelized using MPI. With this hybrid approach, 100 200 compute cores are used to reduce the calibration time from weeks to a few hours for these two applications. This approach is applicable to most of the existing groundwater model codes for many applications.« less

Solar energy collection system

NASA Technical Reports Server (NTRS)

Selcuk, M. K. (Inventor)

1977-01-01

An improved solar energy collection system, having enhanced energy collection and conversion capabilities, is delineated. The system is characterized by a plurality of receivers suspended above a heliostat field comprising a multiplicity of reflector surfaces, each being adapted to direct a concentrated beam of solar energy to illuminate a target surface for a given receiver. A magnitude of efficiency, suitable for effectively competing with systems employed in collecting and converting energy extracted from fossil fuels, is indicated.

Amino acid geochemistry of fossil bones from the Rancho La Brea asphalt deposit, California

USGS Publications Warehouse

McMenamin, M.A.S.; Blunt, D.J.; Kvenvolden, K.A.; Miller, S.E.; Marcus, L.F.; Pardi, R.R.

1982-01-01

Low aspartic acid d:l ratios and modern collagenlike concentration values indicate that amino acids in bones from the Rancho La Brea asphalt deposit, Los Angeles, California are better preserved than amino acids in bones of equivalent age that have not been preserved in asphalt. Amino acids were recovered from 10 Rancho La Brea bone samples which range in age from less than 200 to greater than 36,000 yr. The calibrated rates of aspartic acid racemization range from 2.1 to 5.0 ?? 10-6yr-1. Although this wide range of rate constants decreases the level of confidence for age estimates, use of the larger rate constant of 5.0 ?? 10-6yr-1 provides minimum age estimates which fit the known stratigraphic and chronologic records of the Rancho La Brea deposits. ?? 1982.

Electron spin resonance dating of human teeth from Toca da Santa shelter of São Raimundo Nonato, Piauí, Brazil

NASA Astrophysics Data System (ADS)

Kinoshita, A.; Figueiredo, A. M. G.; Felice, G. D.; Lage, M. C. S. M.; Guidon, N.; Baffa, O.

2008-02-01

Results of the dating of fossil human teeth excavated from a shelter in the surroundings areas of the Serra da Capivara National Park, São Raimundo Nonato, Piauí, Brazil are presented. This shelter was partially excavated to search for more data that could improve the archaeological context of the Garrincho’s limestone hill sites, where the Toca do Gordo do Garrincho shelter provided two human teeth dated by conventional C-14 in (12,170 ± 40) yBP (years before present) and calibrated age (2 Sigma, 95% probability) 15,245 14,690 yBP (Beta 136204) [E. Peyre, C. Guérin, N. Guidon, I. Coppens, CR Acad. Sci. Paris, Sciences de la terre et des planètes/ Earth & Planetary Sciences 327 (1998) 335, [1

General theory of remote gaze estimation using the pupil center and corneal reflections.

PubMed

Guestrin, Elias Daniel; Eizenman, Moshe

2006-06-01

This paper presents a general theory for the remote estimation of the point-of-gaze (POG) from the coordinates of the centers of the pupil and corneal reflections. Corneal reflections are produced by light sources that illuminate the eye and the centers of the pupil and corneal reflections are estimated in video images from one or more cameras. The general theory covers the full range of possible system configurations. Using one camera and one light source, the POG can be estimated only if the head is completely stationary. Using one camera and multiple light sources, the POG can be estimated with free head movements, following the completion of a multiple-point calibration procedure. When multiple cameras and multiple light sources are used, the POG can be estimated following a simple one-point calibration procedure. Experimental and simulation results suggest that the main sources of gaze estimation errors are the discrepancy between the shape of real corneas and the spherical corneal shape assumed in the general theory, and the noise in the estimation of the centers of the pupil and corneal reflections. A detailed example of a system that uses the general theory to estimate the POG on a computer screen is presented.