A new approach to estimate parameters of speciation models with application to apes.

PubMed

Becquet, Celine; Przeworski, Molly

2007-10-01

How populations diverge and give rise to distinct species remains a fundamental question in evolutionary biology, with important implications for a wide range of fields, from conservation genetics to human evolution. A promising approach is to estimate parameters of simple speciation models using polymorphism data from multiple loci. Existing methods, however, make a number of assumptions that severely limit their applicability, notably, no gene flow after the populations split and no intralocus recombination. To overcome these limitations, we developed a new Markov chain Monte Carlo method to estimate parameters of an isolation-migration model. The approach uses summaries of polymorphism data at multiple loci surveyed in a pair of diverging populations or closely related species and, importantly, allows for intralocus recombination. To illustrate its potential, we applied it to extensive polymorphism data from populations and species of apes, whose demographic histories are largely unknown. The isolation-migration model appears to provide a reasonable fit to the data. It suggests that the two chimpanzee species became reproductively isolated in allopatry approximately 850 Kya, while Western and Central chimpanzee populations split approximately 440 Kya but continued to exchange migrants. Similarly, Eastern and Western gorillas and Sumatran and Bornean orangutans appear to have experienced gene flow since their splits approximately 90 and over 250 Kya, respectively.

Dual Extended Kalman Filter for the Identification of Time-Varying Human Manual Control Behavior

NASA Technical Reports Server (NTRS)

Popovici, Alexandru; Zaal, Peter M. T.; Pool, Daan M.

2017-01-01

A Dual Extended Kalman Filter was implemented for the identification of time-varying human manual control behavior. Two filters that run concurrently were used, a state filter that estimates the equalization dynamics, and a parameter filter that estimates the neuromuscular parameters and time delay. Time-varying parameters were modeled as a random walk. The filter successfully estimated time-varying human control behavior in both simulated and experimental data. Simple guidelines are proposed for the tuning of the process and measurement covariance matrices and the initial parameter estimates. The tuning was performed on simulation data, and when applied on experimental data, only an increase in measurement process noise power was required in order for the filter to converge and estimate all parameters. A sensitivity analysis to initial parameter estimates showed that the filter is more sensitive to poor initial choices of neuromuscular parameters than equalization parameters, and bad choices for initial parameters can result in divergence, slow convergence, or parameter estimates that do not have a real physical interpretation. The promising results when applied to experimental data, together with its simple tuning and low dimension of the state-space, make the use of the Dual Extended Kalman Filter a viable option for identifying time-varying human control parameters in manual tracking tasks, which could be used in real-time human state monitoring and adaptive human-vehicle haptic interfaces.

Adaptive Elastic Net for Generalized Methods of Moments.

PubMed

Caner, Mehmet; Zhang, Hao Helen

2014-01-30

Model selection and estimation are crucial parts of econometrics. This paper introduces a new technique that can simultaneously estimate and select the model in generalized method of moments (GMM) context. The GMM is particularly powerful for analyzing complex data sets such as longitudinal and panel data, and it has wide applications in econometrics. This paper extends the least squares based adaptive elastic net estimator of Zou and Zhang (2009) to nonlinear equation systems with endogenous variables. The extension is not trivial and involves a new proof technique due to estimators lack of closed form solutions. Compared to Bridge-GMM of Caner (2009), we allow for the number of parameters to diverge to infinity as well as collinearity among a large number of variables, also the redundant parameters set to zero via a data dependent technique. This method has the oracle property, meaning that we can estimate nonzero parameters with their standard limit and the redundant parameters are dropped from the equations simultaneously. Numerical examples are used to illustrate the performance of the new method.

The effect of multiplicity of stellar encounters and the diffusion coefficients in a locally homogeneous three-dimensional stellar medium: Removing the classical divergence

NASA Astrophysics Data System (ADS)

Rastorguev, A. S.; Utkin, N. D.; Chumak, O. V.

2017-08-01

Agekyan's λ-factor that allows for the effect of multiplicity of stellar encounters with large impact parameters has been used for the first time to directly calculate the diffusion coefficients in the phase space of a stellar system. Simple estimates show that the cumulative effect, i.e., the total contribution of distant encounters to the change in the velocity of a test star, given the multiplicity of stellar encounters, is finite, and the logarithmic divergence inherent in the classical description of diffusion is removed, as was shown previously byKandrup using a different, more complex approach. In this case, the expressions for the diffusion coefficients, as in the classical description, contain the logarithm of the ratio of two independent quantities: the mean interparticle distance and the impact parameter of a close encounter. However, the physical meaning of this logarithmic factor changes radically: it reflects not the divergence but the presence of two characteristic length scales inherent in the stellar medium.

The Efficacy of Consensus Tree Methods for Summarizing Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data.

PubMed

O'Reilly, Joseph E; Donoghue, Philip C J

2018-03-01

Consensus trees are required to summarize trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths, and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are coestimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method. The MCC method assumes that the sampled, fully resolved topology with the highest clade credibility is an adequate summary of the most probable clades, with parameter estimates from compatible sampled trees used to obtain the marginal distributions of parameters such as clade ages and branch lengths. Using both simulated and empirical data, we demonstrate that MCC trees, and trees constructed using the similar maximum a posteriori (MAP) method, often include poorly supported and incorrect clades when summarizing diffuse posterior samples of trees. We demonstrate that the paucity of information in morphological data sets contributes to the inability of MCC and MAP trees to accurately summarise of the posterior distribution. Conversely, majority-rule consensus (MRC) trees represent a lower proportion of incorrect nodes when summarizing the same posterior samples of trees. Thus, we advocate the use of MRC trees, in place of MCC or MAP trees, in attempts to summarize the results of Bayesian phylogenetic analyses of morphological data.

The Efficacy of Consensus Tree Methods for Summarizing Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data

PubMed Central

O’Reilly, Joseph E; Donoghue, Philip C J

2018-01-01

Abstract Consensus trees are required to summarize trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths, and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are coestimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method. The MCC method assumes that the sampled, fully resolved topology with the highest clade credibility is an adequate summary of the most probable clades, with parameter estimates from compatible sampled trees used to obtain the marginal distributions of parameters such as clade ages and branch lengths. Using both simulated and empirical data, we demonstrate that MCC trees, and trees constructed using the similar maximum a posteriori (MAP) method, often include poorly supported and incorrect clades when summarizing diffuse posterior samples of trees. We demonstrate that the paucity of information in morphological data sets contributes to the inability of MCC and MAP trees to accurately summarise of the posterior distribution. Conversely, majority-rule consensus (MRC) trees represent a lower proportion of incorrect nodes when summarizing the same posterior samples of trees. Thus, we advocate the use of MRC trees, in place of MCC or MAP trees, in attempts to summarize the results of Bayesian phylogenetic analyses of morphological data. PMID:29106675

On robust parameter estimation in brain-computer interfacing

NASA Astrophysics Data System (ADS)

Samek, Wojciech; Nakajima, Shinichi; Kawanabe, Motoaki; Müller, Klaus-Robert

2017-12-01

Objective. The reliable estimation of parameters such as mean or covariance matrix from noisy and high-dimensional observations is a prerequisite for successful application of signal processing and machine learning algorithms in brain-computer interfacing (BCI). This challenging task becomes significantly more difficult if the data set contains outliers, e.g. due to subject movements, eye blinks or loose electrodes, as they may heavily bias the estimation and the subsequent statistical analysis. Although various robust estimators have been developed to tackle the outlier problem, they ignore important structural information in the data and thus may not be optimal. Typical structural elements in BCI data are the trials consisting of a few hundred EEG samples and indicating the start and end of a task. Approach. This work discusses the parameter estimation problem in BCI and introduces a novel hierarchical view on robustness which naturally comprises different types of outlierness occurring in structured data. Furthermore, the class of minimum divergence estimators is reviewed and a robust mean and covariance estimator for structured data is derived and evaluated with simulations and on a benchmark data set. Main results. The results show that state-of-the-art BCI algorithms benefit from robustly estimated parameters. Significance. Since parameter estimation is an integral part of various machine learning algorithms, the presented techniques are applicable to many problems beyond BCI.

Perceptual Calibration for Immersive Display Environments

PubMed Central

Ponto, Kevin; Gleicher, Michael; Radwin, Robert G.; Shin, Hyun Joon

2013-01-01

The perception of objects, depth, and distance has been repeatedly shown to be divergent between virtual and physical environments. We hypothesize that many of these discrepancies stem from incorrect geometric viewing parameters, specifically that physical measurements of eye position are insufficiently precise to provide proper viewing parameters. In this paper, we introduce a perceptual calibration procedure derived from geometric models. While most research has used geometric models to predict perceptual errors, we instead use these models inversely to determine perceptually correct viewing parameters. We study the advantages of these new psychophysically determined viewing parameters compared to the commonly used measured viewing parameters in an experiment with 20 subjects. The perceptually calibrated viewing parameters for the subjects generally produced new virtual eye positions that were wider and deeper than standard practices would estimate. Our study shows that perceptually calibrated viewing parameters can significantly improve depth acuity, distance estimation, and the perception of shape. PMID:23428454

Local divergence and curvature divergence in first order optics

NASA Astrophysics Data System (ADS)

Mafusire, Cosmas; Krüger, Tjaart P. J.

2018-06-01

The far-field divergence of a light beam propagating through a first order optical system is presented as a square root of the sum of the squares of the local divergence and the curvature divergence. The local divergence is defined as the ratio of the beam parameter product to the beam width whilst the curvature divergence is a ratio of the space-angular moment also to the beam width. It is established that the beam’s focusing parameter can be defined as a ratio of the local divergence to the curvature divergence. The relationships between the two divergences and other second moment-based beam parameters are presented. Their various mathematical properties are presented such as their evolution through first order systems. The efficacy of the model in the analysis of high power continuous wave laser-based welding systems is briefly discussed.

FRAGS: estimation of coding sequence substitution rates from fragmentary data

PubMed Central

Swart, Estienne C; Hide, Winston A; Seoighe, Cathal

2004-01-01

Background Rates of substitution in protein-coding sequences can provide important insights into evolutionary processes that are of biomedical and theoretical interest. Increased availability of coding sequence data has enabled researchers to estimate more accurately the coding sequence divergence of pairs of organisms. However the use of different data sources, alignment protocols and methods to estimate substitution rates leads to widely varying estimates of key parameters that define the coding sequence divergence of orthologous genes. Although complete genome sequence data are not available for all organisms, fragmentary sequence data can provide accurate estimates of substitution rates provided that an appropriate and consistent methodology is used and that differences in the estimates obtainable from different data sources are taken into account. Results We have developed FRAGS, an application framework that uses existing, freely available software components to construct in-frame alignments and estimate coding substitution rates from fragmentary sequence data. Coding sequence substitution estimates for human and chimpanzee sequences, generated by FRAGS, reveal that methodological differences can give rise to significantly different estimates of important substitution parameters. The estimated substitution rates were also used to infer upper-bounds on the amount of sequencing error in the datasets that we have analysed. Conclusion We have developed a system that performs robust estimation of substitution rates for orthologous sequences from a pair of organisms. Our system can be used when fragmentary genomic or transcript data is available from one of the organisms and the other is a completely sequenced genome within the Ensembl database. As well as estimating substitution statistics our system enables the user to manage and query alignment and substitution data. PMID:15005802

Non-linear dynamics of human locomotion: effects of rhythmic auditory cueing on local dynamic stability.

PubMed

Terrier, Philippe; Dériaz, Olivier

2013-01-01

It has been observed that times series of gait parameters [stride length (SL), stride time (ST), and stride speed (SS)], exhibit long-term persistence and fractal-like properties. Synchronizing steps with rhythmic auditory stimuli modifies the persistent fluctuation pattern to anti-persistence. Another non-linear method estimates the degree of resilience of gait control to small perturbations, i.e., the local dynamic stability (LDS). The method makes use of the maximal Lyapunov exponent, which estimates how fast a non-linear system embedded in a reconstructed state space (attractor) diverges after an infinitesimal perturbation. We propose to use an instrumented treadmill to simultaneously measure basic gait parameters (time series of SL, ST, and SS from which the statistical persistence among consecutive strides can be assessed), and the trajectory of the center of pressure (from which the LDS can be estimated). In 20 healthy participants, the response to rhythmic auditory cueing (RAC) of LDS and of statistical persistence [assessed with detrended fluctuation analysis (DFA)] was compared. By analyzing the divergence curves, we observed that long-term LDS (computed as the reverse of the average logarithmic rate of divergence between the 4th and the 10th strides downstream from nearest neighbors in the reconstructed attractor) was strongly enhanced (relative change +73%). That is likely the indication of a more dampened dynamics. The change in short-term LDS (divergence over one step) was smaller (+3%). DFA results (scaling exponents) confirmed an anti-persistent pattern in ST, SL, and SS. Long-term LDS (but not short-term LDS) and scaling exponents exhibited a significant correlation between them (r = 0.7). Both phenomena probably result from the more conscious/voluntary gait control that is required by RAC. We suggest that LDS and statistical persistence should be used to evaluate the efficiency of cueing therapy in patients with neurological gait disorders.

Understanding the mechanisms of antitropical divergence in the seabird White-faced Storm-petrel (Procellariiformes: Pelagodroma marina) using a multilocus approach.

PubMed

Silva, Mónica C; Matias, Rafael; Wanless, Ross M; Ryan, Peter G; Stephenson, Brent M; Bolton, Mark; Ferrand, Nuno; Coelho, M Manuela

2015-06-01

Analytical methods that apply coalescent theory to multilocus data have improved inferences of demographic parameters that are critical to understanding population divergence and speciation. In particular, at the early stages of speciation, it is important to implement models that accommodate conflicting gene trees, and benefit from the presence of shared polymorphisms. Here, we employ eleven nuclear loci and the mitochondrial control region to investigate the phylogeography and historical demography of the pelagic seabird White-faced Storm-petrel (Pelagodroma marina) by sampling subspecies across its antitropical distribution. Groups are all highly differentiated: global mitochondrial ΦST = 0.89 (P < 0.01) and global nuclear ΦST varies between 0.22 and 0.83 (all P < 0.01). The complete lineage sorting of the mitochondrial locus between hemispheres is corroborated by approximately half of the nuclear genealogies, suggesting a long-term antitropical divergence in isolation. Coalescent-based estimates of demographic parameters suggest that hemispheric divergence of P. marina occurred approximately 840 000 ya (95% HPD 582 000-1 170 000), in the absence of gene flow, and divergence within the Southern Hemisphere occurred 190 000 ya (95% HPD 96 000-600 000), both probably associated with the profound palaeo-oceanographic changes of the Pleistocene. A fledgling sampled in St Helena (tropical South Atlantic) suggests recent colonization from the Northern Hemisphere. Despite the great potential for long-distance dispersal, P. marina antitropical groups have been evolving as independent, allopatric lineages, and divergence is probably maintained by philopatry coupled with asynchronous reproductive phenology and local adaptation. © 2015 John Wiley & Sons Ltd.

A comparison of the genetic basis of wing size divergence in three parallel body size clines of Drosophila melanogaster.

PubMed Central

Gilchrist, A S; Partridge, L

1999-01-01

Body size clines in Drosophila melanogaster have been documented in both Australia and South America, and may exist in Southern Africa. We crossed flies from the northern and southern ends of each of these clines to produce F(1), F(2), and first backcross generations. Our analysis of generation means for wing area and wing length produced estimates of the additive, dominance, epistatic, and maternal effects underlying divergence within each cline. For both females and males of all three clines, the generation means were adequately described by these parameters, indicating that linkage and higher order interactions did not contribute significantly to wing size divergence. Marked differences were apparent between the clines in the occurrence and magnitude of the significant genetic parameters. No cline was adequately described by a simple additive-dominance model, and significant epistatic and maternal effects occurred in most, but not all, of the clines. Generation variances were also analyzed. Only one cline was described sufficiently by a simple additive variance model, indicating significant epistatic, maternal, or linkage effects in the remaining two clines. The diversity in genetic architecture of the clines suggests that natural selection has produced similar phenotypic divergence by different combinations of gene action and interaction. PMID:10581284

Improving the efficiency of feed utilization in poultry by selection. 1. Genetic parameters of anatomy of the gastro-intestinal tract and digestive efficiency.

PubMed

de Verdal, Hugues; Narcy, Agnès; Bastianelli, Denis; Chapuis, Hervé; Même, Nathalie; Urvoix, Séverine; Le Bihan-Duval, Elisabeth; Mignon-Grasteau, Sandrine

2011-07-06

Feed costs represent about 70% of the costs of raising broilers. The main way to decrease these costs is to improve feed efficiency by modification of diet formulation, but one other possibility would be to use genetic selection. Understanding the genetic architecture of the gastro-intestinal tract (GIT) and the impact of the selection criterion on the GIT would be of particular interest. We therefore studied the genetic parameters of AMEn (Apparent metabolisable energy corrected for zero nitrogen balance), feed efficiency, and GIT traits in chickens.Genetic parameters were estimated for 630 broiler chickens of the eighth generation of a divergent selection experiment on AMEn. Birds were reared until 23 d of age and fed a wheat-based diet. The traits measured were body weight (BW), feed conversion ratio (FCR), AMEn, weights of crop, liver, gizzard and proventriculus, and weight, length and density of the duodenum, jejunum and ileum. The heritability estimates of BW, FCR and AMEn were moderate. The heritability estimates were higher for the GIT characteristics except for the weights of the proventriculus and liver. Gizzard weight was negatively correlated with density (weight to length ratio) of duodenum, jejunum and ileum. Proventriculus and gizzard weights were more strongly correlated with AMEn than with FCR, which was not the case for intestine weight and density. GIT traits were largely dependent on genetics and that selecting on AMEn or FCR would modify them. Phenotypic observations carried out in the divergent lines selected on AMEn were consistent with estimated genetic correlations between AMEn and GIT traits.

Estimating Divergence Parameters With Small Samples From a Large Number of Loci

PubMed Central

Wang, Yong; Hey, Jody

2010-01-01

Most methods for studying divergence with gene flow rely upon data from many individuals at few loci. Such data can be useful for inferring recent population history but they are unlikely to contain sufficient information about older events. However, the growing availability of genome sequences suggests a different kind of sampling scheme, one that may be more suited to studying relatively ancient divergence. Data sets extracted from whole-genome alignments may represent very few individuals but contain a very large number of loci. To take advantage of such data we developed a new maximum-likelihood method for genomic data under the isolation-with-migration model. Unlike many coalescent-based likelihood methods, our method does not rely on Monte Carlo sampling of genealogies, but rather provides a precise calculation of the likelihood by numerical integration over all genealogies. We demonstrate that the method works well on simulated data sets. We also consider two models for accommodating mutation rate variation among loci and find that the model that treats mutation rates as random variables leads to better estimates. We applied the method to the divergence of Drosophila melanogaster and D. simulans and detected a low, but statistically significant, signal of gene flow from D. simulans to D. melanogaster. PMID:19917765

Model parameter learning using Kullback-Leibler divergence

NASA Astrophysics Data System (ADS)

Lin, Chungwei; Marks, Tim K.; Pajovic, Milutin; Watanabe, Shinji; Tung, Chih-kuan

2018-02-01

In this paper, we address the following problem: For a given set of spin configurations whose probability distribution is of the Boltzmann type, how do we determine the model coupling parameters? We demonstrate that directly minimizing the Kullback-Leibler divergence is an efficient method. We test this method against the Ising and XY models on the one-dimensional (1D) and two-dimensional (2D) lattices, and provide two estimators to quantify the model quality. We apply this method to two types of problems. First, we apply it to the real-space renormalization group (RG). We find that the obtained RG flow is sufficiently good for determining the phase boundary (within 1% of the exact result) and the critical point, but not accurate enough for critical exponents. The proposed method provides a simple way to numerically estimate amplitudes of the interactions typically truncated in the real-space RG procedure. Second, we apply this method to the dynamical system composed of self-propelled particles, where we extract the parameter of a statistical model (a generalized XY model) from a dynamical system described by the Viscek model. We are able to obtain reasonable coupling values corresponding to different noise strengths of the Viscek model. Our method is thus able to provide quantitative analysis of dynamical systems composed of self-propelled particles.

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

Estimating the components of the sensible heat budget of a tall forest canopy in complex terrain

NASA Astrophysics Data System (ADS)

Moderow, U.; Feigenwinter, C.; Bernhofer, C.

2007-04-01

Ultrasonic wind measurements, sonic temperature and air temperature data at two heights in the advection experiment MORE II were used to establish a complete budget of sensible heat including vertical advection, horizontal advection and horizontal turbulent flux divergence. MORE II took place at the long-term Carbo-Europe IP site in Tharandt, Germany. During the growing period of 2003 three additional towers were established to measure all relevant parameters for an estimation of advective fluxes, primarily of CO2. Additionally, in relation to other advection experiments, a calculation of the horizontal turbulent flux divergence is proposed and the relation of this flux to atmospheric stability and friction velocity is discussed. In order to obtain a complete budget, different scaling heights for horizontal advection and horizontal turbulent flux divergence are tested. It is shown that neglecting advective fluxes may lead to incorrect results. If advective fluxes are taken into account, the sensible heat budget based upon vertical turbulent flux and storage change only, is reduced by approximately 30%. Additional consideration of horizontal turbulent flux divergence would in turn add 5 10% to this sum (i.e., the sum of vertical turbulent flux plus storage change plus horizontal and vertical advection). In comparison with available energy horizontal advection is important at night whilst horizontal turbulent flux divergence is rather insignificant. Obviously, advective fluxes typically improve poor nighttime energy budget closure and might change ecosystem respiration fluxes considerably.

APPROXIMATION AND ESTIMATION OF s-CONCAVE DENSITIES VIA RÉNYI DIVERGENCES.

PubMed

Han, Qiyang; Wellner, Jon A

2016-01-01

In this paper, we study the approximation and estimation of s -concave densities via Rényi divergence. We first show that the approximation of a probability measure Q by an s -concave density exists and is unique via the procedure of minimizing a divergence functional proposed by [ Ann. Statist. 38 (2010) 2998-3027] if and only if Q admits full-dimensional support and a first moment. We also show continuity of the divergence functional in Q : if Q n → Q in the Wasserstein metric, then the projected densities converge in weighted L 1 metrics and uniformly on closed subsets of the continuity set of the limit. Moreover, directional derivatives of the projected densities also enjoy local uniform convergence. This contains both on-the-model and off-the-model situations, and entails strong consistency of the divergence estimator of an s -concave density under mild conditions. One interesting and important feature for the Rényi divergence estimator of an s -concave density is that the estimator is intrinsically related with the estimation of log-concave densities via maximum likelihood methods. In fact, we show that for d = 1 at least, the Rényi divergence estimators for s -concave densities converge to the maximum likelihood estimator of a log-concave density as s ↗ 0. The Rényi divergence estimator shares similar characterizations as the MLE for log-concave distributions, which allows us to develop pointwise asymptotic distribution theory assuming that the underlying density is s -concave.

APPROXIMATION AND ESTIMATION OF s-CONCAVE DENSITIES VIA RÉNYI DIVERGENCES

PubMed Central

Han, Qiyang; Wellner, Jon A.

2017-01-01

In this paper, we study the approximation and estimation of s-concave densities via Rényi divergence. We first show that the approximation of a probability measure Q by an s-concave density exists and is unique via the procedure of minimizing a divergence functional proposed by [Ann. Statist. 38 (2010) 2998–3027] if and only if Q admits full-dimensional support and a first moment. We also show continuity of the divergence functional in Q: if Qn → Q in the Wasserstein metric, then the projected densities converge in weighted L1 metrics and uniformly on closed subsets of the continuity set of the limit. Moreover, directional derivatives of the projected densities also enjoy local uniform convergence. This contains both on-the-model and off-the-model situations, and entails strong consistency of the divergence estimator of an s-concave density under mild conditions. One interesting and important feature for the Rényi divergence estimator of an s-concave density is that the estimator is intrinsically related with the estimation of log-concave densities via maximum likelihood methods. In fact, we show that for d = 1 at least, the Rényi divergence estimators for s-concave densities converge to the maximum likelihood estimator of a log-concave density as s ↗ 0. The Rényi divergence estimator shares similar characterizations as the MLE for log-concave distributions, which allows us to develop pointwise asymptotic distribution theory assuming that the underlying density is s-concave. PMID:28966410

Genetic divergence and phylogeographic history of two closely related species (Leucomeris decora and Nouelia insignis) across the 'Tanaka Line' in Southwest China.

PubMed

Zhao, Yu-Juan; Gong, Xun

2015-07-08

Leucomeris decora and Nouelia insignis (Asteraceae) are narrowly and allopatrically distributed species, separated by the important biogeographic boundary Tanaka Line in Southwest China. Previous morphological, cytogenetic and molecular studies suggested that L. decora is sister to N. insignis. However, it is less clear how the two species diverged, whether in full isolation or occurring gene flow across the Tanaka Line. Here, we performed a molecular study at the population level to characterize genetic differentiation and decipher phylogeographic history in two closely related species based on variation examined in plastid and nuclear DNAs using a coalescent-based approach. These morphologically distinct species share plastid DNA (cpDNA) haplotypes. In contrast, Bayesian analysis of nuclear DNA (nDNA) uncovered two distinct clusters corresponding to L. decora and N. insignis. Based on the IMa analysis, no strong indication of migration was detected based on both cpDNA and nDNA sequences. The molecular data pointed to a major west-east split in nuclear DNA between the two species corresponding with the Tanaka Line. The coalescent time estimate for all cpDNA haplotypes dated to the Mid-Late Pleistocene. The estimated demographic parameters showed that the population size of L. decora was similar to that of N. insignis and both experienced limited demographic fluctuations recently. The study revealed comprehensive species divergence and phylogeographic histories of N. insignis and L. decora divided by the Tanaka Line. The phylogeographic pattern inferred from cpDNA reflected ancestrally shared polymorphisms without post-divergence gene flow between species. The marked genealogical lineage divergence in nDNA provided some indication of Tanaka Line for its role as a barrier to plant dispersal, and lent support to its importance in promoting strong population structure and allopatric divergence.

Maximum Entropy Approach in Dynamic Contrast-Enhanced Magnetic Resonance Imaging.

PubMed

Farsani, Zahra Amini; Schmid, Volker J

2017-01-01

In the estimation of physiological kinetic parameters from Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) data, the determination of the arterial input function (AIF) plays a key role. This paper proposes a Bayesian method to estimate the physiological parameters of DCE-MRI along with the AIF in situations, where no measurement of the AIF is available. In the proposed algorithm, the maximum entropy method (MEM) is combined with the maximum a posterior approach (MAP). To this end, MEM is used to specify a prior probability distribution of the unknown AIF. The ability of this method to estimate the AIF is validated using the Kullback-Leibler divergence. Subsequently, the kinetic parameters can be estimated with MAP. The proposed algorithm is evaluated with a data set from a breast cancer MRI study. The application shows that the AIF can reliably be determined from the DCE-MRI data using MEM. Kinetic parameters can be estimated subsequently. The maximum entropy method is a powerful tool to reconstructing images from many types of data. This method is useful for generating the probability distribution based on given information. The proposed method gives an alternative way to assess the input function from the existing data. The proposed method allows a good fit of the data and therefore a better estimation of the kinetic parameters. In the end, this allows for a more reliable use of DCE-MRI. Schattauer GmbH.

iGLASS: An Improvement to the GLASS Method for Estimating Species Trees from Gene Trees

PubMed Central

Rosenberg, Noah A.

2012-01-01

Abstract Several methods have been designed to infer species trees from gene trees while taking into account gene tree/species tree discordance. Although some of these methods provide consistent species tree topology estimates under a standard model, most either do not estimate branch lengths or are computationally slow. An exception, the GLASS method of Mossel and Roch, is consistent for the species tree topology, estimates branch lengths, and is computationally fast. However, GLASS systematically overestimates divergence times, leading to biased estimates of species tree branch lengths. By assuming a multispecies coalescent model in which multiple lineages are sampled from each of two taxa at L independent loci, we derive the distribution of the waiting time until the first interspecific coalescence occurs between the two taxa, considering all loci and measuring from the divergence time. We then use the mean of this distribution to derive a correction to the GLASS estimator of pairwise divergence times. We show that our improved estimator, which we call iGLASS, consistently estimates the divergence time between a pair of taxa as the number of loci approaches infinity, and that it is an unbiased estimator of divergence times when one lineage is sampled per taxon. We also show that many commonly used clustering methods can be combined with the iGLASS estimator of pairwise divergence times to produce a consistent estimator of the species tree topology. Through simulations, we show that iGLASS can greatly reduce the bias and mean squared error in obtaining estimates of divergence times in a species tree. PMID:22216756

Demographic histories of adaptively diverged riparian and non-riparian species of Ainsliaea (Asteraceae) inferred from coalescent analyses using multiple nuclear loci.

PubMed

Mitsui, Yuki; Setoguchi, Hiroaki

2012-12-28

Understanding demographic histories, such as divergence time, patterns of gene flow, and population size changes, in ecologically diverging lineages provide implications for the process and maintenance of population differentiation by ecological adaptation. This study addressed the demographic histories in two independently derived lineages of flood-resistant riparian plants and their non-riparian relatives [Ainsliaea linearis (riparian) and A. apiculata (non-riparian); A. oblonga (riparian) and A. macroclinidioides (non-riparian); Asteraceae] using an isolation-with-migration (IM) model based on variation at 10 nuclear DNA loci. The highest posterior probabilities of the divergence time parameters were estimated to be ca. 25,000 years ago for A. linearis and A. apiculata and ca. 9000 years ago for A. oblonga and A. macroclinidioides, although the confidence intervals of the parameters had broad ranges. The likelihood ratio tests detected evidence of historical gene flow between both riparian/non-riparian species pairs. The riparian populations showed lower levels of genetic diversity and a significant reduction in effective population sizes compared to the non-riparian populations and their ancestral populations. This study showed the recent origins of flood-resistant riparian plants, which are remarkable examples of plant ecological adaptation. The recent divergence and genetic signatures of historical gene flow among riparian/non-riparian species implied that they underwent morphological and ecological differentiation within short evolutionary timescales and have maintained their species boundaries in the face of gene flow. Comparative analyses of adaptive divergence in two sets of riparian/non-riparian lineages suggested that strong natural selection by flooding had frequently reduced the genetic diversity and size of riparian populations through genetic drift, possibly leading to fixation of adaptive traits in riparian populations. The two sets of riparian/non-riparian lineages showed contrasting patterns of gene flow and genetic differentiation, implying that each lineage showed different degrees of reproductive isolation and that they had experienced unique evolutionary and demographic histories in the process of adaptive divergence.

Image registration based on subpixel localization and Cauchy-Schwarz divergence

NASA Astrophysics Data System (ADS)

Ge, Yongxin; Yang, Dan; Zhang, Xiaohong; Lu, Jiwen

2010-07-01

We define a new matching metric-corner Cauchy-Schwarz divergence (CCSD) and present a new approach based on the proposed CCSD and subpixel localization for image registration. First, we detect the corners in an image by a multiscale Harris operator and take them as initial interest points. And then, a subpixel localization technique is applied to determine the locations of the corners and eliminate the false and unstable corners. After that, CCSD is defined to obtain the initial matching corners. Finally, we use random sample consensus to robustly estimate the parameters based on the initial matching. The experimental results demonstrate that the proposed algorithm has a good performance in terms of both accuracy and efficiency.

Control of linear uncertain systems utilizing mismatched state observers

NASA Technical Reports Server (NTRS)

Goldstein, B.

1972-01-01

The control of linear continuous dynamical systems is investigated as a problem of limited state feedback control. The equations which describe the structure of an observer are developed constrained to time-invarient systems. The optimal control problem is formulated, accounting for the uncertainty in the design parameters. Expressions for bounds on closed loop stability are also developed. The results indicate that very little uncertainty may be tolerated before divergence occurs in the recursive computation algorithms, and the derived stability bound yields extremely conservative estimates of regions of allowable parameter variations.

An adaptive state of charge estimation approach for lithium-ion series-connected battery system

NASA Astrophysics Data System (ADS)

Peng, Simin; Zhu, Xuelai; Xing, Yinjiao; Shi, Hongbing; Cai, Xu; Pecht, Michael

2018-07-01

Due to the incorrect or unknown noise statistics of a battery system and its cell-to-cell variations, state of charge (SOC) estimation of a lithium-ion series-connected battery system is usually inaccurate or even divergent using model-based methods, such as extended Kalman filter (EKF) and unscented Kalman filter (UKF). To resolve this problem, an adaptive unscented Kalman filter (AUKF) based on a noise statistics estimator and a model parameter regulator is developed to accurately estimate the SOC of a series-connected battery system. An equivalent circuit model is first built based on the model parameter regulator that illustrates the influence of cell-to-cell variation on the battery system. A noise statistics estimator is then used to attain adaptively the estimated noise statistics for the AUKF when its prior noise statistics are not accurate or exactly Gaussian. The accuracy and effectiveness of the SOC estimation method is validated by comparing the developed AUKF and UKF when model and measurement statistics noises are inaccurate, respectively. Compared with the UKF and EKF, the developed method shows the highest SOC estimation accuracy.

Multi-locus phylogeny and divergence time estimates of Enallagma damselflies (Odonata: Coenagrionidae).

PubMed

Callahan, Melissa S; McPeek, Mark A

2016-01-01

Reconstructing evolutionary patterns of species and populations provides a framework for asking questions about the impacts of climate change. Here we use a multilocus dataset to estimate gene trees under maximum likelihood and Bayesian models to obtain a robust estimate of relationships for a genus of North American damselflies, Enallagma. Using a relaxed molecular clock, we estimate the divergence times for this group. Furthermore, to account for the fact that gene tree analyses can overestimate ages of population divergences, we use a multi-population coalescent model to gain a more accurate estimate of divergence times. We also infer diversification rates using a method that allows for variation in diversification rate through time and among lineages. Our results reveal a complex evolutionary history of Enallagma, in which divergence events both predate and occur during Pleistocene climate fluctuations. There is also evidence of diversification rate heterogeneity across the tree. These divergence time estimates provide a foundation for addressing the relative significance of historical climatic events in the diversification of this genus. Copyright © 2015 Elsevier Inc. All rights reserved.

Disturbance by an endemic rodent in an arid shrubland is a habitat filter: effects on plant invasion and taxonomical, functional and phylogenetic community structure

PubMed Central

Escobedo, Víctor M.; Rios, Rodrigo S.; Salgado-Luarte, Cristian; Stotz, Gisela C.

2017-01-01

Abstract Background and Aims Disturbance often drives plant invasion and may modify community assembly. However, little is known about how these modifications of community patterns occur in terms of taxonomic, functional and phylogenetic structure. This study evaluated in an arid shrubland the influence of disturbance by an endemic rodent on community functional divergence and phylogenetic structure as well as on plant invasion. It was expected that disturbance would operate as a habitat filter favouring exotic species with short life cycles. Methods Sixteen plots were sampled along a disturbance gradient caused by the endemic fossorial rodent Spalacopus cyanus, measuring community parameters and estimating functional divergence for life history traits (functional dispersion index) and the relative contribution to functional divergence of exotic and native species. The phylogenetic signal (Pagel’s lambda) and phylogenetic community structure (mean phylogenetic distance and mean nearest taxon phylogenetic distance) were also estimated. The use of a continuous approach to the disturbance gradient allowed the identification of non-linear relationships between disturbance and community parameters. Key Results The relationship between disturbance and both species richness and abundance was positive for exotic species and negative for native species. Disturbance modified community composition, and exotic species were associated with more disturbed sites. Disturbance increased trait convergence, which resulted in phylogenetic clustering because traits showed a significant phylogenetic signal. The relative contribution of exotic species to functional divergence increased, while that of natives decreased, with disturbance. Exotic and native species were not phylogenetically distinct. Conclusions Disturbance by rodents in this arid shrubland constitutes a habitat filter over phylogeny-dependent life history traits, leading to phylogenetic clustering, and drives invasion by favouring species with short life cycles. Results can be explained by high phenotypic and phylogenetic resemblance between exotic and native species. The use of continuous gradients when studying the effects of disturbance on community assembly is advocated. PMID:28087661

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.

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 fossilized birth–death process for coherent calibration of divergence-time estimates

PubMed Central

Heath, Tracy A.; Huelsenbeck, John P.; Stadler, Tanja

2014-01-01

Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover patterns of coevolution and diversification. Because molecular sequence data are not informative on absolute time, external data—most commonly, fossil age estimates—are required to calibrate estimates of species divergence dates. For Bayesian divergence time methods, the common practice for calibration using fossil information involves placing arbitrarily chosen parametric distributions on internal nodes, often disregarding most of the information in the fossil record. We introduce the “fossilized birth–death” (FBD) process—a model for calibrating divergence time estimates in a Bayesian framework, explicitly acknowledging that extant species and fossils are part of the same macroevolutionary process. Under this model, absolute node age estimates are calibrated by a single diversification model and arbitrary calibration densities are not necessary. Moreover, the FBD model allows for inclusion of all available fossils. We performed analyses of simulated data and show that node age estimation under the FBD model results in robust and accurate estimates of species divergence times with realistic measures of statistical uncertainty, overcoming major limitations of standard divergence time estimation methods. We used this model to estimate the speciation times for a dataset composed of all living bears, indicating that the genus Ursus diversified in the Late Miocene to Middle Pliocene. PMID:25009181

Exploring the effect of asymmetric mitochondrial DNA introgression on estimating niche divergence in morphologically cryptic species.

PubMed

Wielstra, Ben; Arntzen, Jan W

2014-01-01

If potential morphologically cryptic species, identified based on differentiated mitochondrial DNA, express ecological divergence, this increases support for their treatment as distinct species. However, mitochondrial DNA introgression hampers the correct estimation of ecological divergence. We test the hypothesis that estimated niche divergence differs when considering nuclear DNA composition or mitochondrial DNA type as representing the true species range. We use empirical data of two crested newt species (Amphibia: Triturus) which possess introgressed mitochondrial DNA from a third species in part of their ranges. We analyze the data in environmental space by determining Fisher distances in a principal component analysis and in geographical space by determining geographical overlap of species distribution models. We find that under mtDNA guidance in one of the two study cases niche divergence is overestimated, whereas in the other it is underestimated. In the light of our results we discuss the role of estimated niche divergence in species delineation.

The impact of the rate prior on Bayesian estimation of divergence times with multiple Loci.

PubMed

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

2014-07-01

Bayesian methods provide a powerful way to estimate species divergence times by combining information from molecular sequences with information from the fossil record. With the explosive increase of genomic data, divergence time estimation increasingly uses data of multiple loci (genes or site partitions). Widely used computer programs to estimate divergence times use independent and identically distributed (i.i.d.) priors on the substitution rates for different loci. The i.i.d. prior is problematic. As the number of loci (L) increases, the prior variance of the average rate across all loci goes to zero at the rate 1/L. As a consequence, the rate prior dominates posterior time estimates when many loci are analyzed, and if the rate prior is misspecified, the estimated divergence times will converge to wrong values with very narrow credibility intervals. Here we develop a new prior on the locus rates based on the Dirichlet distribution that corrects the problematic behavior of the i.i.d. prior. We use computer simulation and real data analysis to highlight the differences between the old and new priors. For a dataset for six primate species, we show that with the old i.i.d. prior, if the prior rate is too high (or too low), the estimated divergence times are too young (or too old), outside the bounds imposed by the fossil calibrations. In contrast, with the new Dirichlet prior, posterior time estimates are insensitive to the rate prior and are compatible with the fossil calibrations. We re-analyzed a phylogenomic data set of 36 mammal species and show that using many fossil calibrations can alleviate the adverse impact of a misspecified rate prior to some extent. We recommend the use of the new Dirichlet prior in Bayesian divergence time estimation. [Bayesian inference, divergence time, relaxed clock, rate prior, partition analysis.]. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

A practical divergence measure for survival distributions that can be estimated from Kaplan-Meier curves.

PubMed

Cox, Trevor F; Czanner, Gabriela

2016-06-30

This paper introduces a new simple divergence measure between two survival distributions. For two groups of patients, the divergence measure between their associated survival distributions is based on the integral of the absolute difference in probabilities that a patient from one group dies at time t and a patient from the other group survives beyond time t and vice versa. In the case of non-crossing hazard functions, the divergence measure is closely linked to the Harrell concordance index, C, the Mann-Whitney test statistic and the area under a receiver operating characteristic curve. The measure can be used in a dynamic way where the divergence between two survival distributions from time zero up to time t is calculated enabling real-time monitoring of treatment differences. The divergence can be found for theoretical survival distributions or can be estimated non-parametrically from survival data using Kaplan-Meier estimates of the survivor functions. The estimator of the divergence is shown to be generally unbiased and approximately normally distributed. For the case of proportional hazards, the constituent parts of the divergence measure can be used to assess the proportional hazards assumption. The use of the divergence measure is illustrated on the survival of pancreatic cancer patients. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Phylogeny, time divergence, and historical biogeography of the South American Liolaemus alticolor-bibronii group (Iguania: Liolaemidae)

PubMed Central

2018-01-01

The genus Liolaemus comprises more than 260 species and can be divided in two subgenera: Eulaemus and Liolaemus sensu stricto. In this paper, we present a phylogenetic analysis, divergence times, and ancestral distribution ranges of the Liolaemus alticolor-bibronii group (Liolaemus sensu stricto subgenus). We inferred a total evidence phylogeny combining molecular (Cytb and 12S genes) and morphological characters using Maximum Parsimony and Bayesian Inference. Divergence times were calculated using Bayesian MCMC with an uncorrelated lognormal distributed relaxed clock, calibrated with a fossil record. Ancestral ranges were estimated using the Dispersal-Extinction-Cladogenesis (DEC-Lagrange). Effects of some a priori parameters of DEC were also tested. Distribution ranged from central Perú to southern Argentina, including areas at sea level up to the high Andes. The L. alticolor-bibronii group was recovered as monophyletic, formed by two clades: L. walkeri and L. gracilis, the latter can be split in two groups. Additionally, many species candidates were recognized. We estimate that the L. alticolor-bibronii group diversified 14.5 Myr ago, during the Middle Miocene. Our results suggest that the ancestor of the Liolaemus alticolor-bibronii group was distributed in a wide area including Patagonia and Puna highlands. The speciation pattern follows the South-North Diversification Hypothesis, following the Andean uplift. PMID:29479502

Estimation of divergence from Hardy-Weinberg form.

PubMed

Stark, Alan E

2015-08-01

The Hardy–Weinberg (HW) principle explains how random mating (RM) can produce and maintain a population in equilibrium, that is, with constant genotypic proportions. When proportions diverge from HW form, it is of interest to estimate the fixation index F, which reflects the degree of divergence. Starting from a sample of genotypic counts, a mixed procedure gives first the orthodox estimate of gene frequency q and then a Bayesian estimate of F, based on a credible prior distribution of F, which is described here.

Inferring Species Richness and Turnover by Statistical Multiresolution Texture Analysis of Satellite Imagery

DTIC Science & Technology

2012-10-24

representative pdf’s via the Kullback - Leibler divergence (KL). Species turnover, or b diversity, is estimated using both this KL divergence and the...multiresolution analysis provides a means for estimating divergence between two textures, specifically the Kullback - Leibler divergence between the pair of ...and open challenges. Ecological Informatics 5: 318–329. 19. Ludovisi A, TaticchiM(2006) Investigating beta diversity by kullback - leibler information

SMURC: High-Dimension Small-Sample Multivariate Regression With Covariance Estimation.

PubMed

Bayar, Belhassen; Bouaynaya, Nidhal; Shterenberg, Roman

2017-03-01

We consider a high-dimension low sample-size multivariate regression problem that accounts for correlation of the response variables. The system is underdetermined as there are more parameters than samples. We show that the maximum likelihood approach with covariance estimation is senseless because the likelihood diverges. We subsequently propose a normalization of the likelihood function that guarantees convergence. We call this method small-sample multivariate regression with covariance (SMURC) estimation. We derive an optimization problem and its convex approximation to compute SMURC. Simulation results show that the proposed algorithm outperforms the regularized likelihood estimator with known covariance matrix and the sparse conditional Gaussian graphical model. We also apply SMURC to the inference of the wing-muscle gene network of the Drosophila melanogaster (fruit fly).

Strategies for improving approximate Bayesian computation tests for synchronous diversification.

PubMed

Overcast, Isaac; Bagley, Justin C; Hickerson, Michael J

2017-08-24

Estimating the variability in isolation times across co-distributed taxon pairs that may have experienced the same allopatric isolating mechanism is a core goal of comparative phylogeography. The use of hierarchical Approximate Bayesian Computation (ABC) and coalescent models to infer temporal dynamics of lineage co-diversification has been a contentious topic in recent years. Key issues that remain unresolved include the choice of an appropriate prior on the number of co-divergence events (Ψ), as well as the optimal strategies for data summarization. Through simulation-based cross validation we explore the impact of the strategy for sorting summary statistics and the choice of prior on Ψ on the estimation of co-divergence variability. We also introduce a new setting (β) that can potentially improve estimation of Ψ by enforcing a minimal temporal difference between pulses of co-divergence. We apply this new method to three empirical datasets: one dataset each of co-distributed taxon pairs of Panamanian frogs and freshwater fishes, and a large set of Neotropical butterfly sister-taxon pairs. We demonstrate that the choice of prior on Ψ has little impact on inference, but that sorting summary statistics yields substantially more reliable estimates of co-divergence variability despite violations of assumptions about exchangeability. We find the implementation of β improves estimation of Ψ, with improvement being most dramatic given larger numbers of taxon pairs. We find equivocal support for synchronous co-divergence for both of the Panamanian groups, but we find considerable support for asynchronous divergence among the Neotropical butterflies. Our simulation experiments demonstrate that using sorted summary statistics results in improved estimates of the variability in divergence times, whereas the choice of hyperprior on Ψ has negligible effect. Additionally, we demonstrate that estimating the number of pulses of co-divergence across co-distributed taxon-pairs is improved by applying a flexible buffering regime over divergence times. This improves the correlation between Ψ and the true variability in isolation times and allows for more meaningful interpretation of this hyperparameter. This will allow for more accurate identification of the number of temporally distinct pulses of co-divergence that generated the diversification pattern of a given regional assemblage of sister-taxon-pairs.

Detecting the sampling rate through observations

NASA Astrophysics Data System (ADS)

Shoji, Isao

2018-09-01

This paper proposes a method to detect the sampling rate of discrete time series of diffusion processes. Using the maximum likelihood estimates of the parameters of a diffusion process, we establish a criterion based on the Kullback-Leibler divergence and thereby estimate the sampling rate. Simulation studies are conducted to check whether the method can detect the sampling rates from data and their results show a good performance in the detection. In addition, the method is applied to a financial time series sampled on daily basis and shows the detected sampling rate is different from the conventional rates.

Calibrated tree priors for relaxed phylogenetics and divergence time estimation.

PubMed

Heled, Joseph; Drummond, Alexei J

2012-01-01

The use of fossil evidence to calibrate divergence time estimation has a long history. More recently, Bayesian Markov chain Monte Carlo has become the dominant method of divergence time estimation, and fossil evidence has been reinterpreted as the specification of prior distributions on the divergence times of calibration nodes. These so-called "soft calibrations" have become widely used but the statistical properties of calibrated tree priors in a Bayesian setting hashave not been carefully investigated. Here, we clarify that calibration densities, such as those defined in BEAST 1.5, do not represent the marginal prior distribution of the calibration node. We illustrate this with a number of analytical results on small trees. We also describe an alternative construction for a calibrated Yule prior on trees that allows direct specification of the marginal prior distribution of the calibrated divergence time, with or without the restriction of monophyly. This method requires the computation of the Yule prior conditional on the height of the divergence being calibrated. Unfortunately, a practical solution for multiple calibrations remains elusive. Our results suggest that direct estimation of the prior induced by specifying multiple calibration densities should be a prerequisite of any divergence time dating analysis.

Divergence between human populations estimated from linkage disequilibrium.

PubMed

Sved, John A; McRae, Allan F; Visscher, Peter M

2008-12-01

Observed linkage disequilibrium (LD) between genetic markers in different populations descended independently from a common ancestral population can be used to estimate their absolute time of divergence, because the correlation of LD between populations will be reduced each generation by an amount that, approximately, depends only on the recombination rate between markers. Although drift leads to divergence in allele frequencies, it has less effect on divergence in LD values. We derived the relationship between LD and time of divergence and verified it with coalescent simulations. We then used HapMap Phase II data to estimate time of divergence between human populations. Summed over large numbers of pairs of loci, we find a positive correlation of LD between African and non-African populations at levels of up to approximately 0.3 cM. We estimate that the observed correlation of LD is consistent with an effective separation time of approximately 1,000 generations or approximately 25,000 years before present. The most likely explanation for such relatively low separation times is the existence of substantial levels of migration between populations after the initial separation. Theory and results from coalescent simulations confirm that low levels of migration can lead to a downward bias in the estimate of separation time.

Demographic histories of adaptively diverged riparian and non-riparian species of Ainsliaea (Asteraceae) inferred from coalescent analyses using multiple nuclear loci

PubMed Central

2012-01-01

Background Understanding demographic histories, such as divergence time, patterns of gene flow, and population size changes, in ecologically diverging lineages provide implications for the process and maintenance of population differentiation by ecological adaptation. This study addressed the demographic histories in two independently derived lineages of flood-resistant riparian plants and their non-riparian relatives [Ainsliaea linearis (riparian) and A. apiculata (non-riparian); A. oblonga (riparian) and A. macroclinidioides (non-riparian); Asteraceae] using an isolation-with-migration (IM) model based on variation at 10 nuclear DNA loci. Results The highest posterior probabilities of the divergence time parameters were estimated to be ca. 25,000 years ago for A. linearis and A. apiculata and ca. 9000 years ago for A. oblonga and A. macroclinidioides, although the confidence intervals of the parameters had broad ranges. The likelihood ratio tests detected evidence of historical gene flow between both riparian/non-riparian species pairs. The riparian populations showed lower levels of genetic diversity and a significant reduction in effective population sizes compared to the non-riparian populations and their ancestral populations. Conclusions This study showed the recent origins of flood-resistant riparian plants, which are remarkable examples of plant ecological adaptation. The recent divergence and genetic signatures of historical gene flow among riparian/non-riparian species implied that they underwent morphological and ecological differentiation within short evolutionary timescales and have maintained their species boundaries in the face of gene flow. Comparative analyses of adaptive divergence in two sets of riparian/non-riparian lineages suggested that strong natural selection by flooding had frequently reduced the genetic diversity and size of riparian populations through genetic drift, possibly leading to fixation of adaptive traits in riparian populations. The two sets of riparian/non-riparian lineages showed contrasting patterns of gene flow and genetic differentiation, implying that each lineage showed different degrees of reproductive isolation and that they had experienced unique evolutionary and demographic histories in the process of adaptive divergence. PMID:23273287

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.

Divergences and estimating tight bounds on Bayes error with applications to multivariate Gaussian copula and latent Gaussian copula

NASA Astrophysics Data System (ADS)

Thelen, Brian J.; Xique, Ismael J.; Burns, Joseph W.; Goley, G. Steven; Nolan, Adam R.; Benson, Jonathan W.

2017-04-01

In Bayesian decision theory, there has been a great amount of research into theoretical frameworks and information- theoretic quantities that can be used to provide lower and upper bounds for the Bayes error. These include well-known bounds such as Chernoff, Battacharrya, and J-divergence. Part of the challenge of utilizing these various metrics in practice is (i) whether they are "loose" or "tight" bounds, (ii) how they might be estimated via either parametric or non-parametric methods, and (iii) how accurate the estimates are for limited amounts of data. In general what is desired is a methodology for generating relatively tight lower and upper bounds, and then an approach to estimate these bounds efficiently from data. In this paper, we explore the so-called triangle divergence which has been around for a while, but was recently made more prominent in some recent research on non-parametric estimation of information metrics. Part of this work is motivated by applications for quantifying fundamental information content in SAR/LIDAR data, and to help in this, we have developed a flexible multivariate modeling framework based on multivariate Gaussian copula models which can be combined with the triangle divergence framework to quantify this information, and provide approximate bounds on Bayes error. In this paper we present an overview of the bounds, including those based on triangle divergence and verify that under a number of multivariate models, the upper and lower bounds derived from triangle divergence are significantly tighter than the other common bounds, and often times, dramatically so. We also propose some simple but effective means for computing the triangle divergence using Monte Carlo methods, and then discuss estimation of the triangle divergence from empirical data based on Gaussian Copula models.

On the number of New World founders: a population genetic portrait of the peopling of the Americas.

PubMed

Hey, Jody

2005-06-01

The founding of New World populations by Asian peoples is the focus of considerable archaeological and genetic research, and there persist important questions on when and how these events occurred. Genetic data offer great potential for the study of human population history, but there are significant challenges in discerning distinct demographic processes. A new method for the study of diverging populations was applied to questions on the founding and history of Amerind-speaking Native American populations. The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow. Analyses of data from nine loci are consistent with the general portrait that has emerged from archaeological and other kinds of evidence. The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population. By adding a splitting parameter to population divergence models it becomes possible to develop detailed portraits of human demographic history. Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size.

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

Sequencing of Chloroplast Genomes from Wheat, Barley, Rye and Their Relatives Provides a Detailed Insight into the Evolution of the Triticeae Tribe

PubMed Central

Middleton, Christopher P.; Senerchia, Natacha; Stein, Nils; Akhunov, Eduard D.; Keller, Beat

2014-01-01

Using Roche/454 technology, we sequenced the chloroplast genomes of 12 Triticeae species, including bread wheat, barley and rye, as well as the diploid progenitors and relatives of bread wheat Triticum urartu, Aegilops speltoides and Ae. tauschii. Two wild tetraploid taxa, Ae. cylindrica and Ae. geniculata, were also included. Additionally, we incorporated wild Einkorn wheat Triticum boeoticum and its domesticated form T. monococcum and two Hordeum spontaneum (wild barley) genotypes. Chloroplast genomes were used for overall sequence comparison, phylogenetic analysis and dating of divergence times. We estimate that barley diverged from rye and wheat approximately 8–9 million years ago (MYA). The genome donors of hexaploid wheat diverged between 2.1–2.9 MYA, while rye diverged from Triticum aestivum approximately 3–4 MYA, more recently than previously estimated. Interestingly, the A genome taxa T. boeoticum and T. urartu were estimated to have diverged approximately 570,000 years ago. As these two have a reproductive barrier, the divergence time estimate also provides an upper limit for the time required for the formation of a species boundary between the two. Furthermore, we conclusively show that the chloroplast genome of hexaploid wheat was contributed by the B genome donor and that this unknown species diverged from Ae. speltoides about 980,000 years ago. Additionally, sequence alignments identified a translocation of a chloroplast segment to the nuclear genome which is specific to the rye/wheat lineage. We propose the presented phylogeny and divergence time estimates as a reference framework for future studies on Triticeae. PMID:24614886

Fossils matter: improved estimates of divergence times in Pinus reveal older diversification.

PubMed

Saladin, Bianca; Leslie, Andrew B; Wüest, Rafael O; Litsios, Glenn; Conti, Elena; Salamin, Nicolas; Zimmermann, Niklaus E

2017-04-04

The taxonomy of pines (genus Pinus) is widely accepted and a robust gene tree based on entire plastome sequences exists. However, there is a large discrepancy in estimated divergence times of major pine clades among existing studies, mainly due to differences in fossil placement and dating methods used. We currently lack a dated molecular phylogeny that makes use of the rich pine fossil record, and this study is the first to estimate the divergence dates of pines based on a large number of fossils (21) evenly distributed across all major clades, in combination with applying both node and tip dating methods. We present a range of molecular phylogenetic trees of Pinus generated within a Bayesian framework. We find the origin of crown Pinus is likely up to 30 Myr older (Early Cretaceous) than inferred in most previous studies (Late Cretaceous) and propose generally older divergence times for major clades within Pinus than previously thought. Our age estimates vary significantly between the different dating approaches, but the results generally agree on older divergence times. We present a revised list of 21 fossils that are suitable to use in dating or comparative analyses of pines. Reliable estimates of divergence times in pines are essential if we are to link diversification processes and functional adaptation of this genus to geological events or to changing climates. In addition to older divergence times in Pinus, our results also indicate that node age estimates in pines depend on dating approaches and the specific fossil sets used, reflecting inherent differences in various dating approaches. The sets of dated phylogenetic trees of pines presented here provide a way to account for uncertainties in age estimations when applying comparative phylogenetic methods.

BATMAN beam properties characterization by the beam emission spectroscopy diagnostic

NASA Astrophysics Data System (ADS)

Bonomo, F.; Ruf, B.; Barbisan, M.; Cristofaro, S.; Schiesko, L.; Fantz, U.; Franzen, P.; Pasqualotto, R.; Riedl, R.; Serianni, G.; Wünderlich, D.

2015-04-01

The ITER neutral beam heating systems are based on the production and acceleration of negative ions (H/D) up to 1 MV. The requirements for the beam properties are strict: a low core beam divergence (< 0.4 °) together with a low source pressure (≤ 0.3 Pa) would permit to reduce the ion losses along the beamline, keeping the stripping particle losses below 30%. However, the attainment of such beam properties is not straightforward. At IPP, the negative ion source testbed BATMAN (BAvarian Test MAchine for Negative ions) allows for deepening the knowledge of the determination of the beam properties. One of the diagnostics routinely used to this purpose is the Beam Emission Spectroscopy (BES): the Hα light emitted in the beam is detected and the corresponding spectra are evaluated to estimate the beam divergence and the stripping losses. The BES number of lines of sight in BATMAN has been recently increased: five horizontal lines of sight providing a vertical profile of the beam permit to characterize the negative ion beam properties in relation to the source parameters. Different methods of Hα spectra analysis are here taken into account and compared for the estimation of the beam divergence and the amount of stripping. In particular, to thoroughly study the effect of the space charge compensation on the beam divergence, an additional hydrogen injection line has been added in the tank, which allows for setting different background pressure values (one order of magnitude, from about 0.04 Pa up to the source pressure) in the beam drift region.

Nonnegative matrix factorization with the Itakura-Saito divergence: with application to music analysis.

PubMed

Févotte, Cédric; Bertin, Nancy; Durrieu, Jean-Louis

2009-03-01

This letter presents theoretical, algorithmic, and experimental results about nonnegative matrix factorization (NMF) with the Itakura-Saito (IS) divergence. We describe how IS-NMF is underlaid by a well-defined statistical model of superimposed gaussian components and is equivalent to maximum likelihood estimation of variance parameters. This setting can accommodate regularization constraints on the factors through Bayesian priors. In particular, inverse-gamma and gamma Markov chain priors are considered in this work. Estimation can be carried out using a space-alternating generalized expectation-maximization (SAGE) algorithm; this leads to a novel type of NMF algorithm, whose convergence to a stationary point of the IS cost function is guaranteed. We also discuss the links between the IS divergence and other cost functions used in NMF, in particular, the Euclidean distance and the generalized Kullback-Leibler (KL) divergence. As such, we describe how IS-NMF can also be performed using a gradient multiplicative algorithm (a standard algorithm structure in NMF) whose convergence is observed in practice, though not proven. Finally, we report a furnished experimental comparative study of Euclidean-NMF, KL-NMF, and IS-NMF algorithms applied to the power spectrogram of a short piano sequence recorded in real conditions, with various initializations and model orders. Then we show how IS-NMF can successfully be employed for denoising and upmix (mono to stereo conversion) of an original piece of early jazz music. These experiments indicate that IS-NMF correctly captures the semantics of audio and is better suited to the representation of music signals than NMF with the usual Euclidean and KL costs.

An improved state-parameter analysis of ecosystem models using data assimilation

USGS Publications Warehouse

Chen, M.; Liu, S.; Tieszen, L.L.; Hollinger, D.Y.

2008-01-01

Much of the effort spent in developing data assimilation methods for carbon dynamics analysis has focused on estimating optimal values for either model parameters or state variables. The main weakness of estimating parameter values alone (i.e., without considering state variables) is that all errors from input, output, and model structure are attributed to model parameter uncertainties. On the other hand, the accuracy of estimating state variables may be lowered if the temporal evolution of parameter values is not incorporated. This research develops a smoothed ensemble Kalman filter (SEnKF) by combining ensemble Kalman filter with kernel smoothing technique. SEnKF has following characteristics: (1) to estimate simultaneously the model states and parameters through concatenating unknown parameters and state variables into a joint state vector; (2) to mitigate dramatic, sudden changes of parameter values in parameter sampling and parameter evolution process, and control narrowing of parameter variance which results in filter divergence through adjusting smoothing factor in kernel smoothing algorithm; (3) to assimilate recursively data into the model and thus detect possible time variation of parameters; and (4) to address properly various sources of uncertainties stemming from input, output and parameter uncertainties. The SEnKF is tested by assimilating observed fluxes of carbon dioxide and environmental driving factor data from an AmeriFlux forest station located near Howland, Maine, USA, into a partition eddy flux model. Our analysis demonstrates that model parameters, such as light use efficiency, respiration coefficients, minimum and optimum temperatures for photosynthetic activity, and others, are highly constrained by eddy flux data at daily-to-seasonal time scales. The SEnKF stabilizes parameter values quickly regardless of the initial values of the parameters. Potential ecosystem light use efficiency demonstrates a strong seasonality. Results show that the simultaneous parameter estimation procedure significantly improves model predictions. Results also show that the SEnKF can dramatically reduce the variance in state variables stemming from the uncertainty of parameters and driving variables. The SEnKF is a robust and effective algorithm in evaluating and developing ecosystem models and in improving the understanding and quantification of carbon cycle parameters and processes. ?? 2008 Elsevier B.V.

Variable Autosomal and X Divergence Near and Far from Genes Affects Estimates of Male Mutation Bias in Great Apes

PubMed Central

Narang, Pooja; Wilson Sayres, Melissa A.

2016-01-01

Male mutation bias, when more mutations are passed on via the male germline than via the female germline, is observed across mammals. One common way to infer the magnitude of male mutation bias, α, is to compare levels of neutral sequence divergence between genomic regions that spend different amounts of time in the male and female germline. For great apes, including human, we show that estimates of divergence are reduced in putatively unconstrained regions near genes relative to unconstrained regions far from genes. Divergence increases with increasing distance from genes on both the X chromosome and autosomes, but increases faster on the X chromosome than autosomes. As a result, ratios of X/A divergence increase with increasing distance from genes and corresponding estimates of male mutation bias are significantly higher in intergenic regions near genes versus far from genes. Future studies in other species will need to carefully consider the effect that genomic location will have on estimates of male mutation bias. PMID:27702816

Estimation of hydraulic jump characteristics of channels with sudden diverging side walls via SVM.

PubMed

Roushangar, Kiyoumars; Valizadeh, Reyhaneh; Ghasempour, Roghayeh

2017-10-01

Sudden diverging channels are one of the energy dissipaters which can dissipate most of the kinetic energy of the flow through a hydraulic jump. An accurate prediction of hydraulic jump characteristics is an important step in designing hydraulic structures. This paper focuses on the capability of the support vector machine (SVM) as a meta-model approach for predicting hydraulic jump characteristics in different sudden diverging stilling basins (i.e. basins with and without appurtenances). In this regard, different models were developed and tested using 1,018 experimental data. The obtained results proved the capability of the SVM technique in predicting hydraulic jump characteristics and it was found that the developed models for a channel with a central block performed more successfully than models for channels without appurtenances or with a negative step. The superior performance for the length of hydraulic jump was obtained for the model with parameters F 1 (Froude number) and (h 2- h 1 )/h 1 (h 1 and h 2 are sequent depth of upstream and downstream respectively). Concerning the relative energy dissipation and sequent depth ratio, the model with parameters F 1 and h 1 /B (B is expansion ratio) led to the best results. According to the outcome of sensitivity analysis, Froude number had the most significant effect on the modeling. Also comparison between SVM and empirical equations indicated the great performance of the SVM.

Two-loop hard-thermal-loop thermodynamics with quarks

NASA Astrophysics Data System (ADS)

Andersen, Jens O.; Petitgirard, Emmanuel; Strickland, Michael

2004-08-01

We calculate the quark contribution to the free energy of a hot quark-gluon plasma to two-loop order using hard-thermal-loop (HTL) perturbation theory. All ultraviolet divergences can be absorbed into renormalizations of the vacuum energy and the HTL quark and gluon mass parameters. The quark and gluon HTL mass parameters are determined self-consistently by a variational prescription. Combining the quark contribution with the two-loop HTL perturbation theory free energy for pure glue we obtain the total two-loop QCD free energy. Comparisons are made with lattice estimates of the free energy for Nf=2 and with exact numerical results obtained in the large-Nf limit.

Genetic Divergence Disclosing a Rapid Prehistorical Dispersion of Native Americans in Central and South America

PubMed Central

He, Yungang; Wang, Wei R.; Li, Ran; Wang, Sijia; Jin, Li

2012-01-01

An accurate estimate of the divergence time between Native Americans is important for understanding the initial entry and early dispersion of human beings in the New World. Current methods for estimating the genetic divergence time of populations could seriously depart from a linear relationship with the true divergence for multiple populations of a different population size and significant population expansion. Here, to address this problem, we propose a novel measure to estimate the genetic divergence time of populations. Computer simulation revealed that the new measure maintained an excellent linear correlation with the population divergence time in complicated multi-population scenarios with population expansion. Utilizing the new measure and microsatellite data of 21 Native American populations, we investigated the genetic divergences of the Native American populations. The results indicated that genetic divergences between North American populations are greater than that between Central and South American populations. None of the divergences, however, were large enough to constitute convincing evidence supporting the two-wave or multi-wave migration model for the initial entry of human beings into America. The genetic affinity of the Native American populations was further explored using Neighbor-Net and the genetic divergences suggested that these populations could be categorized into four genetic groups living in four different ecologic zones. The divergence of the population groups suggests that the early dispersion of human beings in America was a multi-step procedure. Further, the divergences suggest the rapid dispersion of Native Americans in Central and South Americas after a long standstill period in North America. PMID:22970308

A Handbook of Sound and Vibration Parameters

DTIC Science & Technology

1978-09-18

fixed in space. (Reference 1.) no motion atay node Static Divergence: (See Divergence.) Statistical Energy Analysis (SEA): Statistical energy analysis is...parameters of the circuits come from statistics of the vibrational characteristics of the structure. Statistical energy analysis is uniquely successful

New robust statistical procedures for the polytomous logistic regression models.

PubMed

Castilla, Elena; Ghosh, Abhik; Martin, Nirian; Pardo, Leandro

2018-05-17

This article derives a new family of estimators, namely the minimum density power divergence estimators, as a robust generalization of the maximum likelihood estimator for the polytomous logistic regression model. Based on these estimators, a family of Wald-type test statistics for linear hypotheses is introduced. Robustness properties of both the proposed estimators and the test statistics are theoretically studied through the classical influence function analysis. Appropriate real life examples are presented to justify the requirement of suitable robust statistical procedures in place of the likelihood based inference for the polytomous logistic regression model. The validity of the theoretical results established in the article are further confirmed empirically through suitable simulation studies. Finally, an approach for the data-driven selection of the robustness tuning parameter is proposed with empirical justifications. © 2018, The International Biometric Society.

Measurement of beam divergence of 30-centimeter dished grids

NASA Technical Reports Server (NTRS)

Danilowicz, R. L.; Rawlin, V. K.; Banks, B. A.; Wintucky, E. G.

1973-01-01

The beam divergence of a 30-centimeter diameter thruster with dished grids was calculated from current densities measured with a probe rake containing seventeen planar molybdenum probes. The measured data were analyzed as a function of a number of parameters. The most sensitive parameters were the amount of compensation of the accelerator grid and the ratio of net to total accelerating voltage. The thrust losses were reduced by over 5 percent with the use of compensated grids alone, and by variation of other parameters the overall thrust losses due to beam divergence were reduced to less than 2 percent.

Measurement of beam divergence of 30-centimeter dished grids

NASA Technical Reports Server (NTRS)

Danilowicz, R. L.; Rawlin, V. K.; Banks, B. A.; Wintucky, E. G.

1973-01-01

The beam divergence of a 30-centimeter diameter thrustor with dished grids was calculated from current densities measured with a probe rake containing seventeen planar molybdenum probes. The measured data were analyzed as a function of a number of parameters. The most sensitive parameters were the amount of compensation of the accelerator grid and the ratio of net to total accelerating voltage. The thrust losses were reduced by over 5 percent with the use of compensated grids alone, and by variation of other parameters the overall thrust losses due to beam divergence were reduced to less than 2 percent.

Analytical estimation on divergence and flutter vibrations of symmetrical three-phase induction stator via field-synchronous coordinates

NASA Astrophysics Data System (ADS)

Xia, Ying; Wang, Shiyu; Sun, Wenjia; Xiu, Jie

2017-01-01

The electromagnetically induced parametric vibration of the symmetrical three-phase induction stator is examined. While it can be analyzed by an approximate analytical or numerical method, more accurate and simple analytical method is desirable. This work proposes a new method based on the field-synchronous coordinates. A mechanical-electromagnetic coupling model is developed under this frame such that a time-invariant governing equation with gyroscopic term can be developed. With the general vibration theory, the eigenvalue is formulated; the transition curves between the stable and unstable regions, and response are all determined as closed-form expressions of basic mechanical-electromagnetic parameters. The dependence of these parameters on the instability behaviors is demonstrated. The results imply that the divergence and flutter instabilities can occur even for symmetrical motors with balanced, constant amplitude and sinusoidal voltage. To verify the analytical predictions, this work also builds up a time-variant model of the same system under the conventional inertial frame. The Floquét theory is employed to predict the parametric instability and the numerical integration is used to obtain the parametric response. The parametric instability and response are both well compared against those under the field-synchronous coordinates. The proposed field-synchronous coordinates allows a quick estimation on the electromagnetically induced vibration. The convenience offered by the body-fixed coordinates is discussed across various fields.

Disturbance by an endemic rodent in an arid shrubland is a habitat filter: effects on plant invasion and taxonomical, functional and phylogenetic community structure.

PubMed

Escobedo, Víctor M; Rios, Rodrigo S; Salgado-Luarte, Cristian; Stotz, Gisela C; Gianoli, Ernesto

2017-03-01

Disturbance often drives plant invasion and may modify community assembly. However, little is known about how these modifications of community patterns occur in terms of taxonomic, functional and phylogenetic structure. This study evaluated in an arid shrubland the influence of disturbance by an endemic rodent on community functional divergence and phylogenetic structure as well as on plant invasion. It was expected that disturbance would operate as a habitat filter favouring exotic species with short life cycles. Sixteen plots were sampled along a disturbance gradient caused by the endemic fossorial rodent Spalacopus cyanus , measuring community parameters and estimating functional divergence for life history traits (functional dispersion index) and the relative contribution to functional divergence of exotic and native species. The phylogenetic signal (Pagel's lambda) and phylogenetic community structure (mean phylogenetic distance and mean nearest taxon phylogenetic distance) were also estimated. The use of a continuous approach to the disturbance gradient allowed the identification of non-linear relationships between disturbance and community parameters. The relationship between disturbance and both species richness and abundance was positive for exotic species and negative for native species. Disturbance modified community composition, and exotic species were associated with more disturbed sites. Disturbance increased trait convergence, which resulted in phylogenetic clustering because traits showed a significant phylogenetic signal. The relative contribution of exotic species to functional divergence increased, while that of natives decreased, with disturbance. Exotic and native species were not phylogenetically distinct. Disturbance by rodents in this arid shrubland constitutes a habitat filter over phylogeny-dependent life history traits, leading to phylogenetic clustering, and drives invasion by favouring species with short life cycles. Results can be explained by high phenotypic and phylogenetic resemblance between exotic and native species. The use of continuous gradients when studying the effects of disturbance on community assembly is advocated. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

History, geography and host use shape genomewide patterns of genetic variation in the redheaded pine sawfly (Neodiprion lecontei).

PubMed

Bagley, Robin K; Sousa, Vitor C; Niemiller, Matthew L; Linnen, Catherine R

2017-02-01

Divergent host use has long been suspected to drive population differentiation and speciation in plant-feeding insects. Evaluating the contribution of divergent host use to genetic differentiation can be difficult, however, as dispersal limitation and population structure may also influence patterns of genetic variation. In this study, we use double-digest restriction-associated DNA (ddRAD) sequencing to test the hypothesis that divergent host use contributes to genetic differentiation among populations of the redheaded pine sawfly (Neodiprion lecontei), a widespread pest that uses multiple Pinus hosts throughout its range in eastern North America. Because this species has a broad range and specializes on host plants known to have migrated extensively during the Pleistocene, we first assess overall genetic structure using model-based and model-free clustering methods and identify three geographically distinct genetic clusters. Next, using a composite-likelihood approach based on the site frequency spectrum and a novel strategy for maximizing the utility of linked RAD markers, we infer the population topology and date divergence to the Pleistocene. Based on existing knowledge of Pinus refugia, estimated demographic parameters and patterns of diversity among sawfly populations, we propose a Pleistocene divergence scenario for N. lecontei. Finally, using Mantel and partial Mantel tests, we identify a significant relationship between genetic distance and geography in all clusters, and between genetic distance and host use in two of three clusters. Overall, our results indicate that Pleistocene isolation, dispersal limitation and ecological divergence all contribute to genomewide differentiation in this species and support the hypothesis that host use is a common driver of population divergence in host-specialized insects. © 2016 John Wiley & Sons Ltd.

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.

A Poisson nonnegative matrix factorization method with parameter subspace clustering constraint for endmember extraction in hyperspectral imagery

NASA Astrophysics Data System (ADS)

Sun, Weiwei; Ma, Jun; Yang, Gang; Du, Bo; Zhang, Liangpei

2017-06-01

A new Bayesian method named Poisson Nonnegative Matrix Factorization with Parameter Subspace Clustering Constraint (PNMF-PSCC) has been presented to extract endmembers from Hyperspectral Imagery (HSI). First, the method integrates the liner spectral mixture model with the Bayesian framework and it formulates endmember extraction into a Bayesian inference problem. Second, the Parameter Subspace Clustering Constraint (PSCC) is incorporated into the statistical program to consider the clustering of all pixels in the parameter subspace. The PSCC could enlarge differences among ground objects and helps finding endmembers with smaller spectrum divergences. Meanwhile, the PNMF-PSCC method utilizes the Poisson distribution as the prior knowledge of spectral signals to better explain the quantum nature of light in imaging spectrometer. Third, the optimization problem of PNMF-PSCC is formulated into maximizing the joint density via the Maximum A Posterior (MAP) estimator. The program is finally solved by iteratively optimizing two sub-problems via the Alternating Direction Method of Multipliers (ADMM) framework and the FURTHESTSUM initialization scheme. Five state-of-the art methods are implemented to make comparisons with the performance of PNMF-PSCC on both the synthetic and real HSI datasets. Experimental results show that the PNMF-PSCC outperforms all the five methods in Spectral Angle Distance (SAD) and Root-Mean-Square-Error (RMSE), and especially it could identify good endmembers for ground objects with smaller spectrum divergences.

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.

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.

Gene flow analysis method, the D-statistic, is robust in a wide parameter space.

PubMed

Zheng, Yichen; Janke, Axel

2018-01-08

We evaluated the sensitivity of the D-statistic, a parsimony-like method widely used to detect gene flow between closely related species. This method has been applied to a variety of taxa with a wide range of divergence times. However, its parameter space and thus its applicability to a wide taxonomic range has not been systematically studied. Divergence time, population size, time of gene flow, distance of outgroup and number of loci were examined in a sensitivity analysis. The sensitivity study shows that the primary determinant of the D-statistic is the relative population size, i.e. the population size scaled by the number of generations since divergence. This is consistent with the fact that the main confounding factor in gene flow detection is incomplete lineage sorting by diluting the signal. The sensitivity of the D-statistic is also affected by the direction of gene flow, size and number of loci. In addition, we examined the ability of the f-statistics, [Formula: see text] and [Formula: see text], to estimate the fraction of a genome affected by gene flow; while these statistics are difficult to implement to practical questions in biology due to lack of knowledge of when the gene flow happened, they can be used to compare datasets with identical or similar demographic background. The D-statistic, as a method to detect gene flow, is robust against a wide range of genetic distances (divergence times) but it is sensitive to population size. The D-statistic should only be applied with critical reservation to taxa where population sizes are large relative to branch lengths in generations.

A mechanistic modeling and data assimilation framework for Mojave Desert ecohydrology

USGS Publications Warehouse

Ng, Gene-Hua Crystal.; Bedford, David; Miller, David

2014-01-01

This study demonstrates and addresses challenges in coupled ecohydrological modeling in deserts, which arise due to unique plant adaptations, marginal growing conditions, slow net primary production rates, and highly variable rainfall. We consider model uncertainty from both structural and parameter errors and present a mechanistic model for the shrub Larrea tridentata (creosote bush) under conditions found in the Mojave National Preserve in southeastern California (USA). Desert-specific plant and soil features are incorporated into the CLM-CN model by Oleson et al. (2010). We then develop a data assimilation framework using the ensemble Kalman filter (EnKF) to estimate model parameters based on soil moisture and leaf-area index observations. A new implementation procedure, the “multisite loop EnKF,” tackles parameter estimation difficulties found to affect desert ecohydrological applications. Specifically, the procedure iterates through data from various observation sites to alleviate adverse filter impacts from non-Gaussianity in small desert vegetation state values. It also readjusts inconsistent parameters and states through a model spin-up step that accounts for longer dynamical time scales due to infrequent rainfall in deserts. Observation error variance inflation may also be needed to help prevent divergence of estimates from true values. Synthetic test results highlight the importance of adequate observations for reducing model uncertainty, which can be achieved through data quality or quantity.

Summary of directional divergence characteristics of several high performance aircraft configurations

NASA Technical Reports Server (NTRS)

Greer, H. D.

1972-01-01

The present paper summarizes the high-angle-of-attack characteristics of a number of high-performance aircraft as determined from model force tests and free-flight model tests and correlates these characteristics with the dynamic directional-stability parameter. This correlation shows that the dynamic directional-stability parameter correlates fairly well with directional divergence. Data are also presented to show the effect of some airframe modifications on the directional divergence potential of the configuration. These results show that leading-edge slates seem to be the most effective airframe modification for reducing or eliminating the directional divergence potential of aircraft with moderately swept wings.

Analytic calculation of finite-population reproductive numbers for direct- and vector-transmitted diseases with homogeneous mixing.

PubMed

Keegan, Lindsay; Dushoff, Jonathan

2014-05-01

The basic reproductive number, R0, provides a foundation for evaluating how various factors affect the incidence of infectious diseases. Recently, it has been suggested that, particularly for vector-transmitted diseases, R0 should be modified to account for the effects of finite host population within a single disease transmission generation. Here, we use a transmission factor approach to calculate such "finite-population reproductive numbers," under the assumption of homogeneous mixing, for both vector-borne and directly transmitted diseases. In the case of vector-borne diseases, we estimate finite-population reproductive numbers for both host-to-host and vector-to-vector generations, assuming that the vector population is effectively infinite. We find simple, interpretable formulas for all three of these quantities. In the direct case, we find that finite-population reproductive numbers diverge from R0 before R0 reaches half of the population size. In the vector-transmitted case, we find that the host-to-host number diverges at even lower values of R0, while the vector-to-vector number diverges very little over realistic parameter ranges.

DNA Barcoding in Pencilfishes (Lebiasinidae: Nannostomus) Reveals Cryptic Diversity across the Brazilian Amazon

PubMed Central

Benzaquem, Denise Corrêa; Oliveira, Claudio; da Silva Batista, Jaqueline; Zuanon, Jansen; Porto, Jorge Ivan Rebelo

2015-01-01

Nannostomus is comprised of 20 species. Popularly known as pencilfishes the vast majority of these species lives in the flooded forests of the Amazon basin and are popular in the ornamental trade. Among the lebiasinids, it is the only genus to have undergone more than one taxonomic revision. Even so, it still possesses poorly defined species. Here, we report the results of an application of DNA barcoding to the identification of pencilfishes and highlight the deeply divergent clades within four nominal species. We surveyed the sequence variation in the mtDNA cytochrome c oxidase subunit I gene among 110 individuals representing 14 nominal species that were collected from several rivers along the Amazon basin. The mean Kimura-2-parameter distances within species and genus were 2% and 19,0%, respectively. The deep lineage divergences detected in N. digrammus, N. trifasciatus, N. unifasciatus and N. eques suggest the existence of hidden diversity in Nannostomus species. For N. digrammus and N. trifasciatus, in particular, the estimated divergences in some lineages were so high that doubt about their conspecific status is raised. PMID:25658694

Fundamental Parameters Line Profile Fitting in Laboratory Diffractometers

PubMed Central

Cheary, R. W.; Coelho, A. A.; Cline, J. P.

2004-01-01

The fundamental parameters approach to line profile fitting uses physically based models to generate the line profile shapes. Fundamental parameters profile fitting (FPPF) has been used to synthesize and fit data from both parallel beam and divergent beam diffractometers. The refined parameters are determined by the diffractometer configuration. In a divergent beam diffractometer these include the angular aperture of the divergence slit, the width and axial length of the receiving slit, the angular apertures of the axial Soller slits, the length and projected width of the x-ray source, the absorption coefficient and axial length of the sample. In a parallel beam system the principal parameters are the angular aperture of the equatorial analyser/Soller slits and the angular apertures of the axial Soller slits. The presence of a monochromator in the beam path is normally accommodated by modifying the wavelength spectrum and/or by changing one or more of the axial divergence parameters. Flat analyzer crystals have been incorporated into FPPF as a Lorentzian shaped angular acceptance function. One of the intrinsic benefits of the fundamental parameters approach is its adaptability any laboratory diffractometer. Good fits can normally be obtained over the whole 20 range without refinement using the known properties of the diffractometer, such as the slit sizes and diffractometer radius, and emission profile. PMID:27366594

The evolutionary stability of cross-sex, cross-trait genetic covariances.

PubMed

Gosden, Thomas P; Chenoweth, Stephen F

2014-06-01

Although knowledge of the selective agents behind the evolution of sexual dimorphism has advanced considerably in recent years, we still lack a clear understanding of the evolutionary durability of cross-sex genetic covariances that often constrain its evolution. We tested the relative stability of cross-sex genetic covariances for a suite of homologous contact pheromones of the fruit fly Drosophila serrata, along a latitudinal gradient where these traits have diverged in mean. Using a Bayesian framework, which allowed us to account for uncertainty in all parameter estimates, we compared divergence in the total amount and orientation of genetic variance across populations, finding divergence in orientation but not total variance. We then statistically compared orientation divergence of within-sex (G) to cross-sex (B) covariance matrices. In line with a previous theoretical prediction, we find that the cross-sex covariance matrix, B, is more variable than either within-sex G matrix. Decomposition of B matrices into their symmetrical and nonsymmetrical components revealed that instability is linked to the degree of asymmetry. We also find that the degree of asymmetry correlates with latitude suggesting a role for spatially varying natural selection in shaping genetic constraints on the evolution of sexual dimorphism. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

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

Linear theory for filtering nonlinear multiscale systems with model error

PubMed Central

Berry, Tyrus; Harlim, John

2014-01-01

In this paper, we study filtering of multiscale dynamical systems with model error arising from limitations in resolving the smaller scale processes. In particular, the analysis assumes the availability of continuous-time noisy observations of all components of the slow variables. Mathematically, this paper presents new results on higher order asymptotic expansion of the first two moments of a conditional measure. In particular, we are interested in the application of filtering multiscale problems in which the conditional distribution is defined over the slow variables, given noisy observation of the slow variables alone. From the mathematical analysis, we learn that for a continuous time linear model with Gaussian noise, there exists a unique choice of parameters in a linear reduced model for the slow variables which gives the optimal filtering when only the slow variables are observed. Moreover, these parameters simultaneously give the optimal equilibrium statistical estimates of the underlying system, and as a consequence they can be estimated offline from the equilibrium statistics of the true signal. By examining a nonlinear test model, we show that the linear theory extends in this non-Gaussian, nonlinear configuration as long as we know the optimal stochastic parametrization and the correct observation model. However, when the stochastic parametrization model is inappropriate, parameters chosen for good filter performance may give poor equilibrium statistical estimates and vice versa; this finding is based on analytical and numerical results on our nonlinear test model and the two-layer Lorenz-96 model. Finally, even when the correct stochastic ansatz is given, it is imperative to estimate the parameters simultaneously and to account for the nonlinear feedback of the stochastic parameters into the reduced filter estimates. In numerical experiments on the two-layer Lorenz-96 model, we find that the parameters estimated online, as part of a filtering procedure, simultaneously produce accurate filtering and equilibrium statistical prediction. In contrast, an offline estimation technique based on a linear regression, which fits the parameters to a training dataset without using the filter, yields filter estimates which are worse than the observations or even divergent when the slow variables are not fully observed. This finding does not imply that all offline methods are inherently inferior to the online method for nonlinear estimation problems, it only suggests that an ideal estimation technique should estimate all parameters simultaneously whether it is online or offline. PMID:25002829

What You Don't Know Can Hurt You: Missing Data and Partial Credit Model Estimates

PubMed Central

Thomas, Sarah L.; Schmidt, Karen M.; Erbacher, Monica K.; Bergeman, Cindy S.

2017-01-01

The authors investigated the effect of Missing Completely at Random (MCAR) item responses on partial credit model (PCM) parameter estimates in a longitudinal study of Positive Affect. Participants were 307 adults from the older cohort of the Notre Dame Study of Health and Well-Being (Bergeman and Deboeck, 2014) who completed questionnaires including Positive Affect items for 56 days. Additional missing responses were introduced to the data, randomly replacing 20%, 50%, and 70% of the responses on each item and each day with missing values, in addition to the existing missing data. Results indicated that item locations and person trait level measures diverged from the original estimates as the level of degradation from induced missing data increased. In addition, standard errors of these estimates increased with the level of degradation. Thus, MCAR data does damage the quality and precision of PCM estimates. PMID:26784376

Robust estimation for partially linear models with large-dimensional covariates

PubMed Central

Zhu, LiPing; Li, RunZe; Cui, HengJian

2014-01-01

We are concerned with robust estimation procedures to estimate the parameters in partially linear models with large-dimensional covariates. To enhance the interpretability, we suggest implementing a noncon-cave regularization method in the robust estimation procedure to select important covariates from the linear component. We establish the consistency for both the linear and the nonlinear components when the covariate dimension diverges at the rate of o(n), where n is the sample size. We show that the robust estimate of linear component performs asymptotically as well as its oracle counterpart which assumes the baseline function and the unimportant covariates were known a priori. With a consistent estimator of the linear component, we estimate the nonparametric component by a robust local linear regression. It is proved that the robust estimate of nonlinear component performs asymptotically as well as if the linear component were known in advance. Comprehensive simulation studies are carried out and an application is presented to examine the finite-sample performance of the proposed procedures. PMID:24955087

Robust estimation for partially linear models with large-dimensional covariates.

PubMed

Zhu, LiPing; Li, RunZe; Cui, HengJian

2013-10-01

We are concerned with robust estimation procedures to estimate the parameters in partially linear models with large-dimensional covariates. To enhance the interpretability, we suggest implementing a noncon-cave regularization method in the robust estimation procedure to select important covariates from the linear component. We establish the consistency for both the linear and the nonlinear components when the covariate dimension diverges at the rate of [Formula: see text], where n is the sample size. We show that the robust estimate of linear component performs asymptotically as well as its oracle counterpart which assumes the baseline function and the unimportant covariates were known a priori. With a consistent estimator of the linear component, we estimate the nonparametric component by a robust local linear regression. It is proved that the robust estimate of nonlinear component performs asymptotically as well as if the linear component were known in advance. Comprehensive simulation studies are carried out and an application is presented to examine the finite-sample performance of the proposed procedures.

Active learning for noisy oracle via density power divergence.

PubMed

Sogawa, Yasuhiro; Ueno, Tsuyoshi; Kawahara, Yoshinobu; Washio, Takashi

2013-10-01

The accuracy of active learning is critically influenced by the existence of noisy labels given by a noisy oracle. In this paper, we propose a novel pool-based active learning framework through robust measures based on density power divergence. By minimizing density power divergence, such as β-divergence and γ-divergence, one can estimate the model accurately even under the existence of noisy labels within data. Accordingly, we develop query selecting measures for pool-based active learning using these divergences. In addition, we propose an evaluation scheme for these measures based on asymptotic statistical analyses, which enables us to perform active learning by evaluating an estimation error directly. Experiments with benchmark datasets and real-world image datasets show that our active learning scheme performs better than several baseline methods. Copyright © 2013 Elsevier Ltd. All rights reserved.

A Coalescent-Based Estimator of Admixture From DNA Sequences

PubMed Central

Wang, Jinliang

2006-01-01

A variety of estimators have been developed to use genetic marker information in inferring the admixture proportions (parental contributions) of a hybrid population. The majority of these estimators used allele frequency data, ignored molecular information that is available in markers such as microsatellites and DNA sequences, and assumed that mutations are absent since the admixture event. As a result, these estimators may fail to deliver an estimate or give rather poor estimates when admixture is ancient and thus mutations are not negligible. A previous molecular estimator based its inference of admixture proportions on the average coalescent times between pairs of genes taken from within and between populations. In this article I propose an estimator that considers the entire genealogy of all of the sampled genes and infers admixture proportions from the numbers of segregating sites in DNA sequence samples. By considering the genealogy of all sequences rather than pairs of sequences, this new estimator also allows the joint estimation of other interesting parameters in the admixture model, such as admixture time, divergence time, population size, and mutation rate. Comparative analyses of simulated data indicate that the new coalescent estimator generally yields better estimates of admixture proportions than the previous molecular estimator, especially when the parental populations are not highly differentiated. It also gives reasonably accurate estimates of other admixture parameters. A human mtDNA sequence data set was analyzed to demonstrate the method, and the analysis results are discussed and compared with those from previous studies. PMID:16624918

Do stochastic inhomogeneities affect dark-energy precision measurements?

PubMed

Ben-Dayan, I; Gasperini, M; Marozzi, G; Nugier, F; Veneziano, G

2013-01-11

The effect of a stochastic background of cosmological perturbations on the luminosity-redshift relation is computed to second order through a recently proposed covariant and gauge-invariant light-cone averaging procedure. The resulting expressions are free from both ultraviolet and infrared divergences, implying that such perturbations cannot mimic a sizable fraction of dark energy. Different averages are estimated and depend on the particular function of the luminosity distance being averaged. The energy flux being minimally affected by perturbations at large z is proposed as the best choice for precision estimates of dark-energy parameters. Nonetheless, its irreducible (stochastic) variance induces statistical errors on Ω(Λ)(z) typically lying in the few-percent range.

Variable Autosomal and X Divergence Near and Far from Genes Affects Estimates of Male Mutation Bias in Great Apes.

PubMed

Narang, Pooja; Wilson Sayres, Melissa A

2016-12-31

Male mutation bias, when more mutations are passed on via the male germline than via the female germline, is observed across mammals. One common way to infer the magnitude of male mutation bias, α, is to compare levels of neutral sequence divergence between genomic regions that spend different amounts of time in the male and female germline. For great apes, including human, we show that estimates of divergence are reduced in putatively unconstrained regions near genes relative to unconstrained regions far from genes. Divergence increases with increasing distance from genes on both the X chromosome and autosomes, but increases faster on the X chromosome than autosomes. As a result, ratios of X/A divergence increase with increasing distance from genes and corresponding estimates of male mutation bias are significantly higher in intergenic regions near genes versus far from genes. Future studies in other species will need to carefully consider the effect that genomic location will have on estimates of male mutation bias. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Sexual selection and population divergence II. Divergence in different sexual traits and signal modalities in field crickets (Teleogryllus oceanicus).

PubMed

Pascoal, Sonia; Mendrok, Magdalena; Wilson, Alastair J; Hunt, John; Bailey, Nathan W

2017-06-01

Sexual selection can target many different types of traits. However, the relative influence of different sexually selected traits during evolutionary divergence is poorly understood. We used the field cricket Teleogryllus oceanicus to quantify and compare how five traits from each of three sexual signal modalities and components diverge among allopatric populations: male advertisement song, cuticular hydrocarbon (CHC) profiles and forewing morphology. Population divergence was unexpectedly consistent: we estimated the among-population (genetic) variance-covariance matrix, D, for all 15 traits, and D max explained nearly two-thirds of its variation. CHC and wing traits were most tightly integrated, whereas song varied more independently. We modeled the dependence of among-population trait divergence on genetic distance estimated from neutral markers to test for signatures of selection versus neutral divergence. For all three sexual trait types, phenotypic variation among populations was largely explained by a neutral model of divergence. Our findings illustrate how phenotypic integration across different types of sexual traits might impose constraints on the evolution of mating isolation and divergence via sexual selection. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Feasibility of Measuring Mean Vertical Motion for Estimating Advection. Chapter 6

NASA Technical Reports Server (NTRS)

Vickers, Dean; Mahrt, L.

2005-01-01

Numerous recent studies calculate horizontal and vertical advection terms for budget studies of net ecosystem exchange of carbon. One potential uncertainty in such studies is the estimate of mean vertical motion. This work addresses the reliability of vertical advection estimates by contrasting the vertical motion obtained from the standard practise of measuring the vertical velocity and applying a tilt correction, to the vertical motion calculated from measurements of the horizontal divergence of the flow using a network of towers. Results are compared for three different tilt correction methods. Estimates of mean vertical motion are sensitive to the choice of tilt correction method. The short-term mean (10 to 60 minutes) vertical motion based on the horizontal divergence is more realistic compared to the estimates derived from the standard practise. The divergence shows long-term mean (days to months) sinking motion at the site, apparently due to the surface roughness change. Because all the tilt correction methods rely on the assumption that the long-term mean vertical motion is zero for a given wind direction, they fail to reproduce the vertical motion based on the divergence.

Two is better than one: joint statistics of density and velocity in concentric spheres as a cosmological probe

NASA Astrophysics Data System (ADS)

Uhlemann, C.; Codis, S.; Hahn, O.; Pichon, C.; Bernardeau, F.

2017-08-01

The analytical formalism to obtain the probability distribution functions (PDFs) of spherically averaged cosmic densities and velocity divergences in the mildly non-linear regime is presented. A large-deviation principle is applied to those cosmic fields assuming their most likely dynamics in spheres is set by the spherical collapse model. We validate our analytical results using state-of-the-art dark matter simulations with a phase-space resolved velocity field finding a 2 per cent level agreement for a wide range of velocity divergences and densities in the mildly non-linear regime (˜10 Mpc h-1 at redshift zero), usually inaccessible to perturbation theory. From the joint PDF of densities and velocity divergences measured in two concentric spheres, we extract with the same accuracy velocity profiles and conditional velocity PDF subject to a given over/underdensity that are of interest to understand the non-linear evolution of velocity flows. Both PDFs are used to build a simple but accurate maximum likelihood estimator for the redshift evolution of the variance of both the density and velocity divergence fields, which have smaller relative errors than their sample variances when non-linearities appear. Given the dependence of the velocity divergence on the growth rate, there is a significant gain in using the full knowledge of both PDFs to derive constraints on the equation of state-of-dark energy. Thanks to the insensitivity of the velocity divergence to bias, its PDF can be used to obtain unbiased constraints on the growth of structures (σ8, f) or it can be combined with the galaxy density PDF to extract bias parameters.

Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates

PubMed Central

Tamura, Koichiro; Tao, Qiqing; Kumar, Sudhir

2018-01-01

Abstract RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It shows excellent performance in estimating divergence times for both simulated and empirical molecular sequence data sets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of data sets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between evolutionary lineages and their respective descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits. PMID:29893954

Scale dependence of the 200-mb divergence inferred from EOLE data.

NASA Technical Reports Server (NTRS)

Morel, P.; Necco, G.

1973-01-01

The EOLE experiment with 480 constant-volume balloons distributed over the Southern Hemisphere approximately at the 200-mb level, has provided a unique, highly accurate set of tracer trajectories in the general westerly circulation. The trajectories of neighboring balloons are analyzed to estimate the horizontal divergence from the Lagrangian derivative of the area of one cluster. The variance of the divergence estimates results from two almost comparable effects: the true divergence of the horizontal flow and eddy diffusion due to small-scale, two-dimensional turbulence. Taking this into account, the rms divergence is found to be of the order of 0.00001 per sec and decreases logarithmically with cluster size. This scale dependence is shown to be consistent with the quasi-geostrophic turbulence model of the general circulation in midlatitudes.

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

PubMed Central

Gutenkunst, Ryan N.; Hernandez, Ryan D.; Williamson, Scott H.; Bustamante, Carlos D.

2009-01-01

Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic variants within and between populations. For candidate models we numerically compute the expected spectrum using a diffusion approximation to the one-locus, two-allele Wright-Fisher process, involving up to three simultaneous populations. Our approach is a composite likelihood scheme, since linkage between neutral loci alters the variance but not the expectation of the frequency spectrum. We thus use bootstraps incorporating linkage to estimate uncertainties for parameters and significance values for hypothesis tests. Our method can also incorporate selection on single sites, predicting the joint distribution of selected alleles among populations experiencing a bevy of evolutionary forces, including expansions, contractions, migrations, and admixture. We model human expansion out of Africa and the settlement of the New World, using 5 Mb of noncoding DNA resequenced in 68 individuals from 4 populations (YRI, CHB, CEU, and MXL) by the Environmental Genome Project. We infer divergence between West African and Eurasian populations 140 thousand years ago (95% confidence interval: 40–270 kya). This is earlier than other genetic studies, in part because we incorporate migration. We estimate the European (CEU) and East Asian (CHB) divergence time to be 23 kya (95% c.i.: 17–43 kya), long after archeological evidence places modern humans in Europe. Finally, we estimate divergence between East Asians (CHB) and Mexican-Americans (MXL) of 22 kya (95% c.i.: 16.3–26.9 kya), and our analysis yields no evidence for subsequent migration. Furthermore, combining our demographic model with a previously estimated distribution of selective effects among newly arising amino acid mutations accurately predicts the frequency spectrum of nonsynonymous variants across three continental populations (YRI, CHB, CEU). PMID:19851460

Ignoring heterozygous sites biases phylogenomic estimates of divergence times: implications for the evolutionary history of microtus voles.

PubMed

Lischer, Heidi E L; Excoffier, Laurent; Heckel, Gerald

2014-04-01

Phylogenetic reconstruction of the evolutionary history of closely related organisms may be difficult because of the presence of unsorted lineages and of a relatively high proportion of heterozygous sites that are usually not handled well by phylogenetic programs. Genomic data may provide enough fixed polymorphisms to resolve phylogenetic trees, but the diploid nature of sequence data remains analytically challenging. Here, we performed a phylogenomic reconstruction of the evolutionary history of the common vole (Microtus arvalis) with a focus on the influence of heterozygosity on the estimation of intraspecific divergence times. We used genome-wide sequence information from 15 voles distributed across the European range. We provide a novel approach to integrate heterozygous information in existing phylogenetic programs by repeated random haplotype sampling from sequences with multiple unphased heterozygous sites. We evaluated the impact of the use of full, partial, or no heterozygous information for tree reconstructions on divergence time estimates. All results consistently showed four deep and strongly supported evolutionary lineages in the vole data. These lineages undergoing divergence processes split only at the end or after the last glacial maximum based on calibration with radiocarbon-dated paleontological material. However, the incorporation of information from heterozygous sites had a significant impact on absolute and relative branch length estimations. Ignoring heterozygous information led to an overestimation of divergence times between the evolutionary lineages of M. arvalis. We conclude that the exclusion of heterozygous sites from evolutionary analyses may cause biased and misleading divergence time estimates in closely related taxa.

Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals

NASA Technical Reports Server (NTRS)

Foote, M.; Hunter, J. P.; Janis, C. M.; Sepkoski, J. J. Jr

1999-01-01

Some molecular clock estimates of divergence times of taxonomic groups undergoing evolutionary radiation are much older than the groups' first observed fossil record. Mathematical models of branching evolution are used to estimate the maximal rate of fossil preservation consistent with a postulated missing history, given the sum of species durations implied by early origins under a range of species origination and extinction rates. The plausibility of postulated divergence times depends on origination, extinction, and preservation rates estimated from the fossil record. For eutherian mammals, this approach suggests that it is unlikely that many modern orders arose much earlier than their oldest fossil records.

Genetic Divergence of an Avian Endemic on the Californian Channel Islands

PubMed Central

Wilson, Amy G.; Chan, Yvonne; Taylor, Sabrina S.; Arcese, Peter

2015-01-01

The Californian Channel Islands are near–shore islands with high levels of endemism, but extensive habitat loss has contributed to the decline or extinction of several endemic taxa. A key parameter for understanding patterns of endemism and demography in island populations is the magnitude of inter–island dispersal. This paper estimates the extent of migration and genetic differentiation in three extant and two extinct populations of Channel Island song sparrows (Melospiza melodia graminea). Inter–island differentiation was substantial (G''ST: 0.14–0.37), with San Miguel Island having the highest genetic divergence and lowest migration rates. Santa Rosa and Santa Cruz Island populations were less diverged with higher migration rates. Genetic signals of past population declines were detected in all of the extant populations. The Channel Island populations were significantly diverged from mainland populations of M. m. heermanni (G''ST: 0.30–0.64). Ten mtDNA haplotypes were recovered across the extant and extinct Channel Island population samples. Two of the ten haplotypes were shared between the Northern and Southern Channel Islands, with one of these haplotypes being detected on the Californian mainland. Our results suggest that there is little contemporary migration between islands, consistent with early explanations of avian biogeography in the Channel Islands, and that song sparrow populations on the northern Channel Islands are demographically independent. PMID:26308717

Unsupervised Learning for Monaural Source Separation Using Maximization–Minimization Algorithm with Time–Frequency Deconvolution †

PubMed Central

Bouridane, Ahmed; Ling, Bingo Wing-Kuen

2018-01-01

This paper presents an unsupervised learning algorithm for sparse nonnegative matrix factor time–frequency deconvolution with optimized fractional β-divergence. The β-divergence is a group of cost functions parametrized by a single parameter β. The Itakura–Saito divergence, Kullback–Leibler divergence and Least Square distance are special cases that correspond to β=0, 1, 2, respectively. This paper presents a generalized algorithm that uses a flexible range of β that includes fractional values. It describes a maximization–minimization (MM) algorithm leading to the development of a fast convergence multiplicative update algorithm with guaranteed convergence. The proposed model operates in the time–frequency domain and decomposes an information-bearing matrix into two-dimensional deconvolution of factor matrices that represent the spectral dictionary and temporal codes. The deconvolution process has been optimized to yield sparse temporal codes through maximizing the likelihood of the observations. The paper also presents a method to estimate the fractional β value. The method is demonstrated on separating audio mixtures recorded from a single channel. The paper shows that the extraction of the spectral dictionary and temporal codes is significantly more efficient by using the proposed algorithm and subsequently leads to better source separation performance. Experimental tests and comparisons with other factorization methods have been conducted to verify its efficacy. PMID:29702629

Pulse rate variability compared with Heart Rate Variability in children with and without sleep disordered breathing.

PubMed

Dehkordi, Parastoo; Garde, Ainara; Karlen, Walter; Wensley, David; Ansermino, J Mark; Dumont, Guy A

2013-01-01

Heart Rate Variability (HRV), the variation of time intervals between heartbeats, is one of the most promising and widely used quantitative markers of autonomic activity. Traditionally, HRV is measured as the series of instantaneous cycle intervals obtained from the electrocardiogram (ECG). In this study, we investigated the estimation of variation in heart rate from a photoplethysmography (PPG) signal, called pulse rate variability (PRV), and assessed its accuracy as an estimate of HRV in children with and without sleep disordered breathing (SDB). We recorded raw PPGs from 72 children using the Phone Oximeter, an oximeter connected to a mobile phone. Full polysomnography including ECG was simultaneously recorded for each subject. We used correlation and Bland-Altman analysis for comparing the parameters of HRV and PRV between two groups of children. Significant correlation (r > 0.90, p < 0.05) and close agreement were found between HRV and PRV for mean intervals, standard deviation of intervals (SDNN) and the root-mean square of the difference of successive intervals (RMSSD). However Bland-Altman analysis showed a large divergence for LF/HF ratio parameter. In addition, children with SDB had depressed SDNN and RMSSD and elevated LF/HF in comparison to children without SDB. In conclusion, PRV provides the accurate estimate of HRV in time domain analysis but does not reflect precise estimation for parameters in frequency domain.

Maternal and child mortality indicators across 187 countries of the world: converging or diverging.

PubMed

Goli, Srinivas; Arokiasamy, Perianayagam

2014-01-01

This study reassessed the progress achieved since 1990 in maternal and child mortality indicators to test whether the progress is converging or diverging across countries worldwide. The convergence process is examined using standard parametric and non-parametric econometric models of convergence. The results of absolute convergence estimates reveal that progress in maternal and child mortality indicators is diverging for the entire period of 1990-2010 [maternal mortality ratio (MMR) - β = .00033, p < .574; neonatal mortality rate (NNMR) - β = .04367, p < .000; post-neonatal mortality rate (PNMR) - β = .02677, p < .000; under-five mortality rate (U5MR) - β = .00828, p < .000)]. In the recent period, such divergence is replaced with convergence for MMR but diverged for all the child mortality indicators. The results of Kernel density estimate reveal considerable reduction in divergence of MMR for the recent period; however, the Kernel density distribution plots show more than one 'peak' which indicates the emergence of convergence clubs based on their mortality levels. For child mortality indicators, the Kernel estimates suggest that divergence is in progress across the countries worldwide but tended to converge for countries with low mortality levels. A mere progress in global averages of maternal and child mortality indicators among a global cross-section of countries does not warranty convergence unless there is a considerable reduction in variance, skewness and range of change.

Experiences in multiyear combined state-parameter estimation with an ecosystem model of the North Atlantic and Arctic Oceans using the Ensemble Kalman Filter

NASA Astrophysics Data System (ADS)

Simon, Ehouarn; Samuelsen, Annette; Bertino, Laurent; Mouysset, Sandrine

2015-12-01

A sequence of one-year combined state-parameter estimation experiments has been conducted in a North Atlantic and Arctic Ocean configuration of the coupled physical-biogeochemical model HYCOM-NORWECOM over the period 2007-2010. The aim is to evaluate the ability of an ensemble-based data assimilation method to calibrate ecosystem model parameters in a pre-operational setting, namely the production of the MyOcean pilot reanalysis of the Arctic biology. For that purpose, four biological parameters (two phyto- and two zooplankton mortality rates) are estimated by assimilating weekly data such as, satellite-derived Sea Surface Temperature, along-track Sea Level Anomalies, ice concentrations and chlorophyll-a concentrations with an Ensemble Kalman Filter. The set of optimized parameters locally exhibits seasonal variations suggesting that time-dependent parameters should be used in ocean ecosystem models. A clustering analysis of the optimized parameters is performed in order to identify consistent ecosystem regions. In the north part of the domain, where the ecosystem model is the most reliable, most of them can be associated with Longhurst provinces and new provinces emerge in the Arctic Ocean. However, the clusters do not coincide anymore with the Longhurst provinces in the Tropics due to large model errors. Regarding the ecosystem state variables, the assimilation of satellite-derived chlorophyll concentration leads to significant reduction of the RMS errors in the observed variables during the first year, i.e. 2008, compared to a free run simulation. However, local filter divergences of the parameter component occur in 2009 and result in an increase in the RMS error at the time of the spring bloom.

[Phylogeny and divergence time estimation of Schizothoracinae fishes in Xinjiang].

PubMed

Ayelhan, Haysa; Guo, Yan; Meng, Wei; Yang, Tianyan; Ma, Yanwu

2014-10-01

Based on combined data of mitochondrial COI, ND4 and 16S RNA genes, molecular phylogeny of 4 genera, 10 species or subspecies of Schizothoracinae fishes distributed in Xinjiang were analyzed. The molecular clock was calibrated by divergence time of Cyprininae and geological segregation event between the upper Yellow River and Qinghai Lake. Divergence time of Schizothoracinae fishes was calculated, and its relationship with the major geological events and the climate changes in surrounding areas of Tarim Basin was discussed. The results showed that genus Aspiorhynchus did not form an independent clade, but clustered with Schizothorax biddulphi and S. irregularis. Kimura 2-parameter model was used to calculate the genetic distance of COI gene, the genetic distance between genus Aspiorhynchus and Schizothorax did not reach genus level, and Aspiorhynchus laticeps might be a specialized species of genus Schizothorax. Cluster analysis showed a different result with morphological classification method, and it did not support the subgenus division of Schizothorax fishes. Divergence of two groups of primitive Schizothoracinae (8.18Ma) and divergence of Gymnodiptychus dybowskii and Diptychus maculates (7.67Ma) occurred in late Miocene, which might be related with the separation of Kunlun Mountain and north Tianshan Mountain River system that was caused by the uplift of Qinghai-Tibet Plateau and Tianshan Mountain, and the aridification of Tarim Basin. The terrain of Tarim Basin that was affected by Quaternary Himalayan movement was high in west but low in east, as a result, Lop Nor became the center of surrounding mountain rivers in Tarim Basin, which shaped the distribution pattern of genus Schizothorax.

Statistics of surface divergence and their relation to air-water gas transfer velocity

NASA Astrophysics Data System (ADS)

Asher, William E.; Liang, Hanzhuang; Zappa, Christopher J.; Loewen, Mark R.; Mukto, Moniz A.; Litchendorf, Trina M.; Jessup, Andrew T.

2012-05-01

Air-sea gas fluxes are generally defined in terms of the air/water concentration difference of the gas and the gas transfer velocity,kL. Because it is difficult to measure kLin the ocean, it is often parameterized using more easily measured physical properties. Surface divergence theory suggests that infrared (IR) images of the water surface, which contain information concerning the movement of water very near the air-water interface, might be used to estimatekL. Therefore, a series of experiments testing whether IR imagery could provide a convenient means for estimating the surface divergence applicable to air-sea exchange were conducted in a synthetic jet array tank embedded in a wind tunnel. Gas transfer velocities were measured as a function of wind stress and mechanically generated turbulence; laser-induced fluorescence was used to measure the concentration of carbon dioxide in the top 300 μm of the water surface; IR imagery was used to measure the spatial and temporal distribution of the aqueous skin temperature; and particle image velocimetry was used to measure turbulence at a depth of 1 cm below the air-water interface. It is shown that an estimate of the surface divergence for both wind-shear driven turbulence and mechanically generated turbulence can be derived from the surface skin temperature. The estimates derived from the IR images are compared to velocity field divergences measured by the PIV and to independent estimates of the divergence made using the laser-induced fluorescence data. Divergence is shown to scale withkLvalues measured using gaseous tracers as predicted by conceptual models for both wind-driven and mechanically generated turbulence.

Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies.

PubMed

Pohl, Nélida; Sison-Mangus, Marilou P; Yee, Emily N; Liswi, Saif W; Briscoe, Adriana D

2009-05-13

The increase in availability of genomic sequences for a wide range of organisms has revealed gene duplication to be a relatively common event. Encounters with duplicate gene copies have consequently become almost inevitable in the context of collecting gene sequences for inferring species trees. Here we examine the effect of incorporating duplicate gene copies evolving at different rates on tree reconstruction and time estimation of recent and deep divergences in butterflies. Sequences from ultraviolet-sensitive (UVRh), blue-sensitive (BRh), and long-wavelength sensitive (LWRh) opsins,EF-1 and COI were obtained from 27 taxa representing the five major butterfly families (5535 bp total). Both BRh and LWRh are present in multiple copies in some butterfly lineages and the different copies evolve at different rates. Regardless of the phylogenetic reconstruction method used, we found that analyses of combined data sets using either slower or faster evolving copies of duplicate genes resulted in a single topology in agreement with our current understanding of butterfly family relationships based on morphology and molecules. Interestingly, individual analyses of BRh and LWRh sequences also recovered these family-level relationships. Two different relaxed clock methods resulted in similar divergence time estimates at the shallower nodes in the tree, regardless of whether faster or slower evolving copies were used, with larger discrepancies observed at deeper nodes in the phylogeny. The time of divergence between the monarch butterfly Danaus plexippus and the queen D. gilippus (15.3-35.6 Mya) was found to be much older than the time of divergence between monarch co-mimic Limenitis archippus and red-spotted purple L. arthemis (4.7-13.6 Mya), and overlapping with the time of divergence of the co-mimetic passionflower butterflies Heliconius erato and H. melpomene (13.5-26.1 Mya). Our family-level results are congruent with recent estimates found in the literature and indicate an age of 84-113 million years for the divergence of all butterfly families. These results are consistent with diversification of the butterfly families following the radiation of angiosperms and suggest that some classes of opsin genes may be usefully employed for both phylogenetic reconstruction and divergence time estimation.

Convexity of quantum χ2-divergence.

PubMed

Hansen, Frank

2011-06-21

The general quantum χ(2)-divergence has recently been introduced by Temme et al. [Temme K, Kastoryano M, Ruskai M, Wolf M, Verstrate F (2010) J Math Phys 51:122201] and applied to quantum channels (quantum Markov processes). The quantum χ(2)-divergence is not unique, as opposed to the classical χ(2)-divergence, but depends on the choice of quantum statistics. It was noticed that the elements in a particular one-parameter family of quantum χ(2)-divergences are convex functions in the density matrices (ρ,σ), thus mirroring the convexity of the classical χ(2)(p,q)-divergence in probability distributions (p,q). We prove that any quantum χ(2)-divergence is a convex function in its two arguments.

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.

Vanishing Point Extraction and Refinement for Robust Camera Calibration

PubMed Central

Tsai, Fuan

2017-01-01

This paper describes a flexible camera calibration method using refined vanishing points without prior information. Vanishing points are estimated from human-made features like parallel lines and repeated patterns. With the vanishing points extracted from the three mutually orthogonal directions, the interior and exterior orientation parameters can be further calculated using collinearity condition equations. A vanishing point refinement process is proposed to reduce the uncertainty caused by vanishing point localization errors. The fine-tuning algorithm is based on the divergence of grouped feature points projected onto the reference plane, minimizing the standard deviation of each of the grouped collinear points with an O(1) computational complexity. This paper also presents an automated vanishing point estimation approach based on the cascade Hough transform. The experiment results indicate that the vanishing point refinement process can significantly improve camera calibration parameters and the root mean square error (RMSE) of the constructed 3D model can be reduced by about 30%. PMID:29280966

Application of Johnson et al.'s speciation threshold model to apparent colonization times of island biotas.

PubMed

Ricklefs, Robert E; Bermingham, Eldredge

2004-08-01

Understanding patterns of diversity can be furthered by analysis of the dynamics of colonization, speciation, and extinction on islands using historical information provided by molecular phylogeography. The land birds of the Lesser Antilles are one of the most thoroughly described regional faunas in this context. In an analysis of colonization times, Ricklefs and Bermingham (2001) found that the cumulative distribution of lineages with respect to increasing time since colonization exhibits a striking change in slope at a genetic distance of about 2% mitochondrial DNA sequence divergence (about one million years). They further showed how this heterogeneity could be explained by either an abrupt increase in colonization rates or a mass extinction event. Cherry et al. (2002), referring to a model developed by Johnson et al. (2000), argued instead that the pattern resulted from a speciation threshold for reproductive isolation of island populations from their continental source populations. Prior to this threshold, genetic divergence is slowed by migration from the source, and species of varying age accumulate at a low genetic distance. After the threshold is reached, source and island populations diverge more rapidly, creating heterogeneity in the distribution of apparent ages of island taxa. We simulated of Johnson et al.'s speciation-threshold model, incorporating genetic divergence at rate k and fixation at rate M of genes that have migrated between the source and the island population. Fixation resets the divergence clock to zero. The speciation-threshold model fits the distribution of divergence times of Lesser Antillean birds well with biologically plausible parameter estimates. Application of the model to the Hawaiian avifauna, which does not exhibit marked heterogeneity of genetic divergence, and the West Indian herpetofauna, which does, required unreasonably high migration-fixation rates, several orders of magnitude greater than the colonization rate. However, the plausibility of the speciation-divergence model for Lesser Antillean birds emphasizes the importance of further investigation of historical biogeography on a regional scale for whole biotas, as well as the migration of genes between populations on long time scales and the achievement of reproductive isolation.

Phylogeny and niche conservatism in North and Central American triatomine bugs (Hemiptera: Reduviidae: Triatominae), vectors of Chagas' disease.

PubMed

Ibarra-Cerdeña, Carlos N; Zaldívar-Riverón, Alejandro; Peterson, A Townsend; Sánchez-Cordero, Víctor; Ramsey, Janine M

2014-10-01

The niche conservatism hypothesis states that related species diverge in niche characteristics at lower rates than expected, given their lineage divergence. Here we analyze whether niche conservatism is a common pattern among vector species (Hemiptera: Reduviidae: Triatominae) of Trypanosoma cruzi that inhabit North and Central America, a highly heterogeneous landmass in terms of environmental gradients. Mitochondrial and nuclear loci were used in a multi-locus phylogenetic framework to reconstruct phylogenetic relationships among species and estimate time of divergence of selected clades to draw biogeographic inferences. Then, we estimated similarity between the ecological niche of sister species and tested the niche conservatism hypothesis using our best estimate of phylogeny. Triatoma is not monophyletic. A primary clade with all North and Central American (NCA) triatomine species from the genera Triatoma, Dipetalogaster, and Panstrongylus, was consistently recovered. Nearctic species within the NCA clade (T. p. protracta, T. r. rubida) diverged during the Pliocene, whereas the Neotropical species (T. phyllosoma, T. longipennis, T. dimidiata complex) are estimated to have diverged more recently, during the Pleistocene. The hypothesis of niche conservatism could not be rejected for any of six sister species pairs. Niche similarity between sister species best fits a retention model. While this framework is used here to infer niche evolution, it has a direct impact on spatial vector dynamics driven by human population movements, expansion of transportation networks and climate change scenarios.

Angular ellipticity correlations in a composite alignment model for elliptical and spiral galaxies and inference from weak lensing

NASA Astrophysics Data System (ADS)

Tugendhat, Tim M.; Schäfer, Björn Malte

2018-05-01

We investigate a physical, composite alignment model for both spiral and elliptical galaxies and its impact on cosmological parameter estimation from weak lensing for a tomographic survey. Ellipticity correlation functions and angular ellipticity spectra for spiral and elliptical galaxies are derived on the basis of tidal interactions with the cosmic large-scale structure and compared to the tomographic weak-lensing signal. We find that elliptical galaxies cause a contribution to the weak-lensing dominated ellipticity correlation on intermediate angular scales between ℓ ≃ 40 and ℓ ≃ 400 before that of spiral galaxies dominates on higher multipoles. The predominant term on intermediate scales is the negative cross-correlation between intrinsic alignments and weak gravitational lensing (GI-alignment). We simulate parameter inference from weak gravitational lensing with intrinsic alignments unaccounted; the bias induced by ignoring intrinsic alignments in a survey like Euclid is shown to be several times larger than the statistical error and can lead to faulty conclusions when comparing to other observations. The biases generally point into different directions in parameter space, such that in some cases one can observe a partial cancellation effect. Furthermore, it is shown that the biases increase with the number of tomographic bins used for the parameter estimation process. We quantify this parameter estimation bias in units of the statistical error and compute the loss of Bayesian evidence for a model due to the presence of systematic errors as well as the Kullback-Leibler divergence to quantify the distance between the true model and the wrongly inferred one.

Molecular survey of basidiomycetes and divergence time estimation: An Indian perspective

PubMed Central

Bhatt, Meghna; Mistri, Pankti; Joshi, Ishita; Ram, Hemal; Raval, Rinni; Thoota, Sruthi; Patel, Ankur; Raval, Dhrupa; Bhargava, Poonam; Soni, Subhash; Bagatharia, Snehal

2018-01-01

This study outlines the biodiversity of mushrooms of India. It reveals the molecular biodiversity and divergence time estimation of basidiomycetes from Gujarat, India. A total of 267 mushrooms were collected from 10 locations across the state. 225 ITS sequences were generated belonging to 105 species, 59 genera and 29 families. Phylogenetic analysis of Agaricaceae reveals monophyletic clade of Podaxis differentiating it from Coprinus. Further, the ancient nature of Podaxis supports the hypothesis that gasteroid forms evolved from secotioid forms. Members of Polyporaceae appeared polyphyletic. Further, our results of a close phylogenetic relationship between Trametes and Lenziteslead us to propose that the genera Trametes may by enlarged to include Lenzites. The tricholomatoid clade shows a clear demarcation for Entolomataceae. However, Lyophyllaceae and Tricholomataceae could not be distinguished clearly. Distribution studies of the mushrooms showed omnipresence of Ganoderma and Schizophyllum. Further, divergence time estimation shows that Dacrymycetes evolved in the Neoproterozoic Era and Hymenochaetales diverged from Agaricomycetes during the Silurian period. PMID:29771956

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

Riihimaki, L.; McFarlane, S.; Sivaraman, C.

The ndrop_mfrsr value-added product (VAP) provides an estimate of the cloud droplet number concentration of overcast water clouds retrieved from cloud optical depth from the multi-filter rotating shadowband radiometer (MFRSR) instrument and liquid water path (LWP) retrieved from the microwave radiometer (MWR). When cloud layer information is available from vertically pointing lidar and radars in the Active Remote Sensing of Clouds (ARSCL) product, the VAP also provides estimates of the adiabatic LWP and an adiabatic parameter (beta) that indicates how divergent the LWP is from the adiabatic case. quality control (QC) flags (qc_drop_number_conc), an uncertainty estimate (drop_number_conc_toterr), and a cloudmore » layer type flag (cloud_base_type) are useful indicators of the quality and accuracy of any given value of the retrieval. Examples of these major input and output variables are given in sample plots in section 6.0.« less

Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data.

PubMed

Fourment, Mathieu; Holmes, Edward C

2014-07-24

Early methods for estimating divergence times from gene sequence data relied on the assumption of a molecular clock. More sophisticated methods were created to model rate variation and used auto-correlation of rates, local clocks, or the so called "uncorrelated relaxed clock" where substitution rates are assumed to be drawn from a parametric distribution. In the case of Bayesian inference methods the impact of the prior on branching times is not clearly understood, and if the amount of data is limited the posterior could be strongly influenced by the prior. We develop a maximum likelihood method--Physher--that uses local or discrete clocks to estimate evolutionary rates and divergence times from heterochronous sequence data. Using two empirical data sets we show that our discrete clock estimates are similar to those obtained by other methods, and that Physher outperformed some methods in the estimation of the root age of an influenza virus data set. A simulation analysis suggests that Physher can outperform a Bayesian method when the real topology contains two long branches below the root node, even when evolution is strongly clock-like. These results suggest it is advisable to use a variety of methods to estimate evolutionary rates and divergence times from heterochronous sequence data. Physher and the associated data sets used here are available online at http://code.google.com/p/physher/.

Strong gravitational lensing by a Konoplya-Zhidenko rotating non-Kerr compact object

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

Wang, Shangyun; Chen, Songbai; Jing, Jiliang, E-mail: shangyun_wang@163.com, E-mail: csb3752@hunnu.edu.cn, E-mail: jljing@hunnu.edu.cn

Konoplya and Zhidenko have proposed recently a rotating non-Kerr black hole metric beyond General Relativity and make an estimate for the possible deviations from the Kerr solution with the data of GW 150914. We here study the strong gravitational lensing in such a rotating non-Kerr spacetime with an extra deformation parameter. We find that the condition of existence of horizons is not inconsistent with that of the marginally circular photon orbit. Moreover, the deflection angle of the light ray near the weakly naked singularity covered by the marginally circular orbit diverges logarithmically in the strong-field limit. In the case ofmore » the completely naked singularity, the deflection angle near the singularity tends to a certain finite value, whose sign depends on the rotation parameter and the deformation parameter. These properties of strong gravitational lensing are different from those in the Johannsen-Psaltis rotating non-Kerr spacetime and in the Janis-Newman-Winicour spacetime. Modeling the supermassive central object of the Milk Way Galaxy as a Konoplya-Zhidenko rotating non-Kerr compact object, we estimated the numerical values of observables for the strong gravitational lensing including the time delay between two relativistic images.« less

Detection of a coherent population trapping resonance in a beam of {sup 87}Rb atoms by the Ramsey method

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

Sokolov, I M

2015-10-31

Formation of a coherent population trapping (CPT) resonance is studied in the interaction of a beam of {sup 87}Rb atoms with two spatially separated domains of the dichromatic field. Various resonance excitation schemes are compared depending on the choice of operation transitions and type of the polarisation scheme. In the case of a single-velocity atomic beam, the dependence of the CPT resonance profile is studied as a function of principal parameters of the system: beam velocity, distance between optical fields, laser beam dimensions and intensities, and applied permanent magnetic field. Influence of the atomic beam angular divergence and residual beammore » velocity spread on the resonance quality parameter is estimated. (atomic beams)« less

Fine-Tuning Cross-Battery Assessment Procedures: After Follow-Up Testing, Use All Valid Scores, Cohesive or Not

ERIC Educational Resources Information Center

Schneider, W. Joel; Roman, Zachary

2018-01-01

We used data simulations to test whether composites consisting of cohesive subtest scores are more accurate than composites consisting of divergent subtest scores. We demonstrate that when multivariate normality holds, divergent and cohesive scores are equally accurate. Furthermore, excluding divergent scores results in biased estimates of…

The close relationship between estimated divergent selection and observed differentiation supports the selective origin of a marine snail hybrid zone.

PubMed

Cruz, R; Vilas, C; Mosquera, J; García, C

2004-11-01

To study the role of divergent selection in the differentiation of the two morphs in a hybrid zone of the intertidal snail Littorina saxatilis, we compared the strength of the divergent selection acting on a series of shell characters (as estimated by the viability of snails in a reciprocal transplant experiment) with the contribution of these characters to the phenotypic differences between the morphs. We found a close correlation between selection and differentiation, which suggests a cause-effect relationship, i.e. that all present differentiation is the result of past divergent selection. In addition, divergent selection was a very important component of the total natural selection acting on shell measures. These novel results support previous evidence, based on allozyme analysis, of a parapatric origin for this hybrid zone. We discuss possible limitations of this interpretation and the circumstances under which allopatric differentiation would produce the same results. Phenotypic analysis of divergent selection may be a useful method of investigating the evolutionary mechanisms involved in differentiation processes.

Quantum chi-squared and goodness of fit testing

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

Temme, Kristan; Verstraete, Frank

2015-01-15

A quantum mechanical hypothesis test is presented for the hypothesis that a certain setup produces a given quantum state. Although the classical and the quantum problems are very much related to each other, the quantum problem is much richer due to the additional optimization over the measurement basis. A goodness of fit test for i.i.d quantum states is developed and a max-min characterization for the optimal measurement is introduced. We find the quantum measurement which leads both to the maximal Pitman and Bahadur efficiencies, and determine the associated divergence rates. We discuss the relationship of the quantum goodness of fitmore » test to the problem of estimating multiple parameters from a density matrix. These problems are found to be closely related and we show that the largest error of an optimal strategy, determined by the smallest eigenvalue of the Fisher information matrix, is given by the divergence rate of the goodness of fit test.« less

Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies

PubMed Central

Pohl, Nélida; Sison-Mangus, Marilou P; Yee, Emily N; Liswi, Saif W; Briscoe, Adriana D

2009-01-01

Background The increase in availability of genomic sequences for a wide range of organisms has revealed gene duplication to be a relatively common event. Encounters with duplicate gene copies have consequently become almost inevitable in the context of collecting gene sequences for inferring species trees. Here we examine the effect of incorporating duplicate gene copies evolving at different rates on tree reconstruction and time estimation of recent and deep divergences in butterflies. Results Sequences from ultraviolet-sensitive (UVRh), blue-sensitive (BRh), and long-wavelength sensitive (LWRh) opsins,EF-1α and COI were obtained from 27 taxa representing the five major butterfly families (5535 bp total). Both BRh and LWRh are present in multiple copies in some butterfly lineages and the different copies evolve at different rates. Regardless of the phylogenetic reconstruction method used, we found that analyses of combined data sets using either slower or faster evolving copies of duplicate genes resulted in a single topology in agreement with our current understanding of butterfly family relationships based on morphology and molecules. Interestingly, individual analyses of BRh and LWRh sequences also recovered these family-level relationships. Two different relaxed clock methods resulted in similar divergence time estimates at the shallower nodes in the tree, regardless of whether faster or slower evolving copies were used, with larger discrepancies observed at deeper nodes in the phylogeny. The time of divergence between the monarch butterfly Danaus plexippus and the queen D. gilippus (15.3–35.6 Mya) was found to be much older than the time of divergence between monarch co-mimic Limenitis archippus and red-spotted purple L. arthemis (4.7–13.6 Mya), and overlapping with the time of divergence of the co-mimetic passionflower butterflies Heliconius erato and H. melpomene (13.5–26.1 Mya). Our family-level results are congruent with recent estimates found in the literature and indicate an age of 84–113 million years for the divergence of all butterfly families. Conclusion These results are consistent with diversification of the butterfly families following the radiation of angiosperms and suggest that some classes of opsin genes may be usefully employed for both phylogenetic reconstruction and divergence time estimation. PMID:19439087

Detecting climatically driven phylogenetic and morphological divergence among spruce (Picea) species worldwide

NASA Astrophysics Data System (ADS)

Wang, Guo-Hong; Li, He; Zhao, Hai-Wei; Zhang, Wei-Kang

2017-05-01

This study aimed to elucidate the relationship between climate and the phylogenetic and morphological divergence of spruces (Picea) worldwide. Climatic and georeferenced data were collected from a total of 3388 sites distributed within the global domain of spruce species. A phylogenetic tree and a morphological tree for the global spruces were reconstructed based on DNA sequences and morphological characteristics. Spatial evolutionary and ecological vicariance analysis (SEEVA) was used to detect the ecological divergence among spruces. A divergence index (D) with (0, 1) scaling was calculated for each climatic factor at each node for both trees. The annual mean values, extreme values and annual range of the climatic variables were among the major determinants for spruce divergence. The ecological divergence was significant (P < 0. 001) for 185 of the 279 comparisons at 31 nodes in the phylogenetic tree, as well as for 196 of the 288 comparisons at 32 nodes in the morphological tree. Temperature parameters and precipitation parameters tended to be the main driving factors for the primary divergences of spruce phylogeny and morphology, respectively. Generally, the maximum D of the climatic variables was smaller in the basal nodes than in the remaining nodes. Notably, the primary divergence of morphology and phylogeny among the investigated spruces tended to be driven by different selective pressures. Given the climate scenario of severe and widespread drought over land areas in the next 30-90 years, our findings shed light on the prediction of spruce distribution under future climate change.

Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)

PubMed Central

Larson, Wesley A; Seeb, Lisa W; Everett, Meredith V; Waples, Ryan K; Templin, William D; Seeb, James E

2014-01-01

Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high-resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure. PMID:24665338

Hypergeometric continuation of divergent perturbation series: I. Critical exponents of the Bose-Hubbard model

NASA Astrophysics Data System (ADS)

Sanders, Sören; Holthaus, Martin

2017-10-01

We study the connection between the exponent of the order parameter of the Mott insulator-to-superfluid transition occurring in the two-dimensional Bose-Hubbard model, and the divergence exponents of its one- and two-particle correlation functions. We find that at the multicritical points all divergence exponents are related to each other, allowing us to express the critical exponent in terms of one single divergence exponent. This approach correctly reproduces the critical exponent of the three-dimensional XY universality class. Because divergence exponents can be computed in an efficient manner by hypergeometric analytic continuation, our strategy is applicable to a wide class of systems.

Divergent selection on home pen locomotor activity in a chicken model: Selection program, genetic parameters and direct response on activity and body weight

PubMed Central

2017-01-01

General locomotor activity (GLA) in poultry has attracted attention, as it negatively influences production costs (energy expenditure and feed consumption) and welfare parameters (bone strength, litter quality, feather pecking and cannibalism). Laying hen lines diverging in the average level of spontaneous locomotor activity in the home pen were developed by genetic selection using the founder New Hampshire line. Activity was recorded using RFID technology at around five weeks of age during four to five days in the home pen. After initial phenotyping, the least active birds were selected for the low activity line and the most active for the high activity line, with no gene transfer between lines. In each of six generations, approximately ten sires were mated to twenty dams producing 158 to 334 offspring per line per generation. The response to selection was rapid and of a considerable magnitude. In sixth generation, the level of GLA was approximately halved in the low and doubled in the high line compared to the control (7.2, 14.9 and 28.7 recordings/h). Estimated heritability of locomotor activity in the low and high line was 0.38 and 0.33, respectively. Males, in general, were more active than females. High line birds were significantly heavier than low line birds. In fourth, fifth, and sixth generation, low as well as high line birds were lighter than control line birds. This selection experiment demonstrates variation in heritability for GLA and, as a result, genetically diverged lines have been developed. These lines can be used as models for further studies of underlying physiological, neural and molecular genetic mechanisms of spontaneous locomotor activity. PMID:28796792

Divergent selection on home pen locomotor activity in a chicken model: Selection program, genetic parameters and direct response on activity and body weight.

PubMed

Kjaer, Joergen B

2017-01-01

General locomotor activity (GLA) in poultry has attracted attention, as it negatively influences production costs (energy expenditure and feed consumption) and welfare parameters (bone strength, litter quality, feather pecking and cannibalism). Laying hen lines diverging in the average level of spontaneous locomotor activity in the home pen were developed by genetic selection using the founder New Hampshire line. Activity was recorded using RFID technology at around five weeks of age during four to five days in the home pen. After initial phenotyping, the least active birds were selected for the low activity line and the most active for the high activity line, with no gene transfer between lines. In each of six generations, approximately ten sires were mated to twenty dams producing 158 to 334 offspring per line per generation. The response to selection was rapid and of a considerable magnitude. In sixth generation, the level of GLA was approximately halved in the low and doubled in the high line compared to the control (7.2, 14.9 and 28.7 recordings/h). Estimated heritability of locomotor activity in the low and high line was 0.38 and 0.33, respectively. Males, in general, were more active than females. High line birds were significantly heavier than low line birds. In fourth, fifth, and sixth generation, low as well as high line birds were lighter than control line birds. This selection experiment demonstrates variation in heritability for GLA and, as a result, genetically diverged lines have been developed. These lines can be used as models for further studies of underlying physiological, neural and molecular genetic mechanisms of spontaneous locomotor activity.

Divergence Times and the Evolutionary Radiation of New World Monkeys (Platyrrhini, Primates): An Analysis of Fossil and Molecular Data.

PubMed

Perez, S Ivan; Tejedor, Marcelo F; Novo, Nelson M; Aristide, Leandro

2013-01-01

The estimation of phylogenetic relationships and divergence times among a group of organisms is a fundamental first step toward understanding its biological diversification. The time of the most recent or last common ancestor (LCA) of extant platyrrhines is one of the most controversial among scholars of primate evolution. Here we use two molecular based approaches to date the initial divergence of the platyrrhine clade, Bayesian estimations under a relaxed-clock model and substitution rate plus generation time and body size, employing the fossil record and genome datasets. We also explore the robustness of our estimations with respect to changes in topology, fossil constraints and substitution rate, and discuss the implications of our findings for understanding the platyrrhine radiation. Our results suggest that fossil constraints, topology and substitution rate have an important influence on our divergence time estimates. Bayesian estimates using conservative but realistic fossil constraints suggest that the LCA of extant platyrrhines existed at ca. 29 Ma, with the 95% confidence limit for the node ranging from 27-31 Ma. The LCA of extant platyrrhine monkeys based on substitution rate corrected by generation time and body size was established between 21-29 Ma. The estimates based on the two approaches used in this study recalibrate the ages of the major platyrrhine clades and corroborate the hypothesis that they constitute very old lineages. These results can help reconcile several controversial points concerning the affinities of key early Miocene fossils that have arisen among paleontologists and molecular systematists. However, they cannot resolve the controversy of whether these fossil species truly belong to the extant lineages or to a stem platyrrhine clade. That question can only be resolved by morphology. Finally, we show that the use of different approaches and well supported fossil information gives a more robust divergence time estimate of a clade.

Divergence Times and the Evolutionary Radiation of New World Monkeys (Platyrrhini, Primates): An Analysis of Fossil and Molecular Data

PubMed Central

Perez, S. Ivan; Tejedor, Marcelo F.; Novo, Nelson M.; Aristide, Leandro

2013-01-01

The estimation of phylogenetic relationships and divergence times among a group of organisms is a fundamental first step toward understanding its biological diversification. The time of the most recent or last common ancestor (LCA) of extant platyrrhines is one of the most controversial among scholars of primate evolution. Here we use two molecular based approaches to date the initial divergence of the platyrrhine clade, Bayesian estimations under a relaxed-clock model and substitution rate plus generation time and body size, employing the fossil record and genome datasets. We also explore the robustness of our estimations with respect to changes in topology, fossil constraints and substitution rate, and discuss the implications of our findings for understanding the platyrrhine radiation. Our results suggest that fossil constraints, topology and substitution rate have an important influence on our divergence time estimates. Bayesian estimates using conservative but realistic fossil constraints suggest that the LCA of extant platyrrhines existed at ca. 29 Ma, with the 95% confidence limit for the node ranging from 27–31 Ma. The LCA of extant platyrrhine monkeys based on substitution rate corrected by generation time and body size was established between 21–29 Ma. The estimates based on the two approaches used in this study recalibrate the ages of the major platyrrhine clades and corroborate the hypothesis that they constitute very old lineages. These results can help reconcile several controversial points concerning the affinities of key early Miocene fossils that have arisen among paleontologists and molecular systematists. However, they cannot resolve the controversy of whether these fossil species truly belong to the extant lineages or to a stem platyrrhine clade. That question can only be resolved by morphology. Finally, we show that the use of different approaches and well supported fossil information gives a more robust divergence time estimate of a clade. PMID:23826358

Bayesian hierarchical piecewise regression models: a tool to detect trajectory divergence between groups in long-term observational studies.

PubMed

Buscot, Marie-Jeanne; Wotherspoon, Simon S; Magnussen, Costan G; Juonala, Markus; Sabin, Matthew A; Burgner, David P; Lehtimäki, Terho; Viikari, Jorma S A; Hutri-Kähönen, Nina; Raitakari, Olli T; Thomson, Russell J

2017-06-06

Bayesian hierarchical piecewise regression (BHPR) modeling has not been previously formulated to detect and characterise the mechanism of trajectory divergence between groups of participants that have longitudinal responses with distinct developmental phases. These models are useful when participants in a prospective cohort study are grouped according to a distal dichotomous health outcome. Indeed, a refined understanding of how deleterious risk factor profiles develop across the life-course may help inform early-life interventions. Previous techniques to determine between-group differences in risk factors at each age may result in biased estimate of the age at divergence. We demonstrate the use of Bayesian hierarchical piecewise regression (BHPR) to generate a point estimate and credible interval for the age at which trajectories diverge between groups for continuous outcome measures that exhibit non-linear within-person response profiles over time. We illustrate our approach by modeling the divergence in childhood-to-adulthood body mass index (BMI) trajectories between two groups of adults with/without type 2 diabetes mellitus (T2DM) in the Cardiovascular Risk in Young Finns Study (YFS). Using the proposed BHPR approach, we estimated the BMI profiles of participants with T2DM diverged from healthy participants at age 16 years for males (95% credible interval (CI):13.5-18 years) and 21 years for females (95% CI: 19.5-23 years). These data suggest that a critical window for weight management intervention in preventing T2DM might exist before the age when BMI growth rate is naturally expected to decrease. Simulation showed that when using pairwise comparison of least-square means from categorical mixed models, smaller sample sizes tended to conclude a later age of divergence. In contrast, the point estimate of the divergence time is not biased by sample size when using the proposed BHPR method. BHPR is a powerful analytic tool to model long-term non-linear longitudinal outcomes, enabling the identification of the age at which risk factor trajectories diverge between groups of participants. The method is suitable for the analysis of unbalanced longitudinal data, with only a limited number of repeated measures per participants and where the time-related outcome is typically marked by transitional changes or by distinct phases of change over time.

Phylogeny and Niche Conservatism in North and Central American Triatomine Bugs (Hemiptera: Reduviidae: Triatominae), Vectors of Chagas' Disease

PubMed Central

Ibarra-Cerdeña, Carlos N.; Zaldívar-Riverón, Alejandro; Peterson, A. Townsend; Sánchez-Cordero, Víctor; Ramsey, Janine M.

2014-01-01

The niche conservatism hypothesis states that related species diverge in niche characteristics at lower rates than expected, given their lineage divergence. Here we analyze whether niche conservatism is a common pattern among vector species (Hemiptera: Reduviidae: Triatominae) of Trypanosoma cruzi that inhabit North and Central America, a highly heterogeneous landmass in terms of environmental gradients. Mitochondrial and nuclear loci were used in a multi-locus phylogenetic framework to reconstruct phylogenetic relationships among species and estimate time of divergence of selected clades to draw biogeographic inferences. Then, we estimated similarity between the ecological niche of sister species and tested the niche conservatism hypothesis using our best estimate of phylogeny. Triatoma is not monophyletic. A primary clade with all North and Central American (NCA) triatomine species from the genera Triatoma, Dipetalogaster, and Panstrongylus, was consistently recovered. Nearctic species within the NCA clade (T. p. protracta, T. r. rubida) diverged during the Pliocene, whereas the Neotropical species (T. phyllosoma, T. longipennis, T. dimidiata complex) are estimated to have diverged more recently, during the Pleistocene. The hypothesis of niche conservatism could not be rejected for any of six sister species pairs. Niche similarity between sister species best fits a retention model. While this framework is used here to infer niche evolution, it has a direct impact on spatial vector dynamics driven by human population movements, expansion of transportation networks and climate change scenarios. PMID:25356550

Exact Results for the Nonergodicity of d -Dimensional Generalized Lévy Walks

NASA Astrophysics Data System (ADS)

Albers, Tony; Radons, Günter

2018-03-01

We provide analytical results for the ensemble-averaged and time-averaged squared displacement, and the randomness of the latter, in the full two-dimensional parameter space of the d -dimensional generalized Lévy walk introduced by Shlesinger et al. [Phys. Rev. Lett. 58, 1100 (1987), 10.1103/PhysRevLett.58.1100]. In certain regions of the parameter plane, we obtain surprising results such as the divergence of the mean-squared displacements, the divergence of the ergodicity breaking parameter despite a finite mean-squared displacement, and subdiffusion which appears superdiffusive when one only considers time averages.

Flutter and divergence instability of supported piezoelectric nanotubes conveying fluid

NASA Astrophysics Data System (ADS)

Bahaadini, Reza; Hosseini, Mohammad; Jamali, Behnam

2018-01-01

In this paper, divergence and flutter instabilities of supported piezoelectric nanotubes containing flowing fluid are investigated. To take the size effects into account, the nonlocal elasticity theory is implemented in conjunction with the Euler-Bernoulli beam theory incorporating surface stress effects. The Knudsen number is applied to investigate the slip boundary conditions between the flow and wall of nanotube. The nonlocal governing equations of nanotube are obtained using Newtonian method, including the influence of piezoelectric voltage, surface effects, Knudsen number and nonlocal parameter. Applying Galerkin approach to transform resulting equations into a set of eigenvalue equations under the simple-simple (S-S) and clamped-clamped (C-C) boundary conditions. The effects of the piezoelectric voltage, surface effects, Knudsen number, nonlocal parameter and boundary conditions on the divergence and flutter boundaries of nanotubes are discussed. It is observed that the fluid-conveying nanotubes with both ends supported lose their stability by divergence first and then by flutter with increase in fluid velocity. Results indicate the importance of using piezoelectric voltage, nonlocal parameter and Knudsen number in decrease of critical flow velocities of system. Moreover, the surface effects have a significant role on the eigenfrequencies and critical fluid velocity.

Estimation of divergence times in litostomatean ciliates (Ciliophora: Intramacronucleata), using Bayesian relaxed clock and 18S rRNA gene.

PubMed

Vďačný, Peter

2015-08-01

The class Litostomatea comprises a diverse assemblage of free-living and endosymbiotic ciliates. To understand diversification dynamic of litostomateans, divergence times of their main groups were estimated with the Bayesian molecular dating, a technique allowing relaxation of molecular clock and incorporation of flexible calibration points. The class Litostomatea very likely emerged during the Cryogenian around 680 Mya. The origin of the subclass Rhynchostomatia is dated to about 415 Mya, while that of the subclass Haptoria to about 654 Mya. The order Pleurostomatida, emerging about 556 Mya, was recognized as the oldest group within the subclass Haptoria. The order Spathidiida appeared in the Paleozoic about 442 Mya. The three remaining haptorian orders evolved in the Paleozoic/Mesozoic periods: Didiniida about 419 Mya, Lacrymariida about 269 Mya, and Haptorida about 194 Mya. The subclass Trichostomatia originated from a spathidiid ancestor in the Mesozoic about 260 Mya. A further goal of this study was to investigate the impact of various settings on posterior divergence time estimates. The root placement and tree topology as well as the priors of the rate-drift model, birth-death process and nucleotide substitution rate, had no significant effect on calculation of posterior divergence time estimates. However, removal of calibration points could significantly change time estimates at some nodes. Copyright © 2015 Elsevier GmbH. All rights reserved.

Estimates of radiative flux divergence in the atmosphere from satellite data

NASA Technical Reports Server (NTRS)

Smith, G. L.; Charlock, Thomas P.; Bess, T. D.; Gupta, Shashi; Rutan, David; Rose, Fred G.

1990-01-01

Several options for the inference of the atmospheric radiative flux divergence (ARD) on the basis of satellite data are discussed. Attention is given to the clear-sky case and the cloudy-sky case. LW ARD profiles for different climatological regimes are presented and the effect of cloud base height on LW ARD divergence at various heights is illustrated.

Convergence from divergence

NASA Astrophysics Data System (ADS)

Costin, Ovidiu; Dunne, Gerald V.

2018-01-01

We show how to convert divergent series, which typically occur in many applications in physics, into rapidly convergent inverse factorial series. This can be interpreted physically as a novel resummation of perturbative series. Being convergent, these new series allow rigorous extrapolation from an asymptotic region with a large parameter, to the opposite region where the parameter is small. We illustrate the method with various physical examples, and discuss how these convergent series relate to standard methods such as Borel summation, and also how they incorporate the physical Stokes phenomenon. We comment on the relation of these results to Dyson’s physical argument for the divergence of perturbation theory. This approach also leads naturally to a wide class of relations between bosonic and fermionic partition functions, and Klein-Gordon and Dirac determinants.

The influence of taxon sampling on Bayesian divergence time inference under scenarios of rate heterogeneity among lineages.

PubMed

Soares, André E R; Schrago, Carlos G

2015-01-07

Although taxon sampling is commonly considered an important issue in phylogenetic inference, it is rarely considered in the Bayesian estimation of divergence times. In fact, the studies conducted to date have presented ambiguous results, and the relevance of taxon sampling for molecular dating remains unclear. In this study, we developed a series of simulations that, after six hundred Bayesian molecular dating analyses, allowed us to evaluate the impact of taxon sampling on chronological estimates under three scenarios of among-lineage rate heterogeneity. The first scenario allowed us to examine the influence of the number of terminals on the age estimates based on a strict molecular clock. The second scenario imposed an extreme example of lineage specific rate variation, and the third scenario permitted extensive rate variation distributed along the branches. We also analyzed empirical data on selected mitochondrial genomes of mammals. Our results showed that in the strict molecular-clock scenario (Case I), taxon sampling had a minor impact on the accuracy of the time estimates, although the precision of the estimates was greater with an increased number of terminals. The effect was similar in the scenario (Case III) based on rate variation distributed among the branches. Only under intensive rate variation among lineages (Case II) taxon sampling did result in biased estimates. The results of an empirical analysis corroborated the simulation findings. We demonstrate that taxonomic sampling affected divergence time inference but that its impact was significant if the rates deviated from those derived for the strict molecular clock. Increased taxon sampling improved the precision and accuracy of the divergence time estimates, but the impact on precision is more relevant. On average, biased estimates were obtained only if lineage rate variation was pronounced. Copyright © 2014 Elsevier Ltd. All rights reserved.

Data assimilation method based on the constraints of confidence region

NASA Astrophysics Data System (ADS)

Li, Yong; Li, Siming; Sheng, Yao; Wang, Luheng

2018-03-01

The ensemble Kalman filter (EnKF) is a distinguished data assimilation method that is widely used and studied in various fields including methodology and oceanography. However, due to the limited sample size or imprecise dynamics model, it is usually easy for the forecast error variance to be underestimated, which further leads to the phenomenon of filter divergence. Additionally, the assimilation results of the initial stage are poor if the initial condition settings differ greatly from the true initial state. To address these problems, the variance inflation procedure is usually adopted. In this paper, we propose a new method based on the constraints of a confidence region constructed by the observations, called EnCR, to estimate the inflation parameter of the forecast error variance of the EnKF method. In the new method, the state estimate is more robust to both the inaccurate forecast models and initial condition settings. The new method is compared with other adaptive data assimilation methods in the Lorenz-63 and Lorenz-96 models under various model parameter settings. The simulation results show that the new method performs better than the competing methods.

PopHuman: the human population genomics browser

PubMed Central

Mulet, Roger; Villegas-Mirón, Pablo; Hervas, Sergi; Sanz, Esteve; Velasco, Daniel; Bertranpetit, Jaume; Laayouni, Hafid

2018-01-01

Abstract The 1000 Genomes Project (1000GP) represents the most comprehensive world-wide nucleotide variation data set so far in humans, providing the sequencing and analysis of 2504 genomes from 26 populations and reporting >84 million variants. The availability of this sequence data provides the human lineage with an invaluable resource for population genomics studies, allowing the testing of molecular population genetics hypotheses and eventually the understanding of the evolutionary dynamics of genetic variation in human populations. Here we present PopHuman, a new population genomics-oriented genome browser based on JBrowse that allows the interactive visualization and retrieval of an extensive inventory of population genetics metrics. Efficient and reliable parameter estimates have been computed using a novel pipeline that faces the unique features and limitations of the 1000GP data, and include a battery of nucleotide variation measures, divergence and linkage disequilibrium parameters, as well as different tests of neutrality, estimated in non-overlapping windows along the chromosomes and in annotated genes for all 26 populations of the 1000GP. PopHuman is open and freely available at http://pophuman.uab.cat. PMID:29059408

Fully probabilistic control for stochastic nonlinear control systems with input dependent noise.

PubMed

Herzallah, Randa

2015-03-01

Robust controllers for nonlinear stochastic systems with functional uncertainties can be consistently designed using probabilistic control methods. In this paper a generalised probabilistic controller design for the minimisation of the Kullback-Leibler divergence between the actual joint probability density function (pdf) of the closed loop control system, and an ideal joint pdf is presented emphasising how the uncertainty can be systematically incorporated in the absence of reliable systems models. To achieve this objective all probabilistic models of the system are estimated from process data using mixture density networks (MDNs) where all the parameters of the estimated pdfs are taken to be state and control input dependent. Based on this dependency of the density parameters on the input values, explicit formulations to the construction of optimal generalised probabilistic controllers are obtained through the techniques of dynamic programming and adaptive critic methods. Using the proposed generalised probabilistic controller, the conditional joint pdfs can be made to follow the ideal ones. A simulation example is used to demonstrate the implementation of the algorithm and encouraging results are obtained. Copyright © 2014 Elsevier Ltd. All rights reserved.

Reevaluation of a classic phylogeographic barrier: new techniques reveal the influence of microgeographic climate variation on population divergence

PubMed Central

Soto-Centeno, J Angel; Barrow, Lisa N; Allen, Julie M; Reed, David L

2013-01-01

We evaluated the mtDNA divergence and relationships within Geomys pinetis to assess the status of formerly recognized Geomys taxa. Additionally, we integrated new hypothesis-based tests in ecological niche models (ENM) to provide greater insight into causes for divergence and potential barriers to gene flow in Southeastern United States (Alabama, Florida, and Georgia). Our DNA sequence dataset confirmed and strongly supported two distinct lineages within G. pinetis occurring east and west of the ARD. Divergence date estimates showed that eastern and western lineages diverged about 1.37 Ma (1.9 Ma–830 ka). Predicted distributions from ENMs were consistent with molecular data and defined each population east and west of the ARD with little overlap. Niche identity and background similarity tests were statistically significant suggesting that ENMs from eastern and western lineages are not identical or more similar than expected based on random localities drawn from the environmental background. ENMs also support the hypothesis that the ARD represents a ribbon of unsuitable climate between more suitable areas where these populations are distributed. The estimated age of divergence between eastern and western lineages of G. pinetis suggests that the divergence was driven by climatic conditions during Pleistocene glacial–interglacial cycles. The ARD at the contact zone of eastern and western lineages of G. pinetis forms a significant barrier promoting microgeographic isolation that helps maintain ecological and genetic divergence. PMID:23789071

Spectrum transformation for divergent iterations

NASA Technical Reports Server (NTRS)

Gupta, Murli M.

1991-01-01

Certain spectrum transformation techniques are described that can be used to transform a diverging iteration into a converging one. Two techniques are considered called spectrum scaling and spectrum enveloping and how to obtain the optimum values of the transformation parameters is discussed. Numerical examples are given to show how this technique can be used to transform diverging iterations into converging ones; this technique can also be used to accelerate the convergence of otherwise convergent iterations.

Leaf anatomy does not explain apparent short-term responses of mesophyll conductance to light and CO2 in tobacco.

PubMed

Carriquí, Marc; Douthe, Cyril; Molins, Arántzazu; Flexas, Jaume

2018-05-10

Mesophyll conductance to CO 2 (g m ), a key photosynthetic trait, is strongly constrained by leaf anatomy. Leaf anatomical parameters such as cell wall thickness and chloroplast area exposed to the mesophyll intercellular airspace have been demonstrated to determine g m in species with diverging phylogeny, leaf structure and ontogeny. However, the potential implication of leaf anatomy, especially chloroplast movement, on the short-term response of g m to rapid changes (i.e. seconds to minutes) under different environmental conditions (CO 2 , light or temperature) has not been examined. The aim of this study was to determine whether the observed rapid variations of g m in response to variations of light and CO 2 could be explained by changes in any leaf anatomical arrangements. When compared to high light and ambient CO 2 , the values of g m estimated by chlorophyll fluorescence decreased under high CO 2 and increased at low CO 2 , while it decreased with decreasing light. Nevertheless, no changes in anatomical parameters, including chloroplast distribution, were found. Hence, the g m estimated by analytical models based on anatomical parameters was constant under varying light and CO 2 . Considering this discrepancy between anatomy and chlorophyll fluorescence estimates, it is concluded that apparent fast g m variations should be due to artifacts in its estimation and/or to changes in the biochemical components acting on diffusional properties of the leaf (e.g. aquaporins and carbonic anhydrase). This article is protected by copyright. All rights reserved.

Bounding filter - A simple solution to lack of exact a priori statistics.

NASA Technical Reports Server (NTRS)

Nahi, N. E.; Weiss, I. M.

1972-01-01

Wiener and Kalman-Bucy estimation problems assume that models describing the signal and noise stochastic processes are exactly known. When this modeling information, i.e., the signal and noise spectral densities for Wiener filter and the signal and noise dynamic system and disturbing noise representations for Kalman-Bucy filtering, is inexactly known, then the filter's performance is suboptimal and may even exhibit apparent divergence. In this paper a system is designed whereby the actual estimation error covariance is bounded by the covariance calculated by the estimator. Therefore, the estimator obtains a bound on the actual error covariance which is not available, and also prevents its apparent divergence.

Low-light divergence in photovoltaic parameter fluctuations

NASA Astrophysics Data System (ADS)

Shvydka, Diana; Karpov, V. G.; Compaan, A. D.

2003-03-01

We study statistics of the major photovoltaic (PV) parameters, such as open-circuit voltage, short-circuit current, etc., versus light intensity on a set of nominally identical thin-film CdTe/CdS solar cells. A crossover light intensity is found, below which the relative fluctuations of the PV parameters diverge inversely proportional to the square root of the light intensity. We propose a model in which the observed fluctuations are due to lateral nonuniformities in the device structure. The crossover is attributed to the lateral nonuniformity screening length exceeding the device size. From the practical standpoint, our study introduces a simple uniformity diagnostic technique.

Vortex gas lens

NASA Technical Reports Server (NTRS)

Bogdanoff, David W.; Berschauer, Andrew; Parker, Timothy W.; Vickers, Jesse E.

1989-01-01

A vortex gas lens concept is presented. Such a lens has a potential power density capability of 10 to the 9th - 10 to the 10th w/sq cm. An experimental prototype was constructed, and the divergence half angle of the exiting beam was measured as a function of the lens operating parameters. Reasonably good agreement is found between the experimental results and theoretical calculations. The expanded beam was observed to be steady, and no strong, potentially beam-degrading jets were found to issue from the ends of the lens. Estimates of random beam deflection angles to be expected due to boundary layer noise are presented; these angles are very small.

Aboriginal population prospects.

PubMed

Gray, A; Tesfaghiorghis, H

1993-11-01

The authors examine data from the 1986 and 1991 Australian censuses to assess discrepancies between the census data and past projections of the size and structure of the Aboriginal population. They also "comment on ways in which determinants of Aboriginal population change are diverging from the parameters used for previous projections. We pay particular attention to mortality prospects.... We note the evidence for under-enumeration of the Aboriginal population in particular age groups in the 1991 Census as in previous censuses, and estimate the size of adjustments necessary to correct for some, but not all, of these deficiencies. The analysis shows that Aboriginal fertility increased in the second half of the 1980s." excerpt

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

Development of Jet Noise Power Spectral Laws Using SHJAR Data

NASA Technical Reports Server (NTRS)

Khavaran, Abbas; Bridges, James

2009-01-01

High quality jet noise spectral data measured at the Aeroacoustic Propulsion Laboratory at the NASA Glenn Research Center is used to examine a number of jet noise scaling laws. Configurations considered in the present study consist of convergent and convergent-divergent axisymmetric nozzles. Following the work of Viswanathan, velocity power factors are estimated using a least squares fit on spectral power density as a function of jet temperature and observer angle. The regression parameters are scrutinized for their uncertainty within the desired confidence margins. As an immediate application of the velocity power laws, spectral density in supersonic jets are decomposed into their respective components attributed to the jet mixing noise and broadband shock associated noise. Subsequent application of the least squares method on the shock power intensity shows that the latter also scales with some power of the shock parameter. A modified shock parameter is defined in order to reduce the dependency of the regression factors on the nozzle design point within the uncertainty margins of the least squares method.

Decorrelation Times of Photospheric Fields and Flows

NASA Technical Reports Server (NTRS)

Welsch, B. T.; Kusano, K.; Yamamoto, T. T.; Muglach, K.

2012-01-01

We use autocorrelation to investigate evolution in flow fields inferred by applying Fourier Local Correlation Tracking (FLCT) to a sequence of high-resolution (0.3 "), high-cadence (approx = 2 min) line-of-sight magnetograms of NOAA active region (AR) 10930 recorded by the Narrowband Filter Imager (NFI) of the Solar Optical Telescope (SOT) aboard the Hinode satellite over 12 - 13 December 2006. To baseline the timescales of flow evolution, we also autocorrelated the magnetograms, at several spatial binnings, to characterize the lifetimes of active region magnetic structures versus spatial scale. Autocorrelation of flow maps can be used to optimize tracking parameters, to understand tracking algorithms f susceptibility to noise, and to estimate flow lifetimes. Tracking parameters varied include: time interval Delta t between magnetogram pairs tracked, spatial binning applied to the magnetograms, and windowing parameter sigma used in FLCT. Flow structures vary over a range of spatial and temporal scales (including unresolved scales), so tracked flows represent a local average of the flow over a particular range of space and time. We define flow lifetime to be the flow decorrelation time, tau . For Delta t > tau, tracking results represent the average velocity over one or more flow lifetimes. We analyze lifetimes of flow components, divergences, and curls as functions of magnetic field strength and spatial scale. We find a significant trend of increasing lifetimes of flow components, divergences, and curls with field strength, consistent with Lorentz forces partially governing flows in the active photosphere, as well as strong trends of increasing flow lifetime and decreasing magnitudes with increases in both spatial scale and Delta t.

Comparison of turbulence estimation for four- and five-beam ADCP configurations

NASA Astrophysics Data System (ADS)

Togneri, Michael; Masters, Ian; Jones, Dale

2017-04-01

Turbulence is a vital consideration for tidal power generation, as the resulting fluctuating loads greatly impact the fatigue life of tidal turbines and their components. Acoustic Doppler current profilers (ADCPs) are one of the most common tools for measurement of currents in tidal power applications, and although most often used for assessment of mean current properties they are also capable of measuring turbulence parameters. Conventional ADCPs use four diverging beams in a so-called 'Janus' configuration, but more recent models employ an additional vertical beam. In this paper we explore the improvements to turbulence measurements that are made possible by the addition of the fifth beam, with a focus on estimation of turbulent kinetic energy (TKE) density. The standard approach for estimating TKE density from ADCP measurements is the variance method. As each of the diverging beams measures a single velocity component at spatially-separated points, it is not possible to find the TKE density by a straightforward combination of beam measurements. Instead, we must assume that the statistical properties of the turbulence are uniform across the spatial extent of the beams; it is then possible to express the TKE density as a linear combination of the velocity variance as measured by each beam. In the four-beam configuration, an additional assumption regarding the magnitude of the turbulent anisotropy: a parameter ξ is introduced that characterises the proportion of TKE in the vertical fluctuations. With the five-beam configuration, direct measurements of the vertical component are available and this assumption is no longer required. In this paper, turbulence measurements from a five-beam ADCP deployed off the coast of Anglesey in 2014 are analysed. We compare turbulence estimates using all five beams to estimates obtained using only the conventional four-beam setup by discarding the vertical beam data. This allows us to quantify the error in the standard value of ξ. We find that it is on average within 3.4% of the real value, although there are times for which it is much greater. We also discuss the Doppler noise correction in the five-beam case, which is more complex than the four-beam case due to the different noise properties of the vertical beam.

Phylogeographic patterns of genetic diversity in eastern Mediterranean water frogs have been determined by geological processes and climate change in the Late Cenozoic.

PubMed

Akın, Ciğdem; Bilgin, C Can; Beerli, Peter; Westaway, Rob; Ohst, Torsten; Litvinchuk, Spartak N; Uzzell, Thomas; Bilgin, Metin; Hotz, Hansjürg; Guex, Gaston-Denis; Plötner, Jörg

2010-11-01

AIM: Our aims were to assess the phylogeographic patterns of genetic diversity in eastern Mediterranean water frogs and to estimate divergence times using different geological scenarios. We related divergence times to past geological events and discuss the relevance of our data for the systematics of eastern Mediterranean water frogs. LOCATION: The eastern Mediterranean region. METHODS: Genetic diversity and divergence were calculated using sequences of two protein-coding mitochondrial (mt) genes: ND2 (1038 bp, 119 sequences) and ND3 (340 bp, 612 sequences). Divergence times were estimated in a Bayesian framework under four geological scenarios representing alternative possible geological histories for the eastern Mediterranean. We then compared the different scenarios using Bayes factors and additional geological data. RESULTS: Extensive genetic diversity in mtDNA divides eastern Mediterranean water frogs into six main haplogroups (MHG). Three MHGs were identified on the Anatolian mainland; the most widespread MHG with the highest diversity is distributed from western Anatolia to the northern shore of the Caspian Sea, including the type locality of Pelophylax ridibundus. The other two Anatolian MHGs are restricted to south-eastern Turkey, occupying localities west and east of the Amanos mountain range. One of the remaining three MHGs is restricted to Cyprus; a second to the Levant; the third was found in the distribution area of European lake frogs (P. ridibundus group), including the Balkans. MAIN CONCLUSIONS: Based on geological evidence and estimates of genetic divergence we hypothesize that the water frogs of Cyprus have been isolated from the Anatolian mainland populations since the end of the Messinian salinity crisis (MSC), i.e. since c. 5.5-5.3 Ma, while our divergence time estimates indicate that the isolation of Crete from the mainland populations (Peloponnese, Anatolia) most likely pre-dates the MSC. The observed rates of divergence imply a time window of c. 1.6-1.1 million years for diversification of the largest Anatolian MHG; divergence between the two other Anatolian MHGs may have begun about 3.0 Ma, apparently as a result of uplift of the Amanos Mountains. Our mtDNA data suggest that the Anatolian water frogs and frogs from Cyprus represent several undescribed species.

Spectral Entropies as Information-Theoretic Tools for Complex Network Comparison

NASA Astrophysics Data System (ADS)

De Domenico, Manlio; Biamonte, Jacob

2016-10-01

Any physical system can be viewed from the perspective that information is implicitly represented in its state. However, the quantification of this information when it comes to complex networks has remained largely elusive. In this work, we use techniques inspired by quantum statistical mechanics to define an entropy measure for complex networks and to develop a set of information-theoretic tools, based on network spectral properties, such as Rényi q entropy, generalized Kullback-Leibler and Jensen-Shannon divergences, the latter allowing us to define a natural distance measure between complex networks. First, we show that by minimizing the Kullback-Leibler divergence between an observed network and a parametric network model, inference of model parameter(s) by means of maximum-likelihood estimation can be achieved and model selection can be performed with appropriate information criteria. Second, we show that the information-theoretic metric quantifies the distance between pairs of networks and we can use it, for instance, to cluster the layers of a multilayer system. By applying this framework to networks corresponding to sites of the human microbiome, we perform hierarchical cluster analysis and recover with high accuracy existing community-based associations. Our results imply that spectral-based statistical inference in complex networks results in demonstrably superior performance as well as a conceptual backbone, filling a gap towards a network information theory.

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.

Prediction of industrial tomato hybrids from agronomic traits and ISSR molecular markers.

PubMed

Figueiredo, A S T; Resende, J T V; Faria, M V; Da-Silva, P R; Fagundes, B S; Morales, R G F

2016-05-13

Heterosis is a highly relevant phenomenon in plant breeding. This condition is usually established in hybrids derived from crosses of highly divergent parents. The success of a breeder in obtaining heterosis is directly related to the correct identification of genetically contrasting parents. Currently, the diallel cross is the most commonly used methodology to detect contrasting parents; however, it is a time- and cost-consuming procedure. Therefore, new tools capable of performing this task quickly and accurately are required. Thus, the purpose of this study was to estimate the genetic divergence in industrial tomato lines, based on agronomic traits, and to compare with estimates obtained using inter-simple sequence repeat (ISSR) molecular markers. The genetic divergence among 10 industrial tomato lines, based on nine morphological characters and 12 ISSR primers was analyzed. For data analysis, Pearson and Spearman correlation coefficients were calculated between the genetic dissimilarity measures estimated by Mahalanobis distance and Jaccard's coefficient of genetic dissimilarity from the heterosis estimates, combining ability, and means of important traits of industrial tomato. The ISSR markers efficiently detected contrasting parents for hybrid production in tomato. Parent RVTD-08 was indicated as the most divergent, both by molecular and morphological markers, that positively contributed to increased heterosis and by the specific combining ability in the crosses in which it participated. The genetic dissimilarity estimated by ISSR molecular markers aided the identification of the best hybrids of the experiment in terms of total fruit yield, pulp yield, and soluble solids content.

Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion

PubMed Central

Campos, José Luis; Charlesworth, Brian

2017-01-01

We used whole-genome resequencing data from a population of Drosophila melanogaster to investigate the causes of the negative correlation between the within-population synonymous nucleotide site diversity (πS) of a gene and its degree of divergence from related species at nonsynonymous nucleotide sites (KA). By using the estimated distributions of mutational effects on fitness at nonsynonymous and UTR sites, we predicted the effects of background selection at sites within a gene on πS and found that these could account for only part of the observed correlation between πS and KA. We developed a model of the effects of selective sweeps that included gene conversion as well as crossing over. We used this model to estimate the average strength of selection on positively selected mutations in coding sequences and in UTRs, as well as the proportions of new mutations that are selectively advantageous. Genes with high levels of selective constraint on nonsynonymous sites were found to have lower strengths of positive selection and lower proportions of advantageous mutations than genes with low levels of constraint. Overall, background selection and selective sweeps within a typical gene reduce its synonymous diversity to ∼75% of its value in the absence of selection, with larger reductions for genes with high KA. Gene conversion has a major effect on the estimates of the parameters of positive selection, such that the estimated strength of selection on favorable mutations is greatly reduced if it is ignored. PMID:28559322

UV-IR mixing in nonassociative Snyder ϕ4 theory

NASA Astrophysics Data System (ADS)

Meljanac, Stjepan; Mignemi, Salvatore; Trampetic, Josip; You, Jiangyang

2018-03-01

Using a quantization of the nonassociative and noncommutative Snyder ϕ4 scalar field theory in a Hermitian realization, we present in this article analytical formulas for the momentum-conserving part of the one-loop two-point function of this theory in D -, 4-, and 3-dimensional Euclidean spaces, which are exact with respect to the noncommutative deformation parameter β . We prove that these integrals are regularized by the Snyder deformation. These results indicate that the Snyder deformation does partially regularize the UV divergences of the undeformed theory, as it was proposed decades ago. Furthermore, it is observed that different nonassociative ϕ4 products can generate different momentum-conserving integrals. Finally, most importantly, a logarithmic infrared divergence emerges in one of these interaction terms. We then analyze sample momentum nonconserving integral qualitatively and show that it could exhibit IR divergence too. Therefore, infrared divergences should exist, in general, in the Snyder ϕ4 theory. We consider infrared divergences at the limit p →0 as UV/IR mixings induced by nonassociativity, since they are associated to the matching UV divergence in the zero-momentum limit and appear in specific types of nonassociative ϕ4 products. We also discuss the extrapolation of the Snyder deformation parameter β to negative values as well as certain general properties of one-loop quantum corrections in Snyder ϕ4 theory at the zero-momentum limit.

Genetic variation and evolutionary demography of Fenneropenaeus chinensis populations, as revealed by the analysis of mitochondrial control region sequences

PubMed Central

2010-01-01

Genetic variation and evolutionary demography of the shrimp Fenneropenaeus chinensis were investigated using sequence data of the complete mitochondrial control region (CR). Fragments of 993 bp of the CR were sequenced for 93 individuals from five localities over most of the species' range in the Yellow Sea and the Bohai Sea. There were 84 variable sites defining 68 haplotypes. Haplotype diversity levels were very high (0.95 ± 0.03-0.99 ± 0.02) in F. chinensis populations, whereas those of nucleotide diversity were moderate to low (0.66 ± 0.36%-0.84 ± 0.46%). Analysis of molecular variance and conventional population statistics (FST ) revealed no significant genetic structure throughout the range of F. chinensis. Mismatch distribution, estimates of population parameters and neutrality tests revealed that the significant fluctuations and shallow coalescence of mtDNA genealogies observed were coincident with estimated demographic parameters and neutrality tests, in implying important past-population size fluctuations or range expansion. Isolation with Migration (IM) coalescence results suggest that F. chinensis, distributed along the coasts of northern China and the Korean Peninsula (about 1000 km apart), diverged recently, the estimated time-split being 12,800 (7,400-18,600) years ago. PMID:21637498

Influence of gene flow on divergence dating - implications for the speciation history of Takydromus grass lizards.

PubMed

Tseng, Shu-Ping; Li, Shou-Hsien; Hsieh, Chia-Hung; Wang, Hurng-Yi; Lin, Si-Min

2014-10-01

Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species-tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus. © 2014 John Wiley & Sons Ltd.

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.

A well-posed and stable stochastic Galerkin formulation of the incompressible Navier–Stokes equations with random data

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

Pettersson, Per, E-mail: per.pettersson@uib.no; Nordström, Jan, E-mail: jan.nordstrom@liu.se; Doostan, Alireza, E-mail: alireza.doostan@colorado.edu

2016-02-01

We present a well-posed stochastic Galerkin formulation of the incompressible Navier–Stokes equations with uncertainty in model parameters or the initial and boundary conditions. The stochastic Galerkin method involves representation of the solution through generalized polynomial chaos expansion and projection of the governing equations onto stochastic basis functions, resulting in an extended system of equations. A relatively low-order generalized polynomial chaos expansion is sufficient to capture the stochastic solution for the problem considered. We derive boundary conditions for the continuous form of the stochastic Galerkin formulation of the velocity and pressure equations. The resulting problem formulation leads to an energy estimatemore » for the divergence. With suitable boundary data on the pressure and velocity, the energy estimate implies zero divergence of the velocity field. Based on the analysis of the continuous equations, we present a semi-discretized system where the spatial derivatives are approximated using finite difference operators with a summation-by-parts property. With a suitable choice of dissipative boundary conditions imposed weakly through penalty terms, the semi-discrete scheme is shown to be stable. Numerical experiments in the laminar flow regime corroborate the theoretical results and we obtain high-order accurate results for the solution variables and the velocity divergence converges to zero as the mesh is refined.« less

A pair of new moisture-dynamic diagnostic parameters for heavy rain location

NASA Astrophysics Data System (ADS)

Yuan, Kai; Zhu, Zhiwei; Li, Ming

2018-06-01

In this study, the regional persistent heavy rain process occurred in the middle and lower reaches of the Yangtze River valley from 30 June 2016 to 7 July 2016 is analyzed. We find that the pure dynamic parameters [e.g., vorticity ( V) and divergence ( D)] and two-dimensional moisture-dynamic parameters [e.g., moist vorticity ( MV), moist divergence ( MD)] have difficulty in capturing the rainfall location during such a critical process. Given the poor performance of these traditional parameters, a pair of new parameters [namely, one-dimensional moist vorticity ( ODMV) and one-dimensional moist divergence ( ODMD)] based on low-level jet is proposed for diagnosing heavy rain location. The results show that (1) ODMV and ODMD have better relations with rain belt in terms of spatial distribution. Precipitation occurs in positive (negative) region of ODMV ( ODMD), and heavy rainfall accurately locates in the positive (negative) center of ODMV ( ODMD); (2) ODMV and ODMD also have good correlation with the precipitation in terms of temporal variation (significant at the 99% confidence level). When ODMV ( ODMD) is in strong positive (negative) phase, precipitation is large, and vice versa; (3) the threat score of ODMV and ODMD for the areal-mean rainfall is improved by 119% and 16%, respectively, compared to V/ D and MV/ MD. It is anticipated that the proposed new parameters would facilitate the skills of diagnosing and forecasting the heavy rainfall.

A Bayesian framework to estimate diversification rates and their variation through time and space

PubMed Central

2011-01-01

Background Patterns of species diversity are the result of speciation and extinction processes, and molecular phylogenetic data can provide valuable information to derive their variability through time and across clades. Bayesian Markov chain Monte Carlo methods offer a promising framework to incorporate phylogenetic uncertainty when estimating rates of diversification. Results We introduce a new approach to estimate diversification rates in a Bayesian framework over a distribution of trees under various constant and variable rate birth-death and pure-birth models, and test it on simulated phylogenies. Furthermore, speciation and extinction rates and their posterior credibility intervals can be estimated while accounting for non-random taxon sampling. The framework is particularly suitable for hypothesis testing using Bayes factors, as we demonstrate analyzing dated phylogenies of Chondrostoma (Cyprinidae) and Lupinus (Fabaceae). In addition, we develop a model that extends the rate estimation to a meta-analysis framework in which different data sets are combined in a single analysis to detect general temporal and spatial trends in diversification. Conclusions Our approach provides a flexible framework for the estimation of diversification parameters and hypothesis testing while simultaneously accounting for uncertainties in the divergence times and incomplete taxon sampling. PMID:22013891

Multilocus patterns of polymorphism and selection across the X chromosome of Caenorhabditis remanei.

PubMed

Cutter, Asher D

2008-03-01

Natural selection and neutral processes such as demography, mutation, and gene conversion all contribute to patterns of polymorphism within genomes. Identifying the relative importance of these varied components in evolution provides the principal challenge for population genetics. To address this issue in the nematode Caenorhabditis remanei, I sampled nucleotide polymorphism at 40 loci across the X chromosome. The site-frequency spectrum for these loci provides no evidence for population size change, and one locus presents a candidate for linkage to a target of balancing selection. Selection for codon usage bias leads to the non-neutrality of synonymous sites, and despite its weak magnitude of effect (N(e)s approximately 0.1), is responsible for profound patterns of diversity and divergence in the C. remanei genome. Although gene conversion is evident for many loci, biased gene conversion is not identified as a significant evolutionary process in this sample. No consistent association is observed between synonymous-site diversity and linkage-disequilibrium-based estimators of the population recombination parameter, despite theoretical predictions about background selection or widespread genetic hitchhiking, but genetic map-based estimates of recombination are needed to rigorously test for a diversity-recombination relationship. Coalescent simulations also illustrate how a spurious correlation between diversity and linkage-disequilibrium-based estimators of recombination can occur, due in part to the presence of unbiased gene conversion. These results illustrate the influence that subtle natural selection can exert on polymorphism and divergence, in the form of codon usage bias, and demonstrate the potential of C. remanei for detecting natural selection from genomic scans of polymorphism.

Rapid changes in genetic architecture of behavioural syndromes following colonization of a novel environment.

PubMed

Karlsson Green, K; Eroukhmanoff, F; Harris, S; Pettersson, L B; Svensson, E I

2016-01-01

Behavioural syndromes, that is correlated behaviours, may be a result from adaptive correlational selection, but in a new environmental setting, the trait correlation might act as an evolutionary constraint. However, knowledge about the quantitative genetic basis of behavioural syndromes, and the stability and evolvability of genetic correlations under different ecological conditions, is limited. We investigated the quantitative genetic basis of correlated behaviours in the freshwater isopod Asellus aquaticus. In some Swedish lakes, A. aquaticus has recently colonized a novel habitat and diverged into two ecotypes, presumably due to habitat-specific selection from predation. Using a common garden approach and animal model analyses, we estimated quantitative genetic parameters for behavioural traits and compared the genetic architecture between the ecotypes. We report that the genetic covariance structure of the behavioural traits has been altered in the novel ecotype, demonstrating divergence in behavioural correlations. Thus, our study confirms that genetic correlations behind behaviours can change rapidly in response to novel selective environments. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Statistical Field Estimation and Scale Estimation for Complex Coastal Regions and Archipelagos

DTIC Science & Technology

2009-05-01

instruments applied to mode-73. Deep-Sea Research, 23:559–582. Brown , R. G. and Hwang , P. Y. C. (1997). Introduction to Random Signals and Applied Kalman ...the covariance matrix becomes neg- ative due to numerical issues ( Brown and Hwang , 1997). Some useful techniques to counter these divergence problems...equations ( Brown and Hwang , 1997). If the number of observations is large, divergence problems can arise under certain con- ditions due to truncation errors

Regularized minimum I-divergence methods for the inverse blackbody radiation problem

NASA Astrophysics Data System (ADS)

Choi, Kerkil; Lanterman, Aaron D.; Shin, Jaemin

2006-08-01

This paper proposes iterative methods for estimating the area temperature distribution of a blackbody from its total radiated power spectrum measurements. This is called the inverse blackbody radiation problem. This problem is inherently ill-posed due to the characteristics of the kernel in the underlying integral equation given by Planck's law. The functions involved in the problem are all non-negative. Csiszár's I-divergence is an information-theoretic discrepancy measure between two non-negative functions. We derive iterative methods for minimizing Csiszár's I-divergence between the measured power spectrum and the power spectrum arising from the estimate according to the integral equation. Due to the ill-posedness of the problem, unconstrained algorithms often produce poor estimates, especially when the measurements are corrupted by noise. To alleviate this difficulty, we apply regularization methods to our algorithms. Penalties based on Shannon's entropy, the L1-norm and Good's roughness are chosen to suppress the undesirable artefacts. When a penalty is applied, the pertinent optimization that needs to be performed at each iteration is no longer trivial. In particular, Good's roughness causes couplings between estimate components. To handle this issue, we adapt Green's one-step-late method. This choice is based on the important fact that our minimum I-divergence algorithms can be interpreted as asymptotic forms of certain expectation-maximization algorithms. The effectiveness of our methods is illustrated via various numerical experiments.

Budgets of divergent and rotational kinetic energy during two periods of intense convection

NASA Technical Reports Server (NTRS)

Buechler, D. E.; Fuelberg, H. E.

1986-01-01

The derivations of the energy budget equations for divergent and rotational components of kinetic energy are provided. The intense convection periods studied are: (1) synoptic scale data of 3 or 6 hour intervals and (2) mesoalphascale data every 3 hours. Composite energies and averaged budgets for the periods are presented; the effects of random data errors on derived energy parameters is investigated. The divergent kinetic energy and rotational kinetic energy budgets are compared; good correlation of the data is observed. The kinetic energies and budget terms increase with convective development; however, the conversion of the divergent and rotational energies are opposite.

A Photometric Study of Phocaea Group Asteroid 1584 Fuji

NASA Astrophysics Data System (ADS)

Drake, J. S.

2004-05-01

Observations of Phocaea group asteroid 1584 Fuji with the 31-inch telescope at Lowell Observatory in Arizona and the 24-inch telescope at Britton Observatory at Dickinson College in Pennsylvania from 31 January 2004 to 28 February 2004 indicate a sinusoidal lightcurve with a period of 14.89 ± 0.01 hours, in conflict with published results. Reduction of these data to a standard magnitude system indicate a V-band amplitude of 0.13 ± 0.02 magnitudes, further diverging from the accepted value. Application of the IAU Two-Parameter magnitude system for asteroids permits an estimation of the body's diameter. I compare these parameters with those published for Fuji's companions in the Phocaea group, other S-type objects in the main belt, and asteroids of similar size throughout the Solar System. I thank Dickinson College and the Arizona Space Grant Consortium for their financial support.

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.

Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago.

PubMed

Schlebusch, Carina M; Malmström, Helena; Günther, Torsten; Sjödin, Per; Coutinho, Alexandra; Edlund, Hanna; Munters, Arielle R; Vicente, Mário; Steyn, Maryna; Soodyall, Himla; Lombard, Marlize; Jakobsson, Mattias

2017-11-03

Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Bayesian phylogenetic estimation of fossil ages.

PubMed

Drummond, Alexei J; Stadler, Tanja

2016-07-19

Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the 'morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. © 2016 The Authors.

Bayesian phylogenetic estimation of fossil ages

PubMed Central

Drummond, Alexei J.; Stadler, Tanja

2016-01-01

Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth–death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the ‘morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. PMID:27325827

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

PubMed Central

2018-01-01

Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications. However, despite the recent explosion in genomic and transcriptomic data, the utility of these data sources for efficient divergence-time inference remains unexamined. Phylogenomic datasets pose two distinct problems for divergence-time estimation: (i) the volume of data makes inference of the entire dataset intractable, and (ii) the extent of underlying topological and rate heterogeneity across genes makes model mis-specification a real concern. “Gene shopping”, wherein a phylogenomic dataset is winnowed to a set of genes with desirable properties, represents an alternative approach that holds promise in alleviating these issues. We implemented an approach for phylogenomic datasets (available in SortaDate) that filters genes by three criteria: (i) clock-likeness, (ii) reasonable tree length (i.e., discernible information content), and (iii) least topological conflict with a focal species tree (presumed to have already been inferred). Such a winnowing procedure ensures that errors associated with model (both clock and topology) mis-specification are minimized, therefore reducing error in divergence-time estimation. We demonstrated the efficacy of this approach through simulation and applied it to published animal (Aves, Diplopoda, and Hymenoptera) and plant (carnivorous Caryophyllales, broad Caryophyllales, and Vitales) phylogenomic datasets. By quantifying rate heterogeneity across both genes and lineages we found that every empirical dataset examined included genes with clock-like, or nearly clock-like, behavior. Moreover, many datasets had genes that were clock-like, exhibited reasonable evolutionary rates, and were mostly compatible with the species tree. We identified overlap in age estimates when analyzing these filtered genes under strict clock and uncorrelated lognormal (UCLN) models. However, this overlap was often due to imprecise estimates from the UCLN model. We find that “gene shopping” can be an efficient approach to divergence-time inference for phylogenomic datasets that may otherwise be characterized by extensive gene tree heterogeneity. PMID:29772020

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era.

PubMed

Smith, Stephen A; Brown, Joseph W; Walker, Joseph F

2018-01-01

Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications. However, despite the recent explosion in genomic and transcriptomic data, the utility of these data sources for efficient divergence-time inference remains unexamined. Phylogenomic datasets pose two distinct problems for divergence-time estimation: (i) the volume of data makes inference of the entire dataset intractable, and (ii) the extent of underlying topological and rate heterogeneity across genes makes model mis-specification a real concern. "Gene shopping", wherein a phylogenomic dataset is winnowed to a set of genes with desirable properties, represents an alternative approach that holds promise in alleviating these issues. We implemented an approach for phylogenomic datasets (available in SortaDate) that filters genes by three criteria: (i) clock-likeness, (ii) reasonable tree length (i.e., discernible information content), and (iii) least topological conflict with a focal species tree (presumed to have already been inferred). Such a winnowing procedure ensures that errors associated with model (both clock and topology) mis-specification are minimized, therefore reducing error in divergence-time estimation. We demonstrated the efficacy of this approach through simulation and applied it to published animal (Aves, Diplopoda, and Hymenoptera) and plant (carnivorous Caryophyllales, broad Caryophyllales, and Vitales) phylogenomic datasets. By quantifying rate heterogeneity across both genes and lineages we found that every empirical dataset examined included genes with clock-like, or nearly clock-like, behavior. Moreover, many datasets had genes that were clock-like, exhibited reasonable evolutionary rates, and were mostly compatible with the species tree. We identified overlap in age estimates when analyzing these filtered genes under strict clock and uncorrelated lognormal (UCLN) models. However, this overlap was often due to imprecise estimates from the UCLN model. We find that "gene shopping" can be an efficient approach to divergence-time inference for phylogenomic datasets that may otherwise be characterized by extensive gene tree heterogeneity.

Integrating paleoecology and genetics of bird populations in two sky island archipelagos.

PubMed

McCormack, John E; Bowen, Bonnie S; Smith, Thomas B

2008-06-27

Genetic tests of paleoecological hypotheses have been rare, partly because recent genetic divergence is difficult to detect and time. According to fossil plant data, continuous woodland in the southwestern USA and northern Mexico became fragmented during the last 10,000 years, as warming caused cool-adapted species to retreat to high elevations. Most genetic studies of resulting 'sky islands' have either failed to detect recent divergence or have found discordant evidence for ancient divergence. We test this paleoecological hypothesis for the region with intraspecific mitochondrial DNA and microsatellite data from sky-island populations of a sedentary bird, the Mexican jay (Aphelocoma ultramarina). We predicted that populations on different sky islands would share common, ancestral alleles that existed during the last glaciation, but that populations on each sky island, owing to their isolation, would contain unique variants of postglacial origin. We also predicted that divergence times estimated from corrected genetic distance and a coalescence model would post-date the last glacial maximum. Our results provide multiple independent lines of support for postglacial divergence, with the predicted pattern of shared and unique mitochondrial DNA haplotypes appearing in two independent sky-island archipelagos, and most estimates of divergence time based on corrected genetic distance post-dating the last glacial maximum. Likewise, an isolation model based on multilocus gene coalescence indicated postglacial divergence of five pairs of sky islands. In contrast to their similar recent histories, the two archipelagos had dissimilar historical patterns in that sky islands in Arizona showed evidence for older divergence, suggesting different responses to the last glaciation. This study is one of the first to provide explicit support from genetic data for a postglacial divergence scenario predicted by one of the best paleoecological records in the world. Our results demonstrate that sky islands act as generators of genetic diversity at both recent and historical timescales and underscore the importance of thorough sampling and the use of loci with fast mutation rates to studies that test hypotheses concerning recent genetic divergence.

Partitioning the Genetic Diversity of a Virus Family: Approach and Evaluation through a Case Study of Picornaviruses

PubMed Central

Lauber, Chris

2012-01-01

The recent advent of genome sequences as the only source available to classify many newly discovered viruses challenges the development of virus taxonomy by expert virologists who traditionally rely on extensive virus characterization. In this proof-of-principle study, we address this issue by presenting a computational approach (DEmARC) to classify viruses of a family into groups at hierarchical levels using a sole criterion—intervirus genetic divergence. To quantify genetic divergence, we used pairwise evolutionary distances (PEDs) estimated by maximum likelihood inference on a multiple alignment of family-wide conserved proteins. PEDs were calculated for all virus pairs, and the resulting distribution was modeled via a mixture of probability density functions. The model enables the quantitative inference of regions of distance discontinuity in the family-wide PED distribution, which define the levels of hierarchy. For each level, a limit on genetic divergence, below which two viruses join the same group, was objectively selected among a set of candidates by minimizing violations of intragroup PEDs to the limit. In a case study, we applied the procedure to hundreds of genome sequences of picornaviruses and extensively evaluated it by modulating four key parameters. It was found that the genetics-based classification largely tolerates variations in virus sampling and multiple alignment construction but is affected by the choice of protein and the measure of genetic divergence. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3905–3915, 2012), we analyze the substantial insight gained with the genetics-based classification approach by comparing it with the expert-based picornavirus taxonomy. PMID:22278230

Quantifying unpredictability: A multiple-model approach based on satellite imagery data from Mediterranean ponds

PubMed Central

García-Roger, Eduardo Moisés; Franch, Belen; Carmona, María José; Serra, Manuel

2017-01-01

Fluctuations in environmental parameters are increasingly being recognized as essential features of any habitat. The quantification of whether environmental fluctuations are prevalently predictable or unpredictable is remarkably relevant to understanding the evolutionary responses of organisms. However, when characterizing the relevant features of natural habitats, ecologists typically face two problems: (1) gathering long-term data and (2) handling the hard-won data. This paper takes advantage of the free access to long-term recordings of remote sensing data (27 years, Landsat TM/ETM+) to assess a set of environmental models for estimating environmental predictability. The case study included 20 Mediterranean saline ponds and lakes, and the focal variable was the water-surface area. This study first aimed to produce a method for accurately estimating the water-surface area from satellite images. Saline ponds can develop salt-crusted areas that make it difficult to distinguish between soil and water. This challenge was addressed using a novel pipeline that combines band ratio water indices and the short near-infrared band as a salt filter. The study then extracted the predictable and unpredictable components of variation in the water-surface area. Two different approaches, each showing variations in the parameters, were used to obtain the stochastic variation around a regular pattern with the objective of dissecting the effect of assumptions on predictability estimations. The first approach, which is based on Colwell’s predictability metrics, transforms the focal variable into a nominal one. The resulting discrete categories define the relevant variations in the water-surface area. In the second approach, we introduced General Additive Model (GAM) fitting as a new metric for quantifying predictability. Both approaches produced a wide range of predictability for the studied ponds. Some model assumptions–which are considered very different a priori–had minor effects, whereas others produced predictability estimations that showed some degree of divergence. We hypothesize that these diverging estimations of predictability reflect the effect of fluctuations on different types of organisms. The fluctuation analysis described in this manuscript is applicable to a wide variety of systems, including both aquatic and non-aquatic systems, and will be valuable for quantifying and characterizing predictability, which is essential within the expected global increase in the unpredictability of environmental fluctuations. We advocate that a priori information for organisms of interest should be used to select the most suitable metrics for estimating predictability, and we provide some guidelines for this approach. PMID:29121667

Performance of Several Conical Convergent-Divergent Rocket-Type Exhaust Nozzles

NASA Technical Reports Server (NTRS)

Campbell, C. E.; Farley, J. M.

1960-01-01

An investigation was conducted to obtain nozzle performance data with relatively large-scale models at pressure ratios as high as 120. Conical convergent-divergent nozzles with divergence angles alpha of 15, 25, and 29 deg. were each tested at area ratios of approximately 10, 25, and 40. Heated air (1200 F) was supplied at the nozzle inlet at pressures up to 145 pounds per square inch absolute and was exhausted into quiescent air at pressures as low as 1.2 pounds per square inch absolute. Thrust ratios for all nozzle configurations are presented over the range of pressure ratios attainable and were extrapolated when possible to design pressure ratio and beyond. Design thrust ratios decreased with increasing nozzle divergence angle according to the trend predicted by the (1 + cos alpha)/2 parameter. Decreasing the nozzle divergence angle resulted in sizable increases in thrust ratio for a given surface-area ratio (nozzle weight), particularly at low nozzle pressure ratios. Correlations of the nozzle static pressure at separation and of the average static pressure downstream of separation with various nozzle parameters permitted the calculation of thrust in the separated-flow region from unseparated static-pressure distributions. Thrust ratios calculated by this method agreed with measured values within about 1 percent.

Estimating linear-nonlinear models using Rényi divergences

PubMed Central

Kouh, Minjoon; Sharpee, Tatyana O.

2009-01-01

This paper compares a family of methods for characterizing neural feature selectivity using natural stimuli in the framework of the linear-nonlinear model. In this model, the spike probability depends in a nonlinear way on a small number of stimulus dimensions. The relevant stimulus dimensions can be found by optimizing a Rényi divergence that quantifies a change in the stimulus distribution associated with the arrival of single spikes. Generally, good reconstructions can be obtained based on optimization of Rényi divergence of any order, even in the limit of small numbers of spikes. However, the smallest error is obtained when the Rényi divergence of order 1 is optimized. This type of optimization is equivalent to information maximization, and is shown to saturate the Cramér-Rao bound describing the smallest error allowed for any unbiased method. We also discuss conditions under which information maximization provides a convenient way to perform maximum likelihood estimation of linear-nonlinear models from neural data. PMID:19568981

Estimating linear-nonlinear models using Renyi divergences.

PubMed

Kouh, Minjoon; Sharpee, Tatyana O

2009-01-01

This article compares a family of methods for characterizing neural feature selectivity using natural stimuli in the framework of the linear-nonlinear model. In this model, the spike probability depends in a nonlinear way on a small number of stimulus dimensions. The relevant stimulus dimensions can be found by optimizing a Rényi divergence that quantifies a change in the stimulus distribution associated with the arrival of single spikes. Generally, good reconstructions can be obtained based on optimization of Rényi divergence of any order, even in the limit of small numbers of spikes. However, the smallest error is obtained when the Rényi divergence of order 1 is optimized. This type of optimization is equivalent to information maximization, and is shown to saturate the Cramer-Rao bound describing the smallest error allowed for any unbiased method. We also discuss conditions under which information maximization provides a convenient way to perform maximum likelihood estimation of linear-nonlinear models from neural data.

NGSLR's Measurement of the Retro-Reflector Array Response of Various LEO to GNSS Satellites

NASA Technical Reports Server (NTRS)

McGarry, Jan; Clarke, Christopher; Degnan, John; Donovan, Howard; Hall, Benjamin; Hovarth, Julie; Zagwodzki, Thomas

2012-01-01

"NASA's Next Generation Satellite Laser Ranging System (NGSLR) has successfully demonstrated daylight and nighttime tracking this year to s atellites from LEO to GNSS orbits, using a 7-8 arcsecond beam divergence, a 43% QE Hamamatsu MCP-PMT with single photon detection, a narrow field of view (11 arcseconds), and a 1 mJ per pulse 2kHz repetition rate laser. We have compared the actual return rates we are getting against the theoretical link calculations, using the known system confi guration parameters, an estimate of the sky transmission using locall y measured visibility, and signal processing to extract the signal from the background noise. We can achieve good agreement between theory and measurement in most passes by using an estimated pOinting error. We will s.()w the results of this comparison along with our conclusio ns."

A dawn to dusk electric field in the Jovian magnetosphere

NASA Technical Reports Server (NTRS)

Goertz, C. K.; Ip, W. I.

1983-01-01

It is shown that if Io-injected plasma is lost via a planetary wind-fixed Birkeland current system may result. This is due to the fact that the azimuthal centrifugal current flows across a density gradient produced by the loss of plasma through the planetary wind in the tail. The divergent centrifugal current is connected to field-aligned Birkeland currents which flow into the ionosphere at dawn and out of it at dusk. The closure currents in the ionosphere require a dawn to dusk electric field which at the orbit of Io is estimated to have a strength of 0.2 mV/m. However, the values of crucial parameters are not well known and the field at Io's orbit may well be significantly larger. Independent estimates derived from the local time asymmetry of the torus UV emission indicate a field of 1.5 mV/m.

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

Phylogeographic Analyses of American Black Bears (Ursus americanus) Suggest Four Glacial Refugia and Complex Patterns of Postglacial Admixture.

PubMed

Puckett, Emily E; Etter, Paul D; Johnson, Eric A; Eggert, Lori S

2015-09-01

Studies of species with continental distributions continue to identify intraspecific lineages despite continuous habitat. Lineages may form due to isolation by distance, adaptation, divergence across barriers, or genetic drift following range expansion. We investigated lineage diversification and admixture within American black bears (Ursus americanus) across their range using 22 k single nucleotide polymorphisms and mitochondrial DNA sequences. We identified three subcontinental nuclear clusters which we further divided into nine geographic regions: Alaskan (Alaska-East), eastern (Central Interior Highlands, Great Lakes, Northeast, Southeast), and western (Alaska-West, West, Pacific Coast, Southwest). We estimated that the western cluster diverged 67 ka, before eastern and Alaskan divergence 31 ka; these divergence dates contrasted with those from the mitochondrial genome where clades A and B diverged 1.07 Ma, and clades A-east and A-west diverged 169 ka. We combined estimates of divergence timing with hindcast species distribution models to infer glacial refugia for the species in Beringia, Pacific Northwest, Southwest, and Southeast. Our results show a complex arrangement of admixture due to expansion out of multiple refugia. The delineation of the genomic population clusters was inconsistent with the ranges for 16 previously described subspecies. Ranges for U. a. pugnax and U. a. cinnamomum were concordant with admixed clusters, calling into question how to order taxa below the species level. Additionally, our finding that U. a. floridanus has not diverged from U. a. americanus also suggests that morphology and genetics should be reanalyzed to assess taxonomic designations relevant to the conservation management of the species. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.For permissions please email: journals.permissions@oup.com.

Potential estimates for the p-Laplace system with data in divergence form

NASA Astrophysics Data System (ADS)

Cianchi, A.; Schwarzacher, S.

2018-07-01

A pointwise bound for local weak solutions to the p-Laplace system is established in terms of data on the right-hand side in divergence form. The relevant bound involves a Havin-Maz'ya-Wolff potential of the datum, and is a counterpart for data in divergence form of a classical result of [25], recently extended to systems in [28]. A local bound for oscillations is also provided. These results allow for a unified approach to regularity estimates for broad classes of norms, including Banach function norms (e.g. Lebesgue, Lorentz and Orlicz norms), and norms depending on the oscillation of functions (e.g. Hölder, BMO and, more generally, Campanato type norms). In particular, new regularity properties are exhibited, and well-known results are easily recovered.

PopHuman: the human population genomics browser.

PubMed

Casillas, Sònia; Mulet, Roger; Villegas-Mirón, Pablo; Hervas, Sergi; Sanz, Esteve; Velasco, Daniel; Bertranpetit, Jaume; Laayouni, Hafid; Barbadilla, Antonio

2018-01-04

The 1000 Genomes Project (1000GP) represents the most comprehensive world-wide nucleotide variation data set so far in humans, providing the sequencing and analysis of 2504 genomes from 26 populations and reporting >84 million variants. The availability of this sequence data provides the human lineage with an invaluable resource for population genomics studies, allowing the testing of molecular population genetics hypotheses and eventually the understanding of the evolutionary dynamics of genetic variation in human populations. Here we present PopHuman, a new population genomics-oriented genome browser based on JBrowse that allows the interactive visualization and retrieval of an extensive inventory of population genetics metrics. Efficient and reliable parameter estimates have been computed using a novel pipeline that faces the unique features and limitations of the 1000GP data, and include a battery of nucleotide variation measures, divergence and linkage disequilibrium parameters, as well as different tests of neutrality, estimated in non-overlapping windows along the chromosomes and in annotated genes for all 26 populations of the 1000GP. PopHuman is open and freely available at http://pophuman.uab.cat. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Volatilisation and competing processes computed for a pesticide applied to plants in a wind tunnel system.

PubMed

Leistra, Minze; Wolters, André; van den Berg, Frederik

2008-06-01

Volatilisation of pesticides from crop canopies can be an important emission pathway. In addition to pesticide properties, competing processes in the canopy and environmental conditions play a part. A computation model is being developed to simulate the processes, but only some of the input data can be obtained directly from the literature. Three well-defined experiments on the volatilisation of radiolabelled parathion-methyl (as example compound) from plants in a wind tunnel system were simulated with the computation model. Missing parameter values were estimated by calibration against the experimental results. The resulting thickness of the air boundary layer, rate of plant penetation and rate of phototransformation were compared with a diversity of literature data. The sequence of importance of the canopy processes was: volatilisation > plant penetration > phototransformation. Computer simulation of wind tunnel experiments, with radiolabelled pesticide sprayed on plants, yields values for the rate coefficients of processes at the plant surface. As some input data for simulations are not required in the framework of registration procedures, attempts to estimate missing parameter values on the basis of divergent experimental results have to be continued. Copyright (c) 2008 Society of Chemical Industry.

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.

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.

More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure.

PubMed

Stone, Anne C; Battistuzzi, Fabia U; Kubatko, Laura S; Perry, George H; Trudeau, Evan; Lin, Hsiuman; Kumar, Sudhir

2010-10-27

Here, we report the sequencing and analysis of eight complete mitochondrial genomes of chimpanzees (Pan troglodytes) from each of the three established subspecies (P. t. troglodytes, P. t. schweinfurthii and P. t. verus) and the proposed fourth subspecies (P. t. ellioti). Our population genetic analyses are consistent with neutral patterns of evolution that have been shaped by demography. The high levels of mtDNA diversity in western chimpanzees are unlike those seen at nuclear loci, which may reflect a demographic history of greater female to male effective population sizes possibly owing to the characteristics of the founding population. By using relaxed-clock methods, we have inferred a timetree of chimpanzee species and subspecies. The absolute divergence times vary based on the methods and calibration used, but relative divergence times show extensive uniformity. Overall, mtDNA produces consistently older times than those known from nuclear markers, a discrepancy that is reduced significantly by explicitly accounting for chimpanzee population structures in time estimation. Assuming the human-chimpanzee split to be between 7 and 5 Ma, chimpanzee time estimates are 2.1-1.5, 1.1-0.76 and 0.25-0.18 Ma for the chimpanzee/bonobo, western/(eastern + central) and eastern/central chimpanzee divergences, respectively.

Phylogeography of the Western Lyresnake (Trimorphodon biscutatus): testing aridland biogeographical hypotheses across the Nearctic-Neotropical transition.

PubMed

Devitt, Thomas J

2006-12-01

The Western Lyresnake (Trimorphodon biscutatus) is a widespread, polytypic taxon inhabiting arid regions from the warm deserts of the southwestern United States southward along the Pacific versant of Mexico to the tropical deciduous forests of Mesoamerica. This broadly distributed species provides a unique opportunity to evaluate a priori biogeographical hypotheses spanning two major distinct biogeographical realms (the Nearctic and Neotropical) that are usually treated separately in phylogeographical analyses. I investigated the phylogeography of T. biscutatus using maximum likelihood and Bayesian phylogenetic analysis of mitochondrial DNA (mtDNA) from across this species' range. Phylogenetic analyses recovered five well-supported clades whose boundaries are concordant with existing geographical barriers, a pattern consistent with a model of vicariant allopatric divergence. Assuming a vicariance model, divergence times between mitochondrial lineages were estimated using Bayesian relaxed molecular clock methods calibrated using geological information from putative vicariant events. Divergence time point estimates were bounded by broad confidence intervals, and thus these highly conservative estimates should be considered tentative hypotheses at best. Comparison of mtDNA lineages and taxa traditionally recognized as subspecies based on morphology suggest this taxon is comprised of multiple independent lineages at various stages of divergence, ranging from putative secondary contact and hybridization to sympatry of 'subspecies'.

An offline approach for output-only Bayesian identification of stochastic nonlinear systems using unscented Kalman filtering

NASA Astrophysics Data System (ADS)

Erazo, Kalil; Nagarajaiah, Satish

2017-06-01

In this paper an offline approach for output-only Bayesian identification of stochastic nonlinear systems is presented. The approach is based on a re-parameterization of the joint posterior distribution of the parameters that define a postulated state-space stochastic model class. In the re-parameterization the state predictive distribution is included, marginalized, and estimated recursively in a state estimation step using an unscented Kalman filter, bypassing state augmentation as required by existing online methods. In applications expectations of functions of the parameters are of interest, which requires the evaluation of potentially high-dimensional integrals; Markov chain Monte Carlo is adopted to sample the posterior distribution and estimate the expectations. The proposed approach is suitable for nonlinear systems subjected to non-stationary inputs whose realization is unknown, and that are modeled as stochastic processes. Numerical verification and experimental validation examples illustrate the effectiveness and advantages of the approach, including: (i) an increased numerical stability with respect to augmented-state unscented Kalman filtering, avoiding divergence of the estimates when the forcing input is unmeasured; (ii) the ability to handle arbitrary prior and posterior distributions. The experimental validation of the approach is conducted using data from a large-scale structure tested on a shake table. It is shown that the approach is robust to inherent modeling errors in the description of the system and forcing input, providing accurate prediction of the dynamic response when the excitation history is unknown.

Divergence in Siblings' Adult Attachment Security: Potential Contributors and Consequences

ERIC Educational Resources Information Center

Fortuna, Keren

2009-01-01

Previous research has revealed only modest concordance in attachment security between siblings during childhood and adolescence. The first goal of this dissertation was to estimate sibling concordance in adult attachment security and identify factors contributing to divergence. The Adult Attachment Interview (AAI) was administered to young adult…

Dimensional regularization of the IR divergences in the Fokker action of point-particle binaries at the fourth post-Newtonian order

NASA Astrophysics Data System (ADS)

Bernard, Laura; Blanchet, Luc; Bohé, Alejandro; Faye, Guillaume; Marsat, Sylvain

2017-11-01

The Fokker action of point-particle binaries at the fourth post-Newtonian (4PN) approximation of general relativity has been determined previously. However two ambiguity parameters associated with infrared (IR) divergencies of spatial integrals had to be introduced. These two parameters were fixed by comparison with gravitational self-force (GSF) calculations of the conserved energy and periastron advance for circular orbits in the test-mass limit. In the present paper together with a companion paper, we determine both these ambiguities from first principle, by means of dimensional regularization. Our computation is thus entirely defined within the dimensional regularization scheme, for treating at once the IR and ultra-violet (UV) divergencies. In particular, we obtain crucial contributions coming from the Einstein-Hilbert part of the action and from the nonlocal tail term in arbitrary dimensions, which resolve the ambiguities.

DNA barcoding reveals species level divergence between populations of the microhylid frog genus Arcovomer (Anura: Microhylidae) in the Atlantic Rainforest of southeastern Brazil.

PubMed

Jennings, W Bryan; Wogel, Henrique; Bilate, Marcos; Salles, Rodrigo de O L; Buckup, Paulo A

2016-09-01

The microhylid frogs belonging to the genus Arcovomer have been reported from lowland Atlantic Rainforest in the Brazilian states of Espírito Santo, Rio de Janeiro, and São Paulo. Here, we use DNA barcoding to assess levels of genetic divergence between apparently isolated populations in Espírito Santo and Rio de Janeiro. Our mtDNA data consisting of cytochrome oxidase subunit I (COI) nucleotide sequences reveals 13.2% uncorrected and 30.4% TIM2 + I + Γ corrected genetic divergences between these two populations. This level of divergence exceeds the suggested 10% uncorrected divergence threshold for elevating amphibian populations to candidate species using this marker, which implies that the Espírito Santo population is a species distinct from Arcovomer passarellii. Calibration of our model-corrected sequence divergence estimates suggests that the time of population divergence falls between 12 and 29 million years ago.

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.

Functional Bregman Divergence and Bayesian Estimation of Distributions (Preprint)

DTIC Science & Technology

2008-01-01

shows that if the set of possible minimizers A includes EPF [F ], then g∗ = EPF [F ] minimizes the expectation of any Bregman divergence. Note the theorem...probability distribution PF defined over the set M. Let A be a set of functions that includes EPF [F ] if it exists. Suppose the function g∗ minimizes...the expected Bregman divergence between the random function F and any function g ∈ A such that g∗ = arg inf g∈A EPF [dφ(F, g)]. Then, if g∗ exists

Atmospheric Flux Computations in Complex Terrain

NASA Technical Reports Server (NTRS)

Smith, Paul L.; Kopp, Fred J.; Orville, Harold D.

2000-01-01

The greatest challenges in applying atmospheric water budget expressions are in determining the divergence and evapotranspiration terms. The evapotranspiration problem is ubiquitous, and critical issues of spatial and temporal resolution commonly arise in establishing the divergence term. In complex terrain, further difficulties crop up in using typical data on atmospheric profiles of water vapor and wind to estimate the divergence term. Those difficulties are the subject of this paper; considerations related to topographic variations both along and normal to the flow direction are treated.

Estimation of population divergence times from non-overlapping genomic sequences: examples from dogs and wolves.

PubMed

Skoglund, Pontus; Götherström, Anders; Jakobsson, Mattias

2011-04-01

Despite recent technological advances in DNA sequencing, incomplete coverage remains to be an issue in population genomics, in particular for studies that include ancient samples. Here, we describe an approach to estimate population divergence times for non-overlapping sequence data that is based on probabilities of different genealogical topologies under a structured coalescent model. We show that the approach can be adapted to accommodate common problems such as sequencing errors and postmortem nucleotide misincorporations, and we use simulations to investigate biases involved with estimating genealogical topologies from empirical data. The approach relies on three reference genomes and should be particularly useful for future analysis of genomic data that comprise of nonoverlapping sets of sequences, potentially from different points in time. We applied the method to shotgun sequence data from an ancient wolf together with extant dogs and wolves and found striking resemblance to previously described fine-scale population structure among dog breeds. When comparing modern dogs to four geographically distinct wolves, we find that the divergence time between dogs and an Indian wolf is smallest, followed by the divergence times to a Chinese wolf and a Spanish wolf, and a relatively long divergence time to an Alaskan wolf, suggesting that the origin of modern dogs is somewhere in Eurasia, potentially southern Asia. We find that less than two-thirds of all loci in the boxer and poodle genomes are more similar to each other than to a modern gray wolf and that--assuming complete isolation without gene flow--the divergence time between gray wolves and modern European dogs extends to 3,500 generations before the present, corresponding to approximately 10,000 years ago (95% confidence interval [CI]: 9,000-13,000). We explicitly study the effect of gene flow between dogs and wolves on our estimates and show that a low rate of gene flow is compatible with an even earlier domestication date ∼30,000 years ago (95% CI: 15,000-90,000). This observation is in agreement with recent archaeological findings and indicates that human behavior necessary for domestication of wild animals could have appeared much earlier than the development of agriculture.

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.

Founding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska

USGS Publications Warehouse

Ramstad, K.M.; Woody, C.A.; Sage, G.K.; Allendorf, F.W.

2004-01-01

Bottlenecks can have lasting effects on genetic population structure that obscure patterns of contemporary gene flow and drift. Sockeye salmon are vulnerable to bottleneck effects because they are a highly structured species with excellent colonizing abilities and often occupy geologically young habitats. We describe genetic divergence among and genetic variation within spawning populations of sockeye salmon throughout the Lake Clark area of Alaska. Fin tissue was collected from sockeye salmon representing 15 spawning populations of Lake Clark, Six-mile Lake, and Lake Iliamna. Allele frequencies differed significantly at 11 microsatellite loci in 96 of 105 pairwise population comparisons. Pairwise estimates of FST ranged from zero to 0.089. Six-mile Lake and Lake Clark populations have historically been grouped together for management purposes and are geographically proximate. However, Six-mile Lake populations are genetically similar to Lake Iliamna populations and are divergent from Lake Clark populations. The reduced allelic diversity and strong divergence of Lake Clark populations relative to Six-mile Lake and Lake Iliamna populations suggest a bottleneck associated with the colonization of Lake Clark by sockeye salmon. Geographic distance and spawning habitat differences apparently do not contribute to isolation and divergence among populations. However, temporal isolation based on spawning time and founder effects associated with ongoing glacial retreat and colonization of new spawning habitats contribute to the genetic population structure of Lake Clark sock-eye salmon. Nonequilibrium conditions and the strong influence of genetic drift caution against using estimates of divergence to estimate gene flow among populations of Lake Clark sockeye salmon.

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.

Rapid molecular evolution of human bocavirus revealed by Bayesian coalescent inference.

PubMed

Zehender, Gianguglielmo; De Maddalena, Chiara; Canuti, Marta; Zappa, Alessandra; Amendola, Antonella; Lai, Alessia; Galli, Massimo; Tanzi, Elisabetta

2010-03-01

Human bocavirus (HBoV) is a linear single-stranded DNA virus belonging to the Parvoviridae family that has recently been isolated from the upper respiratory tract of children with acute respiratory infection. All of the strains observed so far segregate into two genotypes (1 and 2) with a low level of polymorphism. Given the recent description of the infection and the lack of epidemiological and molecular data, we estimated the virus's rates of molecular evolution and population dynamics. A dataset of forty-nine dated VP2 sequences, including also eight new isolates obtained from pharyngeal swabs of Italian patients with acute respiratory tract infections, was submitted to phylogenetic analysis. The model parameters, evolutionary rates and population dynamics were co-estimated using a Bayesian Markov Chain Monte Carlo approach, and site-specific positive and negative selection was also investigated. Recombination was investigated by seven different methods and one suspected recombinant strain was excluded from further analysis. The estimated mean evolutionary rate of HBoV was 8.6x10(-4)subs/site/year, and that of the 1st+2nd codon positions was more than 15 times less than that of the 3rd codon position. Viral population dynamics analysis revealed that the two known genotypes diverged recently (mean tMRCA: 24 years), and that the epidemic due to HBoV genotype 2 grew exponentially at a rate of 1.01year(-1). Selection analysis of the partial VP2 showed that 8.5% of sites were under significant negative pressure and the absence of positive selection. Our results show that, like other parvoviruses, HBoV is characterised by a rapid evolution. The low level of polymorphism is probably due to a relatively recent divergence between the circulating genotypes and strong purifying selection acting on viral antigens.

Exploration of DGVM Parameter Solution Space Using Simulated Annealing: Implications for Forecast Uncertainties

NASA Astrophysics Data System (ADS)

Wells, J. R.; Kim, J. B.

2011-12-01

Parameters in dynamic global vegetation models (DGVMs) are thought to be weakly constrained and can be a significant source of errors and uncertainties. DGVMs use between 5 and 26 plant functional types (PFTs) to represent the average plant life form in each simulated plot, and each PFT typically has a dozen or more parameters that define the way it uses resource and responds to the simulated growing environment. Sensitivity analysis explores how varying parameters affects the output, but does not do a full exploration of the parameter solution space. The solution space for DGVM parameter values are thought to be complex and non-linear; and multiple sets of acceptable parameters may exist. In published studies, PFT parameters are estimated from published literature, and often a parameter value is estimated from a single published value. Further, the parameters are "tuned" using somewhat arbitrary, "trial-and-error" methods. BIOMAP is a new DGVM created by fusing MAPSS biogeography model with Biome-BGC. It represents the vegetation of North America using 26 PFTs. We are using simulated annealing, a global search method, to systematically and objectively explore the solution space for the BIOMAP PFTs and system parameters important for plant water use. We defined the boundaries of the solution space by obtaining maximum and minimum values from published literature, and where those were not available, using +/-20% of current values. We used stratified random sampling to select a set of grid cells representing the vegetation of the conterminous USA. Simulated annealing algorithm is applied to the parameters for spin-up and a transient run during the historical period 1961-1990. A set of parameter values is considered acceptable if the associated simulation run produces a modern potential vegetation distribution map that is as accurate as one produced by trial-and-error calibration. We expect to confirm that the solution space is non-linear and complex, and that multiple acceptable parameter sets exist. Further we expect to demonstrate that the multiple parameter sets produce significantly divergent future forecasts in NEP, C storage, and ET and runoff; and thereby identify a highly important source of DGVM uncertainty

Analysis of the methods for assessing socio-economic development level of urban areas

NASA Astrophysics Data System (ADS)

Popova, Olga; Bogacheva, Elena

2017-01-01

The present paper provides a targeted analysis of current approaches (ratings) in the assessment of socio-economic development of urban areas. The survey focuses on identifying standardized methodologies to area assessment techniques formation that will result in developing the system of intelligent monitoring, dispatching, building management, scheduling and effective management of an administrative-territorial unit. This system is characterized by complex hierarchical structure, including tangible and intangible properties (parameters, attributes). Investigating the abovementioned methods should increase the administrative-territorial unit's attractiveness for investors and residence. The research aims at studying methods for evaluating socio-economic development level of the Russian Federation territories. Experimental and theoretical territory estimating methods were revealed. Complex analysis of the characteristics of the areas was carried out and evaluation parameters were determined. Integral indicators (resulting rating criteria values) as well as the overall rankings (parameters, characteristics) were analyzed. The inventory of the most widely used partial indicators (parameters, characteristics) of urban areas was revealed. The resulting criteria of rating values homogeneity were verified and confirmed by determining the root mean square deviation, i.e. divergence of indices. The principal shortcomings of assessment methodologies were revealed. The assessment methods with enhanced effectiveness and homogeneity were proposed.

On how to avoid input and structural uncertainties corrupt the inference of hydrological parameters using a Bayesian framework

NASA Astrophysics Data System (ADS)

Hernández, Mario R.; Francés, Félix

2015-04-01

One phase of the hydrological models implementation process, significantly contributing to the hydrological predictions uncertainty, is the calibration phase in which values of the unknown model parameters are tuned by optimizing an objective function. An unsuitable error model (e.g. Standard Least Squares or SLS) introduces noise into the estimation of the parameters. The main sources of this noise are the input errors and the hydrological model structural deficiencies. Thus, the biased calibrated parameters cause the divergence model phenomenon, where the errors variance of the (spatially and temporally) forecasted flows far exceeds the errors variance in the fitting period, and provoke the loss of part or all of the physical meaning of the modeled processes. In other words, yielding a calibrated hydrological model which works well, but not for the right reasons. Besides, an unsuitable error model yields a non-reliable predictive uncertainty assessment. Hence, with the aim of prevent all these undesirable effects, this research focuses on the Bayesian joint inference (BJI) of both the hydrological and error model parameters, considering a general additive (GA) error model that allows for correlation, non-stationarity (in variance and bias) and non-normality of model residuals. As hydrological model, it has been used a conceptual distributed model called TETIS, with a particular split structure of the effective model parameters. Bayesian inference has been performed with the aid of a Markov Chain Monte Carlo (MCMC) algorithm called Dream-ZS. MCMC algorithm quantifies the uncertainty of the hydrological and error model parameters by getting the joint posterior probability distribution, conditioned on the observed flows. The BJI methodology is a very powerful and reliable tool, but it must be used correctly this is, if non-stationarity in errors variance and bias is modeled, the Total Laws must be taken into account. The results of this research show that the application of BJI with a GA error model outperforms the hydrological parameters robustness (diminishing the divergence model phenomenon) and improves the reliability of the streamflow predictive distribution, in respect of the results of a bad error model as SLS. Finally, the most likely prediction in a validation period, for both BJI+GA and SLS error models shows a similar performance.

Intercontinental divergence in the Populus-associated ectomycorrhizal fungus, Tricholoma populinum.

PubMed

Grubisha, Lisa C; Levsen, Nicholas; Olson, Matthew S; Taylor, D Lee

2012-04-01

The ectomycorrhizal fungus Tricholoma populinum is host-specific with Populus species. T. populinum has wind-dispersed progagules and may be capable of long-distance dispersal. In this study, we tested the hypothesis of a panmictic population between Scandinavia and North America. DNA sequences from five nuclear loci were used to assess phylogeographic structure and nucleotide divergence between continents. Tricholoma populinum was composed of Scandinavian and North American lineages with complete absence of shared haplotypes and only one shared nucleotide mutation. Divergence of these lineages was estimated at approx. 1.7-1.0 million yr ago (Ma), which occurred after the estimated divergence of host species Populus tremula and Populus balsamifera/Populus trichocarpa at 5 Ma. Phylogeographic structure was not observed within Scandinavian or North American lineages of T. populinum. Intercontinental divergence appears to have resulted from either allopatric isolation; a recent, rare long-distance dispersal founding event followed by genetic drift; or the response in an obligate mycorrhizal fungus with a narrow host range to contractions and expansion of host distribution during glacial and interglacial episodes within continents. Understanding present genetic variation in populations is important for predicting how obligate symbiotic fungi will adapt to present and future changing climatic conditions. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

Uncertainty Quantification using Epi-Splines and Soft Information

DTIC Science & Technology

2012-06-01

use of the Kullback - Leibler divergence measure. The Kullback - Leibler ...to illustrate the application of soft information related to the Kullback - Leibler (KL) divergence discussed in Chapter 2. The idea behind apply- ing... information for the estimation of system performance density functions in order to quantify uncertainty. We conduct empirical testing of

Integrating paleoecology and genetics of bird populations in two sky island archipelagos

PubMed Central

McCormack, John E; Bowen, Bonnie S; Smith, Thomas B

2008-01-01

Background Genetic tests of paleoecological hypotheses have been rare, partly because recent genetic divergence is difficult to detect and time. According to fossil plant data, continuous woodland in the southwestern USA and northern Mexico became fragmented during the last 10,000 years, as warming caused cool-adapted species to retreat to high elevations. Most genetic studies of resulting 'sky islands' have either failed to detect recent divergence or have found discordant evidence for ancient divergence. We test this paleoecological hypothesis for the region with intraspecific mitochondrial DNA and microsatellite data from sky-island populations of a sedentary bird, the Mexican jay (Aphelocoma ultramarina). We predicted that populations on different sky islands would share common, ancestral alleles that existed during the last glaciation, but that populations on each sky island, owing to their isolation, would contain unique variants of postglacial origin. We also predicted that divergence times estimated from corrected genetic distance and a coalescence model would post-date the last glacial maximum. Results Our results provide multiple independent lines of support for postglacial divergence, with the predicted pattern of shared and unique mitochondrial DNA haplotypes appearing in two independent sky-island archipelagos, and most estimates of divergence time based on corrected genetic distance post-dating the last glacial maximum. Likewise, an isolation model based on multilocus gene coalescence indicated postglacial divergence of five pairs of sky islands. In contrast to their similar recent histories, the two archipelagos had dissimilar historical patterns in that sky islands in Arizona showed evidence for older divergence, suggesting different responses to the last glaciation. Conclusion This study is one of the first to provide explicit support from genetic data for a postglacial divergence scenario predicted by one of the best paleoecological records in the world. Our results demonstrate that sky islands act as generators of genetic diversity at both recent and historical timescales and underscore the importance of thorough sampling and the use of loci with fast mutation rates to studies that test hypotheses concerning recent genetic divergence. PMID:18588695

On the properties of circular beams: normalization, Laguerre-Gauss expansion, and free-space divergence.

PubMed

Vallone, Giuseppe

2015-04-15

Circular beams were introduced as a very general solution to the paraxial wave equation carrying orbital angular momentum. Here, we study their properties by looking at their normalization and their expansion in terms of Laguerre-Gauss modes. We also study their far-field divergence and, for particular cases of the beam parameters, their possible experimental generation.

Observation of divergent-beam X-ray diffraction from a crystal of diamond using synchrotron radiation.

PubMed

Glazer, A M; Collins, S P; Zekria, D; Liu, J; Golshan, M

2004-03-01

In 1947 Kathleen Lonsdale conducted a series of experiments on X-ray diffraction using a divergent beam external to a crystal sample. Unlike the Kossel technique, where divergent X-rays are excited by the presence of fluorescing atoms within the crystal, the use of an external divergent source made it possible to study non-fluorescing crystals. The resulting photographs not only illustrated the complexity of X-ray diffraction from crystals in a truly beautiful way, but also demonstrated unprecedented experimental precision. This long-forgotten work is repeated here using a synchrotron radiation source and, once again, considerable merit is found in Lonsdale's technique. The results of this experiment suggest that, through the use of modern 'third-generation' synchrotron sources, divergent-beam diffraction could soon enjoy a renaissance for high-precision lattice-parameter determination and the study of crystal perfection.

Evolution of a Planktonic Foraminifer during Environmental Changes in the Tropical Oceans.

PubMed

Ujiié, Yurika; Ishitani, Yoshiyuki

2016-01-01

Ecological adaptation to environmental changes is a strong driver of evolution, enabling speciation of pelagic plankton in the open ocean without the presence of effective physical barriers to gene flow. The tropical ocean environment, which plays an important role in shaping marine biodiversity, has drastically and frequently changed since the Pliocene. Nevertheless, the evolutionary history of tropical pelagic plankton has been poorly understood, as phylogeographic investigations are still in the developing state and paleontological approaches are insufficient to obtain a sequential record from the deep-sea sediments. The planktonic foraminifer Pulleniatina obliquiloculata is widely distributed in the tropical area throughout the world's oceans, and its phylogeography is well established. It is thus one of the best candidates to examine how past environmental changes may have shifted the spatial distribution and affected the diversification of tropical pelagic plankton. Such an examination requires the divergence history of the planktonic foraminifers, yet the gene marker (partial small subunit (SSU) rDNA) previously used for phylogeographic studies was not powerful enough to achieve a high accuracy in estimating the divergence times. The present study focuses on improving the precision of divergence time estimates for the splits between sibling species (genetic types) of planktonic foraminifers by increasing the number of genes as well as the number of nucleotide bases used for molecular clock estimates. We have amplified the entire coding regions of two ribosomal RNA genes (SSU rDNA and large subunit (LSU) rDNA) of three genetic types of P. obliquiloculata and two closely related species for the first time and applied them to the Bayesian relaxed clock method. The comparison of the credible intervals of the four datasets consisting either of sequences of the partial SSU rDNA, the complete SSU rDNA, LSU rDNA, or a combination of both genes (SSU+LSU) clearly demonstrated that the two-gene dataset improved the accuracy of divergence time estimates. The P. obliquiloculata lineage diverged twice, first at the end of the Pliocene (3.1 Ma) and again in the middle Pleistocene (1.4 Ma). Both timings coincided with the environmental changes, which indirectly involved geographic separation of populations. The habitat of P. obliquiloculata was expanded toward the higher latitudinal zones during the stable warm periods and subsequently placed on the steep environmental gradients following the global cooling. Different environmental conditions in the stable warm tropics and unstable higher latitudes may have triggered ecological divergence among the populations, leading to adaptive differentiation and eventually speciation. A comprehensive analysis of divergence time estimates combined with phylogeography enabled us to reveal the evolutionary history of the pelagic plankton and to find the potential paleoenvironmental events, which could have changed their biogeography and ecology.

Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds

USGS Publications Warehouse

Oyler-McCance, Sara J.; Cornman, Robert S.; Kenneth L. Jones,; Fike, Jennifer

2015-01-01

Sex chromosomes contribute disproportionately to species boundaries as they diverge faster than autosomes and often have reduced diversity. Their hemizygous nature contributes to faster divergence and reduced diversity, as do some types of selection. In birds, other factors (mating system and bottlenecks) can further decrease the effective population size of Z-linked loci and accelerate divergence (Fast-Z). We assessed Z-linked divergence and effective population sizes for two polygynous sage-grouse species and compared them to estimates from birds with various mating systems. We found lower diversity and higher FST for Z-linked loci than for autosomes, as expected. The πZ/πA ratio was 0.38 in Centrocercus minimus, 0.48 in Centrocercus urophasianus and 0.59 in a diverged, parapatric population of C. urophasianus, a broad range given the mating system among these groups is presumably equivalent. The full data set had unequal males and females across groups, so we compared an equally balanced reduced set of C. minimus and individuals pooled from both C. urophasianus subgroups recovering similar estimates: 0.54 for C. urophasianus and 0.38 for C. minimus. We provide further evidence that NeZ/NeA in birds is often lower than expected under random mating or monogamy. The lower ratio in C. minimus could be a consequence of stronger selection or drift acting on Z loci during speciation, as this species differs strongly from C. urophasianus in sexually selected characters with minimal mitochondrial divergence. As C. minimus also exhibited lower genomic diversity, it is possible that a more severe demographic history may contribute to its lower ratio.

Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds.

PubMed

Oyler-McCance, S J; Cornman, R S; Jones, K L; Fike, J A

2015-11-01

Sex chromosomes contribute disproportionately to species boundaries as they diverge faster than autosomes and often have reduced diversity. Their hemizygous nature contributes to faster divergence and reduced diversity, as do some types of selection. In birds, other factors (mating system and bottlenecks) can further decrease the effective population size of Z-linked loci and accelerate divergence (Fast-Z). We assessed Z-linked divergence and effective population sizes for two polygynous sage-grouse species and compared them to estimates from birds with various mating systems. We found lower diversity and higher FST for Z-linked loci than for autosomes, as expected. The π(Z)/π(A) ratio was 0.38 in Centrocercus minimus, 0.48 in Centrocercus urophasianus and 0.59 in a diverged, parapatric population of C. urophasianus, a broad range given the mating system among these groups is presumably equivalent. The full data set had unequal males and females across groups, so we compared an equally balanced reduced set of C. minimus and individuals pooled from both C. urophasianus subgroups recovering similar estimates: 0.54 for C. urophasianus and 0.38 for C. minimus. We provide further evidence that N(eZ)/N(eA) in birds is often lower than expected under random mating or monogamy. The lower ratio in C. minimus could be a consequence of stronger selection or drift acting on Z loci during speciation, as this species differs strongly from C. urophasianus in sexually selected characters with minimal mitochondrial divergence. As C. minimus also exhibited lower genomic diversity, it is possible that a more severe demographic history may contribute to its lower ratio.

Analysis of sea ice dynamics

NASA Technical Reports Server (NTRS)

Zwally, J.

1988-01-01

The ongoing work has established the basis for using multiyear sea ice concentrations from SMMR passive microwave for studies of largescale advection and convergence/divergence of the Arctic sea ice pack. Comparisons were made with numerical model simulations and buoy data showing qualitative agreement on daily to interannual time scales. Analysis of the 7-year SMMR data set shows significant interannual variations in the total area of multiyear ice. The scientific objective is to investigate the dynamics, mass balance, and interannual variability of the Arctic sea ice pack. The research emphasizes the direct application of sea ice parameters derived from passive microwave data (SMMR and SSMI) and collaborative studies using a sea ice dynamics model. The possible causes of observed interannual variations in the multiyear ice area are being examined. The relative effects of variations in the large scale advection and convergence/divergence within the ice pack on a regional and seasonal basis are investigated. The effects of anomolous atmospheric forcings are being examined, including the long-lived effects of synoptic events and monthly variations in the mean geostrophic winds. Estimates to be made will include the amount of new ice production within the ice pack during winter and the amount of ice exported from the pack.

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.

Analytical solutions for efficient interpretation of single-well push-pull tracer tests

NASA Astrophysics Data System (ADS)

Huang, Junqi; Christ, John A.; Goltz, Mark N.

2010-08-01

Single-well push-pull tracer tests have been used to characterize the extent, fate, and transport of subsurface contamination. Analytical solutions provide one alternative for interpreting test results. In this work, an exact analytical solution to two-dimensional equations describing the governing processes acting on a dissolved compound during a modified push-pull test (advection, longitudinal and transverse dispersion, first-order decay, and rate-limited sorption/partitioning in steady, divergent, and convergent flow fields) is developed. The coupling of this solution with inverse modeling to estimate aquifer parameters provides an efficient methodology for subsurface characterization. Synthetic data for single-well push-pull tests are employed to demonstrate the utility of the solution for determining (1) estimates of aquifer longitudinal and transverse dispersivities, (2) sorption distribution coefficients and rate constants, and (3) non-aqueous phase liquid (NAPL) saturations. Employment of the solution to estimate NAPL saturations based on partitioning and non-partitioning tracers is designed to overcome limitations of previous efforts by including rate-limited mass transfer. This solution provides a new tool for use by practitioners when interpreting single-well push-pull test results.

A dating success story: genomes and fossils converge on placental mammal origins

PubMed Central

2012-01-01

The timing of the placental mammal radiation has been a source of contention for decades. The fossil record of mammals extends over 200 million years, but no confirmed placental mammal fossils are known prior to 64 million years ago, which is approximately 1.5 million years after the Cretaceous-Paleogene (K-Pg) mass extinction that saw the end of non-avian dinosaurs. Thus, it came as a great surprise when the first published molecular clock studies suggested that placental mammals originated instead far back in the Cretaceous, in some cases doubling divergence estimates based on fossils. In the last few decades, more than a hundred new genera of Mesozoic mammals have been discovered, and molecular divergence studies have grown from simple clock-like models applied to a few genes to sophisticated analyses of entire genomes. Yet, molecular and fossil-based divergence estimates for placental mammal origins have remained remote, with knock-on effects for macro-scale reconstructions of mammal evolution. A few recent molecular studies have begun to converge with fossil-based estimates, and a new phylogenomic study in particular shows that the palaeontological record was mostly correct; most placental mammal orders diversified after the K-Pg mass extinction. While a small gap still remains for Late Cretaceous supraordinal divergences, this study has significantly improved the congruence between molecular and palaeontological data and heralds a broader integration of these fields of evolutionary science. PMID:22883371

Divergence times and the evolution of morphological complexity in an early land plant lineage (Marchantiopsida) with a slow molecular rate.

PubMed

Villarreal A, Juan Carlos; Crandall-Stotler, Barbara J; Hart, Michelle L; Long, David G; Forrest, Laura L

2016-03-01

We present a complete generic-level phylogeny of the complex thalloid liverworts, a lineage that includes the model system Marchantia polymorpha. The complex thalloids are remarkable for their slow rate of molecular evolution and for being the only extant plant lineage to differentiate gas exchange tissues in the gametophyte generation. We estimated the divergence times and analyzed the evolutionary trends of morphological traits, including air chambers, rhizoids and specialized reproductive structures. A multilocus dataset was analyzed using maximum likelihood and Bayesian approaches. Relative rates were estimated using local clocks. Our phylogeny cements the early branching in complex thalloids. Marchantia is supported in one of the earliest divergent lineages. The rate of evolution in organellar loci is slower than for other liverwort lineages, except for two annual lineages. Most genera diverged in the Cretaceous. Marchantia polymorpha diversified in the Late Miocene, giving a minimum age estimate for the evolution of its sex chromosomes. The complex thalloid ancestor, excluding Blasiales, is reconstructed as a plant with a carpocephalum, with filament-less air chambers opening via compound pores, and without pegged rhizoids. Our comprehensive study of the group provides a temporal framework for the analysis of the evolution of critical traits essential for plants during land colonization. © 2015 Royal Botanic Garden Edinburgh. New Phytologist © 2015 New Phytologist Trust.

Waveguide and active region structure optimization for low-divergence InAs/InGaAs quantum dot comb lasers

NASA Astrophysics Data System (ADS)

Korenev, Vladimir V.; Savelyev, Artem V.; Zhukov, Alexey E.; Maximov, Mikhail V.; Omelchenko, Alexander V.

2015-05-01

Ways to improve beam divergence and energy consumption of quantum dot lasers emitting via the ground-state optical transitions by optimization of the key parameters of laser active region are discussed. It is shown that there exist an optimal cavity length, dispersion of inhomogeneous broadening and number of QD layers in active region allowing to obtain lasing spectrum of a given width at minimum injection current. The planar dielectric waveguide of the laser is optimized by analytical means for a better trade-off between high Γ-factor and low beam divergence.

LASER APPLICATIONS AND OTHER ASPECTS OF QUANTUM ELECTRONICS Measurement of angular parameters of divergent optical radiation by light diffraction on sound

NASA Astrophysics Data System (ADS)

Kotov, V. M.; Averin, S. V.; Shkerdin, G. N.

2010-12-01

A method is proposed to measure the scattering angle of optical radiation, the method employing two Bragg diffraction processes in which divergent optical radiation propagates close to the optical axis of a uniaxial crystal, while the acoustic wave — orthogonally to this axis. The method does not require additional angular tuning of the acousto-optic cell. We suggest using a mask to measure the light divergence that is larger than the angle of Bragg scattering. The method can be used to measure the size of the polished glass plate inhomogeneities.

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

Parameter Estimation with Entangled Photons Produced by Parametric Down-Conversion

NASA Technical Reports Server (NTRS)

Cable, Hugo; Durkin, Gabriel A.

2010-01-01

We explore the advantages offered by twin light beams produced in parametric down-conversion for precision measurement. The symmetry of these bipartite quantum states, even under losses, suggests that monitoring correlations between the divergent beams permits a high-precision inference of any symmetry-breaking effect, e.g., fiber birefringence. We show that the quantity of entanglement is not the key feature for such an instrument. In a lossless setting, scaling of precision at the ultimate "Heisenberg" limit is possible with photon counting alone. Even as photon losses approach 100% the precision is shot-noise limited, and we identify the crossover point between quantum and classical precision as a function of detected flux. The predicted hypersensitivity is demonstrated with a Bayesian simulation.

Parameter estimation with entangled photons produced by parametric down-conversion.

PubMed

Cable, Hugo; Durkin, Gabriel A

2010-07-02

We explore the advantages offered by twin light beams produced in parametric down-conversion for precision measurement. The symmetry of these bipartite quantum states, even under losses, suggests that monitoring correlations between the divergent beams permits a high-precision inference of any symmetry-breaking effect, e.g., fiber birefringence. We show that the quantity of entanglement is not the key feature for such an instrument. In a lossless setting, scaling of precision at the ultimate "Heisenberg" limit is possible with photon counting alone. Even as photon losses approach 100% the precision is shot-noise limited, and we identify the crossover point between quantum and classical precision as a function of detected flux. The predicted hypersensitivity is demonstrated with a Bayesian simulation.

The historical biogeography of the freshwater knifefishes using mitogenomic approaches: a mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha).

PubMed

Inoue, Jun G; Kumazawa, Yoshinori; Miya, Masaki; Nishida, Mutsumi

2009-06-01

The continental distributions of freshwater fishes in the family Notopteridae (Osteoglossomorpha) across Africa, India, and Southeast Asia constitute a long standing and enigmatic problem of freshwater biogeography. The migrational pathway of the Asian notopterids has been discussed in light of two competing schemes: the first posits recent transcontinental dispersal while the second relies on distributions being shaped by ancient vicariance associated with plate-tectonic events. In this study, we determined complete mitochondrial DNA sequences from 10 osteoglossomorph fishes to estimate phylogenetic relationships using partitioned Bayesian and maximum likelihood methods and divergence dates of the family Notopteridae with a partitioned Bayesian approach. We used six species representing the major lineages of the Notopteridae and seven species from the remaining osteoglossomorph families. Fourteen more-derived teleosts, nine basal actinopterygians, two coelacanths, and one shark were used as outgroups. Phylogenetic analyses indicated that the African and Asian notopterids formed a sister group to each other and that these notopterids were a sister to a clade comprising two African families (Mormyridae and Gymnarchidae). Estimated divergence time between the African and Asian notopterids dated back to the early Cretaceous when India-Madagascar separated from the African part of Gondwanaland. Thus, estimated time of divergence based on the molecular evidence is at odds with the recent dispersal model. It can be reconciled with the geological and paleontological evidence to support the vicariance model in which the Asian notopterids diverged from the African notopterids in Gondwanaland and migrated into Eurasia on the Indian subcontinent from the Cretaceous to the Tertiary. However, we could not exclude an alternative explanation that the African and Asian notopterids diverged in Pangea before its complete separation into Laurasia and Gondwanaland, to which these two lineages were later confined, respectively.

Contributions of divergent and nondivergent winds to the kinetic energy balance of a severe storm environment

NASA Technical Reports Server (NTRS)

Browning, P. A.; Fuelberg, H. E.

1983-01-01

Divergent and rotational components of the synoptic scale kinetic energy balance are presented using rawinsonde data at 3 and 6 h intervals from the Atmospheric Variability Experiment (AVE 4). Two intense thunderstorm complexes occurred during the period. Energy budgets are described for the entire computational region and for limited volumes that enclose and move with the convection. Although small in magnitude, the divergent wind component played an important role in the cross contour generation and horizontal flux divergence of kinetic energy. The importance of V sub D appears directly to the presence and intensity of convection within the area. Although K sub D usually comprised less than 10 percent of the total kinetic energy content within the storm environment, as much as 87 percent of the total horizontal flux divergence and 68 percent of the total cross contour generation was due to the divergent component in the upper atmosphere. Generation of kinetic energy by the divergent component appears to be a major factor in the creation of an upper level wind maximum on the poleward side of one of the complexes. A random error analysis is presented to assess confidence limits in the various energy parameters.

Interpretation of Flow Logs from Nevada Test Site Boreholes to Estimate Hydraulic Conductivity Using Numerical Simulations Constrained by Single-Well Aquifer Tests

USGS Publications Warehouse

Garcia, C. Amanda; Halford, Keith J.; Laczniak, Randell J.

2010-01-01

Hydraulic conductivities of volcanic and carbonate lithologic units at the Nevada Test Site were estimated from flow logs and aquifer-test data. Borehole flow and drawdown were integrated and interpreted using a radial, axisymmetric flow model, AnalyzeHOLE. This integrated approach is used because complex well completions and heterogeneous aquifers and confining units produce vertical flow in the annular space and aquifers adjacent to the wellbore. AnalyzeHOLE simulates vertical flow, in addition to horizontal flow, which accounts for converging flow toward screen ends and diverging flow toward transmissive intervals. Simulated aquifers and confining units uniformly are subdivided by depth into intervals in which the hydraulic conductivity is estimated with the Parameter ESTimation (PEST) software. Between 50 and 150 hydraulic-conductivity parameters were estimated by minimizing weighted differences between simulated and measured flow and drawdown. Transmissivity estimates from single-well or multiple-well aquifer tests were used to constrain estimates of hydraulic conductivity. The distribution of hydraulic conductivity within each lithology had a minimum variance because estimates were constrained with Tikhonov regularization. AnalyzeHOLE simulated hydraulic-conductivity estimates for lithologic units across screened and cased intervals are as much as 100 times less than those estimated using proportional flow-log analyses applied across screened intervals only. Smaller estimates of hydraulic conductivity for individual lithologic units are simulated because sections of the unit behind cased intervals of the wellbore are not assumed to be impermeable, and therefore, can contribute flow to the wellbore. Simulated hydraulic-conductivity estimates vary by more than three orders of magnitude across a lithologic unit, indicating a high degree of heterogeneity in volcanic and carbonate-rock units. The higher water transmitting potential of carbonate-rock units relative to volcanic-rock units is exemplified by the large difference in their estimated maximum hydraulic conductivity; 4,000 and 400 feet per day, respectively. Simulated minimum estimates of hydraulic conductivity are inexact and represent the lower detection limit of the method. Minimum thicknesses of lithologic intervals also were defined for comparing AnalyzeHOLE results to hydraulic properties in regional ground-water flow models.

Kernel and divergence techniques in high energy physics separations

NASA Astrophysics Data System (ADS)

Bouř, Petr; Kůs, Václav; Franc, Jiří

2017-10-01

Binary decision trees under the Bayesian decision technique are used for supervised classification of high-dimensional data. We present a great potential of adaptive kernel density estimation as the nested separation method of the supervised binary divergence decision tree. Also, we provide a proof of alternative computing approach for kernel estimates utilizing Fourier transform. Further, we apply our method to Monte Carlo data set from the particle accelerator Tevatron at DØ experiment in Fermilab and provide final top-antitop signal separation results. We have achieved up to 82 % AUC while using the restricted feature selection entering the signal separation procedure.

Spatial measurement in rotating magnetic field plasma acceleration method by using two-dimensional scanning instrument and thrust stand

NASA Astrophysics Data System (ADS)

Furukawa, T.; Takizawa, K.; Yano, K.; Kuwahara, D.; Shinohara, S.

2018-04-01

A two-dimensional scanning probe instrument has been developed to survey spatial plasma characteristics in our electrodeless plasma acceleration schemes. In particular, diagnostics of plasma parameters, e.g., plasma density, temperature, velocity, and excited magnetic field, are essential for elucidating physical phenomena since we have been concentrating on next generation plasma propulsion methods, e.g., Rotating Magnetic Field plasma acceleration method, by characterizing the plasma performance. Moreover, in order to estimate the thrust performance in our experimental scheme, we have also mounted a thrust stand, which has a target type, on this movable instrument, and scanned the axial profile of the thrust performance in the presence of the external magnetic field generated by using permanent magnets, so as to investigate the plasma captured in a stand area, considering the divergent field lines in the downstream region of a generation antenna. In this paper, we will introduce the novel measurement instrument and describe how to measure these parameters.

Application of a data assimilation method via an ensemble Kalman filter to reactive urea hydrolysis transport modeling

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

Juxiu Tong; Bill X. Hu; Hai Huang

2014-03-01

With growing importance of water resources in the world, remediations of anthropogenic contaminations due to reactive solute transport become even more important. A good understanding of reactive rate parameters such as kinetic parameters is the key to accurately predicting reactive solute transport processes and designing corresponding remediation schemes. For modeling reactive solute transport, it is very difficult to estimate chemical reaction rate parameters due to complex processes of chemical reactions and limited available data. To find a method to get the reactive rate parameters for the reactive urea hydrolysis transport modeling and obtain more accurate prediction for the chemical concentrations,more » we developed a data assimilation method based on an ensemble Kalman filter (EnKF) method to calibrate reactive rate parameters for modeling urea hydrolysis transport in a synthetic one-dimensional column at laboratory scale and to update modeling prediction. We applied a constrained EnKF method to pose constraints to the updated reactive rate parameters and the predicted solute concentrations based on their physical meanings after the data assimilation calibration. From the study results we concluded that we could efficiently improve the chemical reactive rate parameters with the data assimilation method via the EnKF, and at the same time we could improve solute concentration prediction. The more data we assimilated, the more accurate the reactive rate parameters and concentration prediction. The filter divergence problem was also solved in this study.« less

Crystallography of ordered colloids using optical microscopy. 2. Divergent-beam technique.

PubMed

Rogers, Richard B; Lagerlöf, K Peter D

2008-04-10

A technique has been developed to extract quantitative crystallographic data from randomly oriented colloidal crystals using a divergent-beam approach. This technique was tested on a series of diverse experimental images of colloidal crystals formed from monodisperse suspensions of sterically stabilized poly-(methyl methacrylate) spheres suspended in organic index-matching solvents. Complete sets of reciprocal lattice basis vectors were extracted in all but one case. When data extraction was successful, results appeared to be accurate to about 1% for lattice parameters and to within approximately 2 degrees for orientation. This approach is easier to implement than a previously developed parallel-beam approach with the drawback that the divergent-beam approach is not as robust in certain situations with random hexagonal close-packed crystals. The two techniques are therefore complimentary to each other, and between them it should be possible to extract quantitative crystallographic data with a conventional optical microscope from any closely index-matched colloidal crystal whose lattice parameters are compatible with visible wavelengths.

Convex foundations for generalized MaxEnt models

NASA Astrophysics Data System (ADS)

Frongillo, Rafael; Reid, Mark D.

2014-12-01

We present an approach to maximum entropy models that highlights the convex geometry and duality of generalized exponential families (GEFs) and their connection to Bregman divergences. Using our framework, we are able to resolve a puzzling aspect of the bijection of Banerjee and coauthors between classical exponential families and what they call regular Bregman divergences. Their regularity condition rules out all but Bregman divergences generated from log-convex generators. We recover their bijection and show that a much broader class of divergences correspond to GEFs via two key observations: 1) Like classical exponential families, GEFs have a "cumulant" C whose subdifferential contains the mean: Eo˜pθ[φ(o)]∈∂C(θ) ; 2) Generalized relative entropy is a C-Bregman divergence between parameters: DF(pθ,pθ')= D C(θ,θ') , where DF becomes the KL divergence for F = -H. We also show that every incomplete market with cost function C can be expressed as a complete market, where the prices are constrained to be a GEF with cumulant C. This provides an entirely new interpretation of prediction markets, relating their design back to the principle of maximum entropy.

Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs.

PubMed Central

Horai, S; Hayasaka, K; Kondo, R; Tsugane, K; Takahata, N

1995-01-01

We analyzed the complete mitochondrial DNA (mtDNA) sequences of three humans (African, European, and Japanese), three African apes (common and pygmy chimpanzees, and gorilla), and one orangutan in an attempt to estimate most accurately the substitution rates and divergence times of hominoid mtDNAs. Nonsynonymous substitutions and substitutions in RNA genes have accumulated with an approximately clock-like regularity. From these substitutions and under the assumption that the orangutan and African apes diverged 13 million years ago, we obtained a divergence time for humans and chimpanzees of 4.9 million years. This divergence time permitted calibration of the synonymous substitution rate (3.89 x 10(-8)/site per year). To obtain the substitution rate in the displacement (D)-loop region, we compared the three human mtDNAs and measured the relative abundance of substitutions in the D-loop region and at synonymous sites. The estimated substitution rate in the D-loop region was 7.00 x 10(-8)/site per year. Using both synonymous and D-loop substitutions, we inferred the age of the last common ancestor of the human mtDNAs as 143,000 +/- 18,000 years. The shallow ancestry of human mtDNAs, together with the observation that the African sequence is the most diverged among humans, strongly supports the recent African origin of modern humans, Homo sapiens sapiens. PMID:7530363

Analysis of the restricting factors of laser countermeasure active detection technology

NASA Astrophysics Data System (ADS)

Zhang, Yufa; Sun, Xiaoquan

2016-07-01

The detection effect of laser active detection system is affected by various kinds of factors. In view of the application requirement of laser active detection, the influence factors for laser active detection are analyzed. The mathematical model of cat eye target detection distance has been built, influence of the parameters of laser detection system and the environment on detection range and the detection efficiency are analyzed. Various parameters constraint detection performance is simulated. The results show that the discovery distance of laser active detection is affected by the laser divergence angle, the incident angle and the visibility of the atmosphere. For a given detection range, the laser divergence angle and the detection efficiency are mutually restricted. Therefore, in view of specific application environment, it is necessary to select appropriate laser detection parameters to achieve optimal detection effect.

Comparative analysis of gene regulatory networks: from network reconstruction to evolution.

PubMed

Thompson, Dawn; Regev, Aviv; Roy, Sushmita

2015-01-01

Regulation of gene expression is central to many biological processes. Although reconstruction of regulatory circuits from genomic data alone is therefore desirable, this remains a major computational challenge. Comparative approaches that examine the conservation and divergence of circuits and their components across strains and species can help reconstruct circuits as well as provide insights into the evolution of gene regulatory processes and their adaptive contribution. In recent years, advances in genomic and computational tools have led to a wealth of methods for such analysis at the sequence, expression, pathway, module, and entire network level. Here, we review computational methods developed to study transcriptional regulatory networks using comparative genomics, from sequence to functional data. We highlight how these methods use evolutionary conservation and divergence to reliably detect regulatory components as well as estimate the extent and rate of divergence. Finally, we discuss the promise and open challenges in linking regulatory divergence to phenotypic divergence and adaptation.

Role of mantle flow in Nubia-Somalia plate divergence

NASA Astrophysics Data System (ADS)

Stamps, D. S.; Iaffaldano, G.; Calais, E.

2015-01-01

Present-day continental extension along the East African Rift System (EARS) has often been attributed to diverging sublithospheric mantle flow associated with the African Superplume. This implies a degree of viscous coupling between mantle and lithosphere that remains poorly constrained. Recent advances in estimating present-day opening rates along the EARS from geodesy offer an opportunity to address this issue with geodynamic modeling of the mantle-lithosphere system. Here we use numerical models of the global mantle-plates coupled system to test the role of present-day mantle flow in Nubia-Somalia plate divergence across the EARS. The scenario yielding the best fit to geodetic observations is one where torques associated with gradients of gravitational potential energy stored in the African highlands are resisted by weak continental faults and mantle basal drag. These results suggest that shear tractions from diverging mantle flow play a minor role in present-day Nubia-Somalia divergence.

New results on the hydrodynamic behaviour of fossil Nummulites tests from two nummulite banks from the Bartonian and Priabonian of northern Italy

PubMed Central

Seddighi, Mona; Briguglio, Antonino; Hohenegger, Johann; Papazzoni, Cesare Andrea

2015-01-01

Settling velocities of 58 well-preserved tests of fossil Nummulites were experimentally determined using a settling tube. The tests were collected from the nummulite banks of Pederiva di Grancona (A forms of N. lyelli and N. striatus, Middle Eocene) and San Germano dei Berici (A and B forms of N. fabianii, Late Eocene), both in the Berici Mts. (Veneto, northern Italy). The data were compared with estimated settling velocities that the same specimens might have had in life conditions. This was done by reconstructing their densities simulating water-filled condition and, to simulate post-diagenetic effects, under calcite-filled condition. These simulations show that A and B forms, even if they greatly diverge in shape, volume and size, still possess comparable settling velocities, and that each nummulite bank is characterized by specific hydrodynamic parameters. The use of settling velocity as a parameter to quantify the hydrodynamic behaviour of particles in seawater enables estimation of palaeoenvironmental conditions such as depth, substrate and the energy scenario. Such information is useful in obtaining further insights into the genesis of nummulite banks, the autochthony or allochthony of which is still being debated. Our results point to an autochthonous interpretation. PMID:26681827

New results on the hydrodynamic behaviour of fossil Nummulites tests from two nummulite banks from the Bartonian and Priabonian of northern Italy.

PubMed

Seddighi, Mona; Briguglio, Antonino; Hohenegger, Johann; Papazzoni, Cesare Andrea

2015-09-01

Settling velocities of 58 well-preserved tests of fossil Nummulites were experimentally determined using a settling tube. The tests were collected from the nummulite banks of Pederiva di Grancona (A forms of N. lyelli and N. striatus, Middle Eocene) and San Germano dei Berici (A and B forms of N. fabianii, Late Eocene), both in the Berici Mts. (Veneto, northern Italy). The data were compared with estimated settling velocities that the same specimens might have had in life conditions. This was done by reconstructing their densities simulating water-filled condition and, to simulate post-diagenetic effects, under calcite-filled condition. These simulations show that A and B forms, even if they greatly diverge in shape, volume and size, still possess comparable settling velocities, and that each nummulite bank is characterized by specific hydrodynamic parameters. The use of settling velocity as a parameter to quantify the hydrodynamic behaviour of particles in seawater enables estimation of palaeoenvironmental conditions such as depth, substrate and the energy scenario. Such information is useful in obtaining further insights into the genesis of nummulite banks, the autochthony or allochthony of which is still being debated. Our results point to an autochthonous interpretation.

A PDF-based classification of gait cadence patterns in patients with amyotrophic lateral sclerosis.

PubMed

Wu, Yunfeng; Ng, Sin Chun

2010-01-01

Amyotrophic lateral sclerosis (ALS) is a type of neurological disease due to the degeneration of motor neurons. During the course of such a progressive disease, it would be difficult for ALS patients to regulate normal locomotion, so that the gait stability becomes perturbed. This paper presents a pilot statistical study on the gait cadence (or stride interval) in ALS, based on the statistical analysis method. The probability density functions (PDFs) of stride interval were first estimated with the nonparametric Parzen-window method. We computed the mean of the left-foot stride interval and the modified Kullback-Leibler divergence (MKLD) from the PDFs estimated. The analysis results suggested that both of these two statistical parameters were significantly altered in ALS, and the least-squares support vector machine (LS-SVM) may effectively distinguish the stride patterns between the ALS patients and healthy controls, with an accurate rate of 82.8% and an area of 0.87 under the receiver operating characteristic curve.

Dynamo threshold detection in the von Kármán sodium experiment.

PubMed

Miralles, Sophie; Bonnefoy, Nicolas; Bourgoin, Mickael; Odier, Philippe; Pinton, Jean-François; Plihon, Nicolas; Verhille, Gautier; Boisson, Jean; Daviaud, François; Dubrulle, Bérengère

2013-07-01

Predicting dynamo self-generation in liquid metal experiments has been an ongoing question for many years. In contrast to simple dynamical systems for which reliable techniques have been developed, the ability to predict the dynamo capacity of a flow and the estimate of the corresponding critical value of the magnetic Reynolds number (the control parameter of the instability) has been elusive, partly due to the high level of turbulent fluctuations of flows in such experiments (with kinetic Reynolds numbers in excess of 10(6)). We address these issues here, using the von Kármán sodium experiment and studying its response to an externally applied magnetic field. We first show that a dynamo threshold can be estimated from analysis related to critical slowing down and susceptibility divergence, in configurations for which dynamo action is indeed observed. These approaches are then applied to flow configurations that have failed to self-generate magnetic fields within operational limits, and we quantify the dynamo capacity of these configurations.

Resolving Recent Plant Radiations: Power and Robustness of Genotyping-by-Sequencing.

PubMed

Fernández-Mazuecos, Mario; Mellers, Greg; Vigalondo, Beatriz; Sáez, Llorenç; Vargas, Pablo; Glover, Beverley J

2018-03-01

Disentangling species boundaries and phylogenetic relationships within recent evolutionary radiations is a challenge due to the poor morphological differentiation and low genetic divergence between species, frequently accompanied by phenotypic convergence, interspecific gene flow and incomplete lineage sorting. Here we employed a genotyping-by-sequencing (GBS) approach, in combination with morphometric analyses, to investigate a small western Mediterranean clade in the flowering plant genus Linaria that radiated in the Quaternary. After confirming the morphological and genetic distinctness of eight species, we evaluated the relative performances of concatenation and coalescent methods to resolve phylogenetic relationships. Specifically, we focused on assessing the robustness of both approaches to variations in the parameter used to estimate sequence homology (clustering threshold). Concatenation analyses suffered from strong systematic bias, as revealed by the high statistical support for multiple alternative topologies depending on clustering threshold values. By contrast, topologies produced by two coalescent-based methods (NJ$_{\\mathrm{st}}$, SVDquartets) were robust to variations in the clustering threshold. Reticulate evolution may partly explain incongruences between NJ$_{\\mathrm{st}}$, SVDquartets and concatenated trees. Integration of morphometric and coalescent-based phylogenetic results revealed (i) extensive morphological divergence associated with recent splits between geographically close or sympatric sister species and (ii) morphological convergence in geographically disjunct species. These patterns are particularly true for floral traits related to pollinator specialization, including nectar spur length, tube width and corolla color, suggesting pollinator-driven diversification. Given its relatively simple and inexpensive implementation, GBS is a promising technique for the phylogenetic and systematic study of recent radiations, but care must be taken to evaluate the robustness of results to variation of data assembly parameters.

Uncertainty Quantification using Exponential Epi-Splines

DTIC Science & Technology

2013-06-01

Leibler divergence. The choice of κ in applications can be informed by the fact that the Kullback - Leibler divergence between two normal densities, ϕ1... of ran- dom output quantities of interests. The framework systematically incorporates hard information derived from physics-based sensors, field test ... information , and determines the ‘best’ estimate within that family. Bayesian estima- tion makes use of prior soft information

Higher level phylogeny and the first divergence time estimation of Heteroptera (Insecta: Hemiptera) based on multiple genes.

PubMed

Li, Min; Tian, Ying; Zhao, Ying; Bu, Wenjun

2012-01-01

Heteroptera, or true bugs, are the largest, morphologically diverse and economically important group of insects with incomplete metamorphosis. However, the phylogenetic relationships within Heteroptera are still in dispute and most of the previous studies were based on morphological characters or with single gene (partial or whole 18S rDNA). Besides, so far, divergence time estimates for Heteroptera totally rely on the fossil record, while no studies have been performed on molecular divergence rates. Here, for the first time, we used maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) with multiple genes (18S rDNA, 28S rDNA, 16S rDNA and COI) to estimate phylogenetic relationships among the infraorders, and meanwhile, the Penalized Likelihood (r8s) and Bayesian (BEAST) molecular dating methods were employed to estimate divergence time of higher taxa of this suborder. Major results of the present study included: Nepomorpha was placed as the most basal clade in all six trees (MP trees, ML trees and Bayesian trees of nuclear gene data and four-gene combined data, respectively) with full support values. The sister-group relationship of Cimicomorpha and Pentatomomorpha was also strongly supported. Nepomorpha originated in early Triassic and the other six infraorders originated in a very short period of time in middle Triassic. Cimicomorpha and Pentatomomorpha underwent a radiation at family level in Cretaceous, paralleling the proliferation of the flowering plants. Our results indicated that the higher-group radiations within hemimetabolous Heteroptera were simultaneously with those of holometabolous Coleoptera and Diptera which took place in the Triassic. While the aquatic habitat was colonized by Nepomorpha already in the Triassic, the Gerromorpha independently adapted to the semi-aquatic habitat in the Early Jurassic.

Higher Level Phylogeny and the First Divergence Time Estimation of Heteroptera (Insecta: Hemiptera) Based on Multiple Genes

PubMed Central

Zhao, Ying; Bu, Wenjun

2012-01-01

Heteroptera, or true bugs, are the largest, morphologically diverse and economically important group of insects with incomplete metamorphosis. However, the phylogenetic relationships within Heteroptera are still in dispute and most of the previous studies were based on morphological characters or with single gene (partial or whole 18S rDNA). Besides, so far, divergence time estimates for Heteroptera totally rely on the fossil record, while no studies have been performed on molecular divergence rates. Here, for the first time, we used maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) with multiple genes (18S rDNA, 28S rDNA, 16S rDNA and COI) to estimate phylogenetic relationships among the infraorders, and meanwhile, the Penalized Likelihood (r8s) and Bayesian (BEAST) molecular dating methods were employed to estimate divergence time of higher taxa of this suborder. Major results of the present study included: Nepomorpha was placed as the most basal clade in all six trees (MP trees, ML trees and Bayesian trees of nuclear gene data and four-gene combined data, respectively) with full support values. The sister-group relationship of Cimicomorpha and Pentatomomorpha was also strongly supported. Nepomorpha originated in early Triassic and the other six infraorders originated in a very short period of time in middle Triassic. Cimicomorpha and Pentatomomorpha underwent a radiation at family level in Cretaceous, paralleling the proliferation of the flowering plants. Our results indicated that the higher-group radiations within hemimetabolous Heteroptera were simultaneously with those of holometabolous Coleoptera and Diptera which took place in the Triassic. While the aquatic habitat was colonized by Nepomorpha already in the Triassic, the Gerromorpha independently adapted to the semi-aquatic habitat in the Early Jurassic. PMID:22384163

Comparison of information theoretic divergences for sensor management

NASA Astrophysics Data System (ADS)

Yang, Chun; Kadar, Ivan; Blasch, Erik; Bakich, Michael

2011-06-01

In this paper, we compare the information-theoretic metrics of the Kullback-Leibler (K-L) and Renyi (α) divergence formulations for sensor management. Information-theoretic metrics have been well suited for sensor management as they afford comparisons between distributions resulting from different types of sensors under different actions. The difference in distributions can also be measured as entropy formulations to discern the communication channel capacity (i.e., Shannon limit). In this paper, we formulate a sensor management scenario for target tracking and compare various metrics for performance evaluation as a function of the design parameter (α) so as to determine which measures might be appropriate for sensor management given the dynamics of the scenario and design parameter.

Empirically Estimable Classification Bounds Based on a Nonparametric Divergence Measure

PubMed Central

Berisha, Visar; Wisler, Alan; Hero, Alfred O.; Spanias, Andreas

2015-01-01

Information divergence functions play a critical role in statistics and information theory. In this paper we show that a non-parametric f-divergence measure can be used to provide improved bounds on the minimum binary classification probability of error for the case when the training and test data are drawn from the same distribution and for the case where there exists some mismatch between training and test distributions. We confirm the theoretical results by designing feature selection algorithms using the criteria from these bounds and by evaluating the algorithms on a series of pathological speech classification tasks. PMID:26807014

An Algebraic Implicitization and Specialization of Minimum KL-Divergence Models

NASA Astrophysics Data System (ADS)

Dukkipati, Ambedkar; Manathara, Joel George

In this paper we study representation of KL-divergence minimization, in the cases where integer sufficient statistics exists, using tools from polynomial algebra. We show that the estimation of parametric statistical models in this case can be transformed to solving a system of polynomial equations. In particular, we also study the case of Kullback-Csisźar iteration scheme. We present implicit descriptions of these models and show that implicitization preserves specialization of prior distribution. This result leads us to a Gröbner bases method to compute an implicit representation of minimum KL-divergence models.

Learning Multisensory Integration and Coordinate Transformation via Density Estimation

PubMed Central

Sabes, Philip N.

2013-01-01

Sensory processing in the brain includes three key operations: multisensory integration—the task of combining cues into a single estimate of a common underlying stimulus; coordinate transformations—the change of reference frame for a stimulus (e.g., retinotopic to body-centered) effected through knowledge about an intervening variable (e.g., gaze position); and the incorporation of prior information. Statistically optimal sensory processing requires that each of these operations maintains the correct posterior distribution over the stimulus. Elements of this optimality have been demonstrated in many behavioral contexts in humans and other animals, suggesting that the neural computations are indeed optimal. That the relationships between sensory modalities are complex and plastic further suggests that these computations are learned—but how? We provide a principled answer, by treating the acquisition of these mappings as a case of density estimation, a well-studied problem in machine learning and statistics, in which the distribution of observed data is modeled in terms of a set of fixed parameters and a set of latent variables. In our case, the observed data are unisensory-population activities, the fixed parameters are synaptic connections, and the latent variables are multisensory-population activities. In particular, we train a restricted Boltzmann machine with the biologically plausible contrastive-divergence rule to learn a range of neural computations not previously demonstrated under a single approach: optimal integration; encoding of priors; hierarchical integration of cues; learning when not to integrate; and coordinate transformation. The model makes testable predictions about the nature of multisensory representations. PMID:23637588

Behavioral versus genetic determination of lipoproteins andidentical twins discordant for exercise

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

Williams, Paul T.; Blanche, Patricia J.; Krauss, Ronald M.

Lipoprotein and weight differences between vigorously active and sedentary MZ twins are used to: (1) estimate the effects of training while controlling for genotype; (2) estimate genetic concordance in the presence of divergent lifestyles.

Dating Tips for Divergence-Time Estimation.

PubMed

O'Reilly, Joseph E; Dos Reis, Mario; Donoghue, Philip C J

2015-11-01

The molecular clock is the only viable means of establishing an accurate timescale for Life on Earth, but it remains reliant on a capricious fossil record for calibration. 'Tip-dating' promises a conceptual advance, integrating fossil species among their living relatives using molecular/morphological datasets and evolutionary models. Fossil species of known age establish calibration directly, and their phylogenetic uncertainty is accommodated through the co-estimation of time and topology. However, challenges remain, including a dearth of effective models of morphological evolution, rate correlation, the non-random nature of missing characters in fossil data, and, most importantly, accommodating uncertainty in fossil age. We show uncertainty in fossil-dating propagates to divergence-time estimates, yielding estimates that are older and less precise than those based on traditional node calibration. Ultimately, node and tip calibrations are not mutually incompatible and may be integrated to achieve more accurate and precise evolutionary timescales. Copyright © 2015 Elsevier Ltd. All rights reserved.

Reconstructing population histories from single nucleotide polymorphism data.

PubMed

Sirén, Jukka; Marttinen, Pekka; Corander, Jukka

2011-01-01

Population genetics encompasses a strong theoretical and applied research tradition on the multiple demographic processes that shape genetic variation present within a species. When several distinct populations exist in the current generation, it is often natural to consider the pattern of their divergence from a single ancestral population in terms of a binary tree structure. Inference about such population histories based on molecular data has been an intensive research topic in the recent years. The most common approach uses coalescent theory to model genealogies of individuals sampled from the current populations. Such methods are able to compare several different evolutionary scenarios and to estimate demographic parameters. However, their major limitation is the enormous computational complexity associated with the indirect modeling of the demographies, which limits the application to small data sets. Here, we propose a novel Bayesian method for inferring population histories from unlinked single nucleotide polymorphisms, which is applicable also to data sets harboring large numbers of individuals from distinct populations. We use an approximation to the neutral Wright-Fisher diffusion to model random fluctuations in allele frequencies. The population histories are modeled as binary rooted trees that represent the historical order of divergence of the different populations. A combination of analytical, numerical, and Monte Carlo integration techniques are utilized for the inferences. A particularly important feature of our approach is that it provides intuitive measures of statistical uncertainty related with the estimates computed, which may be entirely lacking for the alternative methods in this context. The potential of our approach is illustrated by analyses of both simulated and real data sets.

Segmenting the human genome based on states of neutral genetic divergence.

PubMed

Kuruppumullage Don, Prabhani; Ananda, Guruprasad; Chiaromonte, Francesca; Makova, Kateryna D

2013-09-03

Many studies have demonstrated that divergence levels generated by different mutation types vary and covary across the human genome. To improve our still-incomplete understanding of the mechanistic basis of this phenomenon, we analyze several mutation types simultaneously, anchoring their variation to specific regions of the genome. Using hidden Markov models on insertion, deletion, nucleotide substitution, and microsatellite divergence estimates inferred from human-orangutan alignments of neutrally evolving genomic sequences, we segment the human genome into regions corresponding to different divergence states--each uniquely characterized by specific combinations of divergence levels. We then parsed the mutagenic contributions of various biochemical processes associating divergence states with a broad range of genomic landscape features. We find that high divergence states inhabit guanine- and cytosine (GC)-rich, highly recombining subtelomeric regions; low divergence states cover inner parts of autosomes; chromosome X forms its own state with lowest divergence; and a state of elevated microsatellite mutability is interspersed across the genome. These general trends are mirrored in human diversity data from the 1000 Genomes Project, and departures from them highlight the evolutionary history of primate chromosomes. We also find that genes and noncoding functional marks [annotations from the Encyclopedia of DNA Elements (ENCODE)] are concentrated in high divergence states. Our results provide a powerful tool for biomedical data analysis: segmentations can be used to screen personal genome variants--including those associated with cancer and other diseases--and to improve computational predictions of noncoding functional elements.

Optimal projection method determination by Logdet Divergence and perturbed von-Neumann Divergence.

PubMed

Jiang, Hao; Ching, Wai-Ki; Qiu, Yushan; Cheng, Xiao-Qing

2017-12-14

Positive semi-definiteness is a critical property in kernel methods for Support Vector Machine (SVM) by which efficient solutions can be guaranteed through convex quadratic programming. However, a lot of similarity functions in applications do not produce positive semi-definite kernels. We propose projection method by constructing projection matrix on indefinite kernels. As a generalization of the spectrum method (denoising method and flipping method), the projection method shows better or comparable performance comparing to the corresponding indefinite kernel methods on a number of real world data sets. Under the Bregman matrix divergence theory, we can find suggested optimal λ in projection method using unconstrained optimization in kernel learning. In this paper we focus on optimal λ determination, in the pursuit of precise optimal λ determination method in unconstrained optimization framework. We developed a perturbed von-Neumann divergence to measure kernel relationships. We compared optimal λ determination with Logdet Divergence and perturbed von-Neumann Divergence, aiming at finding better λ in projection method. Results on a number of real world data sets show that projection method with optimal λ by Logdet divergence demonstrate near optimal performance. And the perturbed von-Neumann Divergence can help determine a relatively better optimal projection method. Projection method ia easy to use for dealing with indefinite kernels. And the parameter embedded in the method can be determined through unconstrained optimization under Bregman matrix divergence theory. This may provide a new way in kernel SVMs for varied objectives.

SU-E-T-146: Beam Energy Spread Estimate Based On Bragg Peak Measurement

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

Anferov, V; Derenchuk, V; Moore, R

2015-06-15

Purpose: ProNova is installing and commissioning a two room proton therapy system in Knoxville, TN. Beam energy out of the 230MeV cyclotron was measured on Jan 24, 2015. Cyclotron beam was delivered into a Zebra multi layered IC detector calibrated in terms of penetration range in water. The analysis of the measured Bragg peak determines penetration range in water which can be subsequently converted into proton beam energy. We extended this analysis to obtain an estimate of the beam energy spread out of the cyclotron. Methods: Using Monte Carlo simulations we established the correlation between Bragg peak shape parameters (widthmore » at 50% and 80% dose levels, distal falloff) and penetration range for a monoenergetic proton beam. For large uniform field impinging on a small area detector, we observed linear dependence of each Bragg peak parameter on beam penetration range as shown in Figure A. Then we studied how this correlation changes when the shape of Bragg peak is distorted by the beam focusing conditions. As shown in Figure B, small field size or diverging beam cause Bragg peak deformation predominantly in the proximal region. The distal shape of the renormalized Bragg peaks stays nearly constant. This excludes usage of Bragg peak width parameters for energy spread estimates. Results: The measured Bragg peaks had an average distal falloff of 4.86mm, which corresponds to an effective range of 35.5cm for a monoenergetic beam. The 32.7cm measured penetration range is 2.8cm less. Passage of a 230MeV proton beam through a 2.8cm thick slab of water results in a ±0.56MeV energy spread. As a final check, we confirmed agreement between shapes of the measured Bragg peak and one generated by Monte-Carlo code for proton beam with 0.56 MeV energy spread. Conclusion: Proton beam energy spread can be estimated using Bragg peak analysis.« less

Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution

PubMed Central

2017-01-01

Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions. PMID:28637852

Siberian population of the New Stone Age: mtDNA haplotype diversity in the ancient population from the Ust'-Ida I burial ground, dated 4020-3210 BC by 14C.

PubMed

Naumova O, Y u; Rychkov S, Y u

1998-03-01

On the basis of analysis of mtDNA from skeletal remains, dated by 14C 4020-3210 BC, from the Ust'-Ida I Neolithic burial ground in Cis-Baikal area of Siberia, we obtained genetic characteristics of the ancient Mongoloid population. Using the 7 restriction enzymes for the analysis of site's polymorphism in 16,106-16,545 region of mtDNA, we studied the structure of the most frequent DNA haplotypes, and estimated the intrapopulational nucleotide diversity of the Neolithic population. Comparison of the Neolithic and modern indigeneous populations from Siberia, Mongolia and Ural showed, that the ancient Siberian population is one of the ancestors of the modern population of Siberia. From genetic distance, in the assumption of constant nucleotide substitution rate, we estimated the divergence time between the Neolithic and the modern Siberian population. This divergence time (5572 years ago) is conformed to the age of skeletal remains (5542-5652 years). With use of the 14C dates of the skeletal remains, nucleotide substitution rate in mtDNA was estimated as 1% sequence divergence for 8938-9115 years.

Species history and divergence times of viviparous and oviparous Chinese toad-headed sand lizards (Phrynocephalus) on the Qinghai-Tibetan Plateau.

PubMed

Jin, Y-T; Brown, R P

2013-08-01

The Qinghai-Tibetan Plateau (QTP) is an important biogeographical area and has recently become a focus for biodiversity studies. Phyrnocephalus lizards form a widespread Eurasian group with oviparous and viviparous reproductive modes, but two previous mtDNA studies of species from around the QTP have provided different phylogenetic hypotheses. We analysed three loci (mtDNA, RAG-1, AME) from all recognised Chinese Phrynocephalus species to reconstruct the speciation history of the group and to estimate species divergence times. The effects of mtDNA partitioning strategy on phylogenetic inference were examined. Bayes factor comparisons of marginal likelihoods (mLs) estimated using stepping-stone sampling revealed that partitioning strategy had a major impact on mL. Nevertheless, it had a negligible effect on the inferred tree topology. The impact of hard-bound uniform or equivalent soft-bound gamma speciation time calibration priors as well as the use of a fixed topology (as opposed to integration over all possible species histories) on divergence time estimation were also assessed, and found to have little impact on posterior estimates. All three gene trees and the species tree supported the hypothesis that the Chinese species form oviparous and viviparous sister clades. This was in agreement with an early mtDNA study but differed from a subsequent reanalysis of the mtDNA data. Inclusion of mtDNA from more widely distributed Phrynocephalus (from previous studies) indicates that the oviparous P. interscapularis from Central Asia lies outside the clade of Chinese viviparous and oviparous species, but that other Asian oviparous species lie within the Chinese oviparous clade. The median of the posterior on the divergence time of Chinese oviparous and viviparous species was 9.7 Ma ago (95% interval: 7.2-13.0 Ma ago), which coincides with major uplifting of the QTP and indicates that viviparity evolved when this clade became restricted to regions of high elevation. We also found that cladogenesis within the viviparous clade began around 5 Ma ago whereas those in the oviparous clade began around 8.6 Ma ago. We establish more robust estimates of divergence times and relationships within this important group and so provide improved insights into the origins of Phrynocephalus diversity across the QTP. Copyright © 2013 Elsevier Inc. All rights reserved.

Consequences of Traumatic Brain Injury for Human Vergence Dynamics

PubMed Central

Tyler, Christopher W.; Likova, Lora T.; Mineff, Kristyo N.; Elsaid, Anas M.; Nicholas, Spero C.

2015-01-01

Purpose: Traumatic brain injury involving loss of consciousness has focal effects in the human brainstem, suggesting that it may have particular consequences for eye movement control. This hypothesis was investigated by measurements of vergence eye movement parameters. Methods: Disparity vergence eye movements were measured for a population of 123 normally sighted individuals, 26 of whom had suffered diffuse traumatic brain injury (dTBI) in the past, while the remainder served as controls. Vergence tracking responses were measured to sinusoidal disparity modulation of a random-dot field. Disparity vergence step responses were characterized in terms of their dynamic parameters separately for the convergence and divergence directions. Results: The control group showed notable differences between convergence and divergence dynamics. The dTBI group showed significantly abnormal vergence behavior on many of the dynamic parameters. Conclusion: The results support the hypothesis that occult injury to the oculomotor control system is a common residual outcome of dTBI. PMID:25691880

Effect of divergent selection for intramuscular fat on sensory traits and instrumental texture in rabbit meat.

PubMed

Martínez-Álvaroi, M; Penalba, V; Blasco, A; Hernández, P

2016-12-01

Intramuscular fat (IMF) is one of the main parameters affecting meat quality. This work analyzes the effect of selection for IMF on sensory attributes and instrumental texture parameters in rabbit meat. A total of 115 rabbits after 6 generations of divergent selection for IMF were slaughtered at 9 or 13 wk (57 and 58 animals, respectively). For each animal, the left longissimus dorsi muscle (LD) was analyzed by near-infrared spectroscopy to measure IMF whereas the right LD was used for the sensory or instrumental texture analysis. Sensory attributes measured were rabbit odor, liver odor, rabbit flavor, liver flavor, aniseed flavor, hardness, juiciness, and fibrousness. The instrumental texture parameters maximum shear force, shear firmness, and total work to cut the sample were measured by a Warner-Bratzler shear test. The line selected for high IMF showed 58% greater IMF than the line selected for low IMF. This divergence affected firmness that was 9.9% greater in the low-IMF line, although no effect was found for the other instrumental texture traits. No effect of selection was observed in any odor or flavor, except for aniseed flavor, which was greater in the high-IMF line than in the low-IMF line. Age had an effect on IMF, instrumental texture parameters, and sensory attributes. Rabbits at 13 wk showed greater IMF and instrumental and sensory hardness and more intense odor and flavor and lower juiciness than rabbits at 9 wk.

Prediction of Breakthrough Curves for Conservative and Reactive Transport from the Structural Parameters of Highly Heterogeneous Media

NASA Astrophysics Data System (ADS)

Hansen, S. K.; Haslauer, C. P.; Cirpka, O. A.; Vesselinov, V. V.

2016-12-01

It is desirable to predict the shape of breakthrough curves downgradient of a solute source from subsurface structural parameters (as in the small-perturbation macrodispersion theory) both for realistically heterogeneous fields, and at early time, before any sort of Fickian model is applicable. Using a combination of a priori knowledge, large-scale Monte Carlo simulation, and regression techniques, we have developed closed-form predictive expressions for pre- and post-Fickian flux-weighted solute breakthrough curves as a function of distance from the source (in integral scales) and variance of the log hydraulic conductivity field. Using the ensemble of Monte Carlo realizations, we have simultaneously computed error envelopes for the estimated flux-weighted breakthrough, and for the divergence of point breakthrough curves from the flux-weighted average, as functions of the predictive parameters. We have also obtained implied late-time macrodispersion coefficients for highly heterogeneous environments from the breakthrough statistics. This analysis is relevant for the modelling of reactive as well as conservative transport, since for many kinetic sorption and decay reactions, Laplace-domain modification of the breakthrough curve for conservative solute produces the correct curve for the reactive system.

Senstitivity analysis of horizontal heat and vapor transfer coefficients for a cloud-topped marine boundary layer during cold-air outbreaks. M.S. Thesis

NASA Technical Reports Server (NTRS)

Chang, Y. V.

1986-01-01

The effects of external parameters on the surface heat and vapor fluxes into the marine atmospheric boundary layer (MABL) during cold-air outbreaks are investigated using the numerical model of Stage and Businger (1981a). These fluxes are nondimensionalized using the horizontal heat (g1) and vapor (g2) transfer coefficient method first suggested by Chou and Atlas (1982) and further formulated by Stage (1983a). In order to simplify the problem, the boundary layer is assumed to be well mixed and horizontally homogeneous, and to have linear shoreline soundings of equivalent potential temperature and mixing ratio. Modifications of initial surface flux estimates, time step limitation, and termination conditions are made to the MABL model to obtain accurate computations. The dependence of g1 and g2 in the cloud topped boundary layer on the external parameters (wind speed, divergence, sea surface temperature, radiative sky temperature, cloud top radiation cooling, and initial shoreline soundings of temperature, and mixing ratio) is studied by a sensitivity analysis, which shows that the uncertainties of horizontal transfer coefficients caused by changes in the parameters are reasonably small.

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

Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea).

PubMed

Dornburg, Alex; Brandley, Matthew C; McGowen, Michael R; Near, Thomas J

2012-02-01

Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed "uncorrelated relaxed clock" and "random local clock" (RLC) models allow decoupling of nucleotide substitution rates between descendant lineages and are thus predicted to perform better in the presence of lineage-specific rate heterogeneity. However, it is uncertain how these models perform in the presence of punctuated shifts in substitution rate, especially between closely related clades. Using cetaceans (whales and dolphins) as a case study, we test the performance of these two substitution models in estimating both molecular rates and divergence times in the presence of substantial lineage-specific rate heterogeneity. Our RLC analyses of whole mitochondrial genome alignments find evidence for up to ten clade-specific nucleotide substitution rate shifts in cetaceans. We provide evidence that in the uncorrelated relaxed clock framework, a punctuated shift in the rate of molecular evolution within a subclade results in posterior rate estimates that are either misled or intermediate between the disparate rate classes present in baleen and toothed whales. Using simulations, we demonstrate abrupt changes in rate isolated to one or a few lineages in the phylogeny can mislead rate and age estimation, even when the node of interest is calibrated. We further demonstrate how increasing prior age uncertainty can bias rate and age estimates, even while the 95% highest posterior density around age estimates decreases; in other words, increased precision for an inaccurate estimate. We interpret the use of external calibrations in divergence time studies in light of these results, suggesting that rate shifts at deep time scales may mislead inferences of absolute molecular rates and ages.

Phylogenetic relationships and divergence dates of softshell turtles (Testudines: Trionychidae) inferred from complete mitochondrial genomes.

PubMed

Li, H; Liu, J; Xiong, L; Zhang, H; Zhou, H; Yin, H; Jing, W; Li, J; Shi, Q; Wang, Y; Liu, J; Nie, L

2017-05-01

The softshell turtles (Trionychidae) are one of the most widely distributed reptile groups in the world, and fossils have been found on all continents except Antarctica. The phylogenetic relationships among members of this group have been previously studied; however, disagreements regarding its taxonomy, its phylogeography and divergence times are still poorly understood as well. Here, we present a comprehensive mitogenomic study of softshell turtles. We sequenced the complete mitochondrial genomes of 10 softshell turtles, in addition to the GenBank sequence of Dogania subplana, Lissemys punctata, Trionyx triunguis, which cover all extant genera within Trionychidae except for Cyclanorbis and Cycloderma. These data were combined with other mitogenomes of turtles for phylogenetic analyses. Divergence time calibration and ancestral reconstruction were calculated using BEAST and RASP software, respectively. Our phylogenetic analyses indicate that Trionychidae is the sister taxon of Carettochelyidae, and support the monophyly of Trionychinae and Cyclanorbinae, which is consistent with morphological data and molecular analysis. Our phylogenetic analyses have established a sister taxon relationship between the Asian Rafetus and the Asian Palea + Pelodiscus + Dogania + Nilssonia + Amyda, whereas a previous study grouped the Asian Rafetus with the American Apalone. The results of divergence time estimates and area ancestral reconstruction show that extant Trionychidae originated in Asia at around 108 million years ago (MA), and radiations mainly occurred during two warm periods, namely Late Cretaceous-Early Eocene and Oligocene. By combining the estimated divergence time and the reconstructed ancestral area of softshell turtles, we determined that the dispersal of softshell turtles out of Asia may have taken three routes. Furthermore, the times of dispersal seem to be in agreement with the time of the India-Asia collision and opening of the Bering Strait, which provide evidence for the accuracy of our estimation of divergence time. Overall, the mitogenomes of this group were used to explore the origin and dispersal route of Trionychidae and have provided new insights on the evolution of this group. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

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

Antolin, J.; Instituto Carlos I de Fisica Teorica y Computacional, Universidad de Granada, ES-18071 Granada; Bouvrie, P. A.

An alternative one-parameter measure of divergence is proposed, quantifying the discrepancy among general probability densities. Its main mathematical properties include (i) comparison among an arbitrary number of functions, (ii) the possibility of assigning different weights to each function according to its relevance on the comparative procedure, and (iii) ability to modify the relative contribution of different regions within the domain. Applications to the study of atomic density functions, in both conjugated spaces, show the versatility and universality of this divergence.

Species divergence and phylogenetic variation of ecophysiological traits in lianas and trees.

PubMed

Rios, Rodrigo S; Salgado-Luarte, Cristian; Gianoli, Ernesto

2014-01-01

The climbing habit is an evolutionary key innovation in plants because it is associated with enhanced clade diversification. We tested whether patterns of species divergence and variation of three ecophysiological traits that are fundamental for plant adaptation to light environments (maximum photosynthetic rate [A(max)], dark respiration rate [R(d)], and specific leaf area [SLA]) are consistent with this key innovation. Using data reported from four tropical forests and three temperate forests, we compared phylogenetic distance among species as well as the evolutionary rate, phylogenetic distance and phylogenetic signal of those traits in lianas and trees. Estimates of evolutionary rates showed that R(d) evolved faster in lianas, while SLA evolved faster in trees. The mean phylogenetic distance was 1.2 times greater among liana species than among tree species. Likewise, estimates of phylogenetic distance indicated that lianas were less related than by chance alone (phylogenetic evenness across 63 species), and trees were more related than expected by chance (phylogenetic clustering across 71 species). Lianas showed evenness for R(d), while trees showed phylogenetic clustering for this trait. In contrast, for SLA, lianas exhibited phylogenetic clustering and trees showed phylogenetic evenness. Lianas and trees showed patterns of ecophysiological trait variation among species that were independent of phylogenetic relatedness. We found support for the expected pattern of greater species divergence in lianas, but did not find consistent patterns regarding ecophysiological trait evolution and divergence. R(d) followed the species-level pattern, i.e., greater divergence/evolution in lianas compared to trees, while the opposite occurred for SLA and no pattern was detected for A(max). R(d) may have driven lianas' divergence across forest environments, and might contribute to diversification in climber clades.

Species Divergence and Phylogenetic Variation of Ecophysiological Traits in Lianas and Trees

PubMed Central

Rios, Rodrigo S.; Salgado-Luarte, Cristian; Gianoli, Ernesto

2014-01-01

The climbing habit is an evolutionary key innovation in plants because it is associated with enhanced clade diversification. We tested whether patterns of species divergence and variation of three ecophysiological traits that are fundamental for plant adaptation to light environments (maximum photosynthetic rate [Amax], dark respiration rate [Rd], and specific leaf area [SLA]) are consistent with this key innovation. Using data reported from four tropical forests and three temperate forests, we compared phylogenetic distance among species as well as the evolutionary rate, phylogenetic distance and phylogenetic signal of those traits in lianas and trees. Estimates of evolutionary rates showed that Rd evolved faster in lianas, while SLA evolved faster in trees. The mean phylogenetic distance was 1.2 times greater among liana species than among tree species. Likewise, estimates of phylogenetic distance indicated that lianas were less related than by chance alone (phylogenetic evenness across 63 species), and trees were more related than expected by chance (phylogenetic clustering across 71 species). Lianas showed evenness for Rd, while trees showed phylogenetic clustering for this trait. In contrast, for SLA, lianas exhibited phylogenetic clustering and trees showed phylogenetic evenness. Lianas and trees showed patterns of ecophysiological trait variation among species that were independent of phylogenetic relatedness. We found support for the expected pattern of greater species divergence in lianas, but did not find consistent patterns regarding ecophysiological trait evolution and divergence. Rd followed the species-level pattern, i.e., greater divergence/evolution in lianas compared to trees, while the opposite occurred for SLA and no pattern was detected for Amax. Rd may have driven lianas' divergence across forest environments, and might contribute to diversification in climber clades. PMID:24914958

The effects of Medieval dams on genetic divergence and demographic history in brown trout populations

PubMed Central

2014-01-01

Background Habitat fragmentation has accelerated within the last century, but may have been ongoing over longer time scales. We analyzed the timing and genetic consequences of fragmentation in two isolated lake-dwelling brown trout populations. They are from the same river system (the Gudenå River, Denmark) and have been isolated from downstream anadromous trout by dams established ca. 600–800 years ago. For reference, we included ten other anadromous populations and two hatchery strains. Based on analysis of 44 microsatellite loci we investigated if the lake populations have been naturally genetically differentiated from anadromous trout for thousands of years, or have diverged recently due to the establishment of dams. Results Divergence time estimates were based on 1) Approximate Bayesian Computation and 2) a coalescent-based isolation-with-gene-flow model. Both methods suggested divergence times ca. 600–800 years bp, providing strong evidence for establishment of dams in the Medieval as the factor causing divergence. Bayesian cluster analysis showed influence of stocked trout in several reference populations, but not in the focal lake and anadromous populations. Estimates of effective population size using a linkage disequilibrium method ranged from 244 to > 1,000 in all but one anadromous population, but were lower (153 and 252) in the lake populations. Conclusions We show that genetic divergence of lake-dwelling trout in two Danish lakes reflects establishment of water mills and impassable dams ca. 600–800 years ago rather than a natural genetic population structure. Although effective population sizes of the two lake populations are not critically low they may ultimately limit response to selection and thereby future adaptation. Our results demonstrate that populations may have been affected by anthropogenic disturbance over longer time scales than normally assumed. PMID:24903056

The effects of Medieval dams on genetic divergence and demographic history in brown trout populations.

PubMed

Hansen, Michael M; Limborg, Morten T; Ferchaud, Anne-Laure; Pujolar, José-Martin

2014-06-05

Habitat fragmentation has accelerated within the last century, but may have been ongoing over longer time scales. We analyzed the timing and genetic consequences of fragmentation in two isolated lake-dwelling brown trout populations. They are from the same river system (the Gudenå River, Denmark) and have been isolated from downstream anadromous trout by dams established ca. 600-800 years ago. For reference, we included ten other anadromous populations and two hatchery strains. Based on analysis of 44 microsatellite loci we investigated if the lake populations have been naturally genetically differentiated from anadromous trout for thousands of years, or have diverged recently due to the establishment of dams. Divergence time estimates were based on 1) Approximate Bayesian Computation and 2) a coalescent-based isolation-with-gene-flow model. Both methods suggested divergence times ca. 600-800 years bp, providing strong evidence for establishment of dams in the Medieval as the factor causing divergence. Bayesian cluster analysis showed influence of stocked trout in several reference populations, but not in the focal lake and anadromous populations. Estimates of effective population size using a linkage disequilibrium method ranged from 244 to > 1,000 in all but one anadromous population, but were lower (153 and 252) in the lake populations. We show that genetic divergence of lake-dwelling trout in two Danish lakes reflects establishment of water mills and impassable dams ca. 600-800 years ago rather than a natural genetic population structure. Although effective population sizes of the two lake populations are not critically low they may ultimately limit response to selection and thereby future adaptation. Our results demonstrate that populations may have been affected by anthropogenic disturbance over longer time scales than normally assumed.

EVOLUTION OF DIVERGENT FEMALE MATING PREFERENCE IN RESPONSE TO EXPERIMENTAL SEXUAL SELECTION

PubMed Central

Debelle, Allan; Ritchie, Michael G; Snook, Rhonda R

2014-01-01

Sexual selection is predicted to drive the coevolution of mating signals and preferences (mating traits) within populations, and could play a role in speciation if sexual isolation arises due to mating trait divergence between populations. However, few studies have demonstrated that differences in mating traits between populations result from sexual selection alone. Experimental evolution is a promising approach to directly examine the action of sexual selection on mating trait divergence among populations. We manipulated the opportunity for sexual selection (low vs. high) in populations of Drosophila pseudoobscura. Previous studies on these experimental populations have shown that sexual selection manipulation resulted in the divergence between sexual selection treatments of several courtship song parameters, including interpulse interval (IPI) which markedly influences male mating success. Here, we measure female preference for IPI using a playback design to test for preference divergence between the sexual selection treatments after 130 generations of experimental sexual selection. The results suggest that female preference has coevolved with male signal, in opposite directions between the sexual selection treatments, providing direct evidence of the ability of sexual selection to drive the divergent coevolution of mating traits between populations. We discuss the implications in the context sexual selection and speciation. PMID:24931497

Propose a Wall Shear Stress Divergence to Estimate the Risks of Intracranial Aneurysm Rupture

PubMed Central

Zhang, Y.; Takao, H.; Murayama, Y.; Qian, Y.

2013-01-01

Although wall shear stress (WSS) has long been considered a critical indicator of intracranial aneurysm rupture, there is still no definite conclusion as to whether a high or a low WSS results in aneurysm rupture. The reason may be that the effect of WSS direction has not been fully considered. The objectives of this study are to investigate the magnitude of WSS (|WSS|) and its divergence on the aneurysm surface and to test the significance of both in relation to the aneurysm rupture. Patient-specific computational fluid dynamics (CFD) was used to compute WSS and wall shear stress divergence (WSSD) on the aneurysm surface for nineteen patients. Our results revealed that if high |WSS| is stretching aneurysm luminal surface, and the stretching region is concentrated, the aneurysm is under a high risk of rupture. It seems that, by considering both direction and magnitude of WSS, WSSD may be a better indicator for the risk estimation of aneurysm rupture (154). PMID:24191140

Static internal performance including thrust vectoring and reversing of two-dimensional convergent-divergent nozzles

NASA Technical Reports Server (NTRS)

Re, R. J.; Leavitt, L. D.

1984-01-01

The effects of geometric design parameters on two dimensional convergent-divergent nozzles were investigated at nozzle pressure ratios up to 12 in the static test facility. Forward flight (dry and afterburning power settings), vectored-thrust (afterburning power setting), and reverse-thrust (dry power setting) nozzles were investigated. The nozzles had thrust vector angles from 0 deg to 20.26 deg, throat aspect ratios of 3.696 to 7.612, throat radii from sharp to 2.738 cm, expansion ratios from 1.089 to 1.797, and various sidewall lengths. The results indicate that unvectored two dimensional convergent-divergent nozzles have static internal performance comparable to axisymmetric nozzles with similar expansion ratios.

Estimating the age-specific duration of herpes zoster vaccine protection: a matter of model choice?

PubMed

Bilcke, Joke; Ogunjimi, Benson; Hulstaert, Frank; Van Damme, Pierre; Hens, Niel; Beutels, Philippe

2012-04-05

The estimation of herpes zoster (HZ) vaccine efficacy by time since vaccination and age at vaccination is crucial to assess the effectiveness and cost-effectiveness of HZ vaccination. Published estimates for the duration of protection from the vaccine diverge substantially, although based on data from the same trial for a follow-up period of 5 years. Different models were used to obtain these estimates, but it is unclear which of these models is most appropriate (if any). Only one study estimated vaccine efficacy by age at vaccination and time since vaccination combined. Recently, data became available from the same trial for a follow-up period of 7 years. We aim to elaborate on estimating HZ vaccine efficacy (1) by estimating it as a function of time since vaccination and age at vaccination, (2) by comparing the fits of a range of models, and (3) by fitting these models on data for a follow-up period of 5 and 7 years. Although the models' fit to data are very comparable, they differ substantially in how they estimate vaccine efficacy to change as a function of time since vaccination and age at vaccination. An accurate estimation of HZ vaccine efficacy by time since vaccination and age at vaccination is hampered by the lack of insight in the biological processes underlying HZ vaccine protection, and by the fact that such data are currently not available in sufficient detail. Uncertainty about the choice of model to estimate this important parameter should be acknowledged in cost-effectiveness analyses. Copyright © 2011 Elsevier Ltd. All rights reserved.

Computational Investigations in Rectangular Convergent and Divergent Ribbed Channels

NASA Astrophysics Data System (ADS)

Sivakumar, Karthikeyan; Kulasekharan, N.; Natarajan, E.

2018-05-01

Computational investigations on the rib turbulated flow inside a convergent and divergent rectangular channel with square ribs of different rib heights and different Reynolds numbers (Re=20,000, 40,000 and 60,000). The ribs were arranged in a staggered fashion between the upper and lower surfaces of the test section. Computational investigations are carried out using computational fluid dynamic software ANSYS Fluent 14.0. Suitable solver settings like turbulence models were identified from the literature and the boundary conditions for the simulations on a solution of independent grid. Computations were carried out for both convergent and divergent channels with 0 (smooth duct), 1.5, 3, 6, 9 and 12 mm rib heights, to identify the ribbed channel with optimal performance, assessed using a thermo hydraulic performance parameter. The convergent and divergent rectangular channels show higher Nu values than the standard correlation values.

Patterns of Z chromosome divergence among Heliconius species highlight the importance of historical demography.

PubMed

Van Belleghem, Steven M; Baquero, Margarita; Papa, Riccardo; Salazar, Camilo; McMillan, W Owen; Counterman, Brian A; Jiggins, Chris D; Martin, Simon H

2018-03-22

Sex chromosomes are disproportionately involved in reproductive isolation and adaptation. In support of such a "large-X" effect, genome scans between recently diverged populations and species pairs often identify distinct patterns of divergence on the sex chromosome compared to autosomes. When measures of divergence between populations are higher on the sex chromosome compared to autosomes, such patterns could be interpreted as evidence for faster divergence on the sex chromosome, that is "faster-X", barriers to gene flow on the sex chromosome. However, demographic changes can strongly skew divergence estimates and are not always taken into consideration. We used 224 whole-genome sequences representing 36 populations from two Heliconius butterfly clades (H. erato and H. melpomene) to explore patterns of Z chromosome divergence. We show that increased divergence compared to equilibrium expectations can in many cases be explained by demographic change. Among Heliconius erato populations, for instance, population size increase in the ancestral population can explain increased absolute divergence measures on the Z chromosome compared to the autosomes, as a result of increased ancestral Z chromosome genetic diversity. Nonetheless, we do identify increased divergence on the Z chromosome relative to the autosomes in parapatric or sympatric species comparisons that imply postzygotic reproductive barriers. Using simulations, we show that this is consistent with reduced gene flow on the Z chromosome, perhaps due to greater accumulation of incompatibilities. Our work demonstrates the importance of taking demography into account to interpret patterns of divergence on the Z chromosome, but nonetheless provides evidence to support the Z chromosome as a strong barrier to gene flow in incipient Heliconius butterfly species. © 2018 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Improving the efficiency of feed utilization in poultry by selection. 2. Genetic parameters of excretion traits and correlations with anatomy of the gastro-intestinal tract and digestive efficiency.

PubMed

de Verdal, Hugues; Narcy, Agnès; Bastianelli, Denis; Chapuis, Hervé; Même, Nathalie; Urvoix, Séverine; Le Bihan-Duval, Elisabeth; Mignon-Grasteau, Sandrine

2011-08-17

Poultry production has been widely criticized for its negative environmental impact related to the quantity of manure produced and to its nitrogen and phosphorus content. In this study, we investigated which traits related to excretion could be used to select chickens for lower environmental pollution.The genetic parameters of several excretion traits were estimated on 630 chickens originating from 2 chicken lines divergently selected on apparent metabolisable energy corrected for zero nitrogen (AMEn) at constant body weight. The quantity of excreta relative to feed consumption (CDUDM), the nitrogen and phosphorus excreted, the nitrogen to phosphorus ratio and the water content of excreta were measured, and the consequences of such selection on performance and gastro-intestinal tract (GIT) characteristics estimated. The genetic correlations between excretion, GIT and performance traits were established. Heritability estimates were high for CDUDM and the nitrogen excretion rate (0.30 and 0.29, respectively). The other excretion measurements showed low to moderate heritability estimates, ranging from 0.10 for excreta water content to 0.22 for the phosphorus excretion rate. Except for the excreta water content, the CDUDM was highly correlated with the excretion traits, ranging from -0.64 to -1.00. The genetic correlations between AMEn or CDUDM and the GIT characteristics were very similar and showed that a decrease in chicken excretion involves an increase in weight of the upper part of the GIT, and a decrease in the weight of the small intestine. In order to limit the environmental impact of chicken production, AMEn and CDUDM seem to be more suitable criteria to include in selection schemes than feed efficiency traits.

The oldest platypus and its bearing on divergence timing of the platypus and echidna clades

PubMed Central

Rowe, Timothy; Rich, Thomas H.; Vickers-Rich, Patricia; Springer, Mark; Woodburne, Michael O.

2008-01-01

Monotremes have left a poor fossil record, and paleontology has been virtually mute during two decades of discussion about molecular clock estimates of the timing of divergence between the platypus and echidna clades. We describe evidence from high-resolution x-ray computed tomography indicating that Teinolophos, an Early Cretaceous fossil from Australia's Flat Rocks locality (121–112.5 Ma), lies within the crown clade Monotremata, as a basal platypus. Strict molecular clock estimates of the divergence between platypus and echidnas range from 17 to 80 Ma, but Teinolophos suggests that the two monotreme clades were already distinct in the Early Cretaceous, and that their divergence may predate even the oldest strict molecular estimates by at least 50%. We generated relaxed molecular clock models using three different data sets, but only one yielded a date overlapping with the age of Teinolophos. Morphology suggests that Teinolophos is a platypus in both phylogenetic and ecological aspects, and tends to contradict the popular view of rapid Cenozoic monotreme diversification. Whereas the monotreme fossil record is still sparse and open to interpretation, the new data are consistent with much slower ecological, morphological, and taxonomic diversification rates for monotremes than in their sister taxon, the therian mammals. This alternative view of a deep geological history for monotremes suggests that rate heterogeneities may have affected mammalian evolution in such a way as to defeat strict molecular clock models and to challenge even relaxed molecular clock models when applied to mammalian history at a deep temporal scale. PMID:18216270

The oldest platypus and its bearing on divergence timing of the platypus and echidna clades.

PubMed

Rowe, Timothy; Rich, Thomas H; Vickers-Rich, Patricia; Springer, Mark; Woodburne, Michael O

2008-01-29

Monotremes have left a poor fossil record, and paleontology has been virtually mute during two decades of discussion about molecular clock estimates of the timing of divergence between the platypus and echidna clades. We describe evidence from high-resolution x-ray computed tomography indicating that Teinolophos, an Early Cretaceous fossil from Australia's Flat Rocks locality (121-112.5 Ma), lies within the crown clade Monotremata, as a basal platypus. Strict molecular clock estimates of the divergence between platypus and echidnas range from 17 to 80 Ma, but Teinolophos suggests that the two monotreme clades were already distinct in the Early Cretaceous, and that their divergence may predate even the oldest strict molecular estimates by at least 50%. We generated relaxed molecular clock models using three different data sets, but only one yielded a date overlapping with the age of Teinolophos. Morphology suggests that Teinolophos is a platypus in both phylogenetic and ecological aspects, and tends to contradict the popular view of rapid Cenozoic monotreme diversification. Whereas the monotreme fossil record is still sparse and open to interpretation, the new data are consistent with much slower ecological, morphological, and taxonomic diversification rates for monotremes than in their sister taxon, the therian mammals. This alternative view of a deep geological history for monotremes suggests that rate heterogeneities may have affected mammalian evolution in such a way as to defeat strict molecular clock models and to challenge even relaxed molecular clock models when applied to mammalian history at a deep temporal scale.

Genome Evolution in the Primary Endosymbiont of Whiteflies Sheds Light on Their Divergence

PubMed Central

Santos-Garcia, Diego; Vargas-Chavez, Carlos; Moya, Andrés; Latorre, Amparo; Silva, Francisco J.

2015-01-01

Whiteflies are important agricultural insect pests, whose evolutionary success is related to a long-term association with a bacterial endosymbiont, Candidatus Portiera aleyrodidarum. To completely characterize this endosymbiont clade, we sequenced the genomes of three new Portiera strains covering the two extant whitefly subfamilies. Using endosymbiont and mitochondrial sequences we estimated the divergence dates in the clade and used these values to understand the molecular evolution of the endosymbiont coding sequences. Portiera genomes were maintained almost completely stable in gene order and gene content during more than 125 Myr of evolution, except in the Bemisia tabaci lineage. The ancestor had already lost the genetic information transfer autonomy but was able to participate in the synthesis of all essential amino acids and carotenoids. The time of divergence of the B. tabaci complex was much more recent than previous estimations. The recent divergence of biotypes B (MEAM1 species) and Q (MED species) suggests that they still could be considered strains of the same species. We have estimated the rates of evolution of Portiera genes, synonymous and nonsynonymous, and have detected significant differences among-lineages, with most Portiera lineages evolving very slowly. Although the nonsynonymous rates were much smaller than the synonymous, the genomic dN/dS ratios were similar, discarding selection as the driver of among-lineage variation. We suggest variation in mutation rate and generation time as the responsible factors. In conclusion, the slow evolutionary rates of Portiera may have contributed to its long-term association with whiteflies, avoiding its replacement by a novel and more efficient endosymbiont. PMID:25716826

An error analysis of tropical cyclone divergence and vorticity fields derived from satellite cloud winds on the Atmospheric and Oceanographic Information Processing System (AOIPS)

NASA Technical Reports Server (NTRS)

Hasler, A. F.; Rodgers, E. B.

1977-01-01

An advanced Man-Interactive image and data processing system (AOIPS) was developed to extract basic meteorological parameters from satellite data and to perform further analyses. The errors in the satellite derived cloud wind fields for tropical cyclones are investigated. The propagation of these errors through the AOIPS system and their effects on the analysis of horizontal divergence and relative vorticity are evaluated.

Low X/Y divergence in four pairs of papaya sex-linked genes.

PubMed

Yu, Qingyi; Hou, Shaobin; Feltus, F Alex; Jones, Meghan R; Murray, Jan E; Veatch, Olivia; Lemke, Cornelia; Saw, Jimmy H; Moore, Richard C; Thimmapuram, Jyothi; Liu, Lei; Moore, Paul H; Alam, Maqsudul; Jiang, Jiming; Paterson, Andrew H; Ming, Ray

2008-01-01

Sex chromosomes in flowering plants, in contrast to those in animals, evolved relatively recently and only a few are heteromorphic. The homomorphic sex chromosomes of papaya show features of incipient sex chromosome evolution. We investigated the features of paired X- and Y-specific bacterial artificial chromosomes (BACs), and estimated the time of divergence in four pairs of sex-linked genes. We report the results of a comparative analysis of long contiguous genomic DNA sequences between the X and hermaphrodite Y (Y(h)) chromosomes. Numerous chromosomal rearrangements were detected in the male-specific region of the Y chromosome (MSY), including inversions, deletions, insertions, duplications and translocations, showing the dynamic evolutionary process on the MSY after recombination ceased. DNA sequence expansion was documented in the two regions of the MSY, demonstrating that the cytologically homomorphic sex chromosomes are heteromorphic at the molecular level. Analysis of sequence divergence between four X and Y(h) gene pairs resulted in a estimated age of divergence of between 0.5 and 2.2 million years, supporting a recent origin of the papaya sex chromosomes. Our findings indicate that sex chromosomes did not evolve at the family level in Caricaceae, and reinforce the theory that sex chromosomes evolve at the species level in some lineages.

Mitogenome Sequencing in the Genus Camelus Reveals Evidence for Purifying Selection and Long-term Divergence between Wild and Domestic Bactrian Camels.

PubMed

Mohandesan, Elmira; Fitak, Robert R; Corander, Jukka; Yadamsuren, Adiya; Chuluunbat, Battsetseg; Abdelhadi, Omer; Raziq, Abdul; Nagy, Peter; Stalder, Gabrielle; Walzer, Chris; Faye, Bernard; Burger, Pamela A

2017-08-30

The genus Camelus is an interesting model to study adaptive evolution in the mitochondrial genome, as the three extant Old World camel species inhabit hot and low-altitude as well as cold and high-altitude deserts. We sequenced 24 camel mitogenomes and combined them with three previously published sequences to study the role of natural selection under different environmental pressure, and to advance our understanding of the evolutionary history of the genus Camelus. We confirmed the heterogeneity of divergence across different components of the electron transport system. Lineage-specific analysis of mitochondrial protein evolution revealed a significant effect of purifying selection in the concatenated protein-coding genes in domestic Bactrian camels. The estimated dN/dS < 1 in the concatenated protein-coding genes suggested purifying selection as driving force for shaping mitogenome diversity in camels. Additional analyses of the functional divergence in amino acid changes between species-specific lineages indicated fixed substitutions in various genes, with radical effects on the physicochemical properties of the protein products. The evolutionary time estimates revealed a divergence between domestic and wild Bactrian camels around 1.1 [0.58-1.8] million years ago (mya). This has major implications for the conservation and management of the critically endangered wild species, Camelus ferus.

Renormalization of the one-loop theory of fluctuations in polymer blends and diblock copolymer melts.

PubMed

Grzywacz, Piotr; Qin, Jian; Morse, David C

2007-12-01

Attempts to use coarse-grained molecular theories to calculate corrections to the random-phase approximation (RPA) for correlations in polymer mixtures have been plagued by an unwanted sensitivity to the value of an arbitrary cutoff length, i.e., by an ultraviolet (UV) divergence. We analyze the UV divergence of the inverse structure factor S(-1)(k) predicted by a "one-loop" approximation similar to that used in several previous studies. We consider both miscible homopolymer blends and disordered diblock copolymer melts. We show, in both cases, that all UV divergent contributions can be absorbed into a renormalization of the values of the phenomenological parameters of a generalized self-consistent field theory (SCFT). This observation allows the construction of an UV convergent theory of corrections to SCFT phenomenology. The UV-divergent one-loop contribution to S(-1)(k) is shown to be the sum of (i) a k -independent contribution that arises from a renormalization of the effective chi parameter, (ii) a k-dependent contribution that arises from a renormalization of monomer statistical segment lengths, (iii) a contribution proportional to k(2) that arises from a square-gradient contribution to the one-loop fluctuation free energy, and (iv) a k-dependent contribution that is inversely proportional to the degree of polymerization, which arises from local perturbations in fluid structure near chain ends and near junctions between blocks in block copolymers.

Numerical simulation of divergent rocket-based-combined-cycle performances under the flight condition of Mach 3

NASA Astrophysics Data System (ADS)

Cui, Peng; Xu, WanWu; Li, Qinglian

2018-01-01

Currently, the upper operating limit of the turbine engine is Mach 2+, and the lower limit of the dual-mode scramjet is Mach 4. Therefore no single power systems can operate within the range between Mach 2 + and Mach 4. By using ejector rockets, Rocket-based-combined-cycle can work well in the above scope. As the key component of Rocket-based-combined-cycle, the ejector rocket has significant influence on Rocket-based-combined-cycle performance. Research on the influence of rocket parameters on Rocket-based-combined-cycle in the speed range of Mach 2 + to Mach 4 is scarce. In the present study, influences of Mach number and total pressure of the ejector rocket on Rocket-based-combined-cycle were analyzed numerically. Due to the significant effects of the flight conditions and the Rocket-based-combined-cycle configuration on Rocket-based-combined-cycle performances, flight altitude, flight Mach number, and divergence ratio were also considered. The simulation results indicate that matching lower altitude with higher flight Mach numbers can increase Rocket-based-combined-cycle thrust. For another thing, with an increase of the divergent ratio, the effect of the divergent configuration will strengthen and there is a limit on the divergent ratio. When the divergent ratio is greater than the limit, the effect of divergent configuration will gradually exceed that of combustion on supersonic flows. Further increases in the divergent ratio will decrease Rocket-based-combined-cycle thrust.

Genomic patterns of species diversity and divergence in Eucalyptus.

PubMed

Hudson, Corey J; Freeman, Jules S; Myburg, Alexander A; Potts, Brad M; Vaillancourt, René E

2015-06-01

We examined genome-wide patterns of DNA sequence diversity and divergence among six species of the important tree genus Eucalyptus and investigated their relationship with genomic architecture. Using c. 90 range-wide individuals of each Eucalyptus species (E. grandis, E. urophylla, E. globulus, E. nitens, E. dunnii and E. camaldulensis), genetic diversity and divergence were estimated from 2840 polymorphic diversity arrays technology markers covering the 11 chromosomes. Species differentiating markers (SDMs) identified in each of 15 pairwise species comparisons, along with species diversity (HHW ) and divergence (FST ), were projected onto the E. grandis reference genome. Across all species comparisons, SDMs totalled 1.1-5.3% of markers and were widely distributed throughout the genome. Marker divergence (FST and SDMs) and diversity differed among and within chromosomes. Patterns of diversity and divergence were broadly conserved across species and significantly associated with genomic features, including the proximity of markers to genes, the relative number of clusters of tandem duplications, and gene density within or among chromosomes. These results suggest that genomic architecture influences patterns of species diversity and divergence in the genus. This influence is evident across the six species, encompassing diverse phylogenetic lineages, geography and ecology. © 2015 University of Tasmania New Phytologist © 2015 New Phytologist Trust.

Niche evolution and adaptive radiation: Testing the order of trait divergence

USGS Publications Warehouse

Ackerly, D.D.; Schwilk, D.W.; Webb, C.O.

2006-01-01

In the course of an adaptive radiation, the evolution of niche parameters is of particular interest for understanding modes of speciation and the consequences for coexistence of related species within communities. We pose a general question: In the course of an evolutionary radiation, do traits related to within-community niche differences (?? niche) evolve before or after differentiation of macrohabitat affinity or climatic tolerances (?? niche)? Here we introduce a new test to address this question, based on a modification of the method of independent contrasts. The divergence order test (DOT) is based on the average age of the nodes on a tree, weighted by the absolute magnitude of the contrast at each node for a particular trait. The comparison of these weighted averages reveals whether large divergences for one trait have occurred earlier or later in the course of diversification, relative to a second trait; significance is determined by bootstrapping from maximum-likelihood ancestral state reconstructions. The method is applied to the evolution of Ceanothus, a woody plant group in California, in which co-occurring species exhibit significant differences in a key leaf trait (specific leaf area) associated with contrasting physiological and life history strategies. Co-occurring species differ more for this trait than expected under a null model of community assembly. This ?? niche difference evolved early in the divergence of two major subclades within Ceanothus, whereas climatic distributions (?? niche traits) diversified later within each of the subclades. However, rapid evolution of climate parameters makes inferences of early divergence events highly uncertain, and differentiation of the ?? niche might have taken place throughout the evolution of the group, without leaving a clear phylogenetic signal. Similar patterns observed in several plant and animal groups suggest that early divergence of ?? niche traits might be a common feature of niche evolution in many adaptive radiations. ?? 2006 by the Ecological Society of America.

Roles of divergent and rotational winds in the kinetic energy balance during intense convective activity

NASA Technical Reports Server (NTRS)

Fuelberg, H. E.; Browning, P. A.

1983-01-01

Contributions of divergent and rotational wind components to the synoptic-scale kinetic energy balance are described using rawinsonde data at 3 and 6 h intervals from NASA's fourth Atmospheric Variability experiment. Two intense thunderstorm complexes occurred during the period. Energy budgets are described for the entire computational region and for limited volumes that enclosed storm-induced, upper level wind maxima located poleward of convection. Although small in magnitude, the divergent wind component played an important role in the cross-contour generation and horizontal flux divergence of kinetic energy. The importance of V(D) appears directly related to the presence and intensity of convection. Although K(D) usually comprised less than 10 percent of the total kinetic energy content, generation of kinetic energy by V(D) was a major factor in the creation of upper-level wind maxima to the north of the storm complexes. Omission of the divergent wind apparently would lead to serious misrepresentations of the energy balance. A random error analysis is presented to assess confidence limits in the various energy parameters.

The Effective Mutation Rate at Y Chromosome Short Tandem Repeats, with Application to Human Population-Divergence Time

PubMed Central

Zhivotovsky, Lev A.; Underhill, Peter A.; Cinnioğlu, Cengiz; Kayser, Manfred; Morar, Bharti; Kivisild, Toomas; Scozzari, Rosaria; Cruciani, Fulvio; Destro-Bisol, Giovanni; Spedini, Gabriella; Chambers, Geoffrey K.; Herrera, Rene J.; Yong, Kiau Kiun; Gresham, David; Tournev, Ivailo; Feldman, Marcus W.; Kalaydjieva, Luba

2004-01-01

We estimate an effective mutation rate at an average Y chromosome short-tandem repeat locus as 6.9×10-4 per 25 years, with a standard deviation across loci of 5.7×10-4, using data on microsatellite variation within Y chromosome haplogroups defined by unique-event polymorphisms in populations with documented short-term histories, as well as comparative data on worldwide populations at both the Y chromosome and various autosomal loci. This value is used to estimate the times of the African Bantu expansion, the divergence of Polynesian populations (the Maoris, Cook Islanders, and Samoans), and the origin of Gypsy populations from Bulgaria. PMID:14691732

Effects of Model Choice and Forest Structure on Inventory-Based Estimations of Puerto Rican Forest Biomass.

Treesearch

THOMAS J. BRANDEIS; MARIA DEL ROCIO SUAREZ ROZO

2005-01-01

Total aboveground live tree biomass in Puerto Rican lower montane wet, subtropical wet, subtropical moist and subtropical dry forests was estimated using data from two forest inventories and published regression equations. Multiple potentially-applicable published biomass models existed for some forested life zones, and their estimates tended to diverge with increasing...

Effects of model choice and forest structure on inventory-based estimations of Puerto Rican forest biomass

Treesearch

Thomas J. Brandeis; Maria Del Rocio; Suarez Rozo

2005-01-01

Total aboveground live tree biomass in Puerto Rican lower montane wet, subtropical wet, subtropical moist and subtropical dry forests was estimated using data from two forest inventories and published regression equations. Multiple potentially-applicable published biomass models existed for some forested life zones, and their estimates tended to diverge with increasing...

Concrete ensemble Kalman filters with rigorous catastrophic filter divergence

PubMed Central

Kelly, David; Majda, Andrew J.; Tong, Xin T.

2015-01-01

The ensemble Kalman filter and ensemble square root filters are data assimilation methods used to combine high-dimensional, nonlinear dynamical models with observed data. Ensemble methods are indispensable tools in science and engineering and have enjoyed great success in geophysical sciences, because they allow for computationally cheap low-ensemble-state approximation for extremely high-dimensional turbulent forecast models. From a theoretical perspective, the dynamical properties of these methods are poorly understood. One of the central mysteries is the numerical phenomenon known as catastrophic filter divergence, whereby ensemble-state estimates explode to machine infinity, despite the true state remaining in a bounded region. In this article we provide a breakthrough insight into the phenomenon, by introducing a simple and natural forecast model that transparently exhibits catastrophic filter divergence under all ensemble methods and a large set of initializations. For this model, catastrophic filter divergence is not an artifact of numerical instability, but rather a true dynamical property of the filter. The divergence is not only validated numerically but also proven rigorously. The model cleanly illustrates mechanisms that give rise to catastrophic divergence and confirms intuitive accounts of the phenomena given in past literature. PMID:26261335

Concrete ensemble Kalman filters with rigorous catastrophic filter divergence.

PubMed

Kelly, David; Majda, Andrew J; Tong, Xin T

2015-08-25

The ensemble Kalman filter and ensemble square root filters are data assimilation methods used to combine high-dimensional, nonlinear dynamical models with observed data. Ensemble methods are indispensable tools in science and engineering and have enjoyed great success in geophysical sciences, because they allow for computationally cheap low-ensemble-state approximation for extremely high-dimensional turbulent forecast models. From a theoretical perspective, the dynamical properties of these methods are poorly understood. One of the central mysteries is the numerical phenomenon known as catastrophic filter divergence, whereby ensemble-state estimates explode to machine infinity, despite the true state remaining in a bounded region. In this article we provide a breakthrough insight into the phenomenon, by introducing a simple and natural forecast model that transparently exhibits catastrophic filter divergence under all ensemble methods and a large set of initializations. For this model, catastrophic filter divergence is not an artifact of numerical instability, but rather a true dynamical property of the filter. The divergence is not only validated numerically but also proven rigorously. The model cleanly illustrates mechanisms that give rise to catastrophic divergence and confirms intuitive accounts of the phenomena given in past literature.

Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species.

PubMed

Fietz, Katharina; Rye Hintze, Christian Olaf; Skovrind, Mikkel; Kjærgaard Nielsen, Tue; Limborg, Morten T; Krag, Marcus A; Palsbøll, Per J; Hestbjerg Hansen, Lars; Rask Møller, Peter; Gilbert, M Thomas P

2018-05-02

Deciphering the mechanisms governing population genetic divergence and local adaptation across heterogeneous environments is a central theme in marine ecology and conservation. While population divergence and ecological adaptive potential are classically viewed at the genetic level, it has recently been argued that their microbiomes may also contribute to population genetic divergence. We explored whether this might be plausible along the well-described environmental gradient of the Baltic Sea in two species of sand lance (Ammodytes tobianus and Hyperoplus lanceolatus). Specifically, we assessed both their population genetic and gut microbial composition variation and investigated not only which environmental parameters correlate with the observed variation, but whether host genome also correlates with microbiome variation. We found a clear genetic structure separating the high-salinity North Sea from the low-salinity Baltic Sea sand lances. The observed genetic divergence was not simply a function of isolation by distance, but correlated with environmental parameters, such as salinity, sea surface temperature, and, in the case of A. tobianus, possibly water microbiota. Furthermore, we detected two distinct genetic groups in Baltic A. tobianus that might represent sympatric spawning types. Investigation of possible drivers of gut microbiome composition variation revealed that host species identity was significantly correlated with the microbial community composition of the gut. A potential influence of host genetic factors on gut microbiome composition was further confirmed by the results of a constrained analysis of principal coordinates. The host genetic component was among the parameters that best explain observed variation in gut microbiome composition. Our findings have relevance for the population structure of two commercial species but also provide insights into potentially relevant genomic and microbial factors with regards to sand lance adaptation across the North Sea-Baltic Sea environmental gradient. Furthermore, our findings support the hypothesis that host genetics may play a role in regulating the gut microbiome at both the interspecific and intraspecific levels. As sequencing costs continue to drop, we anticipate that future studies that include full genome and microbiome sequencing will be able to explore the full relationship and its potential adaptive implications for these species.

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.

Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution.

PubMed

Warnock, Rachel C M; Yang, Ziheng; Donoghue, Philip C J

2017-06-28

Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions. © 2017 The Authors.

Multilocus approach to clarify species status and the divergence history of the Bemisia tabaci (Hemiptera: Aleyrodidae) species complex.

PubMed

Hsieh, Chia-Hung; Ko, Chiun-Cheng; Chung, Cheng-Han; Wang, Hurng-Yi

2014-07-01

The sweet potato whitefly, Bemisia tabaci, is a highly differentiated species complex. Despite consisting of several morphologically indistinguishable entities and frequent invasions on all continents with important associated economic losses, the phylogenetic relationships, species status, and evolutionary history of this species complex is still debated. We sequenced and analyzed one mitochondrial and three single-copy nuclear genes from 9 of the 12 genetic groups of B. tabaci and 5 closely related species. Bayesian species delimitation was applied to investigate the speciation events of B. tabaci. The species statuses of the different genetic groups were strongly supported under different prior settings and phylogenetic scenarios. Divergence histories were estimated by a multispecies coalescence approach implemented in (*)BEAST. Based on mitochondrial locus, B. tabaci was originated 6.47 million years ago (MYA). Nevertheless, the time was 1.25MYA based on nuclear loci. According to the method of approximate Bayesian computation, this difference is probably due to different degrees of migration among loci; i.e., although the mitochondrial locus had differentiated, gene flow at nuclear loci was still possible, a scenario similar to parapatric mode of speciation. This is the first study in whiteflies using multilocus data and incorporating Bayesian coalescence approaches, both of which provide a more biologically realistic framework for delimiting species status and delineating the divergence history of B. tabaci. Our study illustrates that gene flow during species divergence should not be overlooked and has a great impact on divergence time estimation. Copyright © 2014 Elsevier Inc. All rights reserved.

Internal performance of two nozzles utilizing gimbal concepts for thrust vectoring

NASA Technical Reports Server (NTRS)

Berrier, Bobby L.; Taylor, John G.

1990-01-01

The internal performance of an axisymmetric convergent-divergent nozzle and a nonaxisymmetric convergent-divergent nozzle, both of which utilized a gimbal type mechanism for thrust vectoring was evaluated in the Static Test Facility of the Langley 16-Foot Transonic Tunnel. The nonaxisymmetric nozzle used the gimbal concept for yaw thrust vectoring only; pitch thrust vectoring was accomplished by simultaneous deflection of the upper and lower divergent flaps. The model geometric parameters investigated were pitch vector angle for the axisymmetric nozzle and pitch vector angle, yaw vector angle, nozzle throat aspect ratio, and nozzle expansion ratio for the nonaxisymmetric nozzle. All tests were conducted with no external flow, and nozzle pressure ratio was varied from 2.0 to approximately 12.0.

Applying species-tree analyses to deep phylogenetic histories: challenges and potential suggested from a survey of empirical phylogenetic studies.

PubMed

Lanier, Hayley C; Knowles, L Lacey

2015-02-01

Coalescent-based methods for species-tree estimation are becoming a dominant approach for reconstructing species histories from multi-locus data, with most of the studies examining these methodologies focused on recently diverged species. However, deeper phylogenies, such as the datasets that comprise many Tree of Life (ToL) studies, also exhibit gene-tree discordance. This discord may also arise from the stochastic sorting of gene lineages during the speciation process (i.e., reflecting the random coalescence of gene lineages in ancestral populations). It remains unknown whether guidelines regarding methodologies and numbers of loci established by simulation studies at shallow tree depths translate into accurate species relationships for deeper phylogenetic histories. We address this knowledge gap and specifically identify the challenges and limitations of species-tree methods that account for coalescent variance for deeper phylogenies. Using simulated data with characteristics informed by empirical studies, we evaluate both the accuracy of estimated species trees and the characteristics associated with recalcitrant nodes, with a specific focus on whether coalescent variance is generally responsible for the lack of resolution. By determining the proportion of coalescent genealogies that support a particular node, we demonstrate that (1) species-tree methods account for coalescent variance at deep nodes and (2) mutational variance - not gene-tree discord arising from the coalescent - posed the primary challenge for accurate reconstruction across the tree. For example, many nodes were accurately resolved despite predicted discord from the random coalescence of gene lineages and nodes with poor support were distributed across a range of depths (i.e., they were not restricted to a particular recent divergences). Given their broad taxonomic scope and large sampling of taxa, deep level phylogenies pose several potential methodological complications including difficulties with MCMC convergence and estimation of requisite population genetic parameters for coalescent-based approaches. Despite these difficulties, the findings generally support the utility of species-tree analyses for the estimation of species relationships throughout the ToL. We discuss strategies for successful application of species-tree approaches to deep phylogenies. Copyright © 2014 Elsevier Inc. All rights reserved.

A novel cooperative localization algorithm using enhanced particle filter technique in maritime search and rescue wireless sensor network.

PubMed

Wu, Huafeng; Mei, Xiaojun; Chen, Xinqiang; Li, Junjun; Wang, Jun; Mohapatra, Prasant

2018-07-01

Maritime search and rescue (MSR) play a significant role in Safety of Life at Sea (SOLAS). However, it suffers from scenarios that the measurement information is inaccurate due to wave shadow effect when utilizing wireless Sensor Network (WSN) technology in MSR. In this paper, we develop a Novel Cooperative Localization Algorithm (NCLA) in MSR by using an enhanced particle filter method to reduce measurement errors on observation model caused by wave shadow effect. First, we take into account the mobility of nodes at sea to develop a motion model-Lagrangian model. Furthermore, we introduce both state model and observation model to constitute a system model for particle filter (PF). To address the impact of the wave shadow effect on the observation model, we develop an optimal parameter derived by Kullback-Leibler divergence (KLD) to mitigate the error. After the optimal parameter is acquired, an improved likelihood function is presented. Finally, the estimated position is acquired. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Island biology and morphological divergence of the Skyros wall lizard Podarcis gaigeae: a combined role for local selection and genetic drift on color morph frequency divergence?

PubMed Central

2010-01-01

Background Patterns of spatial variation in discrete phenotypic traits can be used to draw inferences about the adaptive significance of traits and evolutionary processes, especially when compared to patterns of neutral genetic variation. Population divergence in adaptive traits such as color morphs can be influenced by both local ecology and stochastic factors such as genetic drift or founder events. Here, we use quantitative color measurements of males and females of Skyros wall lizard, Podarcis gaigeae, to demonstrate that this species is polymorphic with respect to throat color, and the morphs form discrete phenotypic clusters with limited overlap between categories. We use divergence in throat color morph frequencies and compare that to neutral genetic variation to infer the evolutionary processes acting on islet- and mainland populations. Results Geographically close islet- and mainland populations of the Skyros wall lizard exhibit strong divergence in throat color morph frequencies. Population variation in throat color morph frequencies between islets was higher than that between mainland populations, and the effective population sizes on the islets were small (Ne:s < 100). Population divergence (FST) for throat color morph frequencies fell within the neutral FST-distribution estimated from microsatellite markers, and genetic drift could thus not be rejected as an explanation for the pattern. Moreover, for both comparisons among mainland-mainland population pairs and between mainland-islet population pairs, morph frequency divergence was significantly correlated with neutral divergence, further pointing to some role for genetic drift in divergence also at the phenotypic level of throat color morphs. Conclusions Genetic drift could not be rejected as an explanation for the pattern of population divergence in morph frequencies. In spite of an expected stabilising selection, throat color frequencies diverged in the islet populations. These results suggest that there is an interaction between selection and genetic drift causing divergence even at a phenotypic level in these small, subdivided populations. PMID:20813033

Closing the gap between rocks and clocks using total-evidence dating

PubMed Central

2016-01-01

Total-evidence dating (TED) allows evolutionary biologists to incorporate a wide range of dating information into a unified statistical analysis. One might expect this to improve the agreement between rocks and clocks but this is not necessarily the case. We explore the reasons for such discordance using a mammalian dataset with rich molecular, morphological and fossil information. There is strong conflict in this dataset between morphology and molecules under standard stochastic models. This causes TED to push divergence events back in time when using inadequate models or vague priors, a phenomenon we term ‘deep root attraction’ (DRA). We identify several causes of DRA. Failure to account for diversified sampling results in dramatic DRA, but this can be addressed using existing techniques. Inadequate morphological models also appear to be a major contributor to DRA. The major reason seems to be that current models do not account for dependencies among morphological characters, causing distorted topology and branch length estimates. This is particularly problematic for huge morphological datasets, which may contain large numbers of correlated characters. Finally, diversification and fossil sampling priors that do not incorporate all the available background information can contribute to DRA, but these priors can also be used to compensate for DRA. Specifically, we show that DRA in the mammalian dataset can be addressed by introducing a modest extra penalty for ghost lineages that are unobserved in the fossil record, for instance by assuming rapid diversification, rare extinction or high fossil sampling rate; any of these assumptions produces highly congruent divergence time estimates with a minimal gap between rocks and clocks. Under these conditions, fossils have a stabilizing influence on divergence time estimates and significantly increase the precision of those estimates, which are generally close to the dates suggested by palaeontologists. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. PMID:27325833

Closing the gap between rocks and clocks using total-evidence dating.

PubMed

Ronquist, Fredrik; Lartillot, Nicolas; Phillips, Matthew J

2016-07-19

Total-evidence dating (TED) allows evolutionary biologists to incorporate a wide range of dating information into a unified statistical analysis. One might expect this to improve the agreement between rocks and clocks but this is not necessarily the case. We explore the reasons for such discordance using a mammalian dataset with rich molecular, morphological and fossil information. There is strong conflict in this dataset between morphology and molecules under standard stochastic models. This causes TED to push divergence events back in time when using inadequate models or vague priors, a phenomenon we term 'deep root attraction' (DRA). We identify several causes of DRA. Failure to account for diversified sampling results in dramatic DRA, but this can be addressed using existing techniques. Inadequate morphological models also appear to be a major contributor to DRA. The major reason seems to be that current models do not account for dependencies among morphological characters, causing distorted topology and branch length estimates. This is particularly problematic for huge morphological datasets, which may contain large numbers of correlated characters. Finally, diversification and fossil sampling priors that do not incorporate all the available background information can contribute to DRA, but these priors can also be used to compensate for DRA. Specifically, we show that DRA in the mammalian dataset can be addressed by introducing a modest extra penalty for ghost lineages that are unobserved in the fossil record, for instance by assuming rapid diversification, rare extinction or high fossil sampling rate; any of these assumptions produces highly congruent divergence time estimates with a minimal gap between rocks and clocks. Under these conditions, fossils have a stabilizing influence on divergence time estimates and significantly increase the precision of those estimates, which are generally close to the dates suggested by palaeontologists.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. © 2016 The Authors.

Expression Divergence Is Correlated with Sequence Evolution but Not Positive Selection in Conifers.

PubMed

Hodgins, Kathryn A; Yeaman, Sam; Nurkowski, Kristin A; Rieseberg, Loren H; Aitken, Sally N

2016-06-01

The evolutionary and genomic determinants of sequence evolution in conifers are poorly understood, and previous studies have found only limited evidence for positive selection. Using RNAseq data, we compared gene expression profiles to patterns of divergence and polymorphism in 44 seedlings of lodgepole pine (Pinus contorta) and 39 seedlings of interior spruce (Picea glauca × engelmannii) to elucidate the evolutionary forces that shape their genomes and their plastic responses to abiotic stress. We found that rapidly diverging genes tend to have greater expression divergence, lower expression levels, reduced levels of synonymous site diversity, and longer proteins than slowly diverging genes. Similar patterns were identified for the untranslated regions, but with some exceptions. We found evidence that genes with low expression levels had a larger fraction of nearly neutral sites, suggesting a primary role for negative selection in determining the association between evolutionary rate and expression level. There was limited evidence for differences in the rate of positive selection among genes with divergent versus conserved expression profiles and some evidence supporting relaxed selection in genes diverging in expression between the species. Finally, we identified a small number of genes that showed evidence of site-specific positive selection using divergence data alone. However, estimates of the proportion of sites fixed by positive selection (α) were in the range of other plant species with large effective population sizes suggesting relatively high rates of adaptive divergence among conifers. © The Author 2016. 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.

Evolution of divergent female mating preference in response to experimental sexual selection.

PubMed

Debelle, Allan; Ritchie, Michael G; Snook, Rhonda R

2014-09-01

Sexual selection is predicted to drive the coevolution of mating signals and preferences (mating traits) within populations, and could play a role in speciation if sexual isolation arises due to mating trait divergence between populations. However, few studies have demonstrated that differences in mating traits between populations result from sexual selection alone. Experimental evolution is a promising approach to directly examine the action of sexual selection on mating trait divergence among populations. We manipulated the opportunity for sexual selection (low vs. high) in populations of Drosophila pseudoobscura. Previous studies on these experimental populations have shown that sexual selection manipulation resulted in the divergence between sexual selection treatments of several courtship song parameters, including interpulse interval (IPI) which markedly influences male mating success. Here, we measure female preference for IPI using a playback design to test for preference divergence between the sexual selection treatments after 130 generations of experimental sexual selection. The results suggest that female preference has coevolved with male signal, in opposite directions between the sexual selection treatments, providing direct evidence of the ability of sexual selection to drive the divergent coevolution of mating traits between populations. We discuss the implications in the context sexual selection and speciation. © 2014 The Authors. Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Neopolyploidy and diversification in Heuchera grossulariifolia

PubMed Central

Oswald, Benjamin P.; Nuismer, Scott L.

2013-01-01

Newly formed polyploid lineages must contend with several obstacles to avoid extinction, including minority cytotype exclusion, competition, and inbreeding depression. If polyploidization results in immediate divergence of phenotypic characters these hurdles may be reduced and establishment made more likely. In addition, if polyploidization alters the phenotypic and genotypic associations between traits, i.e. the P and G matrices, polyploids may be able to explore novel evolutionary paths, facilitating their divergence and successful establishment. Here we report results from a study of the perennial plant Heuchera grossulariifolia in which the phenotypic divergence and changes in phenotypic and genotypic covariance matrices caused by neopolyploidization have been estimated. Our results reveal that polyploidization causes immediate divergence for traits relevant to establishment and results in significant changes in the structure of the phenotypic covariance matrix. In contrast, our results do not provide evidence that polyploidization results in immediate and substantial shifts in the genetic covariance matrix. PMID:21143472

Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at noncoding sites.

PubMed

Almeida, Pedro; Barbosa, Raquel; Bensasson, Douda; Gonçalves, Paula; Sampaio, José Paulo

2017-04-01

In Saccharomyces cerevisiae, the main yeast in wine fermentation, the opportunity to examine divergence at the molecular level between a domesticated lineage and its wild counterpart arose recently due to the identification of the closest relatives of wine strains, a wild population associated with Mediterranean oaks. As genomic data are available for a considerable number of representatives belonging to both groups, we used population genomics to estimate the degree and distribution of nucleotide variation between wine yeasts and their closest wild relatives. We found widespread genomewide divergence, particularly at noncoding sites, which, together with above average divergence in trans-acting DNA binding proteins, may suggest an important role for divergence at the level of transcriptional regulation. Nine outlier regions putatively under strong divergent selection were highlighted by a genomewide scan under stringent conditions. Several cases of introgressions, originating in the sibling species Saccharomyces paradoxus, were also identified in the Mediterranean oak population. FZF1 and SSU1, mostly known for conferring sulphite resistance in wine yeasts, were among the introgressed genes, although not fixed. Because the introgressions detected in our study are not found in wine strains, we hypothesize that ongoing divergent ecological selection segregates the two forms between the different niches. Together, our results provide a first insight into the extent and kind of divergence between wine yeasts and their closest wild relatives. © 2017 John Wiley & Sons Ltd.

Genetic divergence of common bean cultivars.

PubMed

Veloso, J S; Silva, W; Pinheiro, L R; Dos Santos, J B; Fonseca, N S; Euzebio, M P

2015-09-22

The aim of this study was to evaluate genetic divergence in the 'Carioca' (beige with brown stripes) common bean cultivar used by different institutions and in 16 other common bean cultivars used in the Rede Cooperativa de Pesquisa de Feijão (Cooperative Network of Common Bean Research), by using simple sequence repeats associated with agronomic traits that are highly distributed in the common bean genome. We evaluated 22 polymorphic loci using bulks containing DNA from 30 plants. There was genetic divergence among the Carioca cultivar provided by the institutions. Nevertheless, there was lower divergence among them than among the other cultivars. The cultivar used by Instituto Agronômico do Paraná was the most divergent in relation to the Carioca samples. The least divergence was observed among the samples used by Universidade Federal de Lavras and by Embrapa Arroz e Feijão. Of all the cultivars, 'CNFP 10104' and 'BRSMG Realce' showed the greatest dissimilarity. The cultivars were separated in two groups of greatest similarity using the Structure software. Genetic variation among cultivars was greater than the variation within or between the groups formed. This fact, together with the high estimate of heterozygosity observed and the genetic divergence of the samples of the Carioca cultivar in relation to the original provided by Instituto Agronômico de Campinas, indicates a mixture of cultivars. The high divergence among cultivars provides potential for the utilization of this genetic variability in plant breeding.

Total Bregman Divergence and its Applications to Shape Retrieval.

PubMed

Liu, Meizhu; Vemuri, Baba C; Amari, Shun-Ichi; Nielsen, Frank

2010-01-01

Shape database search is ubiquitous in the world of biometric systems, CAD systems etc. Shape data in these domains is experiencing an explosive growth and usually requires search of whole shape databases to retrieve the best matches with accuracy and efficiency for a variety of tasks. In this paper, we present a novel divergence measure between any two given points in [Formula: see text] or two distribution functions. This divergence measures the orthogonal distance between the tangent to the convex function (used in the definition of the divergence) at one of its input arguments and its second argument. This is in contrast to the ordinate distance taken in the usual definition of the Bregman class of divergences [4]. We use this orthogonal distance to redefine the Bregman class of divergences and develop a new theory for estimating the center of a set of vectors as well as probability distribution functions. The new class of divergences are dubbed the total Bregman divergence (TBD). We present the l 1 -norm based TBD center that is dubbed the t-center which is then used as a cluster center of a class of shapes The t-center is weighted mean and this weight is small for noise and outliers. We present a shape retrieval scheme using TBD and the t-center for representing the classes of shapes from the MPEG-7 database and compare the results with other state-of-the-art methods in literature.

Mixed-order phase transition in a two-step contagion model with a single infectious seed.

PubMed

Choi, Wonjun; Lee, Deokjae; Kahng, B

2017-02-01

Percolation is known as one of the most robust continuous transitions, because its occupation rule is intrinsically local. As one of the ways to break the robustness, occupation is allowed to more than one species of particles and they occupy cooperatively. This generalized percolation model undergoes a discontinuous transition. Here we investigate an epidemic model with two contagion steps and characterize its phase transition analytically and numerically. We find that even though the order parameter jumps at a transition point r_{c}, then increases continuously, it does not exhibit any critical behavior: the fluctuations of the order parameter do not diverge at r_{c}. However, critical behavior appears in mean outbreak size, which diverges at the transition point in a manner that the ordinary percolation shows. Such a type of phase transition is regarded as a mixed-order phase transition. We also obtain scaling relations of cascade outbreak statistics when the order parameter jumps at r_{c}.

Experimental validation of a Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography

NASA Astrophysics Data System (ADS)

Buchmann, Jens; Kaplan, Bernhard A.; Prohaska, Steffen; Laufer, Jan

2017-03-01

Quantitative photoacoustic tomography (qPAT) aims to extract physiological parameters, such as blood oxygen saturation (sO2), from measured multi-wavelength image data sets. The challenge of this approach lies in the inherently nonlinear fluence distribution in the tissue, which has to be accounted for by using an appropriate model, and the large scale of the inverse problem. In addition, the accuracy of experimental and scanner-specific parameters, such as the wavelength dependence of the incident fluence, the acoustic detector response, the beam profile and divergence, needs to be considered. This study aims at quantitative imaging of blood sO2, as it has been shown to be a more robust parameter compared to absolute concentrations. We propose a Monte-Carlo-based inversion scheme in conjunction with a reduction in the number of variables achieved using image segmentation. The inversion scheme is experimentally validated in tissue-mimicking phantoms consisting of polymer tubes suspended in a scattering liquid. The tubes were filled with chromophore solutions at different concentration ratios. 3-D multi-spectral image data sets were acquired using a Fabry-Perot based PA scanner. A quantitative comparison of the measured data with the output of the forward model is presented. Parameter estimates of chromophore concentration ratios were found to be within 5 % of the true values.

Sex-biased transcriptome divergence along a latitudinal gradient.

PubMed

Allen, Scott L; Bonduriansky, Russell; Sgro, Carla M; Chenoweth, Stephen F

2017-03-01

Sex-dependent gene expression is likely an important genomic mechanism that allows sex-specific adaptation to environmental changes. Among Drosophila species, sex-biased genes display remarkably consistent evolutionary patterns; male-biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex-biased expression within species. Latitudinal clines offer an opportunity to examine how changes in key ecological parameters also influence sex-specific selection and the evolution of sex-biased gene expression. We assayed male and female gene expression in Drosophila serrata along a latitudinal gradient in eastern Australia spanning most of its endemic distribution. Analysis of 11 631 genes across eight populations revealed strong sex differences in the frequency, mode and strength of divergence. Divergence was far stronger in males than females and while latitudinal clines were evident in both sexes, male divergence was often population specific, suggesting responses to localized selection pressures that do not covary predictably with latitude. While divergence was enriched for male-biased genes, there was no overrepresentation of X-linked genes in males. By contrast, X-linked divergence was elevated in females, especially for female-biased genes. Many genes that diverged in D. serrata have homologs also showing latitudinal divergence in Drosophila simulans and Drosophila melanogaster on other continents, likely indicating parallel adaptation in these distantly related species. Our results suggest that sex differences in selection play an important role in shaping the evolution of gene expression over macro- and micro-ecological spatial scales. © 2017 John Wiley & Sons Ltd.

Using rate of divergence as an objective measure to differentiate between voice signal types based on the amount of disorder in the signal

PubMed Central

Calawerts, William M; Lin, Liyu; Sprott, JC; Jiang, Jack J

2016-01-01

Objective/Hypothesis The purpose of this paper is to introduce rate of divergence as an objective measure to differentiate between the four voice types based on the amount of disorder present in a signal. We hypothesized that rate of divergence would provide an objective measure that can quantify all four voice types. Study Design 150 acoustic voice recordings were randomly selected and analyzed using traditional perturbation, nonlinear, and rate of divergence analysis methods. ty Methods We developed a new parameter, rate of divergence, which uses a modified version of Wolf’s algorithm for calculating Lyapunov exponents of a system. The outcome of this calculation is not a Lyapunov exponent, but rather a description of the divergence of two nearby data points for the next three points in the time series, followed in three time delayed embedding dimensions. This measure was compared to currently existing perturbation and nonlinear dynamic methods of distinguishing between voice signals. Results There was a direct relationship between voice type and rate of divergence. This calculation is especially effective at differentiating between type 3 and type 4 voices (p<0.001), and is equally effective at differentiating type 1, type 2, and type 3 signals as currently existing methods. Conclusion The rate of divergence calculation introduced is an objective measure that can be used to distinguish between all four voice types based on amount of disorder present, leading to quicker and more accurate voice typing as well as an improved understanding of the nonlinear dynamics involved in phonation. PMID:26920858

Biogeography of Speciation of Two Sister Species of Neotropical Amazona (Aves, Psittaciformes) Based on Mitochondrial Sequence Data

PubMed Central

Rocha, Amanda V.; Rivera, Luis O.; Martinez, Jaime; Prestes, Nêmora P.; Caparroz, Renato

2014-01-01

Coalescent theory provides powerful models for population genetic inference and is now increasingly important in estimates of divergence times and speciation research. We use molecular data and methods based on coalescent theory to investigate whether genetic evidence supports the hypothesis of A. pretrei and A. tucumana as separate species and whether genetic data allow us to assess which allopatric model seems to better explain the diversification process in these taxa. We sampled 13 A. tucumana from two provinces in northern Argentina and 28 A. pretrei from nine localities of Rio Grande do Sul, Brazil. A 491 bp segment of the mitochondrial gene cytochrome c oxidase I was evaluated using the haplotype network and phylogenetic methods. The divergence time and other demographic quantities were estimated using the isolation and migration model based on coalescent theory. The network and phylogenetic reconstructions showed similar results, supporting reciprocal monophyly for these two taxa. The divergence time of lineage separation was estimated to be approximately 1.3 million years ago, which corresponds to the lower Pleistocene. Our results enforce the current taxonomic status for these two Amazon species. They also support that A. pretrei and A. tucumana diverged with little or no gene flow approximately 1.3 million years ago, most likely after the establishment of a small population in the Southern Yungas forest by dispersion of a few founders from the A. pretrei ancestral population. This process may have been favored by habitat corridors formed in hot and humid periods of the Quaternary. Considering that these two species are considered threatened, the results were evaluated for their implications for the conservation of these two species. PMID:25251765

Molecular-based estimate of species number, phylogenetic relationships and divergence times for the genus Stenotaenia (Chilopoda, Geophilomorpha) in the Italian region

PubMed Central

Del Latte, Laura; Bortolin, Francesca; Rota-Stabelli, Omar; Fusco, Giuseppe; Bonato, Lucio

2015-01-01

Abstract Stenotaenia is one of the largest and most widespread genera of geophilid centipedes in the Western Palearctic, with a very uniform morphology and about fifteen species provisionally recognized. For a better understanding of Stenotaenia species-level taxonomy, we have explored the possibility of using molecular data. As a preliminary assay, we sampled twelve populations, mainly from the Italian region, and analyzed partial sequences of the two genes COI and 28S. We employed a DNA-barcoding approach, complemented by a phylogenetic analysis coupled with divergence time estimation. Assuming a barcoding gap of 10–16% K2P pairwise distances, we found evidence for the presence of at least six Stenotaenia species in the Italian region, which started diverging about 50 million years ago, only partially matching with previously recognized species. We found that small-sized oligopodous species belong to a single clade that originated about 33 million years ago, and obtained some preliminary evidence of the related genus Tuoba being nested within Stenotaenia. PMID:26257533

Gender-based screening for chlamydial infection and divergent infection trends in men and women.

PubMed

Rogers, Susan M; Turner, Charles F; Miller, William C; Erbelding, Emily; Eggleston, Elizabeth; Tan, Sylvia; Roman, Anthony; Hobbs, Marcia; Chromy, James; Muvva, Ravikiran; Ganapathi, Laxminarayana

2014-01-01

To assess the potential impact of chlamydial screening policy that recommends routine screening of women but not men. Population surveys of probability samples of Baltimore adults aged 18 to 35 years in 1997-1998 and 2006-2009 collected biospecimens to estimate trends in undiagnosed chlamydial infection. Survey estimates are compared to surveillance data on diagnosed chlamydial infections reported to the Health Department. Prevalence of undiagnosed chlamydial infection among men increased from 1.6% to 4.0%, but it declined from 4.3% to 3.1% among women (p = 0.028 for test of interaction). The annual (average) number of diagnosed infections was substantially higher among women than men in both time periods and increased among both men and women. Undiagnosed infection prevalence was substantially higher among black than non-black adults (4.0% vs 1.2%, p = 0.042 in 1997-98 and 5.5% vs 0.7%, p<0.001 in 2006-09). Divergent trends in undiagnosed chlamydial infection by gender parallel divergent screening recommendations that encourage chlamydial testing for women but not for men.

Multilocus phylogeny, divergence times, and a major role for the benthic-to-pelagic axis in the diversification of grunts (Haemulidae).

PubMed

Tavera, Jose; Acero P, Arturo; Wainwright, Peter C

2018-04-01

We present a phylogenetic analysis with divergence time estimates, and an ecomorphological assessment of the role of the benthic-to-pelagic axis of diversification in the history of haemulid fishes. Phylogenetic analyses were performed on 97 grunt species based on sequence data collected from seven loci. Divergence time estimation indicates that Haemulidae originated during the mid Eocene (54.7-42.3 Ma) but that the major lineages were formed during the mid-Oligocene 30-25 Ma. We propose a new classification that reflects the phylogenetic history of grunts. Overall the pattern of morphological and functional diversification in grunts appears to be strongly linked with feeding ecology. Feeding traits and the first principal component of body shape strongly separate species that feed in benthic and pelagic habitats. The benthic-to-pelagic axis has been the major axis of ecomorphological diversification in this important group of tropical shoreline fishes, with about 13 transitions between feeding habitats that have had major consequences for head and body morphology. Copyright © 2017 Elsevier Inc. All rights reserved.

Bayesian estimation of post-Messinian divergence times in Balearic Island lizards.

PubMed

Brown, R P; Terrasa, B; Pérez-Mellado, V; Castro, J A; Hoskisson, P A; Picornell, A; Ramon, M M

2008-07-01

Phylogenetic relationships and timings of major cladogenesis events are investigated in the Balearic Island lizards Podarcislilfordi and P.pityusensis using 2675bp of mitochondrial and nuclear DNA sequences. Partitioned Bayesian and Maximum Parsimony analyses provided a well-resolved phylogeny with high node-support values. Bayesian MCMC estimation of node dates was investigated by comparing means of posterior distributions from different subsets of the sequence against the most robust analysis which used multiple partitions and allowed for rate heterogeneity among branches under a rate-drift model. Evolutionary rates were systematically underestimated and thus divergence times overestimated when sequences containing lower numbers of variable sites were used (based on ingroup node constraints). The following analyses allowed the best recovery of node times under the constant-rate (i.e., perfect clock) model: (i) all cytochrome b sequence (partitioned by codon position), (ii) cytochrome b (codon position 3 alone), (iii) NADH dehydrogenase (subunits 1 and 2; partitioned by codon position), (iv) cytochrome b and NADH dehydrogenase sequence together (six gene-codon partitions), (v) all unpartitioned sequence, (vi) a full multipartition analysis (nine partitions). Of these, only (iv) and (vi) performed well under the rate-drift model. These findings have significant implications for dating of recent divergence times in other taxa. The earliest P.lilfordi cladogenesis event (divergence of Menorcan populations), occurred before the end of the Pliocene, some 2.6Ma. Subsequent events led to a West Mallorcan lineage (2.0Ma ago), followed 1.2Ma ago by divergence of populations from the southern part of the Cabrera archipelago from a widely-distributed group from north Cabrera, northern and southern Mallorcan islets. Divergence within P.pityusensis is more recent with the main Ibiza and Formentera clades sharing a common ancestor at about 1.0Ma ago. Climatic and sea level changes are likely to have initiated cladogenesis, with lineages making secondary contact during periodic landbridge formation. This oscillating cross-archipelago pattern in which ancient divergence is followed by repeated contact resembles that seen between East-West refugia populations from mainland Europe.

Sexual selection drives speciation in an Amazonian frog

USGS Publications Warehouse

Boul, K.E.; Funk, W.C.; Darst, C.R.; Cannatella, D.C.; Ryan, M.J.

2007-01-01

One proposed mechanism of speciation is divergent sexual selection, whereby divergence in female preferences and male signals results in behavioural isolation. Despite the appeal of this hypothesis, evidence for it remains inconclusive. Here, we present several lines of evidence that sexual selection is driving behavioural isolation and speciation among populations of an Amazonian frog (Physalaemus petersi). First, sexual selection has promoted divergence in male mating calls and female preferences for calls between neighbouring populations, resulting in strong behavioural isolation. Second, phylogenetic analysis indicates that populations have become fixed for alternative call types several times throughout the species' range, and coalescent analysis rejects genetic drift as a cause for this pattern, suggesting that this divergence is due to selection. Finally, gene flow estimated with microsatellite loci is an average of 30 times lower between populations with different call types than between populations separated by a similar geographical distance with the same call type, demonstrating genetic divergence and incipient speciation. Taken together, these data provide strong evidence that sexual selection is driving behavioural isolation and speciation, supporting sexual selection as a cause for speciation in the wild. ?? 2006 The Royal Society.

Myopia Glasses and Optical Power Estimation: An Easy Experiment

ERIC Educational Resources Information Center

Ribeiro, Jair Lúcio Prados

2015-01-01

Human eye optics is a common high school physics topic and students usually show a great interest during our presentation of this theme. In this article, we present an easy way to estimate a diverging lens' optical power from a simple experiment involving myopia eyeglasses and a smartphone flashlight.

Myopia Glasses and Optical Power Estimation: An Easy Experiment

NASA Astrophysics Data System (ADS)

Ribeiro, Jair Lúcio Prados

2015-02-01

Human eye optics is a common high school physics topic and students usually show a great interest during our presentation of this theme. In this article, we present an easy way to estimate a diverging lens' optical power from a simple experiment involving myopia eyeglasses and a smartphone flashlight.

Velocity field measurements in oblique static divergent vocal fold models

NASA Astrophysics Data System (ADS)

Erath, Byron

2005-11-01

During normal phonation, the vocal fold cycle is characterized by the glottal opening transitioning from a convergent to a divergent passage and then closing before the cycle is repeated. Under ordinary phonatory conditions, both vocal folds, which form the glottal passage, move in phase with each other, creating a time-varying symmetric opening. However, abnormal pathological conditions, such as unilateral paralysis, and polyps, can result in geometrical asymmetries between the vocal folds throughout the phonatory cycle. This study investigates pulsatile flow fields through 7.5 times life-size vocal fold models with included divergence angles of 5 to 30 degrees, and obliquities between the vocal folds of up to 15 degrees. Flow conditions were scaled to match physiological parameters. Data were taken at the anterior posterior mid-plane using phase-averaged Particle Image Velocimetry (PIV). Viscous flow phenomena including the Coanda effect, flow separation points, and jet "flapping" were investigated. The results are compared to previously reported work of flow through symmetric divergent vocal fold models.

Information gains from cosmic microwave background experiments

NASA Astrophysics Data System (ADS)

Seehars, Sebastian; Amara, Adam; Refregier, Alexandre; Paranjape, Aseem; Akeret, Joël

2014-07-01

To shed light on the fundamental problems posed by dark energy and dark matter, a large number of experiments have been performed and combined to constrain cosmological models. We propose a novel way of quantifying the information gained by updates on the parameter constraints from a series of experiments which can either complement earlier measurements or replace them. For this purpose, we use the Kullback-Leibler divergence or relative entropy from information theory to measure differences in the posterior distributions in model parameter space from a pair of experiments. We apply this formalism to a historical series of cosmic microwave background experiments ranging from Boomerang to WMAP, SPT, and Planck. Considering different combinations of these experiments, we thus estimate the information gain in units of bits and distinguish contributions from the reduction of statistical errors and the "surprise" corresponding to a significant shift of the parameters' central values. For this experiment series, we find individual relative entropy gains ranging from about 1 to 30 bits. In some cases, e.g. when comparing WMAP and Planck results, we find that the gains are dominated by the surprise rather than by improvements in statistical precision. We discuss how this technique provides a useful tool for both quantifying the constraining power of data from cosmological probes and detecting the tensions between experiments.

Efficient Moment-Based Inference of Admixture Parameters and Sources of Gene Flow

PubMed Central

Levin, Alex; Reich, David; Patterson, Nick; Berger, Bonnie

2013-01-01

The recent explosion in available genetic data has led to significant advances in understanding the demographic histories of and relationships among human populations. It is still a challenge, however, to infer reliable parameter values for complicated models involving many populations. Here, we present MixMapper, an efficient, interactive method for constructing phylogenetic trees including admixture events using single nucleotide polymorphism (SNP) genotype data. MixMapper implements a novel two-phase approach to admixture inference using moment statistics, first building an unadmixed scaffold tree and then adding admixed populations by solving systems of equations that express allele frequency divergences in terms of mixture parameters. Importantly, all features of the model, including topology, sources of gene flow, branch lengths, and mixture proportions, are optimized automatically from the data and include estimates of statistical uncertainty. MixMapper also uses a new method to express branch lengths in easily interpretable drift units. We apply MixMapper to recently published data for Human Genome Diversity Cell Line Panel individuals genotyped on a SNP array designed especially for use in population genetics studies, obtaining confident results for 30 populations, 20 of them admixed. Notably, we confirm a signal of ancient admixture in European populations—including previously undetected admixture in Sardinians and Basques—involving a proportion of 20–40% ancient northern Eurasian ancestry. PMID:23709261

Determining the Effect of Natural Selection on Linked Neutral Divergence across Species

PubMed Central

Phung, Tanya N.; Lohmueller, Kirk E.

2016-01-01

A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only if more of the genome is under purifying selection than currently believed. Our work has implications for understanding the evolution of genomes and interpreting patterns of genetic variation. PMID:27508305

Determining the Effect of Natural Selection on Linked Neutral Divergence across Species.

PubMed

Phung, Tanya N; Huber, Christian D; Lohmueller, Kirk E

2016-08-01

A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only if more of the genome is under purifying selection than currently believed. Our work has implications for understanding the evolution of genomes and interpreting patterns of genetic variation.

Flux-tube divergence, coronal heating, and the solar wind

NASA Technical Reports Server (NTRS)

Wang, Y.-M.

1993-01-01

Using model calculations based on a self-consistent treatment of the coronal energy balance, we show how the magnetic flux-tube divergence rate controls the coronal temperature and the properties of the solar wind. For a fixed input of mechanical and Alfven-wave energy at the coronal base, we find that as the divergence rate increases, the maximum coronal temperature decreases but the mass flux leaving the sun gradually increases. As a result, the asymptotic wind speed decreases with increasing expansion factor near the sun, in agreement with empirical studies. As noted earlier by Withbroe, the calculated mass flux at the sun is remarkably insensitive to parameter variations; when combined with magnetohydrodynamic considerations, this self-regulatory property of the model explains the observed constancy of the mass flux at earth.

High levels of effective long-distance dispersal may blur ecotypic divergence in a rare terrestrial orchid.

PubMed

Vanden Broeck, An; Van Landuyt, Wouter; Cox, Karen; De Bruyn, Luc; Gyselings, Ralf; Oostermeijer, Gerard; Valentin, Bertille; Bozic, Gregor; Dolinar, Branko; Illyés, Zoltán; Mergeay, Joachim

2014-07-07

Gene flow and adaptive divergence are key aspects of metapopulation dynamics and ecological speciation. Long-distance dispersal is hard to detect and few studies estimate dispersal in combination with adaptive divergence. The aim of this study was to investigate effective long-distance dispersal and adaptive divergence in the fen orchid (Liparis loeselii (L.) Rich.). We used amplified fragment length polymorphism (AFLP)-based assignment tests to quantify effective long-distance dispersal at two different regions in Northwest Europe. In addition, genomic divergence between fen orchid populations occupying two distinguishable habitats, wet dune slacks and alkaline fens, was investigated by a genome scan approach at different spatial scales (continental, landscape and regional) and based on 451 AFLP loci. We expected that different habitats would contribute to strong divergence and restricted gene flow resulting in isolation-by-adaptation. Instead, we found remarkably high levels of effective long-distance seed dispersal and low levels of adaptive divergence. At least 15% of the assigned individuals likely originated from among-population dispersal events with dispersal distances up to 220 km. Six (1.3%) 'outlier' loci, potentially reflecting local adaptation to habitat-type, were identified with high statistical support. Of these, only one (0.22%) was a replicated outlier in multiple independent dune-fen population comparisons and thus possibly reflecting truly parallel divergence. Signals of adaptation in response to habitat type were most evident at the scale of individual populations. The findings of this study suggest that the homogenizing effect of effective long-distance seed dispersal may overwhelm divergent selection associated to habitat type in fen orchids in Northwest Europe.

High levels of effective long-distance dispersal may blur ecotypic divergence in a rare terrestrial orchid

PubMed Central

2014-01-01

Background Gene flow and adaptive divergence are key aspects of metapopulation dynamics and ecological speciation. Long-distance dispersal is hard to detect and few studies estimate dispersal in combination with adaptive divergence. The aim of this study was to investigate effective long-distance dispersal and adaptive divergence in the fen orchid (Liparis loeselii (L.) Rich.). We used amplified fragment length polymorphism (AFLP)-based assignment tests to quantify effective long-distance dispersal at two different regions in Northwest Europe. In addition, genomic divergence between fen orchid populations occupying two distinguishable habitats, wet dune slacks and alkaline fens, was investigated by a genome scan approach at different spatial scales (continental, landscape and regional) and based on 451 AFLP loci. Results We expected that different habitats would contribute to strong divergence and restricted gene flow resulting in isolation-by-adaptation. Instead, we found remarkably high levels of effective long-distance seed dispersal and low levels of adaptive divergence. At least 15% of the assigned individuals likely originated from among-population dispersal events with dispersal distances up to 220 km. Six (1.3%) ‘outlier’ loci, potentially reflecting local adaptation to habitat-type, were identified with high statistical support. Of these, only one (0.22%) was a replicated outlier in multiple independent dune-fen population comparisons and thus possibly reflecting truly parallel divergence. Signals of adaptation in response to habitat type were most evident at the scale of individual populations. Conclusions The findings of this study suggest that the homogenizing effect of effective long-distance seed dispersal may overwhelm divergent selection associated to habitat type in fen orchids in Northwest Europe. PMID:24998243

The Divergence of Neandertal and Modern Human Y Chromosomes

PubMed Central

Mendez, Fernando L.; Poznik, G. David; Castellano, Sergi; Bustamante, Carlos D.

2016-01-01

Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups. PMID:27058445

Vagaries of the molecular clock

PubMed Central

Ayala, Francisco J.

1997-01-01

The hypothesis of the molecular evolutionary clock asserts that informational macromolecules (i.e., proteins and nucleic acids) evolve at rates that are constant through time and for different lineages. The clock hypothesis has been extremely powerful for determining evolutionary events of the remote past for which the fossil and other evidence is lacking or insufficient. I review the evolution of two genes, Gpdh and Sod. In fruit flies, the encoded glycerol-3-phosphate dehydrogenase (GPDH) protein evolves at a rate of 1.1 × 10−10 amino acid replacements per site per year when Drosophila species are compared that diverged within the last 55 million years (My), but a much faster rate of ≈4.5 × 10−10 replacements per site per year when comparisons are made between mammals (≈70 My) or Dipteran families (≈100 My), animal phyla (≈650 My), or multicellular kingdoms (≈1100 My). The rate of superoxide dismutase (SOD) evolution is very fast between Drosophila species (16.2 × 10−10 replacements per site per year) and remains the same between mammals (17.2) or Dipteran families (15.9), but it becomes much slower between animal phyla (5.3) and still slower between the three kingdoms (3.3). If we assume a molecular clock and use the Drosophila rate for estimating the divergence of remote organisms, GPDH yields estimates of 2,500 My for the divergence between the animal phyla (occurred ≈650 My) and 3,990 My for the divergence of the kingdoms (occurred ≈1,100 My). At the other extreme, SOD yields divergence times of 211 My and 224 My for the animal phyla and the kingdoms, respectively. It remains unsettled how often proteins evolve in such erratic fashion as GPDH and SOD. PMID:9223263

Diversification in North American arid lands: niche conservatism, divergence and expansion of habitat explain speciation in the genus Ephedra.

PubMed

Loera, Israel; Sosa, Victoria; Ickert-Bond, Stefanie M

2012-11-01

A lineage of 12 arid land shrubby species in the gymnosperm genus Ephedra (Gnetales) from North America is used to evaluate the influence of climate on speciation. With a long evolutionary history, and a well documented fossil record this lineage is an ideal model for understanding the process of speciation under a niche conservatism scenario. Using seven DNA molecular markers, Bayesian inference is carried out to uncover sister species and to estimate time of divergence of the lineages. Ecological niche models are generated for four parapatric and sympatric sister species and two analyses of niche evolution are performed, one based on ecological niche models and another using raw data and multivariate analysis. As previous analyses suggest, the diversification of North America Ephedra species may be the result of a recent secondary radiation. Both parapatric and sympatric species diverged mostly in a scenario of climatic niche conservatism. However, we also found strong evidence for niche divergence for one of the sister species pairs (E. californica-E. trifurca). Moreover, the multivariate analysis found environmental differences for some variables between sister species. The estimated divergence time of three pairs of sister species distributed in southwestern North America (E. cutleri-E. aspera, E. californica-E. trifurca and E. torreyana-E. viridis) is inferred to have occurred in the Late Miocene to Pliocene and for the sister species pair E. antisyphilitica-E. coryi distributed in the southern United States and northeastern Mexico, it was inferred from the Pliocene to Pleistocene. The orogenetic and climatic changes documented for these regions related to expansion of arid lands, may have contributed to the diversification in North American Ephedra, rather than adaptations to new climatic conditions. Copyright © 2012 Elsevier Inc. All rights reserved.

The Divergence of Neandertal and Modern Human Y Chromosomes.

PubMed

Mendez, Fernando L; Poznik, G David; Castellano, Sergi; Bustamante, Carlos D

2016-04-07

Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes-including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447-806 kya). This is ∼2.1 (95% CI: 1.7-2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Molecular phylogeny of osteoglossoids: a new model for Gondwanian origin and plate tectonic transportation of the Asian arowana.

PubMed

Kumazawa, Y; Nishida, M

2000-12-01

One of the traditional enigmas in freshwater zoogeography has been the evolutionary origin of Scleropages formosus inhabiting Southeast Asia (the Asian arowana), which is a species threatened with extinction among the highly freshwater-adapted fishes from the order Osteoglossiformes. Dispersalists have hypothesized that it originated from the recent (the Miocene or later) transmarine dispersal of morphologically quite similar Australasian arowanas across Wallace's Line, but this hypothesis has been questioned due to their remarkable adaptation to freshwater. We determined the complete nucleotide sequences of two mitochondrial protein genes from 12 osteoglossiform species, including all members of the suborder Osteoglossoidei, with which robust molecular phylogeny was constructed and divergence times were estimated. In agreement with previous morphology-based phylogenetic studies, our molecular phylogeny suggested that the osteoglossiforms diverged from a basal position of the teleostean lineage, that heterotidines (the Nile arowana and the pirarucu) form a sister group of osteoglossines (arowanas in South America, Australasia, and Southeast Asia), and that the Asian arowana is more closely related to Australasian arowanas than to South American ones. However, molecular distances between the Asian and Australasian arowanas were much larger than expected from the fact that they are classified within the same genus. By using the molecular clock of bony fishes, tested for its good performance for rather deep divergences and calibrated using some reasonable assumptions, the divergence between the Asian and Australasian arowanas was estimated to date back to the early Cretaceous. Based on the molecular and geological evidence, we propose a new model whereby the Asian arowana vicariantly diverged from the Australasian arowanas in the eastern margin of Gondwanaland and migrated into Eurasia on the Indian subcontinent or smaller continental blocks. This study also implicates the relatively long absence of osteoglossiform fossil records from the Mesozoic.

A meta-analysis of neuroimaging studies on divergent thinking using activation likelihood estimation.

PubMed

Wu, Xin; Yang, Wenjing; Tong, Dandan; Sun, Jiangzhou; Chen, Qunlin; Wei, Dongtao; Zhang, Qinglin; Zhang, Meng; Qiu, Jiang

2015-07-01

In this study, an activation likelihood estimation (ALE) meta-analysis was used to conduct a quantitative investigation of neuroimaging studies on divergent thinking. Based on the ALE results, the functional magnetic resonance imaging (fMRI) studies showed that distributed brain regions were more active under divergent thinking tasks (DTTs) than those under control tasks, but a large portion of the brain regions were deactivated. The ALE results indicated that the brain networks of the creative idea generation in DTTs may be composed of the lateral prefrontal cortex, posterior parietal cortex [such as the inferior parietal lobule (BA 40) and precuneus (BA 7)], anterior cingulate cortex (ACC) (BA 32), and several regions in the temporal cortex [such as the left middle temporal gyrus (BA 39), and left fusiform gyrus (BA 37)]. The left dorsolateral prefrontal cortex (BA 46) was related to selecting the loosely and remotely associated concepts and organizing them into creative ideas, whereas the ACC (BA 32) was related to observing and forming distant semantic associations in performing DTTs. The posterior parietal cortex may be involved in the semantic information related to the retrieval and buffering of the formed creative ideas, and several regions in the temporal cortex may be related to the stored long-term memory. In addition, the ALE results of the structural studies showed that divergent thinking was related to the dopaminergic system (e.g., left caudate and claustrum). Based on the ALE results, both fMRI and structural MRI studies could uncover the neural basis of divergent thinking from different aspects (e.g., specific cognitive processing and stable individual difference of cognitive capability). © 2015 Wiley Periodicals, Inc.

Relative information content of polymorphic microsatellites and mitochondrial DNA for inferring dispersal and population genetic structure in the olive sea snake, Aipysurus laevis.

PubMed

Lukoschek, V; Waycott, M; Keogh, J S

2008-07-01

Polymorphic microsatellites are widely considered more powerful for resolving population structure than mitochondrial DNA (mtDNA) markers, particularly for recently diverged lineages or geographically proximate populations. Weaker population subdivision for biparentally inherited nuclear markers than maternally inherited mtDNA may signal male-biased dispersal but can also be attributed to marker-specific evolutionary characteristics and sampling properties. We discriminated between these competing explanations with a population genetic study on olive sea snakes, Aipysurus laevis. A previous mtDNA study revealed strong regional population structure for A. laevis around northern Australia, where Pleistocene sea-level fluctuations have influenced the genetic signatures of shallow-water marine species. Divergences among phylogroups dated to the Late Pleistocene, suggesting recent range expansions by previously isolated matrilines. Fine-scale population structure within regions was, however, poorly resolved for mtDNA. In order to improve estimates of fine-scale genetic divergence and to compare population structure between nuclear and mtDNA, 354 olive sea snakes (previously sequenced for mtDNA) were genotyped for five microsatellite loci. F statistics and Bayesian multilocus genotype clustering analyses found similar regional population structure as mtDNA and, after standardizing microsatellite F statistics for high heterozygosities, regional divergence estimates were quantitatively congruent between marker classes. Over small spatial scales, however, microsatellites recovered almost no genetic structure and standardized F statistics were orders of magnitude smaller than for mtDNA. Three tests for male-biased dispersal were not significant, suggesting that recent demographic expansions to the typically large population sizes of A. laevis have prevented microsatellites from reaching mutation-drift equilibrium and local populations may still be diverging.

Social selection parapatry in Afrotropical sunbirds.

PubMed

McEntee, Jay P; Peñalba, Joshua V; Werema, Chacha; Mulungu, Elia; Mbilinyi, Maneno; Moyer, David; Hansen, Louis; Fjeldså, Jon; Bowie, Rauri C K

2016-06-01

The extent of range overlap of incipient and recent species depends on the type and magnitude of phenotypic divergence that separates them, and the consequences of phenotypic divergence on their interactions. Signal divergence by social selection likely initiates many speciation events, but may yield niche-conserved lineages predisposed to limit each others' ranges via ecological competition. Here, we examine this neglected aspect of social selection speciation theory in relation to the discovery of a nonecotonal species border between sunbirds. We find that Nectarinia moreaui and Nectarinia fuelleborni meet in a ∼6 km wide contact zone, as estimated by molecular cline analysis. These species exploit similar bioclimatic niches, but sing highly divergent learned songs, consistent with divergence by social selection. Cline analyses suggest that within-species stabilizing social selection on song-learning predispositions maintains species differences in song despite both hybridization and cultural transmission. We conclude that ecological competition between moreaui and fuelleborni contributes to the stabilization of the species border, but that ecological competition acts in conjunction with reproductive interference. The evolutionary maintenance of learned song differences in a hybrid zone recommend this study system for future studies on the mechanisms of learned song divergence and its role in speciation. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Theoretical study on second-harmonic generation of focused vortex beams

NASA Astrophysics Data System (ADS)

Tang, Daolong; Wang, Jing; Ma, Jingui; Zhou, Bingjie; Yuan, Peng; Xie, Guoqiang; Zhu, Heyuan; Qian, Liejia

2018-03-01

Second-harmonic generation (SHG) provides a promising route for generating vortex beams of both short wavelength and large topological charge. Here we theoretically investigate the efficiency optimization and beam characteristics of focused vortex-beam SHG. Owing to the increasing beam divergence, vortex beams have distinct features in SHG optimization compared with a Gaussian beam. We show that, under the noncritical phase-matching condition, the Boyd and Kleinman prediction of the optimal focusing parameter for Gaussian-beam SHG remains valid for vortex-beam SHG. However, under the critical phase-matching condition, which is sensitive to the beam divergence, the Boyd and Kleinman prediction is no longer valid. In contrast, the optimal focusing parameter for maximizing the SHG efficiency strongly depends on the vortex order. We also investigate the effects of focusing and phase-matching conditions on the second-harmonic beam characteristics.

Geographical variation in sound production in the anemonefish Amphiprion akallopisos.

PubMed

Parmentier, E; Lagardère, J P; Vandewalle, P; Fine, M L

2005-08-22

Because of pelagic-larval dispersal, coral-reef fishes are distributed widely with minimal genetic differentiation between populations. Amphiprion akallopisos, a clownfish that uses sound production to defend its anemone territory, has a wide but disjunct distribution in the Indian Ocean. We compared sounds produced by these fishes from populations in Madagascar and Indonesia, a distance of 6500 km. Differentiation of agonistic calls into distinct types indicates a complexity not previously recorded in fishes' acoustic communication. Moreover, various acoustic parameters, including peak frequency, pulse duration, number of peaks per pulse, differed between the two populations. The geographic comparison is the first to demonstrate 'dialects' in a marine fish species, and these differences in sound parameters suggest genetic divergence between these two populations. These results highlight the possible approach for investigating the role of sounds in fish behaviour in reproductive divergence and speciation.

Addressing the impact of environmental uncertainty in plankton model calibration with a dedicated software system: the Marine Model Optimization Testbed (MarMOT 1.1 alpha)

NASA Astrophysics Data System (ADS)

Hemmings, J. C. P.; Challenor, P. G.

2012-04-01

A wide variety of different plankton system models have been coupled with ocean circulation models, with the aim of understanding and predicting aspects of environmental change. However, an ability to make reliable inferences about real-world processes from the model behaviour demands a quantitative understanding of model error that remains elusive. Assessment of coupled model output is inhibited by relatively limited observing system coverage of biogeochemical components. Any direct assessment of the plankton model is further inhibited by uncertainty in the physical state. Furthermore, comparative evaluation of plankton models on the basis of their design is inhibited by the sensitivity of their dynamics to many adjustable parameters. Parameter uncertainty has been widely addressed by calibrating models at data-rich ocean sites. However, relatively little attention has been given to quantifying uncertainty in the physical fields required by the plankton models at these sites, and tendencies in the biogeochemical properties due to the effects of horizontal processes are often neglected. Here we use model twin experiments, in which synthetic data are assimilated to estimate a system's known "true" parameters, to investigate the impact of error in a plankton model's environmental input data. The experiments are supported by a new software tool, the Marine Model Optimization Testbed, designed for rigorous analysis of plankton models in a multi-site 1-D framework. Simulated errors are derived from statistical characterizations of the mixed layer depth, the horizontal flux divergence tendencies of the biogeochemical tracers and the initial state. Plausible patterns of uncertainty in these data are shown to produce strong temporal and spatial variability in the expected simulation error variance over an annual cycle, indicating variation in the significance attributable to individual model-data differences. An inverse scheme using ensemble-based estimates of the simulation error variance to allow for this environment error performs well compared with weighting schemes used in previous calibration studies, giving improved estimates of the known parameters. The efficacy of the new scheme in real-world applications will depend on the quality of statistical characterizations of the input data. Practical approaches towards developing reliable characterizations are discussed.

Non-Fickian dispersion of groundwater age

PubMed Central

Engdahl, Nicholas B.; Ginn, Timothy R.; Fogg, Graham E.

2014-01-01

We expand the governing equation of groundwater age to account for non-Fickian dispersive fluxes using continuous random walks. Groundwater age is included as an additional (fifth) dimension on which the volumetric mass density of water is distributed and we follow the classical random walk derivation now in five dimensions. The general solution of the random walk recovers the previous conventional model of age when the low order moments of the transition density functions remain finite at their limits and describes non-Fickian age distributions when the transition densities diverge. Previously published transition densities are then used to show how the added dimension in age affects the governing differential equations. Depending on which transition densities diverge, the resulting models may be nonlocal in time, space, or age and can describe asymptotic or pre-asymptotic dispersion. A joint distribution function of time and age transitions is developed as a conditional probability and a natural result of this is that time and age must always have identical transition rate functions. This implies that a transition density defined for age can substitute for a density in time and this has implications for transport model parameter estimation. We present examples of simulated age distributions from a geologically based, heterogeneous domain that exhibit non-Fickian behavior and show that the non-Fickian model provides better descriptions of the distributions than the Fickian model. PMID:24976651

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

PubMed

Cracraft, Joel; Houde, Peter; Ho, Simon Y W; Mindell, David P; Fjeldså, Jon; Lindow, Bent; Edwards, Scott V; Rahbek, Carsten; Mirarab, Siavash; Warnow, Tandy; Gilbert, M Thomas P; Zhang, Guojie; Braun, Edward L; Jarvis, Erich D

2015-09-25

Mitchell et al. argue that divergence-time estimates for our avian phylogeny were too young because of an "inappropriate" maximum age constraint for the most recent common ancestor of modern birds and that, as a result, most modern bird orders diverged before the Cretaceous-Paleogene mass extinction event 66 million years ago instead of after. However, their interpretations of the fossil record and timetrees are incorrect. Copyright © 2015, American Association for the Advancement of Science.

Selecting broiler chickens for ultimate pH of breast muscle: analysis of divergent selection experiment and phenotypic consequences on meat quality, growth, and body composition traits.

PubMed

Alnahhas, N; Berri, C; Boulay, M; Baéza, E; Jégo, Y; Baumard, Y; Chabault, M; Le Bihan-Duval, E

2014-09-01

Genetic parameters for ultimate pH of pectoralis major muscle (PM-pHu) and sartorius muscle (SART-pHu); color parameters L*, a*, b*; logarithm of drip loss (LogDL) of pectoralis major (PM) muscle; breast meat yield (BMY); thigh and drumstick yield (TY); abdominal fat percentage (AFP); and BW at 6 wk (BW6) were estimated in 2 lines of broiler chickens divergently selected for PM-pHu. Effects of selection on all the previous traits and on glycolytic potential, pectoralis major muscle pH at 15 min postmortem, curing-cooking yield (CCY), cooking loss (CL), and Warner-Bratzler shear force (WBSF) of the PM muscle were also analyzed after 5 generations. Strong genetic determinism of PM-pHu was observed, with estimated h(2) of 0.57 ± 0.02. There was a significant positive genetic correlation (rg) between PM-pHu and SART-pHu (0.54 ± 0.04), indicating that selection had a general rather than a specific effect on energy storage in skeletal muscles. The h(2) estimates of L*, a*, and b* parameters were 0.58 ± 0.02, 0.39 ± 0.02, and 0.48 ± 0.02, respectively. Heritability estimates for TY, BMY, and AFP were 0.39 ± 0.04, 0.52 ± 0.01, and 0.71 ± 0.02, respectively. Our results indicated different genetic control of LogDL and L* of the meat between the 2 lines; these traits had a strong rg with PM-pHu in the line selected for low ultimate pH (pHu) value (pHu-; -0.80 and -0.71, respectively), which was not observed in the line selected for high pHu value (pHu+; -0.04 and -0.29, respectively). A significant positive rg (0.21 ± 0.04) was observed between PM-pHu and BMY but not between PM-pHu and BW6, AFP, or TY. Significant phenotypic differences were observed after 5 generations of selection between the 2 lines. The mean differences (P < 0.001) in pHu between the 2 lines were 0.42 and 0.21 pH units in the breast and thigh muscle, respectively. Breast meat in the pHu+ line exhibited lower L* (-5 units; P < 0.001), a* (-0.22 units; P < 0.001), b* (-1.53 units; P < 0.001), and drip loss (-1.6 units; P < 0.001) than in the pHu- line. Breast meat of the pHu+ line was also characterized by greater CCY (+6.1 units; P < 0.001), lower CL (-1.66 units; P < 0.01), and lower WBSF after cooking (-5.1 units; P < 0.001) compared to the pHu- line. This study highlighted that selection based on pHu can be effective in improving the processing ability of breast meat and reducing the incidence of meat quality defects without affecting chicken growth performance.

Using Rate of Divergence as an Objective Measure to Differentiate between Voice Signal Types Based on the Amount of Disorder in the Signal.

PubMed

Calawerts, William M; Lin, Liyu; Sprott, J C; Jiang, Jack J

2017-01-01

The purpose of this paper is to introduce the rate of divergence as an objective measure to differentiate between the four voice types based on the amount of disorder present in a signal. We hypothesized that rate of divergence would provide an objective measure that can quantify all four voice types. A total of 150 acoustic voice recordings were randomly selected and analyzed using traditional perturbation, nonlinear, and rate of divergence analysis methods. We developed a new parameter, rate of divergence, which uses a modified version of Wolf's algorithm for calculating Lyapunov exponents of a system. The outcome of this calculation is not a Lyapunov exponent, but rather a description of the divergence of two nearby data points for the next three points in the time series, followed in three time-delayed embedding dimensions. This measure was compared to currently existing perturbation and nonlinear dynamic methods of distinguishing between voice signals. There was a direct relationship between voice type and rate of divergence. This calculation is especially effective at differentiating between type 3 and type 4 voices (P < 0.001) and is equally effective at differentiating type 1, type 2, and type 3 signals as currently existing methods. The rate of divergence calculation introduced is an objective measure that can be used to distinguish between all four voice types based on the amount of disorder present, leading to quicker and more accurate voice typing as well as an improved understanding of the nonlinear dynamics involved in phonation. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

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.

Sensitivity of Beam Parameters to a Station C Solenoid Scan on Axis II

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

Schulze, Martin E.

Magnet scans are a standard technique for determining beam parameters in accelerators. Beam parameters are inferred from spot size measurements using a model of the beam optics. The sensitivity of the measured beam spot size to the beam parameters is investigated for typical DARHT Axis II beam energies and currents. In a typical S4 solenoid scan, the downstream transport is tuned to achieve a round beam at Station C with an envelope radius of about 1.5 cm with a very small divergence with S4 off. The typical beam energy and current are 16.0 MeV and 1.625 kA. Figures 1-3 showmore » the sensitivity of the bean size at Station C to the emittance, initial radius and initial angle respectively. To better understand the relative sensitivity of the beam size to the emittance, initial radius and initial angle, linear regressions were performed for each parameter as a function of the S4 setting. The results are shown in Figure 4. The measured slope was scaled to have a maximum value of 1 in order to present the relative sensitivities in a single plot. Figure 4 clearly shows the beam size at the minimum of the S4 scan is most sensitive to emittance and relatively insensitive to initial radius and angle as expected. The beam emittance is also very sensitive to the beam size of the converging beam and becomes insensitive to the beam size of the diverging beam. Measurements of the beam size of the diverging beam provide the greatest sensitivity to the initial beam radius and to a lesser extent the initial beam angle. The converging beam size is initially very sensitive to the emittance and initial angle at low S4 currents. As the S4 current is increased the sensitivity to the emittance remains strong while the sensitivity to the initial angle diminishes.« less

Comparative Study of Three Data Assimilation Methods for Ice Sheet Model Initialisation

NASA Astrophysics Data System (ADS)

Mosbeux, Cyrille; Gillet-Chaulet, Fabien; Gagliardini, Olivier

2015-04-01

The current global warming has direct consequences on ice-sheet mass loss contributing to sea level rise. This loss is generally driven by an acceleration of some coastal outlet glaciers and reproducing these mechanisms is one of the major issues in ice-sheet and ice flow modelling. The construction of an initial state, as close as possible to current observations, is required as a prerequisite before producing any reliable projection of the evolution of ice-sheets. For this step, inverse methods are often used to infer badly known or unknown parameters. For instance, the adjoint inverse method has been implemented and applied with success by different authors in different ice flow models in order to infer the basal drag [ Schafer et al., 2012; Gillet-chauletet al., 2012; Morlighem et al., 2010]. Others data fields, such as ice surface and bedrock topography, are easily measurable with more or less uncertainty but only locally along tracks and interpolated on finer model grid. All these approximations lead to errors on the data elevation model and give rise to an ill-posed problem inducing non-physical anomalies in flux divergence [Seroussi et al, 2011]. A solution to dissipate these divergences of flux is to conduct a surface relaxation step at the expense of the accuracy of the modelled surface [Gillet-Chaulet et al., 2012]. Other solutions, based on the inversion of ice thickness and basal drag were proposed [Perego et al., 2014; Pralong & Gudmundsson, 2011]. In this study, we create a twin experiment to compare three different assimilation algorithms based on inverse methods and nudging to constrain the bedrock friction and the bedrock elevation: (i) cyclic inversion of friction parameter and bedrock topography using adjoint method, (ii) cycles coupling inversion of friction parameter using adjoint method and nudging of bedrock topography, (iii) one step inversion of both parameters with adjoint method. The three methods show a clear improvement in parameters knowledge leading to a significant reduction of flux divergence of the model before forecasting.

Robust mislabel logistic regression without modeling mislabel probabilities.

PubMed

Hung, Hung; Jou, Zhi-Yu; Huang, Su-Yun

2018-03-01

Logistic regression is among the most widely used statistical methods for linear discriminant analysis. In many applications, we only observe possibly mislabeled responses. Fitting a conventional logistic regression can then lead to biased estimation. One common resolution is to fit a mislabel logistic regression model, which takes into consideration of mislabeled responses. Another common method is to adopt a robust M-estimation by down-weighting suspected instances. In this work, we propose a new robust mislabel logistic regression based on γ-divergence. Our proposal possesses two advantageous features: (1) It does not need to model the mislabel probabilities. (2) The minimum γ-divergence estimation leads to a weighted estimating equation without the need to include any bias correction term, that is, it is automatically bias-corrected. These features make the proposed γ-logistic regression more robust in model fitting and more intuitive for model interpretation through a simple weighting scheme. Our method is also easy to implement, and two types of algorithms are included. Simulation studies and the Pima data application are presented to demonstrate the performance of γ-logistic regression. © 2017, The International Biometric Society.

Construction of multiple linear regression models using blood biomarkers for selecting against abdominal fat traits in broilers.

PubMed

Dong, J Q; Zhang, X Y; Wang, S Z; Jiang, X F; Zhang, K; Ma, G W; Wu, M Q; Li, H; Zhang, H

2018-01-01

Plasma very low-density lipoprotein (VLDL) can be used to select for low body fat or abdominal fat (AF) in broilers, but its correlation with AF is limited. We investigated whether any other biochemical indicator can be used in combination with VLDL for a better selective effect. Nineteen plasma biochemical indicators were measured in male chickens from the Northeast Agricultural University broiler lines divergently selected for AF content (NEAUHLF) in the fed state at 46 and 48 d of age. The average concentration of every parameter for the 2 d was used for statistical analysis. Levels of these 19 plasma biochemical parameters were compared between the lean and fat lines. The phenotypic correlations between these plasma biochemical indicators and AF traits were analyzed. Then, multiple linear regression models were constructed to select the best model used for selecting against AF content. and the heritabilities of plasma indicators contained in the best models were estimated. The results showed that 11 plasma biochemical indicators (triglycerides, total bile acid, total protein, globulin, albumin/globulin, aspartate transaminase, alanine transaminase, gamma-glutamyl transpeptidase, uric acid, creatinine, and VLDL) differed significantly between the lean and fat lines (P < 0.01), and correlated significantly with AF traits (P < 0.05). The best multiple linear regression models based on albumin/globulin, VLDL, triglycerides, globulin, total bile acid, and uric acid, had higher R2 (0.73) than the model based only on VLDL (0.21). The plasma parameters included in the best models had moderate heritability estimates (0.21 ≤ h2 ≤ 0.43). These results indicate that these multiple linear regression models can be used to select for lean broiler chickens. © 2017 Poultry Science Association Inc.

Generalized entropies and the similarity of texts

NASA Astrophysics Data System (ADS)

Altmann, Eduardo G.; Dias, Laércio; Gerlach, Martin

2017-01-01

We show how generalized Gibbs-Shannon entropies can provide new insights on the statistical properties of texts. The universal distribution of word frequencies (Zipf’s law) implies that the generalized entropies, computed at the word level, are dominated by words in a specific range of frequencies. Here we show that this is the case not only for the generalized entropies but also for the generalized (Jensen-Shannon) divergences, used to compute the similarity between different texts. This finding allows us to identify the contribution of specific words (and word frequencies) for the different generalized entropies and also to estimate the size of the databases needed to obtain a reliable estimation of the divergences. We test our results in large databases of books (from the google n-gram database) and scientific papers (indexed by Web of Science).

Logarithmic Superdiffusion in Two Dimensional Driven Lattice Gases

NASA Astrophysics Data System (ADS)

Krug, J.; Neiss, R. A.; Schadschneider, A.; Schmidt, J.

2018-03-01

The spreading of density fluctuations in two-dimensional driven diffusive systems is marginally anomalous. Mode coupling theory predicts that the diffusivity in the direction of the drive diverges with time as (ln t)^{2/3} with a prefactor depending on the macroscopic current-density relation and the diffusion tensor of the fluctuating hydrodynamic field equation. Here we present the first numerical verification of this behavior for a particular version of the two-dimensional asymmetric exclusion process. Particles jump strictly asymmetrically along one of the lattice directions and symmetrically along the other, and an anisotropy parameter p governs the ratio between the two rates. Using a novel massively parallel coupling algorithm that strongly reduces the fluctuations in the numerical estimate of the two-point correlation function, we are able to accurately determine the exponent of the logarithmic correction. In addition, the variation of the prefactor with p provides a stringent test of mode coupling theory.

Mixed-order phase transition of the contact process near multiple junctions.

PubMed

Juhász, Róbert; Iglói, Ferenc

2017-02-01

We have studied the phase transition of the contact process near a multiple junction of M semi-infinite chains by Monte Carlo simulations. As opposed to the continuous transitions of the translationally invariant (M=2) and semi-infinite (M=1) system, the local order parameter is found to be discontinuous for M>2. Furthermore, the temporal correlation length diverges algebraically as the critical point is approached, but with different exponents on the two sides of the transition. In the active phase, the estimate is compatible with the bulk value, while in the inactive phase it exceeds the bulk value and increases with M. The unusual local critical behavior is explained by a scaling theory with an irrelevant variable, which becomes dangerous in the inactive phase. Quenched spatial disorder is found to make the transition continuous in agreement with earlier renormalization group results.

Extracting scene feature vectors through modeling, volume 3

NASA Technical Reports Server (NTRS)

Berry, J. K.; Smith, J. A.

1976-01-01

The remote estimation of the leaf area index of winter wheat at Finney County, Kansas was studied. The procedure developed consists of three activities: (1) field measurements; (2) model simulations; and (3) response classifications. The first activity is designed to identify model input parameters and develop a model evaluation data set. A stochastic plant canopy reflectance model is employed to simulate reflectance in the LANDSAT bands as a function of leaf area index for two phenological stages. An atmospheric model is used to translate these surface reflectances into simulated satellite radiance. A divergence classifier determines the relative similarity between model derived spectral responses and those of areas with unknown leaf area index. The unknown areas are assigned the index associated with the closest model response. This research demonstrated that the SRVC canopy reflectance model is appropriate for wheat scenes and that broad categories of leaf area index can be inferred from the procedure developed.

Testing a new Free Core Nutation empirical model

NASA Astrophysics Data System (ADS)

Belda, Santiago; Ferrándiz, José M.; Heinkelmann, Robert; Nilsson, Tobias; Schuh, Harald

2016-03-01

The Free Core Nutation (FCN) is a free mode of the Earth's rotation caused by the different material characteristics of the Earth's core and mantle. This causes the rotational axes of those layers to slightly diverge from each other, resulting in a wobble of the Earth's rotation axis comparable to nutations. In this paper we focus on estimating empirical FCN models using the observed nutations derived from the VLBI sessions between 1993 and 2013. Assuming a fixed value for the oscillation period, the time-variable amplitudes and phases are estimated by means of multiple sliding window analyses. The effects of using different a priori Earth Rotation Parameters (ERP) in the derivation of models are also addressed. The optimal choice of the fundamental parameters of the model, namely the window width and step-size of its shift, is searched by performing a thorough experimental analysis using real data. The former analyses lead to the derivation of a model with a temporal resolution higher than the one used in the models currently available, with a sliding window reduced to 400 days and a day-by-day shift. It is shown that this new model increases the accuracy of the modeling of the observed Earth's rotation. Besides, empirical models determined from USNO Finals as a priori ERP present a slightly lower Weighted Root Mean Square (WRMS) of residuals than IERS 08 C04 along the whole period of VLBI observations, according to our computations. The model is also validated through comparisons with other recognized models. The level of agreement among them is satisfactory. Let us remark that our estimates give rise to the lowest residuals and seem to reproduce the FCN signal in more detail.

Neopolyploidy and diversification in Heuchera grossulariifolia.

PubMed

Oswald, Benjamin P; Nuismer, Scott L

2011-06-01

Newly formed polyploid lineages must contend with several obstacles to avoid extinction, including minority cytotype exclusion, competition, and inbreeding depression. If polyploidization results in immediate divergence of phenotypic characters these hurdles may be reduced and establishment made more likely. In addition, if polyploidization alters the phenotypic and genotypic associations between traits, that is, the P and G matrices, polyploids may be able to explore novel evolutionary paths, facilitating their divergence and successful establishment. Here, we report results from a study of the perennial plant Heuchera grossulariifolia in which the phenotypic divergence and changes in phenotypic and genotypic covariance matrices caused by neopolyploidization have been estimated. Our results reveal that polyploidization causes immediate divergence for traits relevant to establishment and results in significant changes in the structure of the phenotypic covariance matrix. In contrast, our results do not provide evidence that polyploidization results in immediate and substantial shifts in the genetic covariance matrix. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

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.

Host Jumps and Radiation, Not Co-Divergence Drives Diversification of Obligate Pathogens. A Case Study in Downy Mildews and Asteraceae.

PubMed

Choi, Young-Joon; Thines, Marco

2015-01-01

Even though the microevolution of plant hosts and pathogens has been intensely studied, knowledge regarding macro-evolutionary patterns is limited. Having the highest species diversity and host-specificity among Oomycetes, downy mildews are a useful a model for investigating long-term host-pathogen coevolution. We show that phylogenies of Bremia and Asteraceae are significantly congruent. The accepted hypothesis is that pathogens have diverged contemporarily with their hosts. But maximum clade age estimation and sequence divergence comparison reveal that congruence is not due to long-term coevolution but rather due to host-shift driven speciation (pseudo-cospeciation). This pattern results from parasite radiation in related hosts, long after radiation and speciation of the hosts. As large host shifts free pathogens from hosts with effector triggered immunity subsequent radiation and diversification in related hosts with similar innate immunity may follow, resulting in a pattern mimicking true co-divergence, which is probably limited to the terminal nodes in many pathogen groups.

Host Jumps and Radiation, Not Co‐Divergence Drives Diversification of Obligate Pathogens. A Case Study in Downy Mildews and Asteraceae

PubMed Central

Choi, Young-Joon; Thines, Marco

2015-01-01

Even though the microevolution of plant hosts and pathogens has been intensely studied, knowledge regarding macro-evolutionary patterns is limited. Having the highest species diversity and host-specificity among Oomycetes, downy mildews are a useful a model for investigating long-term host-pathogen coevolution. We show that phylogenies of Bremia and Asteraceae are significantly congruent. The accepted hypothesis is that pathogens have diverged contemporarily with their hosts. But maximum clade age estimation and sequence divergence comparison reveal that congruence is not due to long-term coevolution but rather due to host-shift driven speciation (pseudo-cospeciation). This pattern results from parasite radiation in related hosts, long after radiation and speciation of the hosts. As large host shifts free pathogens from hosts with effector triggered immunity subsequent radiation and diversification in related hosts with similar innate immunity may follow, resulting in a pattern mimicking true co-divergence, which is probably limited to the terminal nodes in many pathogen groups. PMID:26230508

Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences.

PubMed

Pryer, Kathleen M; Schuettpelz, Eric; Wolf, Paul G; Schneider, Harald; Smith, Alan R; Cranfill, Raymond

2004-10-01

The phylogenetic structure of ferns (= monilophytes) is explored here, with a special focus on the early divergences among leptosporangiate lineages. Despite considerable progress in our understanding of fern relationships, a rigorous and comprehensive analysis of the early leptosporangiate divergences was lacking. Therefore, a data set was designed here to include critical taxa that were not included in earlier studies. More than 5000 bp from the plastid (rbcL, atpB, rps4) and the nuclear (18S rDNA) genomes were sequenced for 62 taxa. Phylogenetic analyses of these data (1) confirm that Osmundaceae are sister to the rest of the leptosporangiates, (2) resolve a diverse set of ferns formerly thought to be a subsequent grade as possibly monophyletic (((Dipteridaceae, Matoniaceae), Gleicheniaceae), Hymenophyllaceae), and (3) place schizaeoid ferns as sister to a large clade of "core leptosporangiates" that includes heterosporous ferns, tree ferns, and polypods. Divergence time estimates for ferns are reported from penalized likelihood analyses of our molecular data, with constraints from a reassessment of the fossil record.

Application of at-site peak-streamflow frequency analyses for very low annual exceedance probabilities

USGS Publications Warehouse

Asquith, William H.; Kiang, Julie E.; Cohn, Timothy A.

2017-07-17

The U.S. Geological Survey (USGS), in cooperation with the U.S. Nuclear Regulatory Commission, has investigated statistical methods for probabilistic flood hazard assessment to provide guidance on very low annual exceedance probability (AEP) estimation of peak-streamflow frequency and the quantification of corresponding uncertainties using streamgage-specific data. The term “very low AEP” implies exceptionally rare events defined as those having AEPs less than about 0.001 (or 1 × 10–3 in scientific notation or for brevity 10–3). Such low AEPs are of great interest to those involved with peak-streamflow frequency analyses for critical infrastructure, such as nuclear power plants. Flood frequency analyses at streamgages are most commonly based on annual instantaneous peak streamflow data and a probability distribution fit to these data. The fitted distribution provides a means to extrapolate to very low AEPs. Within the United States, the Pearson type III probability distribution, when fit to the base-10 logarithms of streamflow, is widely used, but other distribution choices exist. The USGS-PeakFQ software, implementing the Pearson type III within the Federal agency guidelines of Bulletin 17B (method of moments) and updates to the expected moments algorithm (EMA), was specially adapted for an “Extended Output” user option to provide estimates at selected AEPs from 10–3 to 10–6. Parameter estimation methods, in addition to product moments and EMA, include L-moments, maximum likelihood, and maximum product of spacings (maximum spacing estimation). This study comprehensively investigates multiple distributions and parameter estimation methods for two USGS streamgages (01400500 Raritan River at Manville, New Jersey, and 01638500 Potomac River at Point of Rocks, Maryland). The results of this study specifically involve the four methods for parameter estimation and up to nine probability distributions, including the generalized extreme value, generalized log-normal, generalized Pareto, and Weibull. Uncertainties in streamflow estimates for corresponding AEP are depicted and quantified as two primary forms: quantile (aleatoric [random sampling] uncertainty) and distribution-choice (epistemic [model] uncertainty). Sampling uncertainties of a given distribution are relatively straightforward to compute from analytical or Monte Carlo-based approaches. Distribution-choice uncertainty stems from choices of potentially applicable probability distributions for which divergence among the choices increases as AEP decreases. Conventional goodness-of-fit statistics, such as Cramér-von Mises, and L-moment ratio diagrams are demonstrated in order to hone distribution choice. The results generally show that distribution choice uncertainty is larger than sampling uncertainty for very low AEP values.

Connecting Amazonian, Cerrado, and Atlantic Forest histories: Paraphyly, old divergences, and modern population dynamics in tyrant-manakins (Neopelma/Tyranneutes, Aves: Pipridae).

PubMed

Capurucho, João Marcos Guimarães; Ashley, Mary V; Ribas, Camila C; Bates, John M

2018-06-11

Several biogeographic hypotheses have been proposed to explain connections between Amazonian and Atlantic forest biotas. These hypotheses are related to the timing of the connections and their geographic patterns. We performed a phylogeographic investigation of Tyrant-manakins (Aves: Pipridae, Neopelma/Tyranneutes) which include species inhabiting the Amazon and Atlantic forests, as well as gallery forests of the Cerrado. Using DNA sequence data, we determined phylogenetic relationships, temporal and geographic patterns of diversification, and recent intraspecific population genetic patterns, relative to the history of these biomes. We found Neopelma to be a paraphyletic genus, as N. chrysolophum is sister to Neopelma + Tyranneutes, with an estimated divergence of approximately 18 Myrs BP, within the oldest estimated divergence times of other Amazonian and Atlantic forest avian taxa. Subsequent divergences in the group occurred from Mid Miocene to Early Pliocene and involved mainly the Amazonian species, with an expansion into and subsequent speciation in the Cerrado gallery forests by N. pallescens. We found additional structure within N. chrysocephalum and N. sulphureiventer. Analysis of recent population dynamics in N. chrysocephalum, N. sulphureiventer, and N. pallescens revealed recent demographic fluctuations and restrictions to gene flow related to environmental changes since the last glacial cycle. No genetic structure was detected across the Amazon River in N. pallescens. The tyrant-manakins represent an old historical connection between the Amazon and Atlantic Forest. Copyright © 2018. Published by Elsevier Inc.

The evolution of methods for establishing evolutionary timescales

PubMed Central

2016-01-01

The fossil record is well known to be incomplete. Read literally, it provides a distorted view of the history of species divergence and extinction, because different species have different propensities to fossilize, the amount of rock fluctuates over geological timescales, as does the nature of the environments that it preserves. Even so, patterns in the fossil evidence allow us to assess the incompleteness of the fossil record. While the molecular clock can be used to extend the time estimates from fossil species to lineages not represented in the fossil record, fossils are the only source of information concerning absolute (geological) times in molecular dating analysis. We review different ways of incorporating fossil evidence in modern clock dating analyses, including node-calibrations where lineage divergence times are constrained using probability densities and tip-calibrations where fossil species at the tips of the tree are assigned dates from dated rock strata. While node-calibrations are often constructed by a crude assessment of the fossil evidence and thus involves arbitrariness, tip-calibrations may be too sensitive to the prior on divergence times or the branching process and influenced unduly affected by well-known problems of morphological character evolution, such as environmental influence on morphological phenotypes, correlation among traits, and convergent evolution in disparate species. We discuss the utility of time information from fossils in phylogeny estimation and the search for ancestors in the fossil record. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. PMID:27325838

The evolution of methods for establishing evolutionary timescales.

PubMed

Donoghue, Philip C J; Yang, Ziheng

2016-07-19

The fossil record is well known to be incomplete. Read literally, it provides a distorted view of the history of species divergence and extinction, because different species have different propensities to fossilize, the amount of rock fluctuates over geological timescales, as does the nature of the environments that it preserves. Even so, patterns in the fossil evidence allow us to assess the incompleteness of the fossil record. While the molecular clock can be used to extend the time estimates from fossil species to lineages not represented in the fossil record, fossils are the only source of information concerning absolute (geological) times in molecular dating analysis. We review different ways of incorporating fossil evidence in modern clock dating analyses, including node-calibrations where lineage divergence times are constrained using probability densities and tip-calibrations where fossil species at the tips of the tree are assigned dates from dated rock strata. While node-calibrations are often constructed by a crude assessment of the fossil evidence and thus involves arbitrariness, tip-calibrations may be too sensitive to the prior on divergence times or the branching process and influenced unduly affected by well-known problems of morphological character evolution, such as environmental influence on morphological phenotypes, correlation among traits, and convergent evolution in disparate species. We discuss the utility of time information from fossils in phylogeny estimation and the search for ancestors in the fossil record.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. © 2016 The Authors.

Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars

PubMed Central

Shahin, Arwa; Smulders, Marinus J. M.; van Tuyl, Jaap M.; Arens, Paul; Bakker, Freek T.

2014-01-01

Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium. PMID:25368628

Phylogenomic Analysis Resolves the Interordinal Relationships and Rapid Diversification of the Laurasiatherian Mammals

PubMed Central

Zhou, Xuming; Xu, Shixia; Xu, Junxiao; Chen, Bingyao; Zhou, Kaiya; Yang, Guang

2012-01-01

Abstract Although great progress has been made in resolving the relationships of placental mammals, the position of several clades in Laurasiatheria remain controversial. In this study, we performed a phylogenetic analysis of 97 orthologs (46,152 bp) for 15 taxa, representing all laurasiatherian orders. Additionally, phylogenetic trees of laurasiatherian mammals with draft genome sequences were reconstructed based on 1608 exons (2,175,102 bp). Our reconstructions resolve the interordinal relationships within Laurasiatheria and corroborate the clades Scrotifera, Fereuungulata, and Cetartiodactyla. Furthermore, we tested alternative topologies within Laurasiatheria, and among alternatives for the phylogenetic position of Perissodactyla, a sister-group relationship with Cetartiodactyla receives the highest support. Thus, Pegasoferae (Perissodactyla + Carnivora + Pholidota + Chiroptera) does not appear to be a natural group. Divergence time estimates from these genes were compared with published estimates for splits within Laurasiatheria. Our estimates were similar to those of several studies and suggest that the divergences among these orders occurred within just a few million years. PMID:21900649

An improvement of the measurement of time series irreversibility with visibility graph approach

NASA Astrophysics Data System (ADS)

Wu, Zhenyu; Shang, Pengjian; Xiong, Hui

2018-07-01

We propose a method to improve the measure of real-valued time series irreversibility which contains two tools: the directed horizontal visibility graph and the Kullback-Leibler divergence. The degree of time irreversibility is estimated by the Kullback-Leibler divergence between the in and out degree distributions presented in the associated visibility graph. In our work, we reframe the in and out degree distributions by encoding them with different embedded dimensions used in calculating permutation entropy(PE). With this improved method, we can not only estimate time series irreversibility efficiently, but also detect time series irreversibility from multiple dimensions. We verify the validity of our method and then estimate the amount of time irreversibility of series generated by chaotic maps as well as global stock markets over the period 2005-2015. The result shows that the amount of time irreversibility reaches the peak with embedded dimension d = 3 under circumstances of experiment and financial markets.

Geographical variation in sound production in the anemonefish Amphiprion akallopisos

PubMed Central

Parmentier, E; Lagardère, J.P; Vandewalle, P; Fine, M.L

2005-01-01

Because of pelagic-larval dispersal, coral-reef fishes are distributed widely with minimal genetic differentiation between populations. Amphiprion akallopisos, a clownfish that uses sound production to defend its anemone territory, has a wide but disjunct distribution in the Indian Ocean. We compared sounds produced by these fishes from populations in Madagascar and Indonesia, a distance of 6500 km. Differentiation of agonistic calls into distinct types indicates a complexity not previously recorded in fishes' acoustic communication. Moreover, various acoustic parameters, including peak frequency, pulse duration, number of peaks per pulse, differed between the two populations. The geographic comparison is the first to demonstrate ‘dialects’ in a marine fish species, and these differences in sound parameters suggest genetic divergence between these two populations. These results highlight the possible approach for investigating the role of sounds in fish behaviour in reproductive divergence and speciation. PMID:16087425

The taxonomic placement of three fossil Fundulus species and the timing of divergence within the North American topminnows (Teleostei: Fundulidae).

PubMed

Ghedotti, Michael J; Davis, Matthew P

2017-04-10

The fossils species †Fundulus detillae, †F. lariversi, and †F. nevadensis from localities in the western United States are represented by well-preserved material with date estimations. We combined morphological data for these fossil taxa with morphological and DNA-sequence data to conduct a phylogenetic analysis and a tip-based divergence-time estimation for the family Fundulidae. The resultant phylogeny is largely concordant with the prior total-evidence phylogeny. The fossil species do not form a monophyletic group, and do not represent a discrete western radiation of Fundulus as previously proposed. The genus Fundulus diverged into subgeneric clades likely in the Eocene or Oligocene (mean age 34.6 mya, 53-23 mya), and all subgeneric and most species-group clades had evolved by the middle Miocene. †Fundulus lariversi is a member of subgenus Fundulus in which all extant species are found only in eastern North America, demonstrating that fundulids had a complicated biogeographic history. We confirmed †Fundulus detillae as a member of the subgenus Plancterus. †F. nevadensis is not classified in a subgenus but likely is related to the subgenera Plancterus and Wileyichthys.

No known hominin species matches the expected dental morphology of the last common ancestor of Neanderthals and modern humans

PubMed Central

Gómez-Robles, Aida; Bermúdez de Castro, José María; Arsuaga, Juan-Luis; Carbonell, Eudald; Polly, P. David

2013-01-01

A central problem in paleoanthropology is the identity of the last common ancestor of Neanderthals and modern humans ([N-MH]LCA). Recently developed analytical techniques now allow this problem to be addressed using a probabilistic morphological framework. This study provides a quantitative reconstruction of the expected dental morphology of the [N-MH]LCA and an assessment of whether known fossil species are compatible with this ancestral position. We show that no known fossil species is a suitable candidate for being the [N-MH]LCA and that all late Early and Middle Pleistocene taxa from Europe have Neanderthal dental affinities, pointing to the existence of a European clade originated around 1 Ma. These results are incongruent with younger molecular divergence estimates and suggest at least one of the following must be true: (i) European fossils and the [N-MH]LCA selectively retained primitive dental traits; (ii) molecular estimates of the divergence between Neanderthals and modern humans are underestimated; or (iii) phenotypic divergence and speciation between both species were decoupled such that phenotypic differentiation, at least in dental morphology, predated speciation. PMID:24145426

DIRECTIONAL CULTURAL CHANGE BY MODIFICATION AND REPLACEMENT OF MEMES

PubMed Central

Cardoso, Gonçalo C.; Atwell, Jonathan W.

2017-01-01

Evolutionary approaches to culture remain contentious. A source of contention is that cultural mutation may be substantial and, if it drives cultural change, then current evolutionary models are not adequate. But we lack studies quantifying the contribution of mutations to directional cultural change. We estimated the contribution of one type of cultural mutations—modification of memes—to directional cultural change using an amenable study system: learned birdsongs in a species that recently entered an urban habitat. Many songbirds have higher minimum song frequency in cities, to alleviate masking by low-frequency noise. We estimated that the input of meme modifications in an urban songbird population explains about half the extent of the population divergence in song frequency. This contribution of cultural mutations is large, but insufficient to explain the entire population divergence. The remaining divergence is due to selection of memes or creation of new memes. We conclude that the input of cultural mutations can be quantitatively important, unlike in genetic evolution, and that it operates together with other mechanisms of cultural evolution. For this and other traits, in which the input of cultural mutations might be important, quantitative studies of cultural mutation are necessary to calibrate realistic models of cultural evolution. PMID:20722726

Gender-Based Screening for Chlamydial Infection and Divergent Infection Trends in Men and Women

PubMed Central

Rogers, Susan M.; Turner, Charles F.; Miller, William C.; Erbelding, Emily; Eggleston, Elizabeth; Tan, Sylvia; Roman, Anthony; Hobbs, Marcia; Chromy, James; Muvva, Ravikiran; Ganapathi, Laxminarayana

2014-01-01

Objectives To assess the potential impact of chlamydial screening policy that recommends routine screening of women but not men. Methods Population surveys of probability samples of Baltimore adults aged 18 to 35 years in 1997–1998 and 2006–2009 collected biospecimens to estimate trends in undiagnosed chlamydial infection. Survey estimates are compared to surveillance data on diagnosed chlamydial infections reported to the Health Department. Results Prevalence of undiagnosed chlamydial infection among men increased from 1.6% to 4.0%, but it declined from 4.3% to 3.1% among women (p = 0.028 for test of interaction). The annual (average) number of diagnosed infections was substantially higher among women than men in both time periods and increased among both men and women. Undiagnosed infection prevalence was substantially higher among black than non-black adults (4.0% vs 1.2%, p = 0.042 in 1997–98 and 5.5% vs 0.7%, p<0.001 in 2006–09). Conclusion Divergent trends in undiagnosed chlamydial infection by gender parallel divergent screening recommendations that encourage chlamydial testing for women but not for men. PMID:24586491

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.

DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar

PubMed Central

Smith, M. Alex; Fisher, Brian L; Hebert, Paul D.N

2005-01-01

The role of DNA barcoding as a tool to accelerate the inventory and analysis of diversity for hyperdiverse arthropods is tested using ants in Madagascar. We demonstrate how DNA barcoding helps address the failure of current inventory methods to rapidly respond to pressing biodiversity needs, specifically in the assessment of richness and turnover across landscapes with hyperdiverse taxa. In a comparison of inventories at four localities in northern Madagascar, patterns of richness were not significantly different when richness was determined using morphological taxonomy (morphospecies) or sequence divergence thresholds (Molecular Operational Taxonomic Unit(s); MOTU). However, sequence-based methods tended to yield greater richness and significantly lower indices of similarity than morphological taxonomy. MOTU determined using our molecular technique were a remarkably local phenomenon—indicative of highly restricted dispersal and/or long-term isolation. In cases where molecular and morphological methods differed in their assignment of individuals to categories, the morphological estimate was always more conservative than the molecular estimate. In those cases where morphospecies descriptions collapsed distinct molecular groups, sequence divergences of 16% (on average) were contained within the same morphospecies. Such high divergences highlight taxa for further detailed genetic, morphological, life history, and behavioral studies. PMID:16214741

Heritability and quantitative genetic divergence of serotiny, a fire-persistence plant trait

PubMed Central

Hernández-Serrano, Ana; Verdú, Miguel; Santos-del-Blanco, Luís; Climent, José; González-Martínez, Santiago C.; Pausas, Juli G.

2014-01-01

Background and Aims Although it is well known that fire acts as a selective pressure shaping plant phenotypes, there are no quantitative estimates of the heritability of any trait related to plant persistence under recurrent fires, such as serotiny. In this study, the heritability of serotiny in Pinus halepensis is calculated, and an evaluation is made as to whether fire has left a selection signature on the level of serotiny among populations by comparing the genetic divergence of serotiny with the expected divergence of neutral molecular markers (QST–FST comparison). Methods A common garden of P. halepensis was used, located in inland Spain and composed of 145 open-pollinated families from 29 provenances covering the entire natural range of P. halepensis in the Iberian Peninsula and Balearic Islands. Narrow-sense heritability (h2) and quantitative genetic differentiation among populations for serotiny (QST) were estimated by means of an ‘animal model’ fitted by Bayesian inference. In order to determine whether genetic differentiation for serotiny is the result of differential natural selection, QST estimates for serotiny were compared with FST estimates obtained from allozyme data. Finally, a test was made of whether levels of serotiny in the different provenances were related to different fire regimes, using summer rainfall as a proxy for fire regime in each provenance. Key Results Serotiny showed a significant narrow-sense heritability (h2) of 0·20 (credible interval 0·09–0·40). Quantitative genetic differentiation among provenances for serotiny (QST = 0·44) was significantly higher than expected under a neutral process (FST = 0·12), suggesting adaptive differentiation. A significant negative relationship was found between the serotiny level of trees in the common garden and summer rainfall of their provenance sites. Conclusions Serotiny is a heritable trait in P. halepensis, and selection acts on it, giving rise to contrasting serotiny levels among populations depending on the fire regime, and supporting the role of fire in generating genetic divergence for adaptive traits. PMID:25008363

A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land

NASA Technical Reports Server (NTRS)

Battistuzzi, Fabia U.; Feijao, Andreia; Hedges, S. Blair

2004-01-01

BACKGROUND: The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. We assembled a data set of sequences from 32 proteins (approximately 7600 amino acids) common to 72 species and estimated phylogenetic relationships and divergence times with a local clock method. RESULTS: Our phylogenetic results support most of the currently recognized higher-level groupings of prokaryotes. Of particular interest is a well-supported group of three major lineages of eubacteria (Actinobacteria, Deinococcus, and Cyanobacteria) that we call Terrabacteria and associate with an early colonization of land. Divergence time estimates for the major groups of eubacteria are between 2.5-3.2 billion years ago (Ga) while those for archaebacteria are mostly between 3.1-4.1 Ga. The time estimates suggest a Hadean origin of life (prior to 4.1 Ga), an early origin of methanogenesis (3.8-4.1 Ga), an origin of anaerobic methanotrophy after 3.1 Ga, an origin of phototrophy prior to 3.2 Ga, an early colonization of land 2.8-3.1 Ga, and an origin of aerobic methanotrophy 2.5-2.8 Ga. CONCLUSIONS: Our early time estimates for methanogenesis support the consideration of methane, in addition to carbon dioxide, as a greenhouse gas responsible for the early warming of the Earths' surface. Our divergence times for the origin of anaerobic methanotrophy are compatible with highly depleted carbon isotopic values found in rocks dated 2.8-2.6 Ga. An early origin of phototrophy is consistent with the earliest bacterial mats and structures identified as stromatolites, but a 2.6 Ga origin of cyanobacteria suggests that those Archean structures, if biologically produced, were made by anoxygenic photosynthesizers. The resistance to desiccation of Terrabacteria and their elaboration of photoprotective compounds suggests that the common ancestor of this group inhabited land. If true, then oxygenic photosynthesis may owe its origin to terrestrial adaptations.

Genetic constraints predict evolutionary divergence in Dalechampia blossoms.

PubMed

Bolstad, Geir H; Hansen, Thomas F; Pélabon, Christophe; Falahati-Anbaran, Mohsen; Pérez-Barrales, Rocío; Armbruster, W Scott

2014-08-19

If genetic constraints are important, then rates and direction of evolution should be related to trait evolvability. Here we use recently developed measures of evolvability to test the genetic constraint hypothesis with quantitative genetic data on floral morphology from the Neotropical vine Dalechampia scandens (Euphorbiaceae). These measures were compared against rates of evolution and patterns of divergence among 24 populations in two species in the D. scandens species complex. We found clear evidence for genetic constraints, particularly among traits that were tightly phenotypically integrated. This relationship between evolvability and evolutionary divergence is puzzling, because the estimated evolvabilities seem too large to constitute real constraints. We suggest that this paradox can be explained by a combination of weak stabilizing selection around moving adaptive optima and small realized evolvabilities relative to the observed additive genetic variance.

Phylogeny of world stag beetles (Coleoptera: Lucanidae) reveals a Gondwanan origin of Darwin's stag beetle.

PubMed

Kim, Sang Il; Farrell, Brian D

2015-05-01

Stag beetles (family Lucanidae Latreille, 1804) are one of the earliest branching lineages of scarab beetles that are characterized by the striking development of the male mandibles. Despite stag beetles' popularity among traditional taxonomists and amateur collectors, there has been almost no study of lucanid relationships and evolution. Entomologists, including Jeannel (1942), have long recognized resemblance between the austral stag beetles of the tribes Chiasognathini, Colophonini, Lamprimini, Pholidotini, Rhyssonotini, and Streptocerini, but this hypothesis of their close relationship across the continents has never been tested. To gain further insight into lucanid phylogeny and biogeography, we reconstructed the first molecular phylogeny of world stag beetles using DNA sequences from mitochondrial 16S rDNA, nuclear 18S and 28S rDNA, and the nuclear protein-coding (NPC) gene wingless for 93 lucanid species representing all extant subfamilies and 24 out of the 27 tribes, together with 14 representative samples of other early branching scarabaeoid families and two staphyliniform beetle families as outgroups. Both Bayesian inference (BI) and maximum likelihood inference (MLI) strongly supported the monophyly of Lucanidae sensu lato that includes Diphyllostomatidae. Within Lucanidae sensu stricto, the subfamilies Lucaninae and Lampriminae appeared monophyletic under both methods of phylogenetic inferences; however, Aesalinae and Syndesinae were found to be polyphyletic. A time-calibrated phylogeny based on five fossil data estimated the origin of crown group Lucanidae as circa 160 million years ago (MYA). Divergence between the Neotropical and Australasian groups of the Chiasognathini was estimated to be circa 47MYA, with the South African Colophonini branching off from the ancient Chiasognathini lineage around 87MYA. Another Gondwanan relationship was recovered between the Australasian Eucarteria and the Neotropical Casignetus, which diverged circa 58MYA. Lastly, as Jeannel's hypothesis predicted, divergence within Lampriminae between the Australasian Lamprima and the Neotropical Streptocerus was estimated to be circa 37MYA. The split of these lineages were generally concordant with the pattern of continental break-up of the super-continent Gondwana, and our biogeographic reconstructions based on the dispersal-extinction-cladogenesis model (DEC) corroborate our view that the divergences in these austral lineages were caused by vicariance events following the Gondwanan break-up. In addition, the phylogenetic position and geographic origin of the Hawaiian genus Apterocyclus was revealed for the first time. Overall, our results provide the framework toward studying lucanid relationships and divergence time estimates, which allowed for more accurate biogeographic explanations and discussions on ancestral lucanids and the evolutionary origin of the enlarged male mandibles. Copyright © 2015 Elsevier Inc. All rights reserved.

Three dimensional simulations of viscous folding in diverging microchannels

NASA Astrophysics Data System (ADS)

Xu, Bingrui; Chergui, Jalel; Shin, Seungwon; Juric, Damir

2016-11-01

Three dimensional simulations on the viscous folding in diverging microchannels reported by Cubaud and Mason are performed using the parallel code BLUE for multi-phase flows. The more viscous liquid L1 is injected into the channel from the center inlet, and the less viscous liquid L2 from two side inlets. Liquid L1 takes the form of a thin filament due to hydrodynamic focusing in the long channel that leads to the diverging region. The thread then becomes unstable to a folding instability, due to the longitudinal compressive stress applied to it by the diverging flow of liquid L2. We performed a parameter study in which the flow rate ratio, the viscosity ratio, the Reynolds number, and the shape of the channel were varied relative to a reference model. In our simulations, the cross section of the thread produced by focusing is elliptical rather than circular. The initial folding axis can be either parallel or perpendicular to the narrow dimension of the chamber. In the former case, the folding slowly transforms via twisting to perpendicular folding, or it may remain parallel. The direction of folding onset is determined by the velocity profile and the elliptical shape of the thread cross section in the channel that feeds the diverging part of the cell.

Sensible and latent heat forced divergent circulations in the West African Monsoon System

NASA Astrophysics Data System (ADS)

Hagos, S.; Zhang, C.

2008-12-01

Field properties of divergent circulation are utilized to identify the roles of various diabatic processes in forcing moisture transport in the dynamics of the West African Monsoon and its seasonal cycle. In this analysis, the divergence field is treated as a set of point sources and is partitioned into two sub-sets corresponding to latent heat release and surface sensible heat flux at each respective point. The divergent circulation associated with each set is then calculated from the Poisson's equation using Gauss-Seidel iteration. Moisture transport by each set of divergent circulation is subsequently estimated. The results show different roles of the divergent circulations forced by surface sensible and latent heating in the monsoon dynamics. Surface sensible heating drives a shallow meridional circulation, which transports moisture deep into the continent at the polar side of the monsoon rain band and thereby promotes the seasonal northward migration of monsoon precipitation during the monsoon onset season. In contrast, the circulation directly associated with latent heating is deep and the corresponding moisture convergence is within the region of precipitation. Latent heating also induces dry air advection from the north. Neither effect promotes the seasonal northward migration of precipitation. The relative contributions of the processes associated with latent and sensible heating to the net moisture convergence, and hence the seasonal evolution of monsoon precipitation, depend on the background moisture.

Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset

PubMed Central

Higdon, Jeff W; Bininda-Emonds, Olaf RP; Beck, Robin MD; Ferguson, Steven H

2007-01-01

Background Phylogenetic comparative methods are often improved by complete phylogenies with meaningful branch lengths (e.g., divergence dates). This study presents a dated molecular supertree for all 34 world pinniped species derived from a weighted matrix representation with parsimony (MRP) supertree analysis of 50 gene trees, each determined under a maximum likelihood (ML) framework. Divergence times were determined by mapping the same sequence data (plus two additional genes) on to the supertree topology and calibrating the ML branch lengths against a range of fossil calibrations. We assessed the sensitivity of our supertree topology in two ways: 1) a second supertree with all mtDNA genes combined into a single source tree, and 2) likelihood-based supermatrix analyses. Divergence dates were also calculated using a Bayesian relaxed molecular clock with rate autocorrelation to test the sensitivity of our supertree results further. Results The resulting phylogenies all agreed broadly with recent molecular studies, in particular supporting the monophyly of Phocidae, Otariidae, and the two phocid subfamilies, as well as an Odobenidae + Otariidae sister relationship; areas of disagreement were limited to four more poorly supported regions. Neither the supertree nor supermatrix analyses supported the monophyly of the two traditional otariid subfamilies, supporting suggestions for the need for taxonomic revision in this group. Phocid relationships were similar to other recent studies and deeper branches were generally well-resolved. Halichoerus grypus was nested within a paraphyletic Pusa, although relationships within Phocina tend to be poorly supported. Divergence date estimates for the supertree were in good agreement with other studies and the available fossil record; however, the Bayesian relaxed molecular clock divergence date estimates were significantly older. Conclusion Our results join other recent studies and highlight the need for a re-evaluation of pinniped taxonomy, especially as regards the subfamilial classification of otariids and the generic nomenclature of Phocina. Even with the recent publication of new sequence data, the available genetic sequence information for several species, particularly those in Arctocephalus, remains very limited, especially for nuclear markers. However, resolution of parts of the tree will probably remain difficult, even with additional data, due to apparent rapid radiations. Our study addresses the lack of a recent pinniped phylogeny that includes all species and robust divergence dates for all nodes, and will therefore prove indispensable to comparative and macroevolutionary studies of this group of carnivores. PMID:17996107

Holistic information evaluation of divergence of soil's properties by using of legacy data of large scale monitoring surveys

NASA Astrophysics Data System (ADS)

Mikheeva, Irina

2017-04-01

Identification of tendencies of soil's transformations is very important for adequate ecological and economical assessment of degradation of soils. But monitoring of conditions of soils, and other natural objects, bring up a number of important methodological questions, including the probabilistic and statistical analysis of the accumulated legacy data and their use for verification of quantitative estimates of natural processes. Owing to considerable natural variability there is a problem of a reliable assessment of contemporary soil evolution under the influence of environmental management and climate changes. When studying dynamics of soil quality it is necessary to consider soil as open complex system with parameters which significantly vary in space. The analysis of probabilistic distributions of attributes of studied system is informative for the characteristic of holistic state and behavior of the system. Therefore earlier we had offered the method of evaluation of alterations of soils by analysis of changes of pdf of their properties and their statistical entropy. The executed analysis of dynamics of pdf showed that often opposite tendencies to decrease and to increase of property can be shown at the same time. However to give an adequate quantitative evaluation of changes of soil properties it is necessary to characterize them in general. We proposed that it is reasonable to name processes of modern changes in soil properties concerning their start meaning by the term "divergence" and investigate it quantitatively. For this purpose we suggested to use value of information divergence which is defined as a measure of distinctions of pdf in compared objects or in various time. As the measure of dissimilarity, divergence should satisfy come conditions, the most important is scale-invariance property. Information divergence was used by us for evaluation of distinctions of soils according heterogeneity of factors of soil formation and with course of natural and anthropogenous processes. This characteristic allowed to allocate the most changed and vulnerable kinds and layers of soils, and also to range natural changes and anthropogenous impacts in size of their influence on properties of the soil. Case study was conducted on considerable part of the Priirtyshskaya plain in South of Western Siberia. Climate here is sharply continental and droughty. Soils were formed from ancient lake and alluvial deposits. It determined their mainly easy particle size distribution and spatial diversity of the texture. It is possible to judge rates and extent of manifestation of processes of degradation on alteration of properties of the main types of soils here: chestnut soils and Haplic Chernozems.

Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation.

PubMed

Cornuet, Jean-Marie; Santos, Filipe; Beaumont, Mark A; Robert, Christian P; Marin, Jean-Michel; Balding, David J; Guillemaud, Thomas; Estoup, Arnaud

2008-12-01

Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract part of this information but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIY ABC) for inference based on approximate Bayesian computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and population size changes. DIY ABC can be used to compare competing scenarios, estimate parameters for one or more scenarios and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data). This article describes key methods used in the program and provides its main features. The analysis of one simulated and one real dataset, both with complex evolutionary scenarios, illustrates the main possibilities of DIY ABC. The software DIY ABC is freely available at http://www.montpellier.inra.fr/CBGP/diyabc.

A regularized variable selection procedure in additive hazards model with stratified case-cohort design.

PubMed

Ni, Ai; Cai, Jianwen

2018-07-01

Case-cohort designs are commonly used in large epidemiological studies to reduce the cost associated with covariate measurement. In many such studies the number of covariates is very large. An efficient variable selection method is needed for case-cohort studies where the covariates are only observed in a subset of the sample. Current literature on this topic has been focused on the proportional hazards model. However, in many studies the additive hazards model is preferred over the proportional hazards model either because the proportional hazards assumption is violated or the additive hazards model provides more relevent information to the research question. Motivated by one such study, the Atherosclerosis Risk in Communities (ARIC) study, we investigate the properties of a regularized variable selection procedure in stratified case-cohort design under an additive hazards model with a diverging number of parameters. We establish the consistency and asymptotic normality of the penalized estimator and prove its oracle property. Simulation studies are conducted to assess the finite sample performance of the proposed method with a modified cross-validation tuning parameter selection methods. We apply the variable selection procedure to the ARIC study to demonstrate its practical use.

Personalizing Androgen Suppression for Prostate Cancer Using Mathematical Modeling.

PubMed

Hirata, Yoshito; Morino, Kai; Akakura, Koichiro; Higano, Celestia S; Aihara, Kazuyuki

2018-02-08

Using a dataset of 150 patients treated with intermittent androgen suppression (IAS) through a fixed treatment schedule, we retrospectively designed a personalized treatment schedule mathematically for each patient. We estimated 100 sets of parameter values for each patient by randomly resampling each patient's time points to take into account the uncertainty for observations of prostate specific antigen (PSA). Then, we identified 3 types and classified patients accordingly: in type (i), the relapse, namely the divergence of PSA, can be prevented by IAS; in type (ii), the relapse can be delayed by IAS later than by continuous androgen suppression (CAS); in type (iii) IAS was not beneficial and therefore CAS would have been more appropriate in the long run. Moreover, we obtained a treatment schedule of hormone therapy by minimizing the PSA of 3 years later in the worst case scenario among the 100 parameter sets by searching exhaustively all over the possible treatment schedules. If the most frequent type among 100 sets was type (i), the maximal PSA tended to be kept less than 100 ng/ml longer in IAS than in CAS, while there was no statistical difference for the other cases. Thus, mathematically personalized IAS should be studied prospectively.

An Early Miocene bumble bee from northern Bohemia (Hymenoptera, Apidae).

PubMed

Prokop, Jakub; Dehon, Manuel; Michez, Denis; Engel, Michael S

2017-01-01

A new species of fossil bumble bee (Apinae: Bombini) is described and figured from Early Miocene (Burdigalian) deposits of the Most Basin at the Bílina Mine, Czech Republic. Bombus trophonius sp. n. , is placed within the subgenus Cullumanobombus Vogt and distinguished from the several species groups therein. The species is apparently most similar to the Nearctic B. (Cullumanobombus) rufocinctus Cresson, the earliest-diverging species within the clade and the two may be related only by symplesiomorphies. The age of the fossil is in rough accordance with divergence estimations for Cullumanobombus .

The fossil record and taphonomy of butterflies and moths (Insecta, Lepidoptera): implications for evolutionary diversity and divergence-time estimates.

PubMed

Sohn, Jae-Cheon; Labandeira, Conrad C; Davis, Donald R

2015-02-04

It is conventionally accepted that the lepidopteran fossil record is significantly incomplete when compared to the fossil records of other, very diverse, extant insect orders. Such an assumption, however, has been based on cumulative diversity data rather than using alternative statistical approaches from actual specimen counts. We reviewed documented specimens of the lepidopteran fossil record, currently consisting of 4,593 known specimens that are comprised of 4,262 body fossils and 331 trace fossils. The temporal distribution of the lepidopteran fossil record shows significant bias towards the late Paleocene to middle Eocene time interval. Lepidopteran fossils also record major shifts in preservational style and number of represented localities at the Mesozoic stage and Cenozoic epoch level of temporal resolution. Only 985 of the total known fossil specimens (21.4%) were assigned to 23 of the 40 extant lepidopteran superfamilies. Absolute numbers and proportions of preservation types for identified fossils varied significantly across superfamilies. The secular increase of lepidopteran family-level diversity through geologic time significantly deviates from the general pattern of other hyperdiverse, ordinal-level lineages. Our statistical analyses of the lepidopteran fossil record show extreme biases in preservation type, age, and taxonomic composition. We highlight the scarcity of identified lepidopteran fossils and provide a correspondence between the latest lepidopteran divergence-time estimates and relevant fossil occurrences at the superfamily level. These findings provide caution in interpreting the lepidopteran fossil record through the modeling of evolutionary diversification and in determination of divergence time estimates.

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."

Extended mitogenomic phylogenetic analyses yield new insight into crocodylian evolution and their survival of the Cretaceous-Tertiary boundary.

PubMed

Roos, Jonas; Aggarwal, Ramesh K; Janke, Axel

2007-11-01

The mitochondrial genomes of the dwarf crocodile, Osteolaemus tetraspis, and two species of dwarf caimans, the smooth-fronted caiman, Paleosuchus trigonatus, and Cuvier's dwarf caiman, Paleosuchus palpebrosus, were sequenced and included in a mitogenomic phylogenetic study. The phylogenetic analyses, which included a total of ten crocodylian species, yielded strong support to a basal split between Crocodylidae and Alligatoridae. Osteolaemus fell within the Crocodylidae as the sister group to Crocodylus. Gavialis and Tomistoma, which joined on a common branch, constituted a sister group to Crocodylus/Osteolaemus. This suggests that extant crocodylians are organized in two families: Alligatoridae and Crocodylidae. Within the Alligatoridae there was a basal split between Alligator and a branch that contained Paleosuchus and Caiman. The analyses also provided molecular estimates of various divergences applying recently established crocodylian and outgroup fossil calibration points. Molecular estimates based on amino acid data placed the divergence between Crocodylidae and Alligatoridae at 97-103 million years ago and that between Alligator and Caiman/Paleosuchus at 65-72 million years ago. Other crocodilian divergences were placed after the Cretaceous-Tertiary boundary. Thus, according to the molecular estimates, three extant crocodylian lineages have their roots in the Cretaceous. Considering the crocodylian diversification in the Cretaceous the molecular datings suggest that the extinction of the dinosaurs was also to some extent paralleled in the crocodylian evolution. However, for whatever reason, some crocodylian lineages survived into the Tertiary.

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

Performance mapping of a 30 cm engineering model thruster

NASA Technical Reports Server (NTRS)

Poeschel, R. L.; Vahrenkamp, R. P.

1975-01-01

A 30 cm thruster representative of the engineering model design has been tested over a wide range of operating parameters to document performance characteristics such as electrical and propellant efficiencies, double ion and beam divergence thrust loss, component equilibrium temperatures, operational stability, etc. Data obtained show that optimum power throttling, in terms of maximum thruster efficiency, is not highly sensitive to parameter selection. Consequently, considerations of stability, discharge chamber erosion, thrust losses, etc. can be made the determining factors for parameter selection in power throttling operations. Options in parameter selection based on these considerations are discussed.

Deformation of the quintom cosmological model and its consequences

NASA Astrophysics Data System (ADS)

Sadeghi, J.; Pourhassan, B.; Nekouee, Z.; Shokri, M.

In this paper, we investigate the effects of noncommutative phase-space on the quintom cosmological model. In that case, we discuss about some cosmological parameters and show that they depend on the deformation parameters. We find that the noncommutative parameter plays important role which helps to re-arrange the divergency of cosmological constant. We draw time-dependent scale factor and investigate the effect of noncommutative parameters. Finally, we take advantage from noncommutative phase-space and obtain the deformed Lagrangian for the quintom model. In order to discuss some cosmological phenomena as dark energy and inflation, we employ Noether symmetry.

Mito-nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas).

PubMed

Peters, Jeffrey L; Winker, Kevin; Millam, Kendra C; Lavretsky, Philip; Kulikova, Irina; Wilson, Robert E; Zhuravlev, Yuri N; McCracken, Kevin G

2014-06-01

Many species have Holarctic distributions that extend across Europe, Asia and North America. Most genetics research on these species has examined only mitochondrial (mt) DNA, which has revealed wide variance in divergence between Old World (OW) and New World (NW) populations, ranging from shallow, unstructured genealogies to deeply divergent lineages. In this study, we sequenced 20 nuclear introns to test for concordant patterns of OW-NW differentiation between mtDNA and nuclear (nu) DNA for six lineages of Holarctic ducks (genus Anas). Genetic differentiation for both marker types varied widely among these lineages (idiosyncratic population histories), but mtDNA and nuDNA divergence within lineages was not significantly correlated. Moreover, compared with the association between mtDNA and nuDNA divergence observed among different species, OW-NW nuDNA differentiation was generally lower than mtDNA divergence, at least for lineages with deeply divergent mtDNA. Furthermore, coalescent estimates indicated significantly higher rates of gene flow for nuDNA than mtDNA for four of the six lineages. Thus, Holarctic ducks show prominent mito-nuclear discord between OW and NW populations, and we reject differences in sorting rates as the sole cause of the within-species discord. Male-mediated intercontinental gene flow is likely a leading contributor to this discord, although selection could also cause increased mtDNA divergence relative to weak nuDNA differentiation. The population genetics of these ducks contribute to growing evidence that mtDNA can be an unreliable indicator of stage of speciation and that more holistic approaches are needed for species delimitation. © 2014 John Wiley & Sons Ltd.

Rapid diversification of Tragopogon and ecological associates in Eurasia.

PubMed

Bell, C D; Mavrodiev, E V; Soltis, P S; Calaminus, A K; Albach, D C; Cellinese, N; Garcia-Jacas, N; Soltis, D E

2012-12-01

Tragopogon comprises approximately 150 described species distributed throughout Eurasia from Ireland and the UK to India and China with a few species in North Africa. Most of the species diversity is found in Eastern Europe to Western Asia. Previous phylogenetic analyses identified several major clades, generally corresponding to recognized taxonomic sections, although relationships both among these clades and among species within clades remain largely unresolved. These patterns are consistent with rapid diversification following the origin of Tragopogon, and this study addresses the timing and rate of diversification in Tragopogon. Using BEAST to simultaneously estimate a phylogeny and divergence times, we estimate the age of a major split and subsequent rapid divergence within Tragopogon to be ~2.6 Ma (and 1.7-5.4 Ma using various clock estimates). Based on the age estimates obtained with BEAST (HPD 1.7-5.4 Ma) for the origin of crown group Tragopogon and 200 estimated species (to accommodate a large number of cryptic species), the diversification rate of Tragopogon is approximately 0.84-2.71 species/Myr for the crown group, assuming low levels of extinction. This estimate is comparable in rate to a rapid Eurasian radiation in Dianthus (0.66-3.89 species/Myr), which occurs in the same or similar habitats. Using available data, we show that subclades of various plant taxa that occur in the same semi-arid habitats of Eurasia also represent rapid radiations occurring during roughly the same window of time (1.7-5.4 Ma), suggesting similar causal events. However, not all species-rich plant genera from the same habitats diverged at the same time, or at the same tempo. Radiations of several other clades in this same habitat (e.g. Campanula, Knautia, Scabiosa) occurred at earlier dates (45-4.28 Ma). Existing phylogenetic data and diversification estimates therefore indicate that, although some elements of these semi-arid communities radiated during the Plio-Pleistocene period, other clades sharing the same habitat appear to have diversified earlier. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Neandertal admixture in Eurasia confirmed by maximum-likelihood analysis of three genomes.

PubMed

Lohse, Konrad; Frantz, Laurent A F

2014-04-01

Although there has been much interest in estimating histories of divergence and admixture from genomic data, it has proved difficult to distinguish recent admixture from long-term structure in the ancestral population. Thus, recent genome-wide analyses based on summary statistics have sparked controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. Here we derive the probability of full mutational configurations in nonrecombining sequence blocks under both admixture and ancestral structure scenarios. Dividing the genome into short blocks gives an efficient way to compute maximum-likelihood estimates of parameters. We apply this likelihood scheme to triplets of human and Neandertal genomes and compare the relative support for a model of admixture from Neandertals into Eurasian populations after their expansion out of Africa against a history of persistent structure in their common ancestral population in Africa. Our analysis allows us to conclusively reject a model of ancestral structure in Africa and instead reveals strong support for Neandertal admixture in Eurasia at a higher rate (3.4-7.3%) than suggested previously. Using analysis and simulations we show that our inference is more powerful than previous summary statistics and robust to realistic levels of recombination.

Robust inference under the beta regression model with application to health care studies.

PubMed

Ghosh, Abhik

2017-01-01

Data on rates, percentages, or proportions arise frequently in many different applied disciplines like medical biology, health care, psychology, and several others. In this paper, we develop a robust inference procedure for the beta regression model, which is used to describe such response variables taking values in (0, 1) through some related explanatory variables. In relation to the beta regression model, the issue of robustness has been largely ignored in the literature so far. The existing maximum likelihood-based inference has serious lack of robustness against outliers in data and generate drastically different (erroneous) inference in the presence of data contamination. Here, we develop the robust minimum density power divergence estimator and a class of robust Wald-type tests for the beta regression model along with several applications. We derive their asymptotic properties and describe their robustness theoretically through the influence function analyses. Finite sample performances of the proposed estimators and tests are examined through suitable simulation studies and real data applications in the context of health care and psychology. Although we primarily focus on the beta regression models with a fixed dispersion parameter, some indications are also provided for extension to the variable dispersion beta regression models with an application.

Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes

PubMed Central

Lohse, Konrad; Frantz, Laurent A. F.

2014-01-01

Although there has been much interest in estimating histories of divergence and admixture from genomic data, it has proved difficult to distinguish recent admixture from long-term structure in the ancestral population. Thus, recent genome-wide analyses based on summary statistics have sparked controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. Here we derive the probability of full mutational configurations in nonrecombining sequence blocks under both admixture and ancestral structure scenarios. Dividing the genome into short blocks gives an efficient way to compute maximum-likelihood estimates of parameters. We apply this likelihood scheme to triplets of human and Neandertal genomes and compare the relative support for a model of admixture from Neandertals into Eurasian populations after their expansion out of Africa against a history of persistent structure in their common ancestral population in Africa. Our analysis allows us to conclusively reject a model of ancestral structure in Africa and instead reveals strong support for Neandertal admixture in Eurasia at a higher rate (3.4−7.3%) than suggested previously. Using analysis and simulations we show that our inference is more powerful than previous summary statistics and robust to realistic levels of recombination. PMID:24532731

Importance of the accuracy of experimental data in the nonlinear chromatographic determination of adsorption energy distributions

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

Stanley, B.J.; Guiochon, G.

1994-11-01

Adsorption energy distributions (AEDs) are calculated from the classical, fundamental integral equation of adsorption using adsorption isotherms and the expectation-maximization method of parameter estimation. The adsorption isotherms are calculated from nonlinear elution profiles obtained from gas chromatographic data using the characteristic points method of finite concentration chromatography. Porous layer open tubular capillary columns are used to support the adsorbent. The performance of these columns is compared to that of packed columns in terms of their ability to supply accurate isotherm data and AEDs. The effect of the finite column efficiency and the limited loading factor on the accuracy of themore » estimated energy distributions is presented. This accuracy decreases with decreasing efficiency, and approximately 5000 theoretical plates are needed when the loading factor, L[sub f], equals 0.56 for sampling of a unimodal Gaussian distribution. Increasing L[sub f] further increases the contribution of finite efficiency to the AED and causes a divergence at the low-energy endpoint if too high. This occurs as the retention time approaches the holdup time. Data are presented for diethyl ether adsorption on porous silica and its C-18-bonded derivative. 36 refs., 8 figs., 2 tabs.« less

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

Shi, Chang-Sheng; Zhang, Shuang-Nan; Li, Xiang-Dong, E-mail: zhangsn@ihep.ac.cn

We re-estimate the surface magnetic fields of neutron stars (NSs) in Be X-ray binaries (BeXBs) with different models of torque, improved beyond Klus et al. In particular, a new torque model is applied to three models of magnetosphere radius. Unlike the previous models, the new torque model does not lead to divergent results for any fastness parameter. The inferred surface magnetic fields of these NSs for the two compressed magnetosphere models are much higher than that for the uncompressed magnetosphere model. The new torque model using the compressed magnetosphere radius leads to unique solutions near spin equilibrium in all cases, unlike other modelsmore » that usually give two branches of solutions. Although our conclusions are still affected by the simplistic assumptions about the magnetosphere radius calculations, we show several groups of possible surface magnetic field values with our new models when the interaction between the magnetosphere and the infalling accretion plasma is considered. The estimated surface magnetic fields for NSs BeXBs in the Large Magellanic Cloud, the Small Magellanic Cloud and the Milk Way are between the quantum critical field and the maximum “virial” value by the spin equilibrium condition.« less

Singlet fermionic dark matter with Veltman conditions

NASA Astrophysics Data System (ADS)

Kim, Yeong Gyun; Lee, Kang Young; Nam, Soo-hyeon

2018-07-01

We reexamine a renormalizable model of a fermionic dark matter with a gauge singlet Dirac fermion and a real singlet scalar which can ameliorate the scalar mass hierarchy problem of the Standard Model (SM). Our model setup is the minimal extension of the SM for which a realistic dark matter (DM) candidate is provided and the cancellation of one-loop quadratic divergence to the scalar masses can be achieved by the Veltman condition (VC) simultaneously. This model extension, although renormalizable, can be considered as an effective low-energy theory valid up to cut-off energies about 10 TeV. We calculate the one-loop quadratic divergence contributions of the new scalar and fermionic DM singlets, and constrain the model parameters using the VC and the perturbative unitarity conditions. Taking into account the invisible Higgs decay measurement, we show the allowed region of new physics parameters satisfying the recent measurement of relic abundance. With the obtained parameter set, we predict the elastic scattering cross section of the new singlet fermion into target nuclei for a direct detection of the dark matter. We also perform the full analysis with arbitrary set of parameters without the VC as a comparison, and discuss the implication of the constraints by the VC in detail.

Residual Stress Measurement and Calibration for A7N01 Aluminum Alloy Welded Joints by Using Longitudinal Critically Refracted ( LCR) Wave Transmission Method

NASA Astrophysics Data System (ADS)

Zhu, Qimeng; Chen, Jia; Gou, Guoqing; Chen, Hui; Li, Peng; Gao, W.

2016-10-01

Residual stress measurement and control are highly important for the safety of structures of high-speed trains, which is critical for the structure design. The longitudinal critically refracted wave technology is the most widely used method in measuring residual stress with ultrasonic method, but its accuracy is strongly related to the test parameters, namely the flight time at the free-stress condition ( t 0), stress coefficient ( K), and initial stress (σ0) of the measured materials. The difference of microstructure in the weld zone, heat affected zone, and base metal (BM) results in the divergence of experimental parameters. However, the majority of researchers use the BM parameters to determine the residual stress in other zones and ignore the initial stress (σ0) in calibration samples. Therefore, the measured residual stress in different zones is often high in errors and may result in the miscalculation of the safe design of important structures. A serious problem in the ultrasonic estimation of residual stresses requires separation between the microstructure and the acoustoelastic effects. In this paper, the effects of initial stress and microstructure on stress coefficient K and flight time t 0 at free-stress conditions have been studied. The residual stress with or without different corrections was investigated. The results indicated that the residual stresses obtained with correction are more accurate for structure design.

Bifurcations, chaos and adaptive backstepping sliding mode control of a power system with excitation limitation

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

Min, Fuhong, E-mail: minfuhong@njnu.edu.cn; Wang, Yaoda; Peng, Guangya

2016-08-15

The bifurcation and Lyapunov exponent for a single-machine-infinite bus system with excitation model are carried out by varying the mechanical power, generator damping factor and the exciter gain, from which periodic motions, chaos and the divergence of system are observed respectively. From given parameters and different initial conditions, the coexisting motions are developed in power system. The dynamic behaviors in power system may switch freely between the coexisting motions, which will bring huge security menace to protection operation. Especially, the angle divergences due to the break of stable chaotic oscillation are found which causes the instability of power system. Finally,more » a new adaptive backstepping sliding mode controller is designed which aims to eliminate the angle divergences and make the power system run in stable orbits. Numerical simulations are illustrated to verify the effectivity of the proposed method.« less

Constraining neutron guide optimizations with phase-space considerations

NASA Astrophysics Data System (ADS)

Bertelsen, Mads; Lefmann, Kim

2016-09-01

We introduce a method named the Minimalist Principle that serves to reduce the parameter space for neutron guide optimization when the required beam divergence is limited. The reduced parameter space will restrict the optimization to guides with a minimal neutron intake that are still theoretically able to deliver the maximal possible performance. The geometrical constraints are derived using phase-space propagation from moderator to guide and from guide to sample, while assuming that the optimized guides will achieve perfect transport of the limited neutron intake. Guide systems optimized using these constraints are shown to provide performance close to guides optimized without any constraints, however the divergence received at the sample is limited to the desired interval, even when the neutron transport is not limited by the supermirrors used in the guide. As the constraints strongly limit the parameter space for the optimizer, two control parameters are introduced that can be used to adjust the selected subspace, effectively balancing between maximizing neutron transport and avoiding background from unnecessary neutrons. One parameter is needed to describe the expected focusing abilities of the guide to be optimized, going from perfectly focusing to no correlation between position and velocity. The second parameter controls neutron intake into the guide, so that one can select exactly how aggressively the background should be limited. We show examples of guides optimized using these constraints which demonstrates the higher signal to noise than conventional optimizations. Furthermore the parameter controlling neutron intake is explored which shows that the simulated optimal neutron intake is close to the analytically predicted, when assuming that the guide is dominated by multiple scattering events.

Monthly mean large-scale analyses of upper-tropospheric humidity and wind field divergence derived from three geostationary satellites

NASA Technical Reports Server (NTRS)

Schmetz, Johannes; Menzel, W. Paul; Velden, Christopher; Wu, Xiangqian; Vandeberg, Leo; Nieman, Steve; Hayden, Christopher; Holmlund, Kenneth; Geijo, Carlos

1995-01-01

This paper describes the results from a collaborative study between the European Space Operations Center, the European Organization for the Exploitation of Meteorological Satellites, the National Oceanic and Atmospheric Administration, and the Cooperative Institute for Meteorological Satellite Studies investigating the relationship between satellite-derived monthly mean fields of wind and humidity in the upper troposphere for March 1994. Three geostationary meteorological satellites GOES-7, Meteosat-3, and Meteosat-5 are used to cover an area from roughly 160 deg W to 50 deg E. The wind fields are derived from tracking features in successive images of upper-tropospheric water vapor (WV) as depicted in the 6.5-micron absorption band. The upper-tropospheric relative humidity (UTH) is inferred from measured water vapor radiances with a physical retrieval scheme based on radiative forward calculations. Quantitative information on large-scale circulation patterns in the upper-troposphere is possible with the dense spatial coverage of the WV wind vectors. The monthly mean wind field is used to estimate the large-scale divergence; values range between about-5 x 10(exp -6) and 5 x 10(exp 6)/s when averaged over a scale length of about 1000-2000 km. The spatial patterns of the UTH field and the divergence of the wind field closely resemble one another, suggesting that UTH patterns are principally determined by the large-scale circulation. Since the upper-tropospheric humidity absorbs upwelling radiation from lower-tropospheric levels and therefore contributes significantly to the atmospheric greenhouse effect, this work implies that studies on the climate relevance of water vapor should include three-dimensional modeling of the atmospheric dynamics. The fields of UTH and WV winds are useful parameters for a climate-monitoring system based on satellite data. The results from this 1-month analysis suggest the desirability of further GOES and Meteosat studies to characterize the changes in the upper-tropospheric moisture sources and sinks over the past decade.

Genetic constraints predict evolutionary divergence in Dalechampia blossoms

PubMed Central

Bolstad, Geir H.; Hansen, Thomas F.; Pélabon, Christophe; Falahati-Anbaran, Mohsen; Pérez-Barrales, Rocío; Armbruster, W. Scott

2014-01-01

If genetic constraints are important, then rates and direction of evolution should be related to trait evolvability. Here we use recently developed measures of evolvability to test the genetic constraint hypothesis with quantitative genetic data on floral morphology from the Neotropical vine Dalechampia scandens (Euphorbiaceae). These measures were compared against rates of evolution and patterns of divergence among 24 populations in two species in the D. scandens species complex. We found clear evidence for genetic constraints, particularly among traits that were tightly phenotypically integrated. This relationship between evolvability and evolutionary divergence is puzzling, because the estimated evolvabilities seem too large to constitute real constraints. We suggest that this paradox can be explained by a combination of weak stabilizing selection around moving adaptive optima and small realized evolvabilities relative to the observed additive genetic variance. PMID:25002700

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.

Dispersal and population connectivity in the deep North Atlantic estimated from physical transport processes

NASA Astrophysics Data System (ADS)

Etter, Ron J.; Bower, Amy S.

2015-10-01

Little is known about how larvae disperse in deep ocean currents despite how critical estimates of population connectivity are for ecology, evolution and conservation. Estimates of connectivity can provide important insights about the mechanisms that shape patterns of genetic variation. Strong population genetic divergence above and below about 3000 m has been documented for multiple protobranch bivalves in the western North Atlantic. One possible explanation for this congruent divergence is that the Deep Western Boundary Current (DWBC), which flows southwestward along the slope in this region, entrains larvae and impedes dispersal between the upper/middle slope and the lower slope or abyss. We used Lagrangian particle trajectories based on an eddy-resolving ocean general circulation model (specifically FLAME - Family of Linked Atlantic Model Experiments) to estimate the nature and scale of dispersal of passive larvae released near the sea floor at 4 depths across the continental slope (1500, 2000, 2500 and 3200 m) in the western North Atlantic and to test the potential role of the DWBC in explaining patterns of genetic variation on the continental margin. Passive particles released into the model DWBC followed highly complex trajectories that led to both onshore and offshore transport. Transport averaged about 1 km d-1 with dispersal kernels skewed strongly right indicating that some larvae dispersed much greater distances. Offshore transport was more likely than onshore and, despite a prevailing southwestward flow, some particles drifted north and east. Dispersal trajectories and estimates of population connectivity suggested that the DWBC is unlikely to prevent dispersal among depths, in part because of strong cross-slope forces induced by interactions between the DWBC and the deeper flows of the Gulf Stream. The strong genetic divergence we find in this region of the Northwest Atlantic is therefore likely driven by larval behaviors and/or mortality that limit dispersal, or local selective processes (both pre and post-settlement) that limit recruitment of immigrants from some depths.

Speciation on a conveyor belt: sequential colonization of the hawaiian islands by Orsonwelles spiders (Araneae, Linyphiidae).

PubMed

Hormiga, Gustavo; Arnedo, Miquel; Gillespie, Rosemary G

2003-02-01

Spiders of the recently described linyphiid genus Orsonwelles (Araneae, Linyphiidae) are one of the most conspicuous groups of terrestrial arthropods of Hawaiian native forests. There are 13 known Orsonwelles species, and all are single- island endemics. This radiation provides an excellent example of insular gigantism. We reconstructed the cladistic relationships of Orsonwelles species using a combination of morphological and molecular characters (both mitochondrial and nuclear sequences) within a parsimony framework. We explored and quantified the contribution of different character partitions and their sensitivity to changes in the traditional parameters (gap, transition, and transversion costs). The character data show a strong phylogenetic signal, robust to parameter changes. The monophyly of the genus Orsonwelles is strongly supported. The parsimony analysis of all character evidence combined recovered a clade with of all the non-Kauai Orsonwelles species; the species from Kauai form a paraphyletic assemblage with respect to the latter former clade. The biogeographic pattern of the Hawaiian Orsonwelles species is consistent with colonization by island progression, but alternative explanations for our data exist. Although the geographic origin of the radiation remains unknown, it appears that the ancestral colonizing species arrived first on Kauai (or an older island). The ambiguity in the area cladogram (i.e., post-Oahu colonization) is not derived from conflicting or unresolved phylogenetic signal among Orsonwelles species but rather from the number of taxa on the youngest islands. Speciation in Orsonwelles occurred more often within islands (8 of the 12 cladogenic events) than between islands. A molecular clock was rejected for the sequence data. Divergence times were estimated by using the nonparametric rate smoothing method of Sanderson (1997, Mol. Biol. Evol. 14:1218-1231) and the available geological data for calibration. The results suggest that the oldest divergences of Orsonwelles spiders (on Kauai) go back about 4 million years.

Rate variation and estimation of divergence times using strict and relaxed clocks.

PubMed

Brown, Richard P; Yang, Ziheng

2011-09-26

Understanding causes of biological diversity may be greatly enhanced by knowledge of divergence times. Strict and relaxed clock models are used in Bayesian estimation of divergence times. We examined whether: i) strict clock models are generally more appropriate in shallow phylogenies where rate variation is expected to be low, ii) the likelihood ratio test of the clock (LRT) reliably informs which model is appropriate for dating divergence times. Strict and relaxed models were used to analyse sequences simulated under different levels of rate variation. Published shallow phylogenies (Black bass, Primate-sucking lice, Podarcis lizards, Gallotiinae lizards, and Caprinae mammals) were also analysed to determine natural levels of rate variation relative to the performance of the different models. Strict clock analyses performed well on data simulated under the independent rates model when the standard deviation of log rate on branches, σ, was low (≤ 0.1), but were inappropriate when σ>0.1 (95% of rates fall within 0.0082-0.0121 subs/site/Ma when σ = 0.1, for a mean rate of 0.01). The independent rates relaxed clock model performed well at all levels of rate variation, although posterior intervals on times were significantly wider than for the strict clock. The strict clock is therefore superior when rate variation is low. The performance of a correlated rates relaxed clock model was similar to the strict clock. Increased numbers of independent loci led to slightly narrower posteriors under the relaxed clock while older root ages provided proportionately narrower posteriors. The LRT had low power for σ = 0.01-0.1, but high power for σ = 0.5-2.0. Posterior means of σ2 were useful for assessing rate variation in published datasets. Estimates of natural levels of rate variation ranged from 0.05-3.38 for different partitions. Differences in divergence times between relaxed and strict clock analyses were greater in two datasets with higher σ2 for one or more partitions, supporting the simulation results. The strict clock can be superior for trees with shallow roots because of low levels of rate variation between branches. The LRT allows robust assessment of suitability of the clock model as does examination of posteriors on σ2.

Evolutionary Diversification of Banded Tube-Dwelling Anemones (Cnidaria; Ceriantharia; Isarachnanthus) in the Atlantic Ocean

PubMed Central

Stampar, Sergio N.; Maronna, Maximiliano M.; Vermeij, Mark J. A.; Silveira, Fabio L. d.; Morandini, André C.

2012-01-01

The use of molecular data for species delimitation in Anthozoa is still a very delicate issue. This is probably due to the low genetic variation found among the molecular markers (primarily mitochondrial) commonly used for Anthozoa. Ceriantharia is an anthozoan group that has not been tested for genetic divergence at the species level. Recently, all three Atlantic species described for the genus Isarachnanthus of Atlantic Ocean, were deemed synonyms based on morphological simmilarities of only one species: Isarachnanthus maderensis. Here, we aimed to verify whether genetic relationships (using COI, 16S, ITS1 and ITS2 molecular markers) confirmed morphological affinities among members of Isarachnanthus from different regions across the Atlantic Ocean. Results from four DNA markers were completely congruent and revealed that two different species exist in the Atlantic Ocean. The low identification success and substantial overlap between intra and interspecific COI distances render the Anthozoa unsuitable for DNA barcoding, which is not true for Ceriantharia. In addition, genetic divergence within and between Ceriantharia species is more similar to that found in Medusozoa (Hydrozoa and Scyphozoa) than Anthozoa and Porifera that have divergence rates similar to typical metazoans. The two genetic species could also be separated based on micromorphological characteristics of their cnidomes. Using a specimen of Isarachnanthus bandanensis from Pacific Ocean as an outgroup, it was possible to estimate the minimum date of divergence between the clades. The cladogenesis event that formed the species of the Atlantic Ocean is estimated to have occured around 8.5 million years ago (Miocene) and several possible speciation scenarios are discussed. PMID:22815928

Phylogeny and evolutionary radiation of the marine mussels (Bivalvia: Mytilidae) based on mitochondrial and nuclear genes.

PubMed

Liu, Jun; Liu, Helu; Zhang, Haibin

2018-04-22

The marine mussels (Mytilidae) are distributed in the oceans worldwide and occupy various habitats with diverse life styles. However, their taxonomy and phylogeny remain unclear from genus to family level due to equivocal morphological and anatomical characters among some taxa. In this study, we inferred the deep phylogenetic relationships among 42 mytiloid species, 19 genera, and five subfamilies of the extant marine mussels by using two mitochondrial (COI and 16S rRNA) and three nuclear (18S and 28S rRNA, and histone H3) genes. Phylogeny was reconstructed with a combination of five genes using Bayesian inference and maximum likelihood method, and divergence time was estimated for the major nodes using a relaxed clock model with three fossil calibrations. Phylogenetic trees revealed two major clades (Clades 1 and 2). In Clade 1, the deep-sea mussels (subfamily Bathymodiolinae) were sister to subfamily Modiolinae (represented by Modiolus), and then was clustered with Leiosolenus (subfamily Lithophaginae). Clade 2 comprised Lithophaga (Lithophaginae) and subfamily Mytilinae. Additionally, a Modiolus species and Musculus senhousia (subfamily Crenellinae) were positioned within the subfamily Mytilinae. The phylogenetic results strongly indicated monophyly of Mytilidae and Bathymodiolinae, polyphyly of Modiolinae and Lithophaginae, and paraphyly of Mytilinae. Divergence time estimation showed an ancient and gradual divergence in most mussel groups, whereas the deep-sea mussels originated recently and diverged rapidly during the Paleogene. The present study provides new insight into the evolutionary history of the marine mussels, and supports taxonomic revision for this important bivalve group. Copyright © 2018 Elsevier Inc. All rights reserved.

Perceptual Modification of the Built Environment to Influence Behavior Associated with Physical Activity: Quasi-Experimental Field Studies of a Stair Banister Illusion.

PubMed

Masters, Rich; Capio, Catherine; Poolton, Jamie; Uiga, Liis

2018-06-01

Re-engineering the built environment to influence behaviors associated with physical activity potentially provides an opportunity to promote healthier lifestyles at a population level. Here we present evidence from two quasi-experimental field studies in which we tested a novel, yet deceptively simple, intervention designed to alter perception of, and walking behavior associated with, stairs in an urban area. Our objectives were to examine whether adjusting a stair banister has an influence on perceptions of stair steepness or on walking behavior when approaching the stairs. In study 1, we asked participants (n = 143) to visually estimate the steepness of a set of stairs viewed from the top, when the stair banister was adjusted so that it converged with or diverged from the stairs (± 1.91°) or remained neutral (± 0°). In study 2, the walking behavior of participants (n = 36) was filmed as they approached the stairs to descend, unaware of whether the banister converged, diverged, or was neutral. In study 1, participants estimated the stairs to be steeper if the banister diverged from, rather than converged with, the stairs. The effect was greater when participants were unaware of the adjustment. In study 2, walking speed was significantly slower when the banister diverged from, rather than converged with, the stairs. These findings encourage us to speculate about the potential to economically re-engineer features of the built environment to provide opportunities for action (affordances) that invite physical activity behavior or even promote safer navigation of the environment.

Evolutionary diversification of banded tube-dwelling anemones (Cnidaria; Ceriantharia; Isarachnanthus) in the Atlantic Ocean.

PubMed

Stampar, Sergio N; Maronna, Maximiliano M; Vermeij, Mark J A; Silveira, Fabio L d; Morandini, André C

2012-01-01

The use of molecular data for species delimitation in Anthozoa is still a very delicate issue. This is probably due to the low genetic variation found among the molecular markers (primarily mitochondrial) commonly used for Anthozoa. Ceriantharia is an anthozoan group that has not been tested for genetic divergence at the species level. Recently, all three Atlantic species described for the genus Isarachnanthus of Atlantic Ocean, were deemed synonyms based on morphological simmilarities of only one species: Isarachnanthus maderensis. Here, we aimed to verify whether genetic relationships (using COI, 16S, ITS1 and ITS2 molecular markers) confirmed morphological affinities among members of Isarachnanthus from different regions across the Atlantic Ocean. Results from four DNA markers were completely congruent and revealed that two different species exist in the Atlantic Ocean. The low identification success and substantial overlap between intra and interspecific COI distances render the Anthozoa unsuitable for DNA barcoding, which is not true for Ceriantharia. In addition, genetic divergence within and between Ceriantharia species is more similar to that found in Medusozoa (Hydrozoa and Scyphozoa) than Anthozoa and Porifera that have divergence rates similar to typical metazoans. The two genetic species could also be separated based on micromorphological characteristics of their cnidomes. Using a specimen of Isarachnanthus bandanensis from Pacific Ocean as an outgroup, it was possible to estimate the minimum date of divergence between the clades. The cladogenesis event that formed the species of the Atlantic Ocean is estimated to have occured around 8.5 million years ago (Miocene) and several possible speciation scenarios are discussed.

Genetic diversification without obvious genitalic morphological divergence in harvestmen (Opiliones, Laniatores, Sclerobunus robustus) from montane sky islands of western North America.

PubMed

Derkarabetian, Shahan; Ledford, Joel; Hedin, Marshal

2011-12-01

The southern Rocky Mountains and adjacent Intermontane Plateau Highlands region of western North America is a geographically diverse area with an active geologic history. Given the topological complexity and extensive geologic activity, organisms inhabiting this region are expected to show some degree of morphological and genetic divergence, especially populations found on the southern montane 'sky islands' of this region. Here we examine the phylogeographic history and diversification of a montane forest inhabiting harvestmen, Sclerobunus robustus, using a combination of genetic and morphological data. Divergence time estimates indicate that much of the diversification within and between major groups S. robustus predate the Pleistocene glacial cycles. The most widespread subspecies, Sclerobunus robustus robustus, is recovered as six genetically distinct, geographically cohesive mitochondrial phylogroups. Gene tree data for a single nuclear gene reveals congruent, albeit slightly more conservative, patterns of genetic divergence. Despite high levels of genetic divergence throughout their distribution, phylogroups show extreme conservation in somatic and reproductive morphology. This uncoupling of morphological and genetic differentiation may be due to morphological conservatism associated with a conserved microhabitat preference. Based on these data, it is obvious that S. robustus has undergone some level of cryptic diversification. Copyright © 2011 Elsevier Inc. All rights reserved.

Fast algorithms for computing phylogenetic divergence time.

PubMed

Crosby, Ralph W; Williams, Tiffani L

2017-12-06

The inference of species divergence time is a key step in most phylogenetic studies. Methods have been available for the last ten years to perform the inference, but the performance of the methods does not yet scale well to studies with hundreds of taxa and thousands of DNA base pairs. For example a study of 349 primate taxa was estimated to require over 9 months of processing time. In this work, we present a new algorithm, AncestralAge, that significantly improves the performance of the divergence time process. As part of AncestralAge, we demonstrate a new method for the computation of phylogenetic likelihood and our experiments show a 90% improvement in likelihood computation time on the aforementioned dataset of 349 primates taxa with over 60,000 DNA base pairs. Additionally, we show that our new method for the computation of the Bayesian prior on node ages reduces the running time for this computation on the 349 taxa dataset by 99%. Through the use of these new algorithms we open up the ability to perform divergence time inference on large phylogenetic studies.

Determination of electron energy, spectral width, and beam divergence at the exit window for clinical megavoltage x-ray beams.

PubMed

Sawkey, D L; Faddegon, B A

2009-03-01

Monte Carlo simulations of x-ray beams typically take parameters of the electron beam in the accelerating waveguide to be free parameters. In this paper, a methodology is proposed and implemented to determine the energy, spectral width, and beam divergence of the electron source. All treatment head components were removed from the beam path, leaving only the exit window. With the x-ray target and flattener out of the beam, uncertainties in physical characteristics and relative position of the target and flattening filter, and in spot size, did not contribute to uncertainty in the energy. Beam current was lowered to reduce recombination effects. The measured dose distributions were compared with Monte Carlo simulation of the electron beam through the treatment head to extract the electron source characteristics. For the nominal 6 and 18 MV x-ray beams, the energies were 6.51 +/- 0.15 and 13.9 +/- 0.2 MeV, respectively, with the uncertainties resulting from uncertainties in the detector position in the measurement and in the stopping power in the simulations. Gaussian spectral distributions were used, with full widths at half maximum ranging from 20 +/- 4% at 6 MV to 13 +/- 4% at 18 MV required to match the fall-off portion of the percent-depth ionization curve. Profiles at the depth of maximum dose from simulations that used the manufacturer-specified exit window geometry and no beam divergence were 2-3 cm narrower than measured profiles. Two simulation configurations yielding the measured profile width were the manufacturer-specified exit window thickness with electron source divergences of 3.3 degrees at 6 MV and 1.8 degrees at 18 MV and an exit window 40% thicker than the manufacturer's specification with no beam divergence. With the x-ray target in place (and no flattener), comparison of measured to simulated profiles sets upper limits on the electron source divergences of 0.2 degrees at 6 MV and 0.1 degrees at 18 MV. A method of determining source characteristics without mechanical modification of the treatment head, and therefore feasible in clinics, is presented. The energies and spectral widths determined using this method agree with those determined with only the exit window in the beam path.

Positive selection and propeptide repeats promote rapid interspecific divergence of a gastropod sperm protein.

PubMed

Hellberg, M E; Moy, G W; Vacquier, V D

2000-03-01

Male-specific proteins have increasingly been reported as targets of positive selection and are of special interest because of the role they may play in the evolution of reproductive isolation. We report the rapid interspecific divergence of cDNA encoding a major acrosomal protein of unknown function (TMAP) of sperm from five species of teguline gastropods. A mitochondrial DNA clock (calibrated by congeneric species divided by the Isthmus of Panama) estimates that these five species diverged 2-10 MYA. Inferred amino acid sequences reveal a propeptide that has diverged rapidly between species. The mature protein has diverged faster still due to high nonsynonymous substitution rates (> 25 nonsynonymous substitutions per site per 10(9) years). cDNA encoding the mature protein (89-100 residues) shows evidence of positive selection (Dn/Ds > 1) for 4 of 10 pairwise species comparisons. cDNA and predicted secondary-structure comparisons suggest that TMAP is neither orthologous nor paralogous to abalone lysin, and thus marks a second, phylogenetically independent, protein subject to strong positive selection in free-spawning marine gastropods. In addition, an internal repeat in one species (Tegula aureotincta) produces a duplicated cleavage site which results in two alternatively processed mature proteins differing by nine amino acid residues. Such alternative processing may provide a mechanism for introducing novel amino acid sequence variation at the amino-termini of proteins. Highly divergent TMAP N-termini from two other tegulines (Tegula regina and Norrisia norrisii) may have originated by such a mechanism.

Explosive radiation and spatial expansion across the cold environments of the Old World in an avian family.

PubMed

Liu, Baoyan; Alström, Per; Olsson, Urban; Fjeldså, Jon; Quan, Qing; Roselaar, Kees C S; Saitoh, Takema; Yao, Cheng-Te; Hao, Yan; Wang, Wenjuan; Qu, Yanhua; Lei, Fumin

2017-08-01

Our objective was to elucidate the biogeography and speciation patterns in an entire avian family, which shows a complex pattern of overlapping and nonoverlapping geographical distributions, and much variation in plumage, but less in size and structure. We estimated the phylogeny and divergence times for all of the world's species of Prunella based on multiple genetic loci, and analyzed morphometric divergence and biogeographical history. The common ancestor of Prunella was present in the Sino-Himalayan Mountains or these mountains and Central Asia-Mongolia more than 9 million years ago (mya), but a burst of speciations took place during the mid-Pliocene to early Pleistocene. The relationships among the six primary lineages resulting from that differentiation are unresolved, probably because of the rapid radiation. A general increase in sympatry with increasing time since divergence is evident. With one exception, species in clades younger than c. 3.7 my are allopatric. Species that are widely sympatric, including the most recently diverged (2.4 mya) sympatric sisters, are generally more divergent in size/structure than allo-/parapatric close relatives. The distributional pattern and inferred ages suggest divergence in allopatry and substantial waiting time until secondary contact, likely due to competitive exclusion. All sympatrically breeding species are ecologically segregated, as suggested by differences in size/structure and habitat. Colonizations of new areas were facilitated during glacial periods, followed by fragmentation during interglacials-contrary to the usual view that glacial periods resulted mainly in fragmentations.

A reduced order model based on Kalman filtering for sequential data assimilation of turbulent flows

NASA Astrophysics Data System (ADS)

Meldi, M.; Poux, A.

2017-10-01

A Kalman filter based sequential estimator is presented in this work. The estimator is integrated in the structure of segregated solvers for the analysis of incompressible flows. This technique provides an augmented flow state integrating available observation in the CFD model, naturally preserving a zero-divergence condition for the velocity field. Because of the prohibitive costs associated with a complete Kalman Filter application, two model reduction strategies have been proposed and assessed. These strategies dramatically reduce the increase in computational costs of the model, which can be quantified in an augmentation of 10%- 15% with respect to the classical numerical simulation. In addition, an extended analysis of the behavior of the numerical model covariance Q has been performed. Optimized values are strongly linked to the truncation error of the discretization procedure. The estimator has been applied to the analysis of a number of test cases exhibiting increasing complexity, including turbulent flow configurations. The results show that the augmented flow successfully improves the prediction of the physical quantities investigated, even when the observation is provided in a limited region of the physical domain. In addition, the present work suggests that these Data Assimilation techniques, which are at an embryonic stage of development in CFD, may have the potential to be pushed even further using the augmented prediction as a powerful tool for the optimization of the free parameters in the numerical simulation.

Breeding maize as biogas substrate in Central Europe: I. Quantitative-genetic parameters for testcross performance.

PubMed

Grieder, Christoph; Dhillon, Baldev S; Schipprack, Wolfgang; Melchinger, Albrecht E

2012-04-01

Biofuels have gained importance recently and the use of maize biomass as substrate in biogas plants for production of methane has increased tremendously in Germany. The objectives of our research were to (1) estimate variance components and heritability for different traits relevant to biogas production in testcrosses (TCs) of maize, (2) study correlations among traits, and (3) discuss strategies to breed maize as a substrate for biogas fermenters. We evaluated 570 TCs of 285 diverse dent maize lines crossed with two flint single-cross testers in six environments. Data were recorded on agronomic and quality traits, including dry matter yield (DMY), methane fermentation yield (MFY), and methane yield (MY), the product of DMY and MFY, as the main target trait. Estimates of variance components showed general combining ability (GCA) to be the major source of variation. Estimates of heritability exceeded 0.67 for all traits and were even much greater in most instances. Methane yield was perfectly correlated with DMY but not with MFY, indicating that variation in MY is primarily determined by DMY. Further, DMY had a larger heritability and coefficient of genetic variation than MFY. Hence, for improving MY, selection should primarily focus on DMY rather than MFY. Further, maize breeding for biogas production may diverge from that for forage production because in the former case, quality traits seem to be of much lower importance.

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.

Estimating phylogenetic relationships despite discordant gene trees across loci: the species tree of a diverse species group of feather mites (Acari: Proctophyllodidae).

PubMed

Knowles, Lacey L; Klimov, Pavel B

2011-11-01

With the increased availability of multilocus sequence data, the lack of concordance of gene trees estimated for independent loci has focused attention on both the biological processes producing the discord and the methodologies used to estimate phylogenetic relationships. What has emerged is a suite of new analytical tools for phylogenetic inference--species tree approaches. In contrast to traditional phylogenetic methods that are stymied by the idiosyncrasies of gene trees, approaches for estimating species trees explicitly take into account the cause of discord among loci and, in the process, provides a direct estimate of phylogenetic history (i.e. the history of species divergence, not divergence of specific loci). We illustrate the utility of species tree estimates with an analysis of a diverse group of feather mites, the pinnatus species group (genus Proctophyllodes). Discord among four sequenced nuclear loci is consistent with theoretical expectations, given the short time separating speciation events (as evident by short internodes relative to terminal branch lengths in the trees). Nevertheless, many of the relationships are well resolved in a Bayesian estimate of the species tree; the analysis also highlights ambiguous aspects of the phylogeny that require additional loci. The broad utility of species tree approaches is discussed, and specifically, their application to groups with high speciation rates--a history of diversification with particular prevalence in host/parasite systems where species interactions can drive rapid diversification.

Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow.

PubMed

Sachdeva, Himani; Barton, Nicholas H

2017-06-01

Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Molecular systematics and global phylogeography of angel sharks (genus Squatina).

PubMed

Stelbrink, Björn; von Rintelen, Thomas; Cliff, Geremy; Kriwet, Jürgen

2010-02-01

Angel sharks of the genus Squatina represent a group comprising 22 extant benthic species inhabiting continental shelves and upper slopes. In the present study, a comprehensive phylogenetic reconstruction of 17 Squatina species based on two mitochondrial markers (COI and 16S rRNA) is provided. The phylogenetic reconstructions are used to test biogeographic patterns. In addition, a molecular clock analysis is conducted to estimate divergence times of the emerged clades. All analyses show Squatina to be monophyletic. Four geographic clades are recognized, of which the Europe-North Africa-Asia clade is probably a result of the Tethys Sea closure. A second sister group relationship emerged in the analyses, including S. californica (eastern North Pacific) and S. dumeril (western North Atlantic), probably related to the rise of the Panamanian isthmus. The molecular clock analysis show that both lineage divergences coincide with the estimated time of these two geological events. Copyright (c) 2009. Published by Elsevier Inc.

A novel navigation method used in a ballistic missile

NASA Astrophysics Data System (ADS)

Qian, Hua-ming; Sun, Long; Cai, Jia-nan; Peng, Yu

2013-10-01

The traditional strapdown inertial/celestial integrated navigation method used in a ballistic missile cannot accurately estimate the accelerometer bias. It might cause a divergence of navigation errors. To solve this problem, a new navigation method named strapdown inertial/starlight refractive celestial integrated navigation is proposed. To verify the feasibility of the proposed method, a simulated program of a ballistic missile is presented. The simulation results indicated that, when multiple refraction stars are used, the proposed method can accurately estimate the accelerometer bias, and suppress the divergence of navigation errors completely. Specifically, in order to apply this method to a ballistic missile, a novel measurement equation based on stellar refraction was developed. Furthermore a method to calculate the number of refraction stars observed by the stellar sensor was given. Finally, the relationship between the number of refraction stars used and the navigation accuracy is analysed.

Using land subsidence observations for groundwater model calibration

NASA Astrophysics Data System (ADS)

Tufekci, Nesrin; Schoups, Gerrit; Faitouri, Mohamed Al; Mahapatra, Pooja; van de Giesen, Nick; Hanssen, Ramon

2017-04-01

PS-InSAR derived subsidence and groundwater level time series are used to calibrate a groundwater model of Tazerbo well field, Libya, by estimating spatially varying elastic skeletal storage (Sske) and hydraulic conductivity (Hk) of the model area. Tazerbo well field is a part of the Great Man-Made River Project (GMMRP) designed with 108 wells and total pumping rate of 1 million m3/day. The water is pumped from the deep sandstone aquifer (Nubian sandstone), which is overlaid by a thick mudstone-siltstone aquitard. Pumping related deformation patterns around Tazerbo well field are obtained by processing 20 descending Envisat scenes for the period between 2004 and 2010, which yield a concentrated deformation around the well field with the maximum deformation rate around 4 mm/yr. The trends of time series of groundwater head and subsidence are in good agreement for observation wells located in the vicinity of the pumping wells and the pattern of subsidence correlates with the locations of active wells. At the beginning of calibration, different pairs of Sske and Hk are assigned at observation well locations by trial and error so that the simulation results of the forward model would approximate heads and mean linear deformation velocity at these locations. Accordingly, the estimated initial parameters suggest relatively constant Hk(5 m/d) and increasing Sske from south to north (1x10-6 m-1 - 5x10-6 m-1). In order to refine their spatial distribution, representative values of Sske and Hk are assigned at 25 equidistant points over the area, which are restricted by the predetermined values. To calibrate the parameters at assigned locations UCODE is used along with MATLAB. Once the convergence is achieved the estimated parameter values at these locations are held constant and new "in between - equidistant" locations are determined to estimate Sske and Hk in order to spatially refine their distribution. This approach is followed until the relation between observed and simulated results cannot be improved anymore. The final results, show good relation in the areas close to well sites, while difference between simulated and observed values increases towards the southeast boundary of PS-InSAR observations. This divergence can be explained by i) the uncertainty in the parameters at the southeast part of the model area, due to lack of deformation observations, ii) Sske may have been underestimated at the locations with thin aquifer and thick aquitard material.

A Generalized Least-Squares Estimate for the Origin of Sporophytic Self-Incompatibility

PubMed Central

Uyenoyama, M. K.

1995-01-01

Analysis of nucleotide sequences that regulate the expression of self-incompatibility in flowering plants affords a direct means of examining classical hypotheses for the origin and evolution of this major feature of mating systems. Departing from the classical view of monophyly of all forms of self-incompatibility, the current paradigm for the origin of self-incompatibility postulates multiple episodes of recruitment and modification of preexisting genes. In Brassica, the S locus, which regulates sporophytic self-incompatibility, shows homology to a multigene family present both in self-compatible congeners and in groups for which this form of self-incompatibility is atypical. A phylogenetic analysis of S-allele sequences together with homologous sequences that do not cosegregate with self-incompatibility permits dating the change of function that marked the origin of self-incompatibility. A generalized least-squares method is introduced that provides closed-form expressions for estimates and standard errors for function-specific divergence rates and times of divergence among sequences. This analysis suggests that the age of the sporophytic self-incompatibility system expressed in Brassica exceeds species divergence within the genus by four- to fivefold. The extraordinarily high levels of sequence diversity exhibited by S alleles appears to reflect their ancient derivation, with the alternative hypothesis of hypermutability rejected by the analysis. PMID:7713446

Directional cultural change by modification and replacement of memes.

PubMed

Cardoso, Gonçalo C; Atwell, Jonathan W

2011-01-01

Evolutionary approaches to culture remain contentious. A source of contention is that cultural mutation may be substantial and, if it drives cultural change, then current evolutionary models are not adequate. But we lack studies quantifying the contribution of mutations to directional cultural change. We estimated the contribution of one type of cultural mutations--modification of memes--to directional cultural change using an amenable study system: learned birdsongs in a species that recently entered an urban habitat. Many songbirds have higher minimum song frequency in cities, to alleviate masking by low-frequency noise. We estimated that the input of meme modifications in an urban songbird population explains about half the extent of the population divergence in song frequency. This contribution of cultural mutations is large, but insufficient to explain the entire population divergence. The remaining divergence is due to selection of memes or creation of new memes. We conclude that the input of cultural mutations can be quantitatively important, unlike in genetic evolution, and that it operates together with other mechanisms of cultural evolution. For this and other traits, in which the input of cultural mutations might be important, quantitative studies of cultural mutation are necessary to calibrate realistic models of cultural evolution. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

Probabilistic distance-based quantizer design for distributed estimation

NASA Astrophysics Data System (ADS)

Kim, Yoon Hak

2016-12-01

We consider an iterative design of independently operating local quantizers at nodes that should cooperate without interaction to achieve application objectives for distributed estimation systems. We suggest as a new cost function a probabilistic distance between the posterior distribution and its quantized one expressed as the Kullback Leibler (KL) divergence. We first present the analysis that minimizing the KL divergence in the cyclic generalized Lloyd design framework is equivalent to maximizing the logarithmic quantized posterior distribution on the average which can be further computationally reduced in our iterative design. We propose an iterative design algorithm that seeks to maximize the simplified version of the posterior quantized distribution and discuss that our algorithm converges to a global optimum due to the convexity of the cost function and generates the most informative quantized measurements. We also provide an independent encoding technique that enables minimization of the cost function and can be efficiently simplified for a practical use of power-constrained nodes. We finally demonstrate through extensive experiments an obvious advantage of improved estimation performance as compared with the typical designs and the novel design techniques previously published.

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.].

Does gene flow constrain adaptive divergence or vice versa? A test using ecomorphology and sexual isolation in Timema cristinae walking-sticks.

PubMed

Nosil, P; Crespi, B J

2004-01-01

Population differentiation often reflects a balance between divergent natural selection and the opportunity for homogenizing gene flow to erode the effects of selection. However, during ecological speciation, trait divergence results in reproductive isolation and becomes a cause, rather than a consequence, of reductions in gene flow. To assess both the causes and the reproductive consequences of morphological differentiation, we examined morphological divergence and sexual isolation among 17 populations of Timema cristinae walking-sticks. Individuals from populations adapted to using Adenostoma as a host plant tended to exhibit smaller overall body size, wide heads, and short legs relative to individuals using Ceonothus as a host. However, there was also significant variation in morphology among populations within host-plant species. Mean trait values for each single population could be reliably predicted based upon host-plant used and the potential for homogenizing gene flow, inferred from the size of the neighboring population using the alternate host and mitochondrial DNA estimates of gene flow. Morphology did not influence the probability of copulation in between-population mating trials. Thus, morphological divergence is facilitated by reductions in gene flow, but does not cause reductions in gene flow via the evolution of sexual isolation. Combined with rearing data indicating that size and shape have a partial genetic basis, evidence for parallel origins of the host-associated forms, and inferences from functional morphology, these results indicate that morphological divergence in T. cristinae reflects a balance between the effects of host-specific natural selection and gene flow. Our findings illustrate how data on mating preferences can help determine the causal associations between trait divergence and levels of gene flow.

Numerical integration of KPZ equation with restrictions

NASA Astrophysics Data System (ADS)

Torres, M. F.; Buceta, R. C.

2018-03-01

In this paper, we introduce a novel integration method of Kardar–Parisi–Zhang (KPZ) equation. It is known that if during the discrete integration of the KPZ equation the nearest-neighbor height-difference exceeds a critical value, instabilities appear and the integration diverges. One way to avoid these instabilities is to replace the KPZ nonlinear-term by a function of the same term that depends on a single adjustable parameter which is able to control pillars or grooves growing on the interface. Here, we propose a different integration method which consists of directly limiting the value taken by the KPZ nonlinearity, thereby imposing a restriction rule that is applied in each integration time-step, as if it were the growth rule of a restricted discrete model, e.g. restricted-solid-on-solid (RSOS). Taking the discrete KPZ equation with restrictions to its dimensionless version, the integration depends on three parameters: the coupling constant g, the inverse of the time-step k, and the restriction constant ε which is chosen to eliminate divergences while keeping all the properties of the continuous KPZ equation. We study in detail the conditions in the parameters’ space that avoid divergences in the 1-dimensional integration and reproduce the scaling properties of the continuous KPZ with a particular parameter set. We apply the tested methodology to the d-dimensional case (d = 3, 4 ) with the purpose of obtaining the growth exponent β, by establishing the conditions of the coupling constant g under which we recover known values reached by other authors, particularly for the RSOS model. This method allows us to infer that d  =  4 is not the critical dimension of the KPZ universality class, where the strong-coupling phase disappears.

Subtractive procedure for calculating the anomalous electron magnetic moment in QED and its application for numerical calculation at the three-loop level

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

Volkov, S. A., E-mail: volkoff-sergey@mail.ru

2016-06-15

A new subtractive procedure for canceling ultraviolet and infrared divergences in the Feynman integrals described here is developed for calculating QED corrections to the electron anomalous magnetic moment. The procedure formulated in the form of a forest expression with linear operators applied to Feynman amplitudes of UV-diverging subgraphs makes it possible to represent the contribution of each Feynman graph containing only electron and photon propagators in the form of a converging integral with respect to Feynman parameters. The application of the developed method for numerical calculation of two- and threeloop contributions is described.

Injection-insensitive lateral divergence in broad-area diode lasers achieved by spatial current modulation

NASA Astrophysics Data System (ADS)

Wang, Tao; Tong, Cunzhu; Wang, Lijie; Zeng, Yugang; Tian, Sicong; Shu, Shili; Zhang, Jian; Wang, Lijun

2016-11-01

High-power broad-area (BA) diode lasers often suffer from low beam quality, broad linewidth, and a widened slow-axis far field with increasing current. In this paper, a two-dimensional current-modulated structure is proposed and it is demonstrated that it can reduce not only the far-field sensitivity to the injection current but also the linewidth of the lasing spectra. Injection-insensitive lateral divergence was realized, and the beam parameter product (BPP) was improved by 36.5%. At the same time, the linewidth was decreased by about 45% without significant degradations of emission power and conversion efficiency.

Nuclear magnetic resonance in low-symmetry superconductors

NASA Astrophysics Data System (ADS)

Cavanagh, D. C.; Powell, B. J.

2018-01-01

We consider the nuclear spin-lattice relaxation rate 1 /T1 in superconductors with accidental nodes, i.e., zeros of the order parameter that are not enforced by its symmetries. Such nodes in the superconducting gap are not constrained by symmetry to a particular position on the Fermi surface. We show, analytically and numerically, that a Hebel-Slichter-like peak occurs even in the absence of an isotropic component of the superconducting gap. For a gap with symmetry-required nodes the Fermi velocity at the node must point along the node. For accidental nodes this is not, in general, the case. This leads to additional terms in spectral function and hence the density of states. These terms lead to a logarithmic divergence in 1 /T1T at T →Tc- in models neglecting disorder and interactions [except for those leading to superconductivity; here T is temperature, Tc-=limδ→0(Tc-δ ) , and Tc is the critical temperature]. This contrasts with the usual Hebel-Slichter peak which arises from the coherence factors due to the isotropic component of the gap and leads to a divergence in 1 /T1T somewhat below Tc. The divergence in superconductors with accidental nodes is controlled by either disorder or additional electron-electron interactions. However, for reasonable parameters, neither of these effects removes the peak altogether. This provides a simple experimental method to distinguish between symmetry-required and accidental nodes.

Recombination-Driven Genome Evolution and Stability of Bacterial Species.

PubMed

Dixit, Purushottam D; Pang, Tin Yau; Maslov, Sergei

2017-09-01

While bacteria divide clonally, horizontal gene transfer followed by homologous recombination is now recognized as an important contributor to their evolution. However, the details of how the competition between clonality and recombination shapes genome diversity remains poorly understood. Using a computational model, we find two principal regimes in bacterial evolution and identify two composite parameters that dictate the evolutionary fate of bacterial species. In the divergent regime, characterized by either a low recombination frequency or strict barriers to recombination, cohesion due to recombination is not sufficient to overcome the mutational drift. As a consequence, the divergence between pairs of genomes in the population steadily increases in the course of their evolution. The species lacks genetic coherence with sexually isolated clonal subpopulations continuously formed and dissolved. In contrast, in the metastable regime, characterized by a high recombination frequency combined with low barriers to recombination, genomes continuously recombine with the rest of the population. The population remains genetically cohesive and temporally stable. Notably, the transition between these two regimes can be affected by relatively small changes in evolutionary parameters. Using the Multi Locus Sequence Typing (MLST) data, we classify a number of bacterial species to be either the divergent or the metastable type. Generalizations of our framework to include selection, ecologically structured populations, and horizontal gene transfer of nonhomologous regions are discussed as well. Copyright © 2017 by the Genetics Society of America.

µ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype ... frequencies

USDA-ARS?s Scientific Manuscript database

Genetic marker effects and interactions are estimated with poor precision when minor marker allele frequencies are low. An Angus population was subjected to marker assisted selection for multiple years to increase divergent haplotype and minor marker allele frequencies to 1) estimate effect size an...

Numerical study of neutron beam divergence in a beam-fusion scenario employing laser driven ions

NASA Astrophysics Data System (ADS)

Alejo, A.; Green, A.; Ahmed, H.; Robinson, A. P. L.; Cerchez, M.; Clarke, R.; Doria, D.; Dorkings, S.; Fernandez, J.; McKenna, P.; Mirfayzi, S. R.; Naughton, K.; Neely, D.; Norreys, P.; Peth, C.; Powell, H.; Ruiz, J. A.; Swain, J.; Willi, O.; Borghesi, M.; Kar, S.

2016-09-01

The most established route to create a laser-based neutron source is by employing laser accelerated, low atomic-number ions in fusion reactions. In addition to the high reaction cross-sections at moderate energies of the projectile ions, the anisotropy in neutron emission is another important feature of beam-fusion reactions. Using a simple numerical model based on neutron generation in a pitcher-catcher scenario, anisotropy in neutron emission was studied for the deuterium-deuterium fusion reaction. Simulation results are consistent with the narrow-divergence (∼ 70 ° full width at half maximum) neutron beam recently served in an experiment employing multi-MeV deuteron beams of narrow divergence (up to 30° FWHM, depending on the ion energy) accelerated by a sub-petawatt laser pulse from thin deuterated plastic foils via the Target Normal Sheath Acceleration mechanism. By varying the input ion beam parameters, simulations show that a further improvement in the neutron beam directionality (i.e. reduction in the beam divergence) can be obtained by increasing the projectile ion beam temperature and cut-off energy, as expected from interactions employing higher power lasers at upcoming facilities.

Is competition needed for ecological character displacement? Does displacement decrease competition?

PubMed Central

Abrams, Peter A.; Cortez, Michael H.

2015-01-01

Interspecific competition for resources is generally considered to be the selective force driving ecological character displacement, and displacement is assumed to reduce competition. Skeptics of the prevalence of character displacement often cite lack of evidence of competition. The present article uses a simple model to examine whether competition is needed for character displacement and whether displacement reduces competition. It treats systems with competing resources, and considers cases when only one consumer evolves. It quantifies competition using several different measures. The analysis shows that selection for divergence of consumers occurs regardless of the level of between‐resource competition or whether the indirect interaction between the consumers is competition (−,−), mutualism (+,+), or contramensalism (+,−). Also, divergent evolution always decreases the equilibrium population size of the evolving consumer. Whether divergence of one consumer reduces or increases the impact of a subsequent perturbation of the other consumer depends on the parameters and the method chosen for measuring competition. Divergence in mutualistic interactions may reduce beneficial effects of subsequent increases in the other consumer's population. The evolutionary response is driven by an increase in the relative abundance of the resource the consumer catches more rapidly. Such an increase can occur under several types of interaction. PMID:26548922

Tracing the colonization history of the Indian Ocean scops-owls (Strigiformes: Otus) with further insight into the spatio-temporal origin of the Malagasy avifauna.

PubMed

Fuchs, Jérôme; Pons, Jean-Marc; Goodman, Steven M; Bretagnolle, Vincent; Melo, Martim; Bowie, Rauri C K; Currie, David; Safford, Roger; Virani, Munir Z; Thomsett, Simon; Hija, Alawi; Cruaud, Corinne; Pasquet, Eric

2008-07-09

The island of Madagascar and surrounding volcanic and coralline islands are considered to form a biodiversity hotspot with large numbers of unique taxa. The origin of this endemic fauna can be explained by two different factors: vicariance or over-water-dispersal. Deciphering which factor explains the current distributional pattern of a given taxonomic group requires robust phylogenies as well as estimates of divergence times. The lineage of Indian Ocean scops-owls (Otus: Strigidae) includes six or seven species that are endemic to Madagascar and portions of the Comoros and Seychelles archipelagos; little is known about the species limits, biogeographic affinities and relationships to each other. In the present study, using DNA sequence data gathered from six loci, we examine the biogeographic history of the Indian Ocean scops-owls. We also compare the pattern and timing of colonization of the Indian Ocean islands by scops-owls with divergence times already proposed for other bird taxa. Our analyses revealed that Indian Ocean islands scops-owls do not form a monophyletic assemblage: the Seychelles Otus insularis is genetically closer to the South-East Asian endemic O. sunia than to species from the Comoros and Madagascar. The Pemba Scops-owls O. pembaensis, often considered closely related to, if not conspecific with O. rutilus of Madagascar, is instead closely related to the African mainland O. senegalensis. Relationships among the Indian Ocean taxa from the Comoros and Madagascar are unresolved, despite the analysis of over 4000 bp, suggesting a diversification burst after the initial colonization event. We also highlight one case of putative back-colonization to the Asian mainland from an island ancestor (O. sunia). Our divergence date estimates, using a Bayesian relaxed clock method, suggest that all these events occurred during the last 3.6 myr; albeit colonization of the Indian Ocean islands were not synchronous, O. pembaensis diverged from O. senegalensis about 1.7 mya while species from Madagascar and the Comoro diverged from their continental sister-group about 3.6 mya. We highlight that our estimates coincide with estimates of diversification from other bird lineages. Our analyses revealed the occurrence of multiple synchronous colonization events of the Indian Ocean islands by scops-owls, at a time when faunistic exchanges involving Madagascar was common as a result of lowered sea-level that would have allowed the formation of stepping-stone islands. Patterns of diversification that emerged from the scops-owls data are: 1) a star-like pattern concerning the order of colonization of the Indian Ocean islands and 2) the high genetic distinctiveness among all Indian Ocean taxa, reinforcing their recognition as distinct species.

Tracing the colonization history of the Indian Ocean scops-owls (Strigiformes: Otus) with further insight into the spatio-temporal origin of the Malagasy avifauna

PubMed Central

2008-01-01

Background The island of Madagascar and surrounding volcanic and coralline islands are considered to form a biodiversity hotspot with large numbers of unique taxa. The origin of this endemic fauna can be explained by two different factors: vicariance or over-water-dispersal. Deciphering which factor explains the current distributional pattern of a given taxonomic group requires robust phylogenies as well as estimates of divergence times. The lineage of Indian Ocean scops-owls (Otus: Strigidae) includes six or seven species that are endemic to Madagascar and portions of the Comoros and Seychelles archipelagos; little is known about the species limits, biogeographic affinities and relationships to each other. In the present study, using DNA sequence data gathered from six loci, we examine the biogeographic history of the Indian Ocean scops-owls. We also compare the pattern and timing of colonization of the Indian Ocean islands by scops-owls with divergence times already proposed for other bird taxa. Results Our analyses revealed that Indian Ocean islands scops-owls do not form a monophyletic assemblage: the Seychelles Otus insularis is genetically closer to the South-East Asian endemic O. sunia than to species from the Comoros and Madagascar. The Pemba Scops-owls O. pembaensis, often considered closely related to, if not conspecific with O. rutilus of Madagascar, is instead closely related to the African mainland O. senegalensis. Relationships among the Indian Ocean taxa from the Comoros and Madagascar are unresolved, despite the analysis of over 4000 bp, suggesting a diversification burst after the initial colonization event. We also highlight one case of putative back-colonization to the Asian mainland from an island ancestor (O. sunia). Our divergence date estimates, using a Bayesian relaxed clock method, suggest that all these events occurred during the last 3.6 myr; albeit colonization of the Indian Ocean islands were not synchronous, O. pembaensis diverged from O. senegalensis about 1.7 mya while species from Madagascar and the Comoro diverged from their continental sister-group about 3.6 mya. We highlight that our estimates coincide with estimates of diversification from other bird lineages. Conclusion Our analyses revealed the occurrence of multiple synchronous colonization events of the Indian Ocean islands by scops-owls, at a time when faunistic exchanges involving Madagascar was common as a result of lowered sea-level that would have allowed the formation of stepping-stone islands. Patterns of diversification that emerged from the scops-owls data are: 1) a star-like pattern concerning the order of colonization of the Indian Ocean islands and 2) the high genetic distinctiveness among all Indian Ocean taxa, reinforcing their recognition as distinct species. PMID:18611281

Geodetic measurements and numerical models of the Afar rifting sequence 2005-2010

NASA Astrophysics Data System (ADS)

Ali, T.; Feigl, K.; Calais, E.; Hamling, I. J.; Wright, T. J.

2012-12-01

Rifting episodes are characterized by magma migration and dike intrusions that perturb the stress field within the surrounding lithosphere, inducing viscous flow in the lower crust and upper mantle that leads to observable, transient surface deformation. The Manda Hararo-Dabbahu rifting episode that occurred in the Afar depression between 2005 and 2010 is the first such episode to unfold fully in the era of satellite geodesy, thus providing a unique opportunity to probe the rheology of lithosphere at a divergent plate boundary. GPS and SAR measurements over the region since 2005 show accelerated surface deformation rates during post-diking intervals [Wright et al., Nature Geosci., 2012]. Using these observations in combination with a numerical model, we estimate model parameters that best explain the deformation signal. Our model accounts for three distinct processes: (i) secular plate spreading between Nubian and Arabian plates, (ii) time dependent post-rifting viscoelastic relaxation following the 14 dike intrusions that occurred between 2005 and 2010, including the 60 km long mega dike intrusion of September 2005, and (iii) magma accumulation within crustal reservoirs that feed the dikes. To model the time dependent deformation field, we use the open-source unstructured finite element code, Defmod [Ali, 2011, http://defmod.googlecode.com/]. Using a gradient-based iterative scheme [Ali and Feigl, Geochem. Geophys. Geosyst., 2012], we optimize the fit between observed and modeled deformation to estimate parameters in the model, including the locking depth of the rift zone, geometry and depth of magma reservoirs and rheological properties of lower crust and upper mantle, along with their formal uncertainties.

Genetic analysis for mastitis resistance and milk somatic cell score in French Lacaune dairy sheep

PubMed Central

Barillet, Francis; Rupp, Rachel; Mignon-Grasteau, Sandrine; Astruc, Jean-Michel; Jacquin, Michèle

2001-01-01

Genetic analysis for mastitis resistance was studied from two data sets. Firstly, risk factors for different mastitis traits, i.e. culling due to clinical or chronic mastitis and subclinical mastitis predicted from somatic cell count (SCC), were explored using data from 957 first lactation Lacaune ewes of an experimental INRA flock composed of two divergent lines for milk yield. Secondly, genetic parameters for SCC were estimated from 5 272 first lactation Lacaune ewes recorded among 38 flocks, using an animal model. In the experimental flock, the frequency of culling due to clinical mastitis (5%) was lower than that of subclinical mastitis (10%) predicted from SCC. Predicted subclinical mastitis was unfavourably associated with the milk yield level. Such an antagonism was not detected for clinical mastitis, which could result, to some extent, from its low frequency or from the limited amount of data. In practice, however, selection for mastitis resistance could be limited in a first approach to selection against subclinical mastitis using SCC. The heritability estimate of SCC was 0.15 for the lactation mean trait and varied from 0.04 to 0.12 from the first to the fifth test-day. The genetic correlation between lactation SCC and milk yield was slightly positive (0.15) but showed a strong evolution during lactation, i.e. from favourable (-0.48) to antagonistic (0.27). On a lactation basis, our results suggest that selection for mastitis resistance based on SCC is feasible. Patterns for genetic parameters within first lactation, however, require further confirmation and investigation. PMID:11559483

Molecular insights into the colonization and chromosomal diversification of Madeiran house mice.

PubMed

Förster, D W; Gündüz, I; Nunes, A C; Gabriel, S; Ramalhinho, M G; Mathias, M L; Britton-Davidian, J; Searle, J B

2009-11-01

The colonization history of Madeiran house mice was investigated by analysing the complete mitochondrial (mt) D-loop sequences of 156 mice from the island of Madeira and mainland Portugal, extending on previous studies. The numbers of mtDNA haplotypes from Madeira and mainland Portugal were substantially increased (17 and 14 new haplotypes respectively), and phylogenetic analysis confirmed the previously reported link between the Madeiran archipelago and northern Europe. Sequence analysis revealed the presence of four mtDNA lineages in mainland Portugal, of which one was particularly common and widespread (termed the 'Portugal Main Clade'). There was no support for population bottlenecks during the formation of the six Robertsonian chromosome races on the island of Madeira, and D-loop sequence variation was not found to be structured according to karyotype. The colonization time of the Madeiran archipelago by Mus musculus domesticus was approached using two molecular dating methods (mismatch distribution and Bayesian skyline plot). Time estimates based on D-loop sequence variation at mainland sites (including previously published data from France and Turkey) were evaluated in the context of the zooarchaeological record of M. m. domesticus. A range of values for mutation rate (mu) and number of mouse generations per year was considered in these analyses because of the uncertainty surrounding these two parameters. The colonization of Portugal and Madeira by house mice is discussed in the context of the best-supported parameter values. In keeping with recent studies, our results suggest that mutation rate estimates based on interspecific divergence lead to gross overestimates concerning the timing of recent within-species events.

Molecular phylogenetic analysis of the Persea group (Lauraceae) and its biogeographic implications on the evolution of tropical and subtropical Amphi-Pacific disjunctions.

PubMed

Li, Lang; Li, Jie; Rohwer, Jens G; van der Werff, Henk; Wang, Zhi-Hua; Li, Hsi-Wen

2011-09-01

The Persea group (Lauraceae) has a tropical and subtropical amphi-pacific disjunct distribution with most of its members, and it includes two Macaronesian species. The relationships within the group are still controversial, and its intercontinental disjunction has not been investigated with extensive sampling and precise time dating. • ITS and LEAFY intron II sequences of 78 Persea group species and nine other Lauraceae species were analyzed with maximum parsimony and Bayesian inference. Divergence time estimation employed Bayesian Markov chain Monte Carlo method under a relaxed clock. • Several traditional genera or subgenera within the Persea group form well-supported monophyletic groups except Alseodaphne and Dehaasia. The divergence time of the Persea group is estimated as ∼55.3 (95% higher posterior densities [HPD] 41.4-69.9) million years ago (mya). Two major divergences within the Persea group are estimated as ∼51.9 (95% HPD 38.9-63.9) mya and ∼48.5 (95% HPD 35.9-59.9) mya. • Persea can be retained as a genus by the inclusion of Apollonias barbujana and exclusion a few species that do not fit into the established subgenera. A major revision is recommended for the delimitation between Alseodaphne, Dehaasia, and Nothaphoebe. We suggest that the Persea group originated from the Perseeae-Laureae radiation in early Eocene Laurasia. Its amphi-pacific disjunction results from the disruption of boreotropical flora by climatic cooling during the mid- to late Eocene. The American-Macaronesian disjunction may be explained by the long-distance dispersal.

Mesozoic fossils (>145 Mya) suggest the antiquity of the subgenera of Daphnia and their coevolution with chaoborid predators.

PubMed

Kotov, Alexey A; Taylor, Derek J

2011-05-19

The timescale of the origins of Daphnia O. F. Mueller (Crustacea: Cladocera) remains controversial. The origin of the two main subgenera has been associated with the breakup of the supercontinent Pangaea. This vicariance hypothesis is supported by reciprocal monophyly, present day associations with the former Gondwanaland and Laurasia regions, and mitochondrial DNA divergence estimates. However, previous multilocus nuclear DNA sequence divergence estimates at < 10 Million years are inconsistent with the breakup of Pangaea. We examined new and existing cladoceran fossils from a Mesozoic Mongolian site, in hopes of gaining insights into the timescale of the evolution of Daphnia. We describe new fossils of ephippia from the Khotont site in Mongolia associated with the Jurassic-Cretaceous boundary (about 145 MYA) that are morphologically similar to several modern genera of the family Daphniidae, including the two major subgenera of Daphnia, i.e., Daphnia s. str. and Ctenodaphnia. The daphniid fossils co-occurred with fossils of the predaceous phantom midge (Chaoboridae). Our findings indicate that the main subgenera of Daphnia are likely much older than previously known from fossils (at least 100 MY older) or from nuclear DNA estimates of divergence. The results showing co-occurrence of the main subgenera far from the presumed Laurasia/Gondwanaland dispersal barrier shortly after formation suggests that vicariance from the breakup of Pangaea is an unlikely explanation for the origin of the main subgenera. The fossil impressions also reveal that the coevolution of a dipteran predator (Chaoboridae) with the subgenus Daphnia is much older than previously known -- since the Mesozoic.

Genome-culture coevolution promotes rapid divergence of killer whale ecotypes.

PubMed

Foote, Andrew D; Vijay, Nagarjun; Ávila-Arcos, María C; Baird, Robin W; Durban, John W; Fumagalli, Matteo; Gibbs, Richard A; Hanson, M Bradley; Korneliussen, Thorfinn S; Martin, Michael D; Robertson, Kelly M; Sousa, Vitor C; Vieira, Filipe G; Vinař, Tomáš; Wade, Paul; Worley, Kim C; Excoffier, Laurent; Morin, Phillip A; Gilbert, M Thomas P; Wolf, Jochen B W

2016-05-31

Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and post-zygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step towards an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level.

Genome-culture coevolution promotes rapid divergence of killer whale ecotypes

PubMed Central

Foote, Andrew D.; Vijay, Nagarjun; Ávila-Arcos, María C.; Baird, Robin W.; Durban, John W.; Fumagalli, Matteo; Gibbs, Richard A.; Hanson, M. Bradley; Korneliussen, Thorfinn S.; Martin, Michael D.; Robertson, Kelly M.; Sousa, Vitor C.; Vieira, Filipe G.; Vinař, Tomáš; Wade, Paul; Worley, Kim C.; Excoffier, Laurent; Morin, Phillip A.; Gilbert, M. Thomas P.; Wolf, Jochen B.W.

2016-01-01

Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and post-zygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step towards an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level. PMID:27243207

Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting

PubMed Central

Kamneva, Olga K; Rosenberg, Noah A

2017-01-01

Hybridization events generate reticulate species relationships, giving rise to species networks rather than species trees. We report a comparative study of consensus, maximum parsimony, and maximum likelihood methods of species network reconstruction using gene trees simulated assuming a known species history. We evaluate the role of the divergence time between species involved in a hybridization event, the relative contributions of the hybridizing species, and the error in gene tree estimation. When gene tree discordance is mostly due to hybridization and not due to incomplete lineage sorting (ILS), most of the methods can detect even highly skewed hybridization events between highly divergent species. For recent divergences between hybridizing species, when the influence of ILS is sufficiently high, likelihood methods outperform parsimony and consensus methods, which erroneously identify extra hybridizations. The more sophisticated likelihood methods, however, are affected by gene tree errors to a greater extent than are consensus and parsimony. PMID:28469378

Density profiles of the exclusive queuing process

NASA Astrophysics Data System (ADS)

Arita, Chikashi; Schadschneider, Andreas

2012-12-01

The exclusive queuing process (EQP) incorporates the exclusion principle into classic queuing models. It is characterized by, in addition to the entrance probability α and exit probability β, a third parameter: the hopping probability p. The EQP can be interpreted as an exclusion process of variable system length. Its phase diagram in the parameter space (α,β) is divided into a convergent phase and a divergent phase by a critical line which consists of a curved part and a straight part. Here we extend previous studies of this phase diagram. We identify subphases in the divergent phase, which can be distinguished by means of the shape of the density profile, and determine the velocity of the system length growth. This is done for EQPs with different update rules (parallel, backward sequential and continuous time). We also investigate the dynamics of the system length and the number of customers on the critical line. They are diffusive or subdiffusive with non-universal exponents that also depend on the update rules.

Study of the catastrophic discharge phenomenon in a Hall thruster

NASA Astrophysics Data System (ADS)

Ding, Yongjie; Su, Hongbo; Li, Peng; Wei, Liqiu; Li, Hong; Peng, Wuji; Xu, Yu; Sun, Hezhi; Yu, Daren

2017-10-01

In a 1350-W Hall-effect thruster, in which a technique for pushing down the magnetic field is implemented, a catastrophic discharge phenomenon is identified by varying the magnetic field strength while keeping all other operating parameters constant. According to experiments, before and after the discharge catastrophe, the plume changes from focusing state to a divergent state, and discharge parameters such as discharge current and thrust exhibit noticeable changes. The divergence half-angle of the plume increases from 22° to 46°. The oscillation amplitude and mean values of the discharge current significantly increase from 0.8 A to 4 A and from 4.6 A to 6.3 A, respectively, while the thrust increases from 89.3 mN to 91 mN. Analysis of the experimental results shows that as the maximum magnetic field of the thruster we developed is in the plume region, the acceleration occurs in the plume region and a large number of Xe2+ ions appear in the plume area, the catastrophic discharge phenomenon observed.

Mesoscale kinematics derived from X-band Doppler radar observations of convective versus stratiform precipitation and comparison with GPS radiosonde profiles

NASA Astrophysics Data System (ADS)

Deshpande, Sachin M.; Dhangar, N.; Das, S. K.; Kalapureddy, M. C. R.; Chakravarty, K.; Sonbawne, S.; Konwar, M.

2015-11-01

Single Doppler analysis techniques known as velocity azimuth display (VAD) and volume velocity processing (VVP) are used to analyze kinematics of mesoscale flow such as horizontal wind and divergence using X-band Doppler weather radar observations, for selected cases of convective, stratiform, and shallow cloud systems near tropical Indian sites Pune (18.58°N, 73.92°E, above sea level (asl) 560 m) and Mandhardev (18.51°N, 73.85°E, asl 1297 m). The vertical profiles of horizontal wind estimated from radar VVP/VAD methods agree well with GPS radiosonde profiles, with the low-level jet at about 1.5 km during monsoon season well depicted in both. The vertical structure and temporal variability of divergence and reflectivity profiles are indicative of the dynamical and microphysical characteristics of shallow convective, deep convective, and stratiform cloud systems. In shallow convective systems, vertical development of reflectivity profiles is limited below 5 km. In deep convective systems, reflectivity values as large as 55 dBZ were observed above freezing level. The stratiform system shows the presence of a reflectivity bright band (~35 dBZ) near the melting level. The diagnosed vertical profiles of divergence in convective and stratiform systems are distinct. In shallow convective conditions, convergence was seen below 4 km with divergence above. Low-level convergence and upper level divergence are observed in deep convective profiles, while stratiform precipitation has midlevel convergence present between lower level and upper level divergence. The divergence profiles in stratiform precipitation exhibit intense shallow layers of "melting convergence" at 0°C level, near 4.5 km altitude, with a steep gradient on the both sides of the peak. The level of nondivergence in stratiform situations is lower than that in convective situations. These observed vertical structures of divergence are largely indicative of latent heating profiles in the atmosphere, an important ingredient of monsoon dynamics.

Comparative phylogeography reveals deep lineages and regional evolutionary hotspots in the Mojave and Sonoran Deserts

USGS Publications Warehouse

Wood, Dustin A.; Vandergast, Amy G.; Barr, Kelly R.; Inman, Richard D.; Esque, Todd C.; Nussear, Kenneth E.; Fisher, Robert N.

2013-01-01

Aim: We explored lineage diversification within desert-dwelling fauna. Our goals were (1) to determine whether phylogenetic lineages and population expansions were consistent with younger Pleistocene climate fluctuation hypotheses or much older events predicted by pre-Pleistocene vicariance hypotheses, (2) to assess concordance in spatial patterns of genetic divergence and diversity among species and (3) to identify regional evolutionary hotspots of divergence and diversity and assess their conservation status. Location: Mojave, Colorado, and Sonoran Deserts, USA. Methods: We analysed previously published gene sequence data for twelve species. We used Bayesian gene tree methods to estimate lineages and divergence times. Within each lineage, we tested for population expansion and age of expansion using coalescent approaches. We mapped interpopulation genetic divergence and intra-population genetic diversity in a GIS to identify hotspots of highest genetic divergence and diversity and to assess whether protected lands overlapped with evolutionary hotspots. Results: In seven of the 12 species, lineage divergence substantially predated the Pleistocene. Historical population expansion was found in eight species, but expansion events postdated the Last Glacial Maximum (LGM) in only four. For all species assessed, six hotspots of high genetic divergence and diversity were concentrated in the Colorado Desert, along the Colorado River and in the Mojave/Sonoran ecotone. At least some proportion of the land within each recovered hotspot was categorized as protected, yet four of the six also overlapped with major areas of human development. Main conclusions: Most of the species studied here diversified into distinct Mojave and Sonoran lineages prior to the LGM – supporting older diversification hypotheses. Several evolutionary hotspots were recovered but are not strategically paired with areas of protected land. Long-term preservation of species-level biodiversity would entail selecting areas for protection in Mojave and Sonoran Deserts to retain divergent genetic diversity and ensure connectedness across environmental gradients.

A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land

PubMed Central

Battistuzzi, Fabia U; Feijao, Andreia; Hedges, S Blair

2004-01-01

Background The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. We assembled a data set of sequences from 32 proteins (~7600 amino acids) common to 72 species and estimated phylogenetic relationships and divergence times with a local clock method. Results Our phylogenetic results support most of the currently recognized higher-level groupings of prokaryotes. Of particular interest is a well-supported group of three major lineages of eubacteria (Actinobacteria, Deinococcus, and Cyanobacteria) that we call Terrabacteria and associate with an early colonization of land. Divergence time estimates for the major groups of eubacteria are between 2.5–3.2 billion years ago (Ga) while those for archaebacteria are mostly between 3.1–4.1 Ga. The time estimates suggest a Hadean origin of life (prior to 4.1 Ga), an early origin of methanogenesis (3.8–4.1 Ga), an origin of anaerobic methanotrophy after 3.1 Ga, an origin of phototrophy prior to 3.2 Ga, an early colonization of land 2.8–3.1 Ga, and an origin of aerobic methanotrophy 2.5–2.8 Ga. Conclusions Our early time estimates for methanogenesis support the consideration of methane, in addition to carbon dioxide, as a greenhouse gas responsible for the early warming of the Earths' surface. Our divergence times for the origin of anaerobic methanotrophy are compatible with highly depleted carbon isotopic values found in rocks dated 2.8–2.6 Ga. An early origin of phototrophy is consistent with the earliest bacterial mats and structures identified as stromatolites, but a 2.6 Ga origin of cyanobacteria suggests that those Archean structures, if biologically produced, were made by anoxygenic photosynthesizers. The resistance to desiccation of Terrabacteria and their elaboration of photoprotective compounds suggests that the common ancestor of this group inhabited land. If true, then oxygenic photosynthesis may owe its origin to terrestrial adaptations. PMID:15535883

Estimating JPEG2000 compression for image forensics using Benford's Law

NASA Astrophysics Data System (ADS)

Qadir, Ghulam; Zhao, Xi; Ho, Anthony T. S.

2010-05-01

With the tremendous growth and usage of digital images nowadays, the integrity and authenticity of digital content is becoming increasingly important, and a growing concern to many government and commercial sectors. Image Forensics, based on a passive statistical analysis of the image data only, is an alternative approach to the active embedding of data associated with Digital Watermarking. Benford's Law was first introduced to analyse the probability distribution of the 1st digit (1-9) numbers of natural data, and has since been applied to Accounting Forensics for detecting fraudulent income tax returns [9]. More recently, Benford's Law has been further applied to image processing and image forensics. For example, Fu et al. [5] proposed a Generalised Benford's Law technique for estimating the Quality Factor (QF) of JPEG compressed images. In our previous work, we proposed a framework incorporating the Generalised Benford's Law to accurately detect unknown JPEG compression rates of watermarked images in semi-fragile watermarking schemes. JPEG2000 (a relatively new image compression standard) offers higher compression rates and better image quality as compared to JPEG compression. In this paper, we propose the novel use of Benford's Law for estimating JPEG2000 compression for image forensics applications. By analysing the DWT coefficients and JPEG2000 compression on 1338 test images, the initial results indicate that the 1st digit probability of DWT coefficients follow the Benford's Law. The unknown JPEG2000 compression rates of the image can also be derived, and proved with the help of a divergence factor, which shows the deviation between the probabilities and Benford's Law. Based on 1338 test images, the mean divergence for DWT coefficients is approximately 0.0016, which is lower than DCT coefficients at 0.0034. However, the mean divergence for JPEG2000 images compression rate at 0.1 is 0.0108, which is much higher than uncompressed DWT coefficients. This result clearly indicates a presence of compression in the image. Moreover, we compare the results of 1st digit probability and divergence among JPEG2000 compression rates at 0.1, 0.3, 0.5 and 0.9. The initial results show that the expected difference among them could be used for further analysis to estimate the unknown JPEG2000 compression rates.

Distributed parameterization of complex terrain

NASA Astrophysics Data System (ADS)

Band, Lawrence E.

1991-03-01

This paper addresses the incorporation of high resolution topography, soils and vegetation information into the simulation of land surface processes in atmospheric circulation models (ACM). Recent work has concentrated on detailed representation of one-dimensional exchange processes, implicitly assuming surface homogeneity over the atmospheric grid cell. Two approaches that could be taken to incorporate heterogeneity are the integration of a surface model over distributed, discrete portions of the landscape, or over a distribution function of the model parameters. However, the computational burden and parameter intensive nature of current land surface models in ACM limits the number of independent model runs and parameterizations that are feasible to accomplish for operational purposes. Therefore, simplications in the representation of the vertical exchange processes may be necessary to incorporate the effects of landscape variability and horizontal divergence of energy and water. The strategy is then to trade off the detail and rigor of point exchange calculations for the ability to repeat those calculations over extensive, complex terrain. It is clear the parameterization process for this approach must be automated such that large spatial databases collected from remotely sensed images, digital terrain models and digital maps can be efficiently summarized and transformed into the appropriate parameter sets. Ideally, the landscape should be partitioned into surface units that maximize between unit variance while minimizing within unit variance, although it is recognized that some level of surface heterogeneity will be retained at all scales. Therefore, the geographic data processing necessary to automate the distributed parameterization should be able to estimate or predict parameter distributional information within each surface unit.

Hard-thermal-loop perturbation theory to two loops

NASA Astrophysics Data System (ADS)

Andersen, Jens O.; Braaten, Eric; Petitgirard, Emmanuel; Strickland, Michael

2002-10-01

We calculate the pressure for pure-glue QCD at high temperature to two-loop order using hard-thermal-loop (HTL) perturbation theory. At this order, all the ultraviolet divergences can be absorbed into renormalizations of the vacuum energy density and the HTL mass parameter. We determine the HTL mass parameter by a variational prescription. The resulting predictions for the pressure fail to agree with results from lattice gauge theory at temperatures for which they are available.

A synthetic phylogeny of freshwater crayfish: insights for conservation.

PubMed

Owen, Christopher L; Bracken-Grissom, Heather; Stern, David; Crandall, Keith A

2015-02-19

Phylogenetic systematics is heading for a renaissance where we shift from considering our phylogenetic estimates as a static image in a published paper and taxonomies as a hardcopy checklist to treating both the phylogenetic estimate and dynamic taxonomies as metadata for further analyses. The Open Tree of Life project (opentreeoflife.org) is developing synthesis tools for harnessing the power of phylogenetic inference and robust taxonomy to develop a synthetic tree of life. We capitalize on this approach to estimate a synthesis tree for the freshwater crayfish. The crayfish make an exceptional group to demonstrate the utility of the synthesis approach, as there recently have been a number of phylogenetic studies on the crayfishes along with a robust underlying taxonomic framework. Importantly, the crayfish have also been extensively assessed by an IUCN Red List team and therefore have accurate and up-to-date area and conservation status data available for analysis within a phylogenetic context. Here, we develop a synthesis phylogeny for the world's freshwater crayfish and examine the phylogenetic distribution of threat. We also estimate a molecular phylogeny based on all available GenBank crayfish sequences and use this tree to estimate divergence times and test for divergence rate variation. Finally, we conduct EDGE and HEDGE analyses and identify a number of species of freshwater crayfish of highest priority in conservation efforts. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

A synthetic phylogeny of freshwater crayfish: insights for conservation

PubMed Central

Owen, Christopher L.; Bracken-Grissom, Heather; Stern, David; Crandall, Keith A.

2015-01-01

Phylogenetic systematics is heading for a renaissance where we shift from considering our phylogenetic estimates as a static image in a published paper and taxonomies as a hardcopy checklist to treating both the phylogenetic estimate and dynamic taxonomies as metadata for further analyses. The Open Tree of Life project (opentreeoflife.org) is developing synthesis tools for harnessing the power of phylogenetic inference and robust taxonomy to develop a synthetic tree of life. We capitalize on this approach to estimate a synthesis tree for the freshwater crayfish. The crayfish make an exceptional group to demonstrate the utility of the synthesis approach, as there recently have been a number of phylogenetic studies on the crayfishes along with a robust underlying taxonomic framework. Importantly, the crayfish have also been extensively assessed by an IUCN Red List team and therefore have accurate and up-to-date area and conservation status data available for analysis within a phylogenetic context. Here, we develop a synthesis phylogeny for the world's freshwater crayfish and examine the phylogenetic distribution of threat. We also estimate a molecular phylogeny based on all available GenBank crayfish sequences and use this tree to estimate divergence times and test for divergence rate variation. Finally, we conduct EDGE and HEDGE analyses and identify a number of species of freshwater crayfish of highest priority in conservation efforts. PMID:25561670

A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change.

PubMed

Wan, Yizhen; Schwaninger, Heidi R; Baldo, Angela M; Labate, Joanne A; Zhong, Gan-Yuan; Simon, Charles J

2013-07-05

Grapes are one of the most economically important fruit crops. There are about 60 species in the genus Vitis. The phylogenetic relationships among these species are of keen interest for the conservation and use of this germplasm. We selected 309 accessions from 48 Vitis species,varieties, and outgroups, examined ~11 kb (~3.4 Mb total) of aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic context, and estimated divergence times based on fossil calibrations. Vitis formed a strongly supported clade. There was substantial support for species and less for the higher-level groupings (series). As estimated from extant taxa, the crown age of Vitis was 28 Ma and the divergence of subgenera (Vitis and Muscadinia) occurred at ~18 Ma. Higher clades in subgenus Vitis diverged 16 - 5 Ma with overlapping confidence intervals, and ongoing divergence formed extant species at 12 - 1.3 Ma. Several species had species-specific SNPs. NeighborNet analysis showed extensive reticulation at the core of subgenus Vitis representing the deeper nodes, with extensive reticulation radiating outward. Fitch Parsimony identified North America as the origin of the most recent common ancestor of extant Vitis species. Phylogenetic patterns suggested origination of the genus in North America, fragmentation of an ancestral range during the Miocene, formation of extant species in the late Miocene-Pleistocene, and differentiation of species in the context of Pliocene-Quaternary tectonic and climatic change. Nuclear SNPs effectively resolved relationships at and below the species level in grapes and rectified several misclassifications of accessions in the repositories. Our results challenge current higher-level classifications, reveal the abundance of genetic diversity in the genus that is potentially available for crop improvement, and provide a valuable resource for species delineation, germplasm conservation and use.

The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages

PubMed Central

Iacchei, Matthew; Coleman, Richard R.; Gaither, Michelle R.; Browne, William E.; Bowen, Brian W.; Toonen, Robert J.

2018-01-01

The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120–253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus, we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range. Phylogenetic analyses reveal that S. hispidus has a Western Atlantic lineage and a widely distributed Indo-Pacific lineage, separated by sequence divergence of 2.1%. Genetic diversity is much higher in the Western Atlantic (h = 0.929; π = 0.004) relative to the Indo-Pacific (h = 0.105; π < 0.001), and coalescent analyses indicate that the Indo-Pacific population expanded more recently (95% HPD (highest posterior density) = 60,000–400,000 yr) than the Western Atlantic population (95% HPD = 300,000–760,000 yr). Divergence of the Western Atlantic and Pacific lineages is estimated at 710,000–1.8 million years ago, which does not readily align with commonly implicated colonization events between the ocean basins. The estimated age of populations contradicts the prevailing dispersal route for tropical marine biodiversity (Indo-Pacific to Atlantic) with the oldest and most diverse population in the Atlantic, and a recent population expansion with a single common haplotype shared throughout the vast Indian and Pacific oceans. In contrast to the circumtropical fishes, this diminutive reef shrimp challenges our understanding of conventional dispersal capabilities of marine species. PMID:29527409

Novel Concordance Between Geographic, Environmental, and Genetic Structure in the Ecological Generalist Prickly Sculpin (Cottus asper) in California.

PubMed

Baumsteiger, Jason; Kinziger, Andrew P; Aguilar, Andres

2016-11-01

Ecological generalists may contain a wealth of information concerning diversity, ecology, and geographic connectivity throughout their range. We explored these ideas in prickly sculpin (Cottus asper), a small generalist freshwater fish species where coastal forms have potentially undergone radiations into inland lacustrine and riverine environments. Using a 962bp cytochrome b mtDNA marker and 11 microsatellites, we estimated diversity, divergence times, gene flow, and structure among populations at 43 locations throughout California. We then incorporated genetic and GIS data into ecological niche models to assess ecological conditions within identified groups. Though not reciprocally monophyletic, unique mtDNA haplotypes, microsatellite clustering, and measures of isolation by distance (Coastal: r = 0.960, P < 0.001; Inland: r = 0.277, P = 0.148) suggest 2 novel taxonomic groups, Coastal and Inland (constrained to Great Central Valley). Divergence estimates of 41-191 kya combined with the regional biogeographic history suggest geographic barriers are absent between groups since divergence, but ecological niche modeling revealed significant environmental differences (t = 10.84, P < 0.001). Introgressed individuals were also discovered between groups in an ecologically and geographically intermediate region. Population structure was limited, predominately found in tributaries of the San Joaquin basin in the Inland group. Overall, C. asper exhibited substantial genetic diversity, despite its ecological generality, reflecting California's historically unique and complex hydrology. More broadly, this study illustrates variable environments within the range of a generalist species may mask genetic divergences and should not be overlooked in biodiversity assessments. © The American Genetic Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A Passerine Bird's evolution corroborates the geologic history of the island of New Guinea.

PubMed

Deiner, Kristy; Lemmon, Alan R; Mack, Andrew L; Fleischer, Robert C; Dumbacher, John P

2011-05-06

New Guinea is a biologically diverse island, with a unique geologic history and topography that has likely played a role in the evolution of species. Few island-wide studies, however, have examined the phylogeographic history of lowland species. The objective of this study was to examine patterns of phylogeographic variation of a common and widespread New Guinean bird species (Colluricincla megarhyncha). Specifically, we test the mechanisms hypothesized to cause geographic and genetic variation (e.g., vicariance, isolation by distance and founder-effect with dispersal). To accomplish this, we surveyed three regions of the mitochondrial genome and a nuclear intron and assessed differences among 23 of the 30 described subspecies from throughout their range. We found support for eight highly divergent lineages within C. megarhyncha. Genetic lineages were found within continuous lowland habitat or on smaller islands, but all individuals within clades were not necessarily structured by predicted biogeographic barriers. There was some evidence of isolation by distance and potential founder-effects. Mitochondrial DNA sequence divergence among lineages was at a level often observed among different species or even genera of birds (5-11%), suggesting lineages within regions have been isolated for long periods of time. When topographical barriers were associated with divergence patterns, the estimated divergence date for the clade coincided with the estimated time of barrier formation. We also found that dispersal distance and range size are positively correlated across lineages. Evidence from this research suggests that different phylogeographic mechanisms concurrently structure lineages of C. megarhyncha and are not mutually exclusive. These lineages are a result of evolutionary forces acting at different temporal and spatial scales concordant with New Guinea's geological history.

A Passerine Bird's Evolution Corroborates the Geologic History of the Island of New Guinea

PubMed Central

Deiner, Kristy; Lemmon, Alan R.; Mack, Andrew L.; Fleischer, Robert C.; Dumbacher, John P.

2011-01-01

New Guinea is a biologically diverse island, with a unique geologic history and topography that has likely played a role in the evolution of species. Few island-wide studies, however, have examined the phylogeographic history of lowland species. The objective of this study was to examine patterns of phylogeographic variation of a common and widespread New Guinean bird species (Colluricincla megarhyncha). Specifically, we test the mechanisms hypothesized to cause geographic and genetic variation (e.g., vicariance, isolation by distance and founder-effect with dispersal). To accomplish this, we surveyed three regions of the mitochondrial genome and a nuclear intron and assessed differences among 23 of the 30 described subspecies from throughout their range. We found support for eight highly divergent lineages within C. megarhyncha. Genetic lineages were found within continuous lowland habitat or on smaller islands, but all individuals within clades were not necessarily structured by predicted biogeographic barriers. There was some evidence of isolation by distance and potential founder-effects. Mitochondrial DNA sequence divergence among lineages was at a level often observed among different species or even genera of birds (5–11%), suggesting lineages within regions have been isolated for long periods of time. When topographical barriers were associated with divergence patterns, the estimated divergence date for the clade coincided with the estimated time of barrier formation. We also found that dispersal distance and range size are positively correlated across lineages. Evidence from this research suggests that different phylogeographic mechanisms concurrently structure lineages of C. megarhyncha and are not mutually exclusive. These lineages are a result of evolutionary forces acting at different temporal and spatial scales concordant with New Guinea's geological history. PMID:21573115

Displaced phylogeographic signals from Gyrodactylus arcuatus, a parasite of the three-spined stickleback Gasterosteus aculeatus, suggest freshwater glacial refugia in Europe

USGS Publications Warehouse

Lumme, Jaakko; Mäkinen, Hannu; Ermolenko, Alexey V.; Gregg, Jacob L.; Ziętara, Marek S.

2016-01-01

We examined the global mitochondrial phylogeography of Gyrodactylus arcuatus, a flatworm ectoparasite of three-spined stickleback Gasterosteus aculeatus. In accordance with the suggested high divergence rate of 13%/million years, the genetic variation of the parasite was high: haplotype diversity h = 0.985 and nucleotide diversity π = 0.0161. The differentiation among the parasite populations was substantial (Φst = 0.759), with two main allopatric clades (here termed Euro and North) accounting for 54% of the total genetic variation. The diversity center of the Euro clade was in the Baltic Sea, while the North clade was spread across the Barents and White Seas. A single haplotype within the North clade was found in the western and eastern Pacific Ocean. Divergence of main clades was estimated to be circa 200 thousand years ago. Each main clade was further divided into six distinct subclades, estimated to have diverged in isolation since 135 thousand years ago. This second division corresponds approximately to the Eemian interglacial predating the last glacial maximum. A demographic expansion of the subclades is associated with colonisation of northern Europe since the last glacial maximum, circa 15–40 thousand years ago. The parasite phylogeny is most likely explained by sequential isolated bottlenecks and expansions in numerous allopatric refugia. The postglacial intermingling and high variation in the marine parasite populations, separately in the Baltic and Barents Seas, suggest low competition of divergent parasite matrilines, coupled with a large population size and high rate of dispersal of hosts. The genetic contribution of the assumed refugial fish populations maintaining the parasite during the last glacial maximum was not detected among the marine sticklebacks, which perhaps were infected after range expansion.

On the Evolutionary and Biogeographic History of Saxifraga sect. Trachyphyllum (Gaud.) Koch (Saxifragaceae Juss.)

PubMed Central

DeChaine, Eric G.; Anderson, Stacy A.; McNew, Jennifer M.; Wendling, Barry M.

2013-01-01

Arctic-alpine plants in the genus Saxifraga L. (Saxifragaceae Juss.) provide an excellent system for investigating the process of diversification in northern regions. Yet, sect. Trachyphyllum (Gaud.) Koch, which is comprised of about 8 to 26 species, has still not been explored by molecular systematists even though taxonomists concur that the section needs to be thoroughly re-examined. Our goals were to use chloroplast trnL-F and nuclear ITS DNA sequence data to circumscribe the section phylogenetically, test models of geographically-based population divergence, and assess the utility of morphological characters in estimating evolutionary relationships. To do so, we sequenced both genetic markers for 19 taxa within the section. The phylogenetic inferences of sect. Trachyphyllum using maximum likelihood and Bayesian analyses showed that the section is polyphyletic, with S. aspera L. and S bryoides L. falling outside the main clade. In addition, the analyses supported several taxonomic re-classifications to prior names. We used two approaches to test biogeographic hypotheses: i) a coalescent approach in Mesquite to test the fit of our reconstructed gene trees to geographically-based models of population divergence and ii) a maximum likelihood inference in Lagrange. These tests uncovered strong support for an origin of the clade in the Southern Rocky Mountains of North America followed by dispersal and divergence episodes across refugia. Finally we adopted a stochastic character mapping approach in SIMMAP to investigate the utility of morphological characters in estimating evolutionary relationships among taxa. We found that few morphological characters were phylogenetically informative and many were misleading. Our molecular analyses provide a foundation for the diversity and evolutionary relationships within sect. Trachyphyllum and hypotheses for better understanding the patterns and processes of divergence in this section, other saxifrages, and plants inhabiting the North Pacific Rim. PMID:23922810

Displaced phylogeographic signals from Gyrodactylus arcuatus, a parasite of the three-spined stickleback Gasterosteus aculeatus, suggest freshwater glacial refugia in Europe.

PubMed

Lumme, Jaakko; Mäkinen, Hannu; Ermolenko, Alexey V; Gregg, Jacob L; Ziętara, Marek S

2016-08-01

We examined the global mitochondrial phylogeography of Gyrodactylus arcuatus, a flatworm ectoparasite of three-spined stickleback Gasterosteus aculeatus. In accordance with the suggested high divergence rate of 13%/million years, the genetic variation of the parasite was high: haplotype diversity h=0.985 and nucleotide diversity π=0.0161. The differentiation among the parasite populations was substantial (Φst=0.759), with two main allopatric clades (here termed Euro and North) accounting for 54% of the total genetic variation. The diversity center of the Euro clade was in the Baltic Sea, while the North clade was spread across the Barents and White Seas. A single haplotype within the North clade was found in the western and eastern Pacific Ocean. Divergence of main clades was estimated to be circa 200 thousand years ago. Each main clade was further divided into six distinct subclades, estimated to have diverged in isolation since 135 thousand years ago. This second division corresponds approximately to the Eemian interglacial predating the last glacial maximum. A demographic expansion of the subclades is associated with colonisation of northern Europe since the last glacial maximum, circa 15-40 thousand years ago. The parasite phylogeny is most likely explained by sequential isolated bottlenecks and expansions in numerous allopatric refugia. The postglacial intermingling and high variation in the marine parasite populations, separately in the Baltic and Barents Seas, suggest low competition of divergent parasite matrilines, coupled with a large population size and high rate of dispersal of hosts. The genetic contribution of the assumed refugial fish populations maintaining the parasite during the last glacial maximum was not detected among the marine sticklebacks, which perhaps were infected after range expansion. Copyright © 2016 Australian Society for Parasitology. All rights reserved.

Codon Usage Selection Can Bias Estimation of the Fraction of Adaptive Amino Acid Fixations.

PubMed

Matsumoto, Tomotaka; John, Anoop; Baeza-Centurion, Pablo; Li, Boyang; Akashi, Hiroshi

2016-06-01

A growing number of molecular evolutionary studies are estimating the proportion of adaptive amino acid substitutions (α) from comparisons of ratios of polymorphic and fixed DNA mutations. Here, we examine how violations of two of the model assumptions, neutral evolution of synonymous mutations and stationary base composition, affect α estimation. We simulated the evolution of coding sequences assuming weak selection on synonymous codon usage bias and neutral protein evolution, α = 0. We show that weak selection on synonymous mutations can give polymorphism/divergence ratios that yield α-hat (estimated α) considerably larger than its true value. Nonstationary evolution (changes in population size, selection, or mutation) can exacerbate such biases or, in some scenarios, give biases in the opposite direction, α-hat < α. These results demonstrate that two factors that appear to be prevalent among taxa, weak selection on synonymous mutations and non-steady-state nucleotide composition, should be considered when estimating α. Estimates of the proportion of adaptive amino acid fixations from large-scale analyses of Drosophila melanogaster polymorphism and divergence data are positively correlated with codon usage bias. Such patterns are consistent with α-hat inflation from weak selection on synonymous mutations and/or mutational changes within the examined gene trees. © The Author 2016. 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.

Cultural and climatic changes shape the evolutionary history of the Uralic languages.

PubMed

Honkola, T; Vesakoski, O; Korhonen, K; Lehtinen, J; Syrjänen, K; Wahlberg, N

2013-06-01

Quantitative phylogenetic methods have been used to study the evolutionary relationships and divergence times of biological species, and recently, these have also been applied to linguistic data to elucidate the evolutionary history of language families. In biology, the factors driving macroevolutionary processes are assumed to be either mainly biotic (the Red Queen model) or mainly abiotic (the Court Jester model) or a combination of both. The applicability of these models is assumed to depend on the temporal and spatial scale observed as biotic factors act on species divergence faster and in smaller spatial scale than the abiotic factors. Here, we used the Uralic language family to investigate whether both 'biotic' interactions (i.e. cultural interactions) and abiotic changes (i.e. climatic fluctuations) are also connected to language diversification. We estimated the times of divergence using Bayesian phylogenetics with a relaxed-clock method and related our results to climatic, historical and archaeological information. Our timing results paralleled the previous linguistic studies but suggested a later divergence of Finno-Ugric, Finnic and Saami languages. Some of the divergences co-occurred with climatic fluctuation and some with cultural interaction and migrations of populations. Thus, we suggest that both 'biotic' and abiotic factors contribute either directly or indirectly to the diversification of languages and that both models can be applied when studying language evolution. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Phylogenetic Position and Subspecies Divergence of the Endangered New Zealand Dotterel (Charadrius obscurus)

PubMed Central

Barth, Julia M. I.; Matschiner, Michael; Robertson, Bruce C.

2013-01-01

The New Zealand Dotterel (Charadrius obscurus), an endangered shorebird of the family Charadriidae, is endemic to New Zealand where two subspecies are recognized. These subspecies are not only separated geographically, with C. o. aquilonius being distributed in the New Zealand North Island and C. o. obscurus mostly restricted to Stewart Island, but also differ substantially in morphology and behavior. Despite these divergent traits, previous work has failed to detect genetic differentiation between the subspecies, and the question of when and where the two populations separated is still open. Here, we use mitochondrial and nuclear markers to address molecular divergence between the subspecies, and apply maximum likelihood and Bayesian methods to place C. obscurus within the non-monophyletic genus Charadrius. Despite very little overall differentiation, distinct haplotypes for the subspecies were detected, thus supporting molecular separation of the northern and southern populations. Phylogenetic analysis recovers a monophyletic clade combining the New Zealand Dotterel with two other New Zealand endemic shorebirds, the Wrybill and the Double-Banded Plover, thus suggesting a single dispersal event as the origin of this group. Divergence dates within Charadriidae were estimated with BEAST 2, and our results indicate a Middle Miocene origin of New Zealand endemic Charadriidae, a Late Miocene emergence of the lineage leading to the New Zealand Dotterel, and a Middle to Late Pleistocene divergence of the two New Zealand Dotterel subspecies. PMID:24205094

Role of dimensionality in Axelrod's model for the dissemination of culture

NASA Astrophysics Data System (ADS)

Klemm, Konstantin; Eguíluz, Víctor M.; Toral, Raúl; Miguel, Maxi San

2003-09-01

We analyze a model of social interaction in one- and two-dimensional lattices for a moderate number of features. We introduce an order parameter as a function of the overlap between neighboring sites. In a one-dimensional chain, we observe that the dynamics is consistent with a second-order transition, where the order parameter changes continuously and the average domain diverges at the transition point. However, in a two-dimensional lattice the order parameter is discontinuous at the transition point characteristic of a first-order transition between an ordered and a disordered state.

Global gradient estimates for divergence-type elliptic problems involving general nonlinear operators

NASA Astrophysics Data System (ADS)

Cho, Yumi

2018-05-01

We study nonlinear elliptic problems with nonstandard growth and ellipticity related to an N-function. We establish global Calderón-Zygmund estimates of the weak solutions in the framework of Orlicz spaces over bounded non-smooth domains. Moreover, we prove a global regularity result for asymptotically regular problems which are getting close to the regular problems considered, when the gradient variable goes to infinity.

Plume Characteristics of the Busek 600 W Hall Thruster

DTIC Science & Technology

2006-07-12

that can then be applied to estimate the effect of the energetic plume on complex spacecraft geometries. Early measurement of plume properties, such...produced a measurable effect on ion current density and plume divergence, experimentally showing an increase or decrease of ±15-20%. Ionic energy...can then be applied to estimate the effect of the energetic plume on complex spacecraft geometries. Early measurement of plume properties, such as plume

Analysis of the Command and Control Segment (CCS) attitude estimation algorithm

NASA Technical Reports Server (NTRS)

Stockwell, Catherine

1993-01-01

This paper categorizes the qualitative behavior of the Command and Control Segment (CCS) differential correction algorithm as applied to attitude estimation using simultaneous spin axis sun angle and Earth cord length measurements. The categories of interest are the domains of convergence, divergence, and their boundaries. Three series of plots are discussed that show the dependence of the estimation algorithm on the vehicle radius, the sun/Earth angle, and the spacecraft attitude. Common qualitative dynamics to all three series are tabulated and discussed. Out-of-limits conditions for the estimation algorithm are identified and discussed.

Study of internal gravity waves in the meteor zone

NASA Technical Reports Server (NTRS)

Gavrilov, N. M.

1987-01-01

An important component of the dynamical regime of the atmosphere at heights near 100 km are internal gravity waves (IGW) with periods from about 5 min to about 17.5 hrs which propagate from the lower atmospheric layers and are generated in the uppermost region of the atmosphere. As IGW propagate upwards, their amplitudes increase and they have a considerable effect on upper atmospheric processes: (1) they provide heat flux divergences comparable with solar heating; (2) they influence the gaseous composition and produce wave variations of the concentrations of gaseous components and emissions of the upper atmosphere; and (3) they cause considerable acceleration of the mean stream. It was concluded that the periods, wavelengths, amplitudes and velocities of IGW propagation in the meteor zone are now measured quite reliably. However, for estimating the influence of IGW on the thermal regime and the circulation of the upper atmosphere these parameters are not as important as the values of wave fluxes of energy, heat, moment and mass.

Importance sampling large deviations in nonequilibrium steady states. I.

PubMed

Ray, Ushnish; Chan, Garnet Kin-Lic; Limmer, David T

2018-03-28

Large deviation functions contain information on the stability and response of systems driven into nonequilibrium steady states and in such a way are similar to free energies for systems at equilibrium. As with equilibrium free energies, evaluating large deviation functions numerically for all but the simplest systems is difficult because by construction they depend on exponentially rare events. In this first paper of a series, we evaluate different trajectory-based sampling methods capable of computing large deviation functions of time integrated observables within nonequilibrium steady states. We illustrate some convergence criteria and best practices using a number of different models, including a biased Brownian walker, a driven lattice gas, and a model of self-assembly. We show how two popular methods for sampling trajectory ensembles, transition path sampling and diffusion Monte Carlo, suffer from exponentially diverging correlations in trajectory space as a function of the bias parameter when estimating large deviation functions. Improving the efficiencies of these algorithms requires introducing guiding functions for the trajectories.

Importance sampling large deviations in nonequilibrium steady states. I

NASA Astrophysics Data System (ADS)

Ray, Ushnish; Chan, Garnet Kin-Lic; Limmer, David T.

2018-03-01

Large deviation functions contain information on the stability and response of systems driven into nonequilibrium steady states and in such a way are similar to free energies for systems at equilibrium. As with equilibrium free energies, evaluating large deviation functions numerically for all but the simplest systems is difficult because by construction they depend on exponentially rare events. In this first paper of a series, we evaluate different trajectory-based sampling methods capable of computing large deviation functions of time integrated observables within nonequilibrium steady states. We illustrate some convergence criteria and best practices using a number of different models, including a biased Brownian walker, a driven lattice gas, and a model of self-assembly. We show how two popular methods for sampling trajectory ensembles, transition path sampling and diffusion Monte Carlo, suffer from exponentially diverging correlations in trajectory space as a function of the bias parameter when estimating large deviation functions. Improving the efficiencies of these algorithms requires introducing guiding functions for the trajectories.

Marker-aided genetic divergence analysis in Brassica.

PubMed

Arunachalam, V; Verma, Shefali; Sujata, V; Prabhu, K V

2005-08-01

Genetic divergence was evaluated in 31 breeding lines from four Brassica species using Mahalanobis' D2. A new method of grouping using D2 values was used to group the 31 lines, based on diagnostic morphological traits (called morphoqts). Isozyme variation of the individual enzymes esterase and glutamate oxaloacetate was quantified by five parameters (called isoqts) developed earlier. Grouping by the same method was also done based on the isoqts, and the grouping by isozymes was compared with that by morphoqts. Overall, there was an agreement of 73% suggesting that isoqts can be used in the choice of parents and also first stage selection of segregants in the laboratory. It was suggested that such an exercise would help to take care of season-bound and field-related problems of breeding. The new isozyme QTs, within lane variance of relative mobility and relative absorption, accounted for about 50% of the total divergence. The utility of the new method and isoqts in cost-effective breeding were highlighted.

Turbulence characteristics inferred from time-lagged satellite imagery of surface algae in a shallow tidal sea

NASA Astrophysics Data System (ADS)

Marmorino, George O.; Smith, Geoffrey B.; Miller, W. D.

2017-09-01

A pair of time-lagged satellite images of surface algae in the Great Barrier Reef lagoon is used to investigate characteristics of the horizontal velocity field at a spatial resolution as small as 4 m. A distinctive feature is the occurrence of surface patches that are relatively clear of algae and which grow in size. These patches are interpreted as resulting from the horizontally diverging motion associated with boils. The surface divergence in such boils can be as large as 0.01 s-1, as deduced directly from the imagery. Overall, root-mean-squared values of divergence, vorticity, and strain rate are 45, 58, and 170, respectively, when normalized by the Coriolis parameter. By observing the algae and its fluid environment simultaneously, the analysis thus provides a glimpse of how underlying hydrodynamic processes help shape the distribution of surface algae - under the calm winds that favor the formation of dense surface aggregations.

Jamming/flowing transition of non-Brownian particles suspended in a iso-density fluid flowing in a 2D rectangular duct

NASA Astrophysics Data System (ADS)

Burel, Maxym; Martin, Sylvain; Bonnefoy, Olivier

2017-06-01

We present the results of an experimental study on the jamming/flowing transition. A suspension of neutrally buoyant large particles flows in an horizontal rectangular duct, where an artificial restriction triggers jamming. We show that the avalanche distribution size is exponential, that is memoryless. We further demonstrate that the avalanche size diverges when the restriction size approaches a critical value and that this divergence is well described by a power law. The parameters (critical opening size and divergence velocity) are compared to literature values and show a strong similarity with others systems. Another result of this paper is the study of the influence of the particle morphology. We show that, for a moderate restriction size, the dead-zone formed right upstream of the restriction is larger for angular particles but, paradoxically, that the avalanche size is larger for polyhedra compared to spheres by at least one order of magnitude.

Molecular diversity of some species belonging to the genus Daphnia O. F. Müller, 1785 (Crustacea: Cladocera) in Turkey.

PubMed

Özdemir, Ebru; Altındağ, Ahmet; Kandemir, İrfan

2017-05-01

Daphnia is a freshwater zooplankton species with controversial taxonomy due to its high morphological variation linked to environmental factors and inter-specific hybridization and polyploidy in some groups. The aim of the present study is to examine molecular diversity of some Daphnia species in Turkey and to establish DNA barcodes of Turkish Daphnia species. Sequence analysis was performed using 540 bp region of cytochrome oxidase subunit I gene of mitochondrial DNA. A total of 34 haplotypes have been identified for Turkey. Daphnia pulex complex was divided into two clades with 16.1% sequence divergence according to molecular taxonomy based on Kimura 2-parameter. The clade which was molecularly diverged from Daphnia pulex with 16.1% sequence divergence was found to show 99% similarity with Daphnia cf. pulicaria (sensu Alonso 1996) instead of Daphnia pulicaria Forbes, 1893. Furthermore, this study has contributed to Turkish zoogeography by demonstrating the distribution of Daphnia species in Turkey.

Archimedean Voronoi spiral tilings

NASA Astrophysics Data System (ADS)

Yamagishi, Yoshikazu; Sushida, Takamichi

2018-01-01

We study the transition of the number of spirals (called parastichy in the theory of phyllotaxis) within a Voronoi tiling for Archimedean spiral lattices. The transition of local parastichy numbers within a tiling is regarded as a transition at the base site point in a continuous family of tilings. This gives a natural description of the quasiperiodic structure of the grain boundaries. It is proved that the number of tiles in the grain boundaries are denominators of rational approximations of the argument (called the divergence angle) of the generator. The local parastichy numbers are non-decreasing functions of the plastochron parameter. The bifurcation diagram of local parastichy numbers has a Farey tree structure. We also prove Richards’ formula of spiral phyllotaxis in the case of Archimedean Voronoi spiral tilings, and show that, if the divergence angle is a quadratic irrational number, then the shapes of tiles in the grain boundaries are close to rectangles. If the divergence angle is linearly equivalent to the golden section, then the shape of tiles in the grain boundaries is close to square.

Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation

PubMed Central

Cornuet, Jean-Marie; Santos, Filipe; Beaumont, Mark A.; Robert, Christian P.; Marin, Jean-Michel; Balding, David J.; Guillemaud, Thomas; Estoup, Arnaud

2008-01-01

Summary: Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract part of this information but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIY ABC) for inference based on approximate Bayesian computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and population size changes. DIY ABC can be used to compare competing scenarios, estimate parameters for one or more scenarios and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data). This article describes key methods used in the program and provides its main features. The analysis of one simulated and one real dataset, both with complex evolutionary scenarios, illustrates the main possibilities of DIY ABC. Availability: The software DIY ABC is freely available at http://www.montpellier.inra.fr/CBGP/diyabc. Contact: j.cornuet@imperial.ac.uk Supplementary information: Supplementary data are also available at http://www.montpellier.inra.fr/CBGP/diyabc PMID:18842597

Gone with the plate: the opening of the Western Mediterranean basin drove the diversification of ground-dweller spiders

PubMed Central

2011-01-01

Background The major islands of the Western Mediterranean--Corsica, Sardinia, and the Balearic Islands--are continental terrenes that drifted towards their present day location following a retreat from their original position on the eastern Iberian Peninsula about 30 million years ago. Several studies have taken advantage of this well-dated geological scenario to calibrate molecular rates in species for which distributions seemed to match this tectonic event. Nevertheless, the use of external calibration points has revealed that most of the present-day fauna on these islands post-dated the opening of the western Mediterranean basin. In this study, we use sequence information of the cox1, nad1, 16S, L1, and 12S mitochondrial genes and the 18S, 28S, and h3 nuclear genes, along with relaxed clock models and a combination of biogeographic and fossil external calibration points, to test alternative historical scenarios of the evolutionary history of the ground-dweller spider genus Parachtes (Dysderidae), which is endemic to the region. Results We analyse 49 specimens representing populations of most Parachtes species and close relatives. Our results reveal that both the sequence of species formation in Parachtes and the estimated divergence times match the geochronological sequence of separation of the main islands, suggesting that the diversification of the group was driven by Tertiary plate tectonics. In addition, the confirmation that Parachtes diversification matches well-dated geological events provides a model framework to infer substitution rates of molecular markers. Divergence rates estimates ranged from 3.5% My-1 (nad1) to 0.12% My-1 (28S), and the average divergence rate for the mitochondrial genes was 2.25% My-1, very close to the "standard" arthropod mitochondrial rate (2.3% My-1). Conclusions Our study provides the first unequivocal evidence of terrestrial endemic fauna of the major western Mediterranean islands, whose origin can be traced back to the Oligocene separation of these islands from the continent. Moreover, our study provides useful information on the divergence rate estimates of the most commonly used genes for phylogenetic inference in non-model arthropods. PMID:22039781

Gone with the plate: the opening of the Western Mediterranean basin drove the diversification of ground-dweller spiders.

PubMed

Bidegaray-Batista, Leticia; Arnedo, Miquel A

2011-10-31

The major islands of the Western Mediterranean--Corsica, Sardinia, and the Balearic Islands--are continental terrenes that drifted towards their present day location following a retreat from their original position on the eastern Iberian Peninsula about 30 million years ago. Several studies have taken advantage of this well-dated geological scenario to calibrate molecular rates in species for which distributions seemed to match this tectonic event. Nevertheless, the use of external calibration points has revealed that most of the present-day fauna on these islands post-dated the opening of the western Mediterranean basin. In this study, we use sequence information of the cox1, nad1, 16S, L1, and 12S mitochondrial genes and the 18S, 28S, and h3 nuclear genes, along with relaxed clock models and a combination of biogeographic and fossil external calibration points, to test alternative historical scenarios of the evolutionary history of the ground-dweller spider genus Parachtes (Dysderidae), which is endemic to the region. We analyse 49 specimens representing populations of most Parachtes species and close relatives. Our results reveal that both the sequence of species formation in Parachtes and the estimated divergence times match the geochronological sequence of separation of the main islands, suggesting that the diversification of the group was driven by Tertiary plate tectonics. In addition, the confirmation that Parachtes diversification matches well-dated geological events provides a model framework to infer substitution rates of molecular markers. Divergence rates estimates ranged from 3.5% My(-1) (nad1) to 0.12% My(-1) (28S), and the average divergence rate for the mitochondrial genes was 2.25% My(-1), very close to the "standard" arthropod mitochondrial rate (2.3% My(-1)). Our study provides the first unequivocal evidence of terrestrial endemic fauna of the major western Mediterranean islands, whose origin can be traced back to the Oligocene separation of these islands from the continent. Moreover, our study provides useful information on the divergence rate estimates of the most commonly used genes for phylogenetic inference in non-model arthropods.

Behavioural divergence, interfertility and speciation: a review.

PubMed

Pillay, Neville; Rymer, Tasmin L

2012-11-01

Behavioural compatibility between mates is fundamental for maintaining species boundaries and is achieved through appropriate communication between males and females. A breakdown in communication will lead to behavioural divergence and reduced interfertility. In this review, we summarise the current knowledge on male signals and female perception of these signals, integrating the literature from several taxa. We advocate that signaller-perceiver coevolution, which is usually under strong stabilising selection to enable mating, forms the basis of species-specific mate recognition systems. The mechanisms (phylogeny, geography, ecology, biology) shaping signaller-perceiver systems are briefly discussed to demonstrate the factors underpinning the evolution of signaller-perceiver couplings. Since divergence and diversification of communication systems is driven by changes in the mechanical properties of sensory pathways and morphology of sensory organs, we highlight signal modalities (auditory, olfactory, visual, tactile) and their importance in communication, particularly in mate selection. Next, using available examples and generating a stylised model, we suggest how disruption (biological, ecological, stochastic) of signaller-perceiver systems drives behavioural divergence and consequently results in reduced interfertility and speciation. Future studies should adopt an integrative approach, combining multiple parameters (phylogeny, adaptive utility of communication systems, genetics and biomechanical/biochemical properties of signals and perception) to explore how disruption of signaller-perceiver systems results in behavioural divergence and reduced interfertility. Finally, we question the impact that rapid environmental change will have on disruption of communication systems, potentially interfering with signaller-perceiver couplings. Copyright © 2012 Elsevier B.V. All rights reserved.

Vortical structures and development of laminar flow over convergent-divergent riblets

NASA Astrophysics Data System (ADS)

Xu, Fang; Zhong, Shan; Zhang, Shanying

2018-05-01

In this work, the development of a laminar boundary layer over a rectangular convergent-divergent riblet section with a finite streamwise length is studied experimentally using dye visualization and particle image velocimetry in a water flume. The flow topology over this highly directional spanwise roughness is established from this study. It is shown that convergent-divergent riblets generate a spanwise flow above the riblets from the diverging line toward the adjacent converging line. This consequently leads to the formation of a weak recirculating secondary flow in cross-stream planes across the boundary layer that creates a downwash motion over the diverging line and an upwash motion over the converging line. It is found that the fluid inside the riblet valley follows a helicoidal path and it also interacts with the crossflow boundary layer hence playing a key role in determining the structure of the secondary flow across the boundary layer. The impact of riblet wavelength on vortical structures is also revealed for the first time. A larger riblet wavelength is seen to produce a stronger upwash/downwash and hence a more intense secondary flow as well as a stronger deceleration effect on the crossflow. Furthermore, the streamwise development of the flow over the riblet section can be divided into a developing stage followed by a developed stage. In the developing stage, the magnitude of induced streamwise velocity and vorticity over the converging line continues to increase, whereas in the developed stage the values of these parameters remain essentially unchanged.