Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes.

PubMed

Cisneros, Laura M; Fagan, Matthew E; Willig, Michael R

2016-01-01

Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Variation

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes

PubMed Central

Fagan, Matthew E.; Willig, Michael R.

2016-01-01

Background Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. Methods We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. Results The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or

Quantitative methods in assessment of neurologic function.

PubMed

Potvin, A R; Tourtellotte, W W; Syndulko, K; Potvin, J

1981-01-01

Traditionally, neurologists have emphasized qualitative techniques for assessing results of clinical trials. However, in recent years qualitative evaluations have been increasingly augmented by quantitative tests for measuring neurologic functions pertaining to mental state, strength, steadiness, reactions, speed, coordination, sensation, fatigue, gait, station, and simulated activities of daily living. Quantitative tests have long been used by psychologists for evaluating asymptomatic function, assessing human information processing, and predicting proficiency in skilled tasks; however, their methodology has never been directly assessed for validity in a clinical environment. In this report, relevant contributions from the literature on asymptomatic human performance and that on clinical quantitative neurologic function are reviewed and assessed. While emphasis is focused on tests appropriate for evaluating clinical neurologic trials, evaluations of tests for reproducibility, reliability, validity, and examiner training procedures, and for effects of motivation, learning, handedness, age, and sex are also reported and interpreted. Examples of statistical strategies for data analysis, scoring systems, data reduction methods, and data display concepts are presented. Although investigative work still remains to be done, it appears that carefully selected and evaluated tests of sensory and motor function should be an essential factor for evaluating clinical trials in an objective manner.

Plant DNA barcodes and assessment of phylogenetic community structure of a tropical mixed dipterocarp forest in Brunei Darussalam (Borneo)

PubMed Central

Abu Salim, Kamariah; Chase, Mark W.; Dexter, Kyle G.; Pennington, R. Toby; Tan, Sylvester; Kaye, Maria Ellen; Samuel, Rosabelle

2017-01-01

DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m) of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia). The combined matrix (rbcL + matK) comprised 555 haplotypes (from ≥154 genera, 68 families and 25 orders sensu APG, Angiosperm Phylogeny Group, 2016), making a substantial contribution to tree barcode sequences from Southeast Asia. Barcode sequences were used to reconstruct phylogenetic relationships using maximum likelihood, both with and without constraining the topology of taxonomic orders to match that proposed by the Angiosperm Phylogeny Group. A third phylogenetic tree was reconstructed using the program Phylomatic to investigate the influence of phylogenetic resolution on results. Detection of non-random patterns of community assembly was determined by net relatedness index (NRI) and nearest taxon index (NTI). In most cases, community assembly was either random or phylogenetically clustered, which likely indicates the importance to community structure of habitat filtering based on phylogenetically correlated traits in determining community structure. Different phylogenetic trees gave similar overall results, but the Phylomatic tree produced greater variation across plots for NRI and NTI values, presumably due to noise introduced by using an unresolved phylogenetic tree. Our results suggest that using a DNA barcode tree has benefits over the traditionally used Phylomatic approach by increasing precision and accuracy and allowing the incorporation of taxonomically unidentified individuals into analyses

Quantitative risk assessment system (QRAS)

NASA Technical Reports Server (NTRS)

Tan, Zhibin (Inventor); Mosleh, Ali (Inventor); Weinstock, Robert M (Inventor); Smidts, Carol S (Inventor); Chang, Yung-Hsien (Inventor); Groen, Francisco J (Inventor); Swaminathan, Sankaran (Inventor)

2001-01-01

A quantitative risk assessment system (QRAS) builds a risk model of a system for which risk of failure is being assessed, then analyzes the risk of the system corresponding to the risk model. The QRAS performs sensitivity analysis of the risk model by altering fundamental components and quantifications built into the risk model, then re-analyzes the risk of the system using the modifications. More particularly, the risk model is built by building a hierarchy, creating a mission timeline, quantifying failure modes, and building/editing event sequence diagrams. Multiplicities, dependencies, and redundancies of the system are included in the risk model. For analysis runs, a fixed baseline is first constructed and stored. This baseline contains the lowest level scenarios, preserved in event tree structure. The analysis runs, at any level of the hierarchy and below, access this baseline for risk quantitative computation as well as ranking of particular risks. A standalone Tool Box capability exists, allowing the user to store application programs within QRAS.

Assessment of and standardization for quantitative nondestructive test

NASA Technical Reports Server (NTRS)

Neuschaefer, R. W.; Beal, J. B.

1972-01-01

Present capabilities and limitations of nondestructive testing (NDT) as applied to aerospace structures during design, development, production, and operational phases are assessed. It will help determine what useful structural quantitative and qualitative data may be provided from raw materials to vehicle refurbishment. This assessment considers metal alloys systems and bonded composites presently applied in active NASA programs or strong contenders for future use. Quantitative and qualitative data has been summarized from recent literature, and in-house information, and presented along with a description of those structures or standards where the information was obtained. Examples, in tabular form, of NDT technique capabilities and limitations have been provided. NDT techniques discussed and assessed were radiography, ultrasonics, penetrants, thermal, acoustic, and electromagnetic. Quantitative data is sparse; therefore, obtaining statistically reliable flaw detection data must be strongly emphasized. The new requirements for reusable space vehicles have resulted in highly efficient design concepts operating in severe environments. This increases the need for quantitative NDT evaluation of selected structural components, the end item structure, and during refurbishment operations.

Integrated Environmental Modeling: Quantitative Microbial Risk Assessment

EPA Science Inventory

The presentation discusses the need for microbial assessments and presents a road map associated with quantitative microbial risk assessments, through an integrated environmental modeling approach. A brief introduction and the strengths of the current knowledge are illustrated. W...

Physiologic Basis for Understanding Quantitative Dehydration Assessment

DTIC Science & Technology

2012-01-01

Perspective Physiologic basis for understanding quantitative dehydration assessment1–4 Samuel N Cheuvront, Robert W Kenefick, Nisha Charkoudian, and...Michael N Sawka ABSTRACT Dehydration (body water deficit) is a physiologic state that can have profound implications for human health and performance...review the physiologic basis for understanding quantitative dehydration as- sessment. We highlight how phenomenologic interpretations of de- hydration

Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism.

PubMed

Davies, T Jonathan; Kraft, Nathan J B; Salamin, Nicolas; Wolkovich, Elizabeth M

2012-02-01

The tendency for more closely related species to share similar traits and ecological strategies can be explained by their longer shared evolutionary histories and represents phylogenetic conservatism. How strongly species traits co-vary with phylogeny can significantly impact how we analyze cross-species data and can influence our interpretation of assembly rules in the rapidly expanding field of community phylogenetics. Phylogenetic conservatism is typically quantified by analyzing the distribution of species values on the phylogenetic tree that connects them. Many phylogenetic approaches, however, assume a completely sampled phylogeny: while we have good estimates of deeper phylogenetic relationships for many species-rich groups, such as birds and flowering plants, we often lack information on more recent interspecific relationships (i.e., within a genus). A common solution has been to represent these relationships as polytomies on trees using taxonomy as a guide. Here we show that such trees can dramatically inflate estimates of phylogenetic conservatism quantified using S. P. Blomberg et al.'s K statistic. Using simulations, we show that even randomly generated traits can appear to be phylogenetically conserved on poorly resolved trees. We provide a simple rarefaction-based solution that can reliably retrieve unbiased estimates of K, and we illustrate our method using data on first flowering times from Thoreau's woods (Concord, Massachusetts, USA).

QUANTITATIVE PROCEDURES FOR NEUROTOXICOLOGY RISK ASSESSMENT

EPA Science Inventory

In this project, previously published information on biologically based dose-response model for brain development was used to quantitatively evaluate critical neurodevelopmental processes, and to assess potential chemical impacts on early brain development. This model has been ex...

Evaluation of properties over phylogenetic trees using stochastic logics.

PubMed

Requeno, José Ignacio; Colom, José Manuel

2016-06-14

Model checking has been recently introduced as an integrated framework for extracting information of the phylogenetic trees using temporal logics as a querying language, an extension of modal logics that imposes restrictions of a boolean formula along a path of events. The phylogenetic tree is considered a transition system modeling the evolution as a sequence of genomic mutations (we understand mutation as different ways that DNA can be changed), while this kind of logics are suitable for traversing it in a strict and exhaustive way. Given a biological property that we desire to inspect over the phylogeny, the verifier returns true if the specification is satisfied or a counterexample that falsifies it. However, this approach has been only considered over qualitative aspects of the phylogeny. In this paper, we repair the limitations of the previous framework for including and handling quantitative information such as explicit time or probability. To this end, we apply current probabilistic continuous-time extensions of model checking to phylogenetics. We reinterpret a catalog of qualitative properties in a numerical way, and we also present new properties that couldn't be analyzed before. For instance, we obtain the likelihood of a tree topology according to a mutation model. As case of study, we analyze several phylogenies in order to obtain the maximum likelihood with the model checking tool PRISM. In addition, we have adapted the software for optimizing the computation of maximum likelihoods. We have shown that probabilistic model checking is a competitive framework for describing and analyzing quantitative properties over phylogenetic trees. This formalism adds soundness and readability to the definition of models and specifications. Besides, the existence of model checking tools hides the underlying technology, omitting the extension, upgrade, debugging and maintenance of a software tool to the biologists. A set of benchmarks justify the feasibility of our

Cophenetic metrics for phylogenetic trees, after Sokal and Rohlf.

PubMed

Cardona, Gabriel; Mir, Arnau; Rosselló, Francesc; Rotger, Lucía; Sánchez, David

2013-01-16

Phylogenetic tree comparison metrics are an important tool in the study of evolution, and hence the definition of such metrics is an interesting problem in phylogenetics. In a paper in Taxon fifty years ago, Sokal and Rohlf proposed to measure quantitatively the difference between a pair of phylogenetic trees by first encoding them by means of their half-matrices of cophenetic values, and then comparing these matrices. This idea has been used several times since then to define dissimilarity measures between phylogenetic trees but, to our knowledge, no proper metric on weighted phylogenetic trees with nested taxa based on this idea has been formally defined and studied yet. Actually, the cophenetic values of pairs of different taxa alone are not enough to single out phylogenetic trees with weighted arcs or nested taxa. For every (rooted) phylogenetic tree T, let its cophenetic vectorφ(T) consist of all pairs of cophenetic values between pairs of taxa in T and all depths of taxa in T. It turns out that these cophenetic vectors single out weighted phylogenetic trees with nested taxa. We then define a family of cophenetic metrics dφ,p by comparing these cophenetic vectors by means of Lp norms, and we study, either analytically or numerically, some of their basic properties: neighbors, diameter, distribution, and their rank correlation with each other and with other metrics. The cophenetic metrics can be safely used on weighted phylogenetic trees with nested taxa and no restriction on degrees, and they can be computed in O(n2) time, where n stands for the number of taxa. The metrics dφ,1 and dφ,2 have positive skewed distributions, and they show a low rank correlation with the Robinson-Foulds metric and the nodal metrics, and a very high correlation with each other and with the splitted nodal metrics. The diameter of dφ,p, for p⩾1 , is in O(n(p+2)/p), and thus for low p they are more discriminative, having a wider range of values.

Physiologic basis for understanding quantitative dehydration assessment.

PubMed

Cheuvront, Samuel N; Kenefick, Robert W; Charkoudian, Nisha; Sawka, Michael N

2013-03-01

Dehydration (body water deficit) is a physiologic state that can have profound implications for human health and performance. Unfortunately, dehydration can be difficult to assess, and there is no single, universal gold standard for decision making. In this article, we review the physiologic basis for understanding quantitative dehydration assessment. We highlight how phenomenologic interpretations of dehydration depend critically on the type (dehydration compared with volume depletion) and magnitude (moderate compared with severe) of dehydration, which in turn influence the osmotic (plasma osmolality) and blood volume-dependent compensatory thresholds for antidiuretic and thirst responses. In particular, we review new findings regarding the biological variation in osmotic responses to dehydration and discuss how this variation can help provide a quantitative and clinically relevant link between the physiology and phenomenology of dehydration. Practical measures with empirical thresholds are provided as a starting point for improving the practice of dehydration assessment.

Assessing the reporting of categorised quantitative variables in observational epidemiological studies.

PubMed

Mabikwa, Onkabetse V; Greenwood, Darren C; Baxter, Paul D; Fleming, Sarah J

2017-03-14

One aspect to consider when reporting results of observational studies in epidemiology is how quantitative risk factors are analysed. The STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines recommend that researchers describe how they handle quantitative variables when analysing data. For categorised quantitative variables, the authors are required to provide reasons and justifications informing their practice. We investigated and assessed the practices and reporting of categorised quantitative variables in epidemiology. The assessment was based on five medical journals that publish epidemiological research. Observational studies published between April and June 2015 and investigating the relationships between quantitative exposures (or risk factors) and the outcomes were considered for assessment. A standard form was used to collect the data, and the reporting patterns amongst eligible studies were quantified and described. Out of 61 articles assessed for eligibility, 23 observational studies were included in the assessment. Categorisation of quantitative exposures occurred in 61% of these studies and reasons informing the practice were rarely provided. Only one article explained the choice of categorisation in the analysis. Transformation of quantitative exposures into four or five groups was common and dominant amongst studies using equally spaced categories. Dichotomisation was not popular; the practice featured in one article. Overall, the majority (86%) of the studies preferred ordered or arbitrary group categories. Other criterions used to decide categorical boundaries were based on established guidelines such as consensus statements and WHO standards. Categorisation of continuous variables remains a dominant practice in epidemiological studies. The reasons informing the practice of categorisation within published work are limited and remain unknown in most articles. The existing STROBE guidelines could provide stronger

Phylogenetics.

PubMed

Sleator, Roy D

2011-04-01

The recent rapid expansion in the DNA and protein databases, arising from large-scale genomic and metagenomic sequence projects, has forced significant development in the field of phylogenetics: the study of the evolutionary relatedness of the planet's inhabitants. Advances in phylogenetic analysis have greatly transformed our view of the landscape of evolutionary biology, transcending the view of the tree of life that has shaped evolutionary theory since Darwinian times. Indeed, modern phylogenetic analysis no longer focuses on the restricted Darwinian-Mendelian model of vertical gene transfer, but must also consider the significant degree of lateral gene transfer, which connects and shapes almost all living things. Herein, I review the major tree-building methods, their strengths, weaknesses and future prospects.

A taxonomic and phylogenetic re-appraisal of the genus Curvularia

USDA-ARS?s Scientific Manuscript database

Species of Curvularia are important plant and human pathogens worldwide. In this study, the genus Curvularia is re-assessed based on molecular phylogenetic analysis and morphological observations of available isolates and specimens. A multi-gene phylogenetic tree inferred from ITS, TEF and GPDH gene...

Phylogenetic community structure: temporal variation in fish assemblage

PubMed Central

Santorelli, Sergio; Magnusson, William; Ferreira, Efrem; Caramaschi, Erica; Zuanon, Jansen; Amadio, Sidnéia

2014-01-01

Hypotheses about phylogenetic relationships among species allow inferences about the mechanisms that affect species coexistence. Nevertheless, most studies assume that phylogenetic patterns identified are stable over time. We used data on monthly samples of fish from a single lake over 10 years to show that the structure in phylogenetic assemblages varies over time and conclusions depend heavily on the time scale investigated. The data set was organized in guild structures and temporal scales (grouped at three temporal scales). Phylogenetic distance was measured as the mean pairwise distances (MPD) and as mean nearest-neighbor distance (MNTD). Both distances were based on counts of nodes. We compared the observed values of MPD and MNTD with values that were generated randomly using null model independent swap. A serial runs test was used to assess the temporal independence of indices over time. The phylogenetic pattern in the whole assemblage and the functional groups varied widely over time. Conclusions about phylogenetic clustering or dispersion depended on the temporal scales. Conclusions about the frequency with which biotic processes and environmental filters affect the local assembly do not depend only on taxonomic grouping and spatial scales. While these analyzes allow the assertion that all proposed patterns apply to the fish assemblages in the floodplain, the assessment of the relative importance of these processes, and how they vary depending on the temporal scale and functional group studied, cannot be determined with the effort commonly used. It appears that, at least in the system that we studied, the assemblages are forming and breaking continuously, resulting in various phylogeny-related structures that makes summarizing difficult. PMID:25360256

A measure of the denseness of a phylogenetic network. [by sequenced proteins from extant species

NASA Technical Reports Server (NTRS)

Holmquist, R.

1978-01-01

An objective measure of phylogenetic denseness is developed to examine various phylogenetic criteria: alpha- and beta-hemoglobin, myoglobin, cytochrome c, and the parvalbumin family. Attention is given to the number of nucleotide replacements separating homologous sequences, and to the topology of the network (in other words, to the qualitative nature of the network as defined by how closely the studied species are related). Applications include quantitative comparisons of species origin, relation, and rates of evolution.

Rock Slide Risk Assessment: A Semi-Quantitative Approach

NASA Astrophysics Data System (ADS)

Duzgun, H. S. B.

2009-04-01

Rock slides can be better managed by systematic risk assessments. Any risk assessment methodology for rock slides involves identification of rock slide risk components, which are hazard, elements at risk and vulnerability. For a quantitative/semi-quantitative risk assessment for rock slides, a mathematical value the risk has to be computed and evaluated. The quantitative evaluation of risk for rock slides enables comparison of the computed risk with the risk of other natural and/or human-made hazards and providing better decision support and easier communication for the decision makers. A quantitative/semi-quantitative risk assessment procedure involves: Danger Identification, Hazard Assessment, Elements at Risk Identification, Vulnerability Assessment, Risk computation, Risk Evaluation. On the other hand, the steps of this procedure require adaptation of existing or development of new implementation methods depending on the type of landslide, data availability, investigation scale and nature of consequences. In study, a generic semi-quantitative risk assessment (SQRA) procedure for rock slides is proposed. The procedure has five consecutive stages: Data collection and analyses, hazard assessment, analyses of elements at risk and vulnerability and risk assessment. The implementation of the procedure for a single rock slide case is illustrated for a rock slope in Norway. Rock slides from mountain Ramnefjell to lake Loen are considered to be one of the major geohazards in Norway. Lake Loen is located in the inner part of Nordfjord in Western Norway. Ramnefjell Mountain is heavily jointed leading to formation of vertical rock slices with height between 400-450 m and width between 7-10 m. These slices threaten the settlements around Loen Valley and tourists visiting the fjord during summer season, as the released slides have potential of creating tsunami. In the past, several rock slides had been recorded from the Mountain Ramnefjell between 1905 and 1950. Among them

A Deliberate Practice Approach to Teaching Phylogenetic Analysis

PubMed Central

Hobbs, F. Collin; Johnson, Daniel J.; Kearns, Katherine D.

2013-01-01

One goal of postsecondary education is to assist students in developing expert-level understanding. Previous attempts to encourage expert-level understanding of phylogenetic analysis in college science classrooms have largely focused on isolated, or “one-shot,” in-class activities. Using a deliberate practice instructional approach, we designed a set of five assignments for a 300-level plant systematics course that incrementally introduces the concepts and skills used in phylogenetic analysis. In our assignments, students learned the process of constructing phylogenetic trees through a series of increasingly difficult tasks; thus, skill development served as a framework for building content knowledge. We present results from 5 yr of final exam scores, pre- and postconcept assessments, and student surveys to assess the impact of our new pedagogical materials on student performance related to constructing and interpreting phylogenetic trees. Students improved in their ability to interpret relationships within trees and improved in several aspects related to between-tree comparisons and tree construction skills. Student feedback indicated that most students believed our approach prepared them to engage in tree construction and gave them confidence in their abilities. Overall, our data confirm that instructional approaches implementing deliberate practice address student misconceptions, improve student experiences, and foster deeper understanding of difficult scientific concepts. PMID:24297294

Some suggested future directions of quantitative resource assessments

USGS Publications Warehouse

Singer, D.A.

2001-01-01

Future quantitative assessments will be expected to estimate quantities, values, and locations of undiscovered mineral resources in a form that conveys both economic viability and uncertainty associated with the resources. Historically, declining metal prices point to the need for larger deposits over time. Sensitivity analysis demonstrates that the greatest opportunity for reducing uncertainty in assessments lies in lowering uncertainty associated with tonnage estimates. Of all errors possible in assessments, those affecting tonnage estimates are by far the most important. Selecting the correct deposit model is the most important way of controlling errors because the dominance of tonnage-deposit models are the best known predictor of tonnage. Much of the surface is covered with apparently barren rocks and sediments in many large regions. Because many exposed mineral deposits are believed to have been found, a prime concern is the presence of possible mineralized rock under cover. Assessments of areas with resources under cover must rely on extrapolation from surrounding areas, new geologic maps of rocks under cover, or analogy with other well-explored areas that can be considered training tracts. Cover has a profound effect on uncertainty and on methods and procedures of assessments because geology is seldom known and geophysical methods typically have attenuated responses. Many earlier assessment methods were based on relationships of geochemical and geophysical variables to deposits learned from deposits exposed on the surface-these will need to be relearned based on covered deposits. Mineral-deposit models are important in quantitative resource assessments for two reasons: (1) grades and tonnages of most deposit types are significantly different, and (2) deposit types are present in different geologic settings that can be identified from geologic maps. Mineral-deposit models are the keystone in combining the diverse geoscience information on geology, mineral

Toward Quantitative Small Animal Pinhole SPECT: Assessment of Quantitation Accuracy Prior to Image Compensations

PubMed Central

Chen, Chia-Lin; Wang, Yuchuan; Lee, Jason J. S.; Tsui, Benjamin M. W.

2011-01-01

Purpose We assessed the quantitation accuracy of small animal pinhole single photon emission computed tomography (SPECT) under the current preclinical settings, where image compensations are not routinely applied. Procedures The effects of several common image-degrading factors and imaging parameters on quantitation accuracy were evaluated using Monte-Carlo simulation methods. Typical preclinical imaging configurations were modeled, and quantitative analyses were performed based on image reconstructions without compensating for attenuation, scatter, and limited system resolution. Results Using mouse-sized phantom studies as examples, attenuation effects alone degraded quantitation accuracy by up to −18% (Tc-99m or In-111) or −41% (I-125). The inclusion of scatter effects changed the above numbers to −12% (Tc-99m or In-111) and −21% (I-125), respectively, indicating the significance of scatter in quantitative I-125 imaging. Region-of-interest (ROI) definitions have greater impacts on regional quantitation accuracy for small sphere sources as compared to attenuation and scatter effects. For the same ROI, SPECT acquisitions using pinhole apertures of different sizes could significantly affect the outcome, whereas the use of different radii-of-rotation yielded negligible differences in quantitation accuracy for the imaging configurations simulated. Conclusions We have systematically quantified the influence of several factors affecting the quantitation accuracy of small animal pinhole SPECT. In order to consistently achieve accurate quantitation within 5% of the truth, comprehensive image compensation methods are needed. PMID:19048346

Biodiversity assessment among two Nebraska prairies: a comparison between traditional and phylogenetic diversity indices.

PubMed

Aust, Shelly K; Ahrendsen, Dakota L; Kellar, P Roxanne

2015-01-01

Conservation of the evolutionary diversity among organisms should be included in the selection of priority regions for preservation of Earth's biodiversity. Traditionally, biodiversity has been determined from an assessment of species richness (S), abundance, evenness, rarity, etc. of organisms but not from variation in species' evolutionary histories. Phylogenetic diversity (PD) measures evolutionary differences between taxa in a community and is gaining acceptance as a biodiversity assessment tool. However, with the increase in the number of ways to calculate PD, end-users and decision-makers are left wondering how metrics compare and what data are needed to calculate various metrics. In this study, we used massively parallel sequencing to generate over 65,000 DNA characters from three cellular compartments for over 60 species in the asterid clade of flowering plants. We estimated asterid phylogenies from character datasets of varying nucleotide quantities, and then assessed the effect of varying character datasets on resulting PD metric values. We also compared multiple PD metrics with traditional diversity indices (including S) among two endangered grassland prairies in Nebraska (U.S.A.). Our results revealed that PD metrics varied based on the quantity of genes used to infer the phylogenies; therefore, when comparing PD metrics between sites, it is vital to use comparable datasets. Additionally, various PD metrics and traditional diversity indices characterize biodiversity differently and should be chosen depending on the research question. Our study provides empirical results that reveal the value of measuring PD when considering sites for conservation, and it highlights the usefulness of using PD metrics in combination with other diversity indices when studying community assembly and ecosystem functioning. Ours is just one example of the types of investigations that need to be conducted across the tree of life and across varying ecosystems in order to build

Biodiversity assessment among two Nebraska prairies: a comparison between traditional and phylogenetic diversity indices

PubMed Central

Aust, Shelly K.; Ahrendsen, Dakota L.

2015-01-01

Abstract Background Conservation of the evolutionary diversity among organisms should be included in the selection of priority regions for preservation of Earth’s biodiversity. Traditionally, biodiversity has been determined from an assessment of species richness (S), abundance, evenness, rarity, etc. of organisms but not from variation in species’ evolutionary histories. Phylogenetic diversity (PD) measures evolutionary differences between taxa in a community and is gaining acceptance as a biodiversity assessment tool. However, with the increase in the number of ways to calculate PD, end-users and decision-makers are left wondering how metrics compare and what data are needed to calculate various metrics. New information In this study, we used massively parallel sequencing to generate over 65,000 DNA characters from three cellular compartments for over 60 species in the asterid clade of flowering plants. We estimated asterid phylogenies from character datasets of varying nucleotide quantities, and then assessed the effect of varying character datasets on resulting PD metric values. We also compared multiple PD metrics with traditional diversity indices (including S) among two endangered grassland prairies in Nebraska (U.S.A.). Our results revealed that PD metrics varied based on the quantity of genes used to infer the phylogenies; therefore, when comparing PD metrics between sites, it is vital to use comparable datasets. Additionally, various PD metrics and traditional diversity indices characterize biodiversity differently and should be chosen depending on the research question. Our study provides empirical results that reveal the value of measuring PD when considering sites for conservation, and it highlights the usefulness of using PD metrics in combination with other diversity indices when studying community assembly and ecosystem functioning. Ours is just one example of the types of investigations that need to be conducted across the tree of life and

Distinguishing nanomaterial particles from background airborne particulate matter for quantitative exposure assessment

NASA Astrophysics Data System (ADS)

Ono-Ogasawara, Mariko; Serita, Fumio; Takaya, Mitsutoshi

2009-10-01

As the production of engineered nanomaterials quantitatively expands, the chance that workers involved in the manufacturing process will be exposed to nanoparticles also increases. A risk management system is needed for workplaces in the nanomaterial industry based on the precautionary principle. One of the problems in the risk management system is difficulty of exposure assessment. In this article, examples of exposure assessment in nanomaterial industries are reviewed with a focus on distinguishing engineered nanomaterial particles from background nanoparticles in workplace atmosphere. An approach by JNIOSH (Japan National Institute of Occupational Safety and Health) to quantitatively measure exposure to carbonaceous nanomaterials is also introduced. In addition to real-time measurements and qualitative analysis by electron microscopy, quantitative chemical analysis is necessary for quantitatively assessing exposure to nanomaterials. Chemical analysis is suitable for quantitative exposure measurement especially at facilities with high levels of background NPs.

The phylogenetic roots of human lethal violence.

PubMed

Gómez, José María; Verdú, Miguel; González-Megías, Adela; Méndez, Marcos

2016-10-13

The psychological, sociological and evolutionary roots of conspecific violence in humans are still debated, despite attracting the attention of intellectuals for over two millennia. Here we propose a conceptual approach towards understanding these roots based on the assumption that aggression in mammals, including humans, has a significant phylogenetic component. By compiling sources of mortality from a comprehensive sample of mammals, we assessed the percentage of deaths due to conspecifics and, using phylogenetic comparative tools, predicted this value for humans. The proportion of human deaths phylogenetically predicted to be caused by interpersonal violence stood at 2%. This value was similar to the one phylogenetically inferred for the evolutionary ancestor of primates and apes, indicating that a certain level of lethal violence arises owing to our position within the phylogeny of mammals. It was also similar to the percentage seen in prehistoric bands and tribes, indicating that we were as lethally violent then as common mammalian evolutionary history would predict. However, the level of lethal violence has changed through human history and can be associated with changes in the socio-political organization of human populations. Our study provides a detailed phylogenetic and historical context against which to compare levels of lethal violence observed throughout our history.

BIMLR: a method for constructing rooted phylogenetic networks from rooted phylogenetic trees.

PubMed

Wang, Juan; Guo, Maozu; Xing, Linlin; Che, Kai; Liu, Xiaoyan; Wang, Chunyu

2013-09-15

Rooted phylogenetic trees constructed from different datasets (e.g. from different genes) are often conflicting with one another, i.e. they cannot be integrated into a single phylogenetic tree. Phylogenetic networks have become an important tool in molecular evolution, and rooted phylogenetic networks are able to represent conflicting rooted phylogenetic trees. Hence, the development of appropriate methods to compute rooted phylogenetic networks from rooted phylogenetic trees has attracted considerable research interest of late. The CASS algorithm proposed by van Iersel et al. is able to construct much simpler networks than other available methods, but it is extremely slow, and the networks it constructs are dependent on the order of the input data. Here, we introduce an improved CASS algorithm, BIMLR. We show that BIMLR is faster than CASS and less dependent on the input data order. Moreover, BIMLR is able to construct much simpler networks than almost all other methods. BIMLR is available at http://nclab.hit.edu.cn/wangjuan/BIMLR/. © 2013 Elsevier B.V. All rights reserved.

How Accurate and Robust Are the Phylogenetic Estimates of Austronesian Language Relationships?

PubMed Central

Greenhill, Simon J.; Drummond, Alexei J.; Gray, Russell D.

2010-01-01

We recently used computational phylogenetic methods on lexical data to test between two scenarios for the peopling of the Pacific. Our analyses of lexical data supported a pulse-pause scenario of Pacific settlement in which the Austronesian speakers originated in Taiwan around 5,200 years ago and rapidly spread through the Pacific in a series of expansion pulses and settlement pauses. We claimed that there was high congruence between traditional language subgroups and those observed in the language phylogenies, and that the estimated age of the Austronesian expansion at 5,200 years ago was consistent with the archaeological evidence. However, the congruence between the language phylogenies and the evidence from historical linguistics was not quantitatively assessed using tree comparison metrics. The robustness of the divergence time estimates to different calibration points was also not investigated exhaustively. Here we address these limitations by using a systematic tree comparison metric to calculate the similarity between the Bayesian phylogenetic trees and the subgroups proposed by historical linguistics, and by re-estimating the age of the Austronesian expansion using only the most robust calibrations. The results show that the Austronesian language phylogenies are highly congruent with the traditional subgroupings, and the date estimates are robust even when calculated using a restricted set of historical calibrations. PMID:20224774

Maximizing the phylogenetic diversity of seed banks.

PubMed

Griffiths, Kate E; Balding, Sharon T; Dickie, John B; Lewis, Gwilym P; Pearce, Tim R; Grenyer, Richard

2015-04-01

Ex situ conservation efforts such as those of zoos, botanical gardens, and seed banks will form a vital complement to in situ conservation actions over the coming decades. It is therefore necessary to pay the same attention to the biological diversity represented in ex situ conservation facilities as is often paid to protected-area networks. Building the phylogenetic diversity of ex situ collections will strengthen our capacity to respond to biodiversity loss. Since 2000, the Millennium Seed Bank Partnership has banked seed from 14% of the world's plant species. We assessed the taxonomic, geographic, and phylogenetic diversity of the Millennium Seed Bank collection of legumes (Leguminosae). We compared the collection with all known legume genera, their known geographic range (at country and regional levels), and a genus-level phylogeny of the legume family constructed for this study. Over half the phylogenetic diversity of legumes at the genus level was represented in the Millennium Seed Bank. However, pragmatic prioritization of species of economic importance and endangerment has led to the banking of a less-than-optimal phylogenetic diversity and prioritization of range-restricted species risks an underdispersed collection. The current state of the phylogenetic diversity of legumes in the Millennium Seed Bank could be substantially improved through the strategic banking of relatively few additional taxa. Our method draws on tools that are widely applied to in situ conservation planning, and it can be used to evaluate and improve the phylogenetic diversity of ex situ collections. © 2014 Society for Conservation Biology.

A framework for organizing and selecting quantitative approaches for benefit-harm assessment.

PubMed

Puhan, Milo A; Singh, Sonal; Weiss, Carlos O; Varadhan, Ravi; Boyd, Cynthia M

2012-11-19

Several quantitative approaches for benefit-harm assessment of health care interventions exist but it is unclear how the approaches differ. Our aim was to review existing quantitative approaches for benefit-harm assessment and to develop an organizing framework that clarifies differences and aids selection of quantitative approaches for a particular benefit-harm assessment. We performed a review of the literature to identify quantitative approaches for benefit-harm assessment. Our team, consisting of clinicians, epidemiologists, and statisticians, discussed the approaches and identified their key characteristics. We developed a framework that helps investigators select quantitative approaches for benefit-harm assessment that are appropriate for a particular decisionmaking context. Our framework for selecting quantitative approaches requires a concise definition of the treatment comparison and population of interest, identification of key benefit and harm outcomes, and determination of the need for a measure that puts all outcomes on a single scale (which we call a benefit and harm comparison metric). We identified 16 quantitative approaches for benefit-harm assessment. These approaches can be categorized into those that consider single or multiple key benefit and harm outcomes, and those that use a benefit-harm comparison metric or not. Most approaches use aggregate data and can be used in the context of single studies or systematic reviews. Although the majority of approaches provides a benefit and harm comparison metric, only four approaches provide measures of uncertainty around the benefit and harm comparison metric (such as a 95 percent confidence interval). None of the approaches considers the actual joint distribution of benefit and harm outcomes, but one approach considers competing risks when calculating profile-specific event rates. Nine approaches explicitly allow incorporating patient preferences. The choice of quantitative approaches depends on the

A framework for organizing and selecting quantitative approaches for benefit-harm assessment

PubMed Central

2012-01-01

Background Several quantitative approaches for benefit-harm assessment of health care interventions exist but it is unclear how the approaches differ. Our aim was to review existing quantitative approaches for benefit-harm assessment and to develop an organizing framework that clarifies differences and aids selection of quantitative approaches for a particular benefit-harm assessment. Methods We performed a review of the literature to identify quantitative approaches for benefit-harm assessment. Our team, consisting of clinicians, epidemiologists, and statisticians, discussed the approaches and identified their key characteristics. We developed a framework that helps investigators select quantitative approaches for benefit-harm assessment that are appropriate for a particular decisionmaking context. Results Our framework for selecting quantitative approaches requires a concise definition of the treatment comparison and population of interest, identification of key benefit and harm outcomes, and determination of the need for a measure that puts all outcomes on a single scale (which we call a benefit and harm comparison metric). We identified 16 quantitative approaches for benefit-harm assessment. These approaches can be categorized into those that consider single or multiple key benefit and harm outcomes, and those that use a benefit-harm comparison metric or not. Most approaches use aggregate data and can be used in the context of single studies or systematic reviews. Although the majority of approaches provides a benefit and harm comparison metric, only four approaches provide measures of uncertainty around the benefit and harm comparison metric (such as a 95 percent confidence interval). None of the approaches considers the actual joint distribution of benefit and harm outcomes, but one approach considers competing risks when calculating profile-specific event rates. Nine approaches explicitly allow incorporating patient preferences. Conclusion The choice of

Threatened species and the potential loss of phylogenetic diversity: conservation scenarios based on estimated extinction probabilities and phylogenetic risk analysis.

PubMed

Faith, Daniel P

2008-12-01

New species conservation strategies, including the EDGE of Existence (EDGE) program, have expanded threatened species assessments by integrating information about species' phylogenetic distinctiveness. Distinctiveness has been measured through simple scores that assign shared credit among species for evolutionary heritage represented by the deeper phylogenetic branches. A species with a high score combined with a high extinction probability receives high priority for conservation efforts. Simple hypothetical scenarios for phylogenetic trees and extinction probabilities demonstrate how such scoring approaches can provide inefficient priorities for conservation. An existing probabilistic framework derived from the phylogenetic diversity measure (PD) properly captures the idea of shared responsibility for the persistence of evolutionary history. It avoids static scores, takes into account the status of close relatives through their extinction probabilities, and allows for the necessary updating of priorities in light of changes in species threat status. A hypothetical phylogenetic tree illustrates how changes in extinction probabilities of one or more species translate into changes in expected PD. The probabilistic PD framework provided a range of strategies that moved beyond expected PD to better consider worst-case PD losses. In another example, risk aversion gave higher priority to a conservation program that provided a smaller, but less risky, gain in expected PD. The EDGE program could continue to promote a list of top species conservation priorities through application of probabilistic PD and simple estimates of current extinction probability. The list might be a dynamic one, with all the priority scores updated as extinction probabilities change. Results of recent studies suggest that estimation of extinction probabilities derived from the red list criteria linked to changes in species range sizes may provide estimated probabilities for many different species

Towards quantitative condition assessment of biodiversity outcomes: Insights from Australian marine protected areas.

PubMed

Addison, Prue F E; Flander, Louisa B; Cook, Carly N

2017-08-01

Protected area management effectiveness (PAME) evaluation is increasingly undertaken to evaluate governance, assess conservation outcomes and inform evidence-based management of protected areas (PAs). Within PAME, quantitative approaches to assess biodiversity outcomes are now emerging, where biological monitoring data are directly assessed against quantitative (numerically defined) condition categories (termed quantitative condition assessments). However, more commonly qualitative condition assessments are employed in PAME, which use descriptive condition categories and are evaluated largely with expert judgement that can be subject to a range of biases, such as linguistic uncertainty and overconfidence. Despite the benefits of increased transparency and repeatability of evaluations, quantitative condition assessments are rarely used in PAME. To understand why, we interviewed practitioners from all Australian marine protected area (MPA) networks, which have access to long-term biological monitoring data and are developing or conducting PAME evaluations. Our research revealed that there is a desire within management agencies to implement quantitative condition assessment of biodiversity outcomes in Australian MPAs. However, practitioners report many challenges in transitioning from undertaking qualitative to quantitative condition assessments of biodiversity outcomes, which are hampering progress. Challenges include a lack of agency capacity (staff numbers and money), knowledge gaps, and diminishing public and political support for PAs. We point to opportunities to target strategies that will assist agencies overcome these challenges, including new decision support tools, approaches to better finance conservation efforts, and to promote more management relevant science. While a single solution is unlikely to achieve full evidence-based conservation, we suggest ways for agencies to target strategies and advance PAME evaluations toward best practice. Copyright �

Teaching Molecular Phylogenetics through Investigating a Real-World Phylogenetic Problem

ERIC Educational Resources Information Center

Zhang, Xiaorong

2012-01-01

A phylogenetics exercise is incorporated into the "Introduction to biocomputing" course, a junior-level course at Savannah State University. This exercise is designed to help students learn important concepts and practical skills in molecular phylogenetics through solving a real-world problem. In this application, students are required to identify…

A new phylogenetic diversity measure generalizing the shannon index and its application to phyllostomid bats.

PubMed

Allen, Benjamin; Kon, Mark; Bar-Yam, Yaneer

2009-08-01

Protecting biodiversity involves preserving the maximum number and abundance of species while giving special attention to species with unique genetic or morphological characteristics. In balancing different priorities, conservation policymakers may consider quantitative measures that compare diversity across ecological communities. To serve this purpose, a measure should increase or decrease with changes in community composition in a way that reflects what is valued, including species richness, evenness, and distinctness. However, counterintuitively, studies have shown that established indices, including those that emphasize average interspecies phylogenetic distance, may increase with the elimination of species. We introduce a new diversity index, the phylogenetic entropy, which generalizes in a natural way the Shannon index to incorporate species relatedness. Phylogenetic entropy favors communities in which highly distinct species are more abundant, but it does not advocate decreasing any species proportion below a community structure-dependent threshold. We contrast the behavior of multiple indices on a community of phyllostomid bats in the Selva Lacandona. The optimal genus distribution for phylogenetic entropy populates all genera in a linear relationship to their total phylogenetic distance to other genera. Two other indices favor eliminating 12 out of the 23 genera.

Nonbinary Tree-Based Phylogenetic Networks.

PubMed

Jetten, Laura; van Iersel, Leo

2018-01-01

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can, for example, represent gene transfer events. Such phylogenetic networks are called tree-based. Here, we consider two possible generalizations of this concept to nonbinary networks, which we call tree-based and strictly-tree-based nonbinary phylogenetic networks. We give simple graph-theoretic characterizations of tree-based and strictly-tree-based nonbinary phylogenetic networks. Moreover, we show for each of these two classes that it can be decided in polynomial time whether a given network is contained in the class. Our approach also provides a new view on tree-based binary phylogenetic networks. Finally, we discuss two examples of nonbinary phylogenetic networks in biology and show how our results can be applied to them.

A continuous morphological approach to study the evolution of pollen in a phylogenetic context: An example with the order Myrtales.

PubMed

Kriebel, Ricardo; Khabbazian, Mohammad; Sytsma, Kenneth J

2017-01-01

The study of pollen morphology has historically allowed evolutionary biologists to assess phylogenetic relationships among Angiosperms, as well as to better understand the fossil record. During this process, pollen has mainly been studied by discretizing some of its main characteristics such as size, shape, and exine ornamentation. One large plant clade in which pollen has been used this way for phylogenetic inference and character mapping is the order Myrtales, composed by the small families Alzateaceae, Crypteroniaceae, and Penaeaceae (collectively the "CAP clade"), as well as the large families Combretaceae, Lythraceae, Melastomataceae, Myrtaceae, Onagraceae and Vochysiaceae. In this study, we present a novel way to study pollen evolution by using quantitative size and shape variables. We use morphometric and morphospace methods to evaluate pollen change in the order Myrtales using a time-calibrated, supermatrix phylogeny. We then test for conservatism, divergence, and morphological convergence of pollen and for correlation between the latitudinal gradient and pollen size and shape. To obtain an estimate of shape, Myrtales pollen images were extracted from the literature, and their outlines analyzed using elliptic Fourier methods. Shape and size variables were then analyzed in a phylogenetic framework under an Ornstein-Uhlenbeck process to test for shifts in size and shape during the evolutionary history of Myrtales. Few shifts in Myrtales pollen morphology were found which indicates morphological conservatism. Heterocolpate, small pollen is ancestral with largest pollen in Onagraceae. Convergent shifts in shape but not size occurred in Myrtaceae and Onagraceae and are correlated to shifts in latitude and biogeography. A quantitative approach was applied for the first time to examine pollen evolution across a large time scale. Using phylogenetic based morphometrics and an OU process, hypotheses of pollen size and shape were tested across Myrtales. Convergent

A continuous morphological approach to study the evolution of pollen in a phylogenetic context: An example with the order Myrtales

PubMed Central

Khabbazian, Mohammad; Sytsma, Kenneth J.

2017-01-01

The study of pollen morphology has historically allowed evolutionary biologists to assess phylogenetic relationships among Angiosperms, as well as to better understand the fossil record. During this process, pollen has mainly been studied by discretizing some of its main characteristics such as size, shape, and exine ornamentation. One large plant clade in which pollen has been used this way for phylogenetic inference and character mapping is the order Myrtales, composed by the small families Alzateaceae, Crypteroniaceae, and Penaeaceae (collectively the “CAP clade”), as well as the large families Combretaceae, Lythraceae, Melastomataceae, Myrtaceae, Onagraceae and Vochysiaceae. In this study, we present a novel way to study pollen evolution by using quantitative size and shape variables. We use morphometric and morphospace methods to evaluate pollen change in the order Myrtales using a time-calibrated, supermatrix phylogeny. We then test for conservatism, divergence, and morphological convergence of pollen and for correlation between the latitudinal gradient and pollen size and shape. To obtain an estimate of shape, Myrtales pollen images were extracted from the literature, and their outlines analyzed using elliptic Fourier methods. Shape and size variables were then analyzed in a phylogenetic framework under an Ornstein-Uhlenbeck process to test for shifts in size and shape during the evolutionary history of Myrtales. Few shifts in Myrtales pollen morphology were found which indicates morphological conservatism. Heterocolpate, small pollen is ancestral with largest pollen in Onagraceae. Convergent shifts in shape but not size occurred in Myrtaceae and Onagraceae and are correlated to shifts in latitude and biogeography. A quantitative approach was applied for the first time to examine pollen evolution across a large time scale. Using phylogenetic based morphometrics and an OU process, hypotheses of pollen size and shape were tested across Myrtales. Convergent

Quantitative Procedures for the Assessment of Quality in Higher Education Institutions.

ERIC Educational Resources Information Center

Moran, Tom; Rowse, Glenwood

The development of procedures designed to provide quantitative assessments of quality in higher education institutions are reviewed. These procedures employ a systems framework and utilize quantitative data to compare institutions or programs of similar types with one another. Three major elements essential in the development of models focusing on…

Assessing the influence of biogeographical region and phylogenetic history on chemical defences and herbivory in Quercus species.

PubMed

Moreira, Xoaquín; Abdala-Roberts, Luis; Galmán, Andrea; Francisco, Marta; Fuente, María de la; Butrón, Ana; Rasmann, Sergio

2018-06-07

Biogeographical factors and phylogenetic history are key determinants of inter-specific variation in plant defences. However, few studies have conducted broad-scale geographical comparisons of plant defences while controlling for phylogenetic relationships, and, in doing so, none have separated constitutive from induced defences. This gap has limited our understanding of how historical or large-scale processes mediate biogeographical patterns in plant defences since these may be contingent upon shared evolutionary history and phylogenetic constraints. We conducted a phylogenetically-controlled experiment testing for differences in constitutive leaf chemical defences and their inducibility between Palearctic and Nearctic oak species (Quercus, total 18 species). We induced defences in one-year old plants by inflicting damage by gypsy moth larvae (Lymantria dispar), estimated the amount of leaf area consumed, and quantified various groups of phenolic compounds. There was no detectable phylogenetic signal for constitutive or induced levels of most defensive traits except for constitutive condensed tannins, as well as no phylogenetic signal in leaf herbivory. We did, however, find marked differences in defence levels between oak species from each region: Palearctic species had higher levels of constitutive condensed tannins, but less constitutive lignins and less constitutive and induced hydrolysable tannins compared with Nearctic species. Additionally, Palearctic species had lower levels of leaf damage compared with Nearctic species. These differences in leaf damage, lignins and hydrolysable (but not condensed) tannins were lost after accounting for phylogeny, suggesting that geographical structuring of phylogenetic relationships mediated biogeographical differences in defences and herbivore resistance. Together, these findings suggest that historical processes and large-scale drivers have shaped differences in allocation to constitutive defences (and in turn

Facilitation can increase the phylogenetic diversity of plant communities.

PubMed

Valiente-Banuet, Alfonso; Verdú, Miguel

2007-11-01

With the advent of molecular phylogenies the assessment of community assembly processes has become a central topic in community ecology. These processes have focused almost exclusively on habitat filtering and competitive exclusion. Recent evidence, however, indicates that facilitation has been important in preserving biodiversity over evolutionary time, with recent lineages conserving the regeneration niches of older, distant lineages. Here we test whether, if facilitation among distant-related species has preserved the regeneration niche of plant lineages, this has increased the phylogenetic diversity of communities. By analyzing a large worldwide database of species, we showed that the regeneration niches were strongly conserved across evolutionary history. Likewise, a phylogenetic supertree of all species of three communities driven by facilitation showed that nurse species facilitated distantly related species and increased phylogenetic diversity.

[Research progress and development trend of quantitative assessment techniques for urban thermal environment.

PubMed

Sun, Tie Gang; Xiao, Rong Bo; Cai, Yun Nan; Wang, Yao Wu; Wu, Chang Guang

2016-08-01

Quantitative assessment of urban thermal environment has become a focus for urban climate and environmental science since the concept of urban heat island has been proposed. With the continual development of space information and computer simulation technology, substantial progresses have been made on quantitative assessment techniques and methods of urban thermal environment. The quantitative assessment techniques have been developed to dynamics simulation and forecast of thermal environment at various scales based on statistical analysis of thermal environment on urban-scale using the historical data of weather stations. This study reviewed the development progress of ground meteorological observation, thermal infrared remote sensing and numerical simulation. Moreover, the potential advantages and disadvantages, applicability and the development trends of these techniques were also summarized, aiming to add fundamental knowledge of understanding the urban thermal environment assessment and optimization.

Relationship between Plaque Echo, Thickness and Neovascularization Assessed by Quantitative and Semi-quantitative Contrast-Enhanced Ultrasonography in Different Stenosis Groups.

PubMed

Song, Yan; Feng, Jun; Dang, Ying; Zhao, Chao; Zheng, Jie; Ruan, Litao

2017-12-01

The aim of this study was to determine the relationship between plaque echo, thickness and neovascularization in different stenosis groups using quantitative and semi-quantitative contrast-enhanced ultrasound (CEUS) in patients with carotid atherosclerosis plaque. A total of 224 plaques were divided into mild stenosis (<50%; 135 plaques, 60.27%), moderate stenosis (50%-69%; 39 plaques, 17.41%) and severe stenosis (70%-99%; 50 plaques, 22.32%) groups. Quantitative and semi-quantitative methods were used to assess plaque neovascularization and determine the relationship between plaque echo, thickness and neovascularization. Correlation analysis revealed no relationship of neovascularization with plaque echo in the groups using either quantitative or semi-quantitative methods. Furthermore, there was no correlation of neovascularization with plaque thickness using the semi-quantitative method. The ratio of areas under the curve (RAUC) was negatively correlated with plaque thickness (r = -0.317, p = 0.001) in the mild stenosis group. With the quartile method, plaque thickness of the mild stenosis group was divided into four groups, with significant differences between the 1.5-2.2 mm and ≥3.5 mm groups (p = 0.002), 2.3-2.8 mm and ≥3.5 mm groups (p <0.001) and 2.9-3.4 mm and ≥3.5 mm groups (p <0.001). Both semi-quantitative and quantitative CEUS methods characterizing neovascularization of plaque are equivalent with respect to assessing relationships between neovascularization, echogenicity and thickness. However, the quantitative method could fail for plaque <3.5 mm because of motion artifacts. Copyright © 2017 World Federation for Ultrasound in Medicine and Biology. Published by Elsevier Inc. All rights reserved.

The Use of Quantitative SPECT/CT Imaging to Assess Residual Limb Health

DTIC Science & Technology

2016-10-01

AWARD NUMBER: W81XWH-15-1-0669 TITLE: The Use of Quantitative SPECT/CT Imaging to Assess Residual Limb Health PRINCIPAL INVESTIGATOR...3. DATES COVERED 30 Sep 2015 - 29 Sep 2016 4. TITLE AND SUBTITLE The Use of Quantitative SPECT/CT Imaging to Assess Residual Limb Health 5a...amputation and subsequently evaluate the utility of non-invasive imaging for evaluating the impact of next-generation socket technologies on the health of

Assessing framing assumptions in quantitative health impact assessments: a housing intervention example.

PubMed

Mesa-Frias, Marco; Chalabi, Zaid; Foss, Anna M

2013-09-01

Health impact assessment (HIA) is often used to determine ex ante the health impact of an environmental policy or an environmental intervention. Underpinning any HIA is the framing assumption, which defines the causal pathways mapping environmental exposures to health outcomes. The sensitivity of the HIA to the framing assumptions is often ignored. A novel method based on fuzzy cognitive map (FCM) is developed to quantify the framing assumptions in the assessment stage of a HIA, and is then applied to a housing intervention (tightening insulation) as a case-study. Framing assumptions of the case-study were identified through a literature search of Ovid Medline (1948-2011). The FCM approach was used to identify the key variables that have the most influence in a HIA. Changes in air-tightness, ventilation, indoor air quality and mould/humidity have been identified as having the most influence on health. The FCM approach is widely applicable and can be used to inform the formulation of the framing assumptions in any quantitative HIA of environmental interventions. We argue that it is necessary to explore and quantify framing assumptions prior to conducting a detailed quantitative HIA during the assessment stage. Copyright © 2013 Elsevier Ltd. All rights reserved.

Spatial phylogenetics of the vascular flora of Chile.

PubMed

Scherson, Rosa A; Thornhill, Andrew H; Urbina-Casanova, Rafael; Freyman, William A; Pliscoff, Patricio A; Mishler, Brent D

2017-07-01

Current geographic patterns of biodiversity are a consequence of the evolutionary history of the lineages that comprise them. This study was aimed at exploring how evolutionary features of the vascular flora of Chile are distributed across the landscape. Using a phylogeny at the genus level for 87% of the Chilean vascular flora, and a geographic database of sample localities, we calculated phylogenetic diversity (PD), phylogenetic endemism (PE), relative PD (RPD), and relative PE (RPE). Categorical Analyses of Neo- and Paleo-Endemism (CANAPE) were also performed, using a spatial randomization to assess statistical significance. A cluster analysis using range-weighted phylogenetic turnover was used to compare among grid cells, and with known Chilean bioclimates. PD patterns were concordant with known centers of high taxon richness and the Chilean biodiversity hotspot. In addition, several other interesting areas of concentration of evolutionary history were revealed as potential conservation targets. The south of the country shows areas of significantly high RPD and a concentration of paleo-endemism, and the north shows areas of significantly low PD and RPD, and a concentration of neo-endemism. Range-weighted phylogenetic turnover shows high congruence with the main macrobioclimates of Chile. Even though the study was done at the genus level, the outcome provides an accurate outline of phylogenetic patterns that can be filled in as more fine-scaled information becomes available. Copyright © 2017 Elsevier Inc. All rights reserved.

A qualitative and quantitative assessment for a bone marrow harvest simulator.

PubMed

Machado, Liliane S; Moraes, Ronei M

2009-01-01

Several approaches to perform assessment in training simulators based on virtual reality have been proposed. There are two kinds of assessment methods: offline and online. The main requirements related to online training assessment methodologies applied to virtual reality systems are the low computational complexity and the high accuracy. In the literature it can be found several approaches for general cases which can satisfy such requirements. An inconvenient about those approaches is related to an unsatisfactory solution for specific cases, as in some medical procedures, where there are quantitative and qualitative information available to perform the assessment. In this paper, we present an approach to online training assessment based on a Modified Naive Bayes which can manipulate qualitative and quantitative variables simultaneously. A special medical case was simulated in a bone marrow harvest simulator. The results obtained were satisfactory and evidenced the applicability of the method.

Computational Tools for Parsimony Phylogenetic Analysis of Omics Data

PubMed Central

Salazar, Jose; Amri, Hakima; Noursi, David

2015-01-01

Abstract High-throughput assays from genomics, proteomics, metabolomics, and next generation sequencing produce massive omics datasets that are challenging to analyze in biological or clinical contexts. Thus far, there is no publicly available program for converting quantitative omics data into input formats to be used in off-the-shelf robust phylogenetic programs. To the best of our knowledge, this is the first report on creation of two Windows-based programs, OmicsTract and SynpExtractor, to address this gap. We note, as a way of introduction and development of these programs, that one particularly useful bioinformatics inferential modeling is the phylogenetic cladogram. Cladograms are multidimensional tools that show the relatedness between subgroups of healthy and diseased individuals and the latter's shared aberrations; they also reveal some characteristics of a disease that would not otherwise be apparent by other analytical methods. The OmicsTract and SynpExtractor were written for the respective tasks of (1) accommodating advanced phylogenetic parsimony analysis (through standard programs of MIX [from PHYLIP] and TNT), and (2) extracting shared aberrations at the cladogram nodes. OmicsTract converts comma-delimited data tables through assigning each data point into a binary value (“0” for normal states and “1” for abnormal states) then outputs the converted data tables into the proper input file formats for MIX or with embedded commands for TNT. SynapExtractor uses outfiles from MIX and TNT to extract the shared aberrations of each node of the cladogram, matching them with identifying labels from the dataset and exporting them into a comma-delimited file. Labels may be gene identifiers in gene-expression datasets or m/z values in mass spectrometry datasets. By automating these steps, OmicsTract and SynpExtractor offer a veritable opportunity for rapid and standardized phylogenetic analyses of omics data; their model can also be extended to next

One tree to link them all: a phylogenetic dataset for the European tetrapoda.

PubMed

Roquet, Cristina; Lavergne, Sébastien; Thuiller, Wilfried

2014-08-08

Since the ever-increasing availability of phylogenetic informative data, the last decade has seen an upsurge of ecological studies incorporating information on evolutionary relationships among species. However, detailed species-level phylogenies are still lacking for many large groups and regions, which are necessary for comprehensive large-scale eco-phylogenetic analyses. Here, we provide a dataset of 100 dated phylogenetic trees for all European tetrapods based on a mixture of supermatrix and supertree approaches. Phylogenetic inference was performed separately for each of the main Tetrapoda groups of Europe except mammals (i.e. amphibians, birds, squamates and turtles) by means of maximum likelihood (ML) analyses of supermatrix applying a tree constraint at the family (amphibians and squamates) or order (birds and turtles) levels based on consensus knowledge. For each group, we inferred 100 ML trees to be able to provide a phylogenetic dataset that accounts for phylogenetic uncertainty, and assessed node support with bootstrap analyses. Each tree was dated using penalized-likelihood and fossil calibration. The trees obtained were well-supported by existing knowledge and previous phylogenetic studies. For mammals, we modified the most complete supertree dataset available on the literature to include a recent update of the Carnivora clade. As a final step, we merged the phylogenetic trees of all groups to obtain a set of 100 phylogenetic trees for all European Tetrapoda species for which data was available (91%). We provide this phylogenetic dataset (100 chronograms) for the purpose of comparative analyses, macro-ecological or community ecology studies aiming to incorporate phylogenetic information while accounting for phylogenetic uncertainty.

Phylogenetic assessment of heterotrophic bacteria from a water distribution system using 16S rDNA sequencing.

PubMed

Tokajian, Sima T; Hashwa, Fuad A; Hancock, Ian C; Zalloua, Pierre A

2005-04-01

Determination of a heterotrophic plate count (HPC) for drinking-water samples alone is not enough to assess possible health hazards associated with sudden changes in the bacterial count. Speciation is very crucial to determine whether the population includes pathogens and (or) opportunistic pathogens. Most of the isolates recovered from drinking water samples could not be allocated to a specific phylogenetic branch based on the use of conventional diagnostic methods. The present study had to use phylogenetic analysis, which was simplified by determining and using the first 500-bp sequence of the 16S rDNA, to successfully identify the type and species of bacteria found in the samples. Gram-positive bacteria alpha-, beta-, and gamma-Proteobacteria were found to be the major groups representing the heterotrophic bacteria in drinking water. The study also revealed that the presence of sphingomonads in drinking water supplies may be much more common than has been reported so far and thus further studies are merited. The intermittent mode of supply, mainly characterized by water stagnation and flow interruption associated possibly with biofilm detachment, raised the possibility that the studied bacterial populations in such systems represented organisms coming from 2 different niches, the biofilm and the water column.

Repeatability Assessment by ISO 11843-7 in Quantitative HPLC for Herbal Medicines.

PubMed

Chen, Liangmian; Kotani, Akira; Hakamata, Hideki; Tsutsumi, Risa; Hayashi, Yuzuru; Wang, Zhimin; Kusu, Fumiyo

2015-01-01

We have proposed an assessment methods to estimate the measurement relative standard deviation (RSD) of chromatographic peaks in quantitative HPLC for herbal medicines by the methodology of ISO 11843 Part 7 (ISO 11843-7:2012), which provides detection limits stochastically. In quantitative HPLC with UV detection (HPLC-UV) of Scutellaria Radix for the determination of baicalin, the measurement RSD of baicalin by ISO 11843-7:2012 stochastically was within a 95% confidence interval of the statistically obtained RSD by repetitive measurements (n = 6). Thus, our findings show that it is applicable for estimating of the repeatability of HPLC-UV for determining baicalin without repeated measurements. In addition, the allowable limit of the "System repeatability" in "Liquid Chromatography" regulated in a pharmacopoeia can be obtained by the present assessment method. Moreover, the present assessment method was also successfully applied to estimate the measurement RSDs of quantitative three-channel liquid chromatography with electrochemical detection (LC-3ECD) of Chrysanthemi Flos for determining caffeoylquinic acids and flavonoids. By the present repeatability assessment method, reliable measurement RSD was obtained stochastically, and the experimental time was remarkably reduced.

Mitochondrial comparative genomics and phylogenetic signal assessment of mtDNA among arbuscular mycorrhizal fungi.

PubMed

Nadimi, Maryam; Daubois, Laurence; Hijri, Mohamed

2016-05-01

Mitochondrial (mt) genes, such as cytochrome C oxidase genes (cox), have been widely used for barcoding in many groups of organisms, although this approach has been less powerful in the fungal kingdom due to the rapid evolution of their mt genomes. The use of mt genes in phylogenetic studies of Dikarya has been met with success, while early diverging fungal lineages remain less studied, particularly the arbuscular mycorrhizal fungi (AMF). Advances in next-generation sequencing have substantially increased the number of publically available mtDNA sequences for the Glomeromycota. As a result, comparison of mtDNA across key AMF taxa can now be applied to assess the phylogenetic signal of individual mt coding genes, as well as concatenated subsets of coding genes. Here we show comparative analyses of publically available mt genomes of Glomeromycota, augmented with two mtDNA genomes that were newly sequenced for this study (Rhizophagus irregularis DAOM240159 and Glomus aggregatum DAOM240163), resulting in 16 complete mtDNA datasets. R. irregularis isolate DAOM240159 and G. aggregatum isolate DAOM240163 showed mt genomes measuring 72,293bp and 69,505bp with G+C contents of 37.1% and 37.3%, respectively. We assessed the phylogenies inferred from single mt genes and complete sets of coding genes, which are referred to as "supergenes" (16 concatenated coding genes), using Shimodaira-Hasegawa tests, in order to identify genes that best described AMF phylogeny. We found that rnl, nad5, cox1, and nad2 genes, as well as concatenated subset of these genes, provided phylogenies that were similar to the supergene set. This mitochondrial genomic analysis was also combined with principal coordinate and partitioning analyses, which helped to unravel certain evolutionary relationships in the Rhizophagus genus and for G. aggregatum within the Glomeromycota. We showed evidence to support the position of G. aggregatum within the R. irregularis 'species complex'. Copyright © 2016

An integrated environmental modeling framework for performing Quantitative Microbial Risk Assessments

EPA Science Inventory

Standardized methods are often used to assess the likelihood of a human-health effect from exposure to a specified hazard, and inform opinions and decisions about risk management and communication. A Quantitative Microbial Risk Assessment (QMRA) is specifically adapted to detail ...

NecroQuant: quantitative assessment of radiological necrosis

NASA Astrophysics Data System (ADS)

Hwang, Darryl H.; Mohamed, Passant; Varghese, Bino A.; Cen, Steven Y.; Duddalwar, Vinay

2017-11-01

Clinicians can now objectively quantify tumor necrosis by Hounsfield units and enhancement characteristics from multiphase contrast enhanced CT imaging. NecroQuant has been designed to work as part of a radiomics pipelines. The software is a departure from the conventional qualitative assessment of tumor necrosis, as it provides the user (radiologists and researchers) a simple interface to precisely and interactively define and measure necrosis in contrast-enhanced CT images. Although, the software is tested here on renal masses, it can be re-configured to assess tumor necrosis across variety of tumors from different body sites, providing a generalized, open, portable, and extensible quantitative analysis platform that is widely applicable across cancer types to quantify tumor necrosis.

Combined visual and semi-quantitative assessment of 123I-FP-CIT SPECT for the diagnosis of dopaminergic neurodegenerative diseases.

PubMed

Ueda, Jun; Yoshimura, Hajime; Shimizu, Keiji; Hino, Megumu; Kohara, Nobuo

2017-07-01

Visual and semi-quantitative assessments of 123 I-FP-CIT single-photon emission computed tomography (SPECT) are useful for the diagnosis of dopaminergic neurodegenerative diseases (dNDD), including Parkinson's disease, dementia with Lewy bodies, progressive supranuclear palsy, multiple system atrophy, and corticobasal degeneration. However, the diagnostic value of combined visual and semi-quantitative assessment in dNDD remains unclear. Among 239 consecutive patients with a newly diagnosed possible parkinsonian syndrome who underwent 123 I-FP-CIT SPECT in our medical center, 114 patients with a disease duration less than 7 years were diagnosed as dNDD with the established criteria or as non-dNDD according to clinical judgment. We retrospectively examined their clinical characteristics and visual and semi-quantitative assessments of 123 I-FP-CIT SPECT. The striatal binding ratio (SBR) was used as a semi-quantitative measure of 123 I-FP-CIT SPECT. We calculated the sensitivity and specificity of visual assessment alone, semi-quantitative assessment alone, and combined visual and semi-quantitative assessment for the diagnosis of dNDD. SBR was correlated with visual assessment. Some dNDD patients with a normal visual assessment had an abnormal SBR, and vice versa. There was no statistically significant difference between sensitivity of the diagnosis with visual assessment alone and semi-quantitative assessment alone (91.2 vs. 86.8%, respectively, p = 0.29). Combined visual and semi-quantitative assessment demonstrated superior sensitivity (96.7%) to visual assessment (p = 0.03) or semi-quantitative assessment (p = 0.003) alone with equal specificity. Visual and semi-quantitative assessments of 123 I-FP-CIT SPECT are helpful for the diagnosis of dNDD, and combined visual and semi-quantitative assessment shows superior sensitivity with equal specificity.

Objective, Quantitative, Data-Driven Assessment of Chemical Probes.

PubMed

Antolin, Albert A; Tym, Joseph E; Komianou, Angeliki; Collins, Ian; Workman, Paul; Al-Lazikani, Bissan

2018-02-15

Chemical probes are essential tools for understanding biological systems and for target validation, yet selecting probes for biomedical research is rarely based on objective assessment of all potential compounds. Here, we describe the Probe Miner: Chemical Probes Objective Assessment resource, capitalizing on the plethora of public medicinal chemistry data to empower quantitative, objective, data-driven evaluation of chemical probes. We assess >1.8 million compounds for their suitability as chemical tools against 2,220 human targets and dissect the biases and limitations encountered. Probe Miner represents a valuable resource to aid the identification of potential chemical probes, particularly when used alongside expert curation. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Transforming phylogenetic networks: Moving beyond tree space.

PubMed

Huber, Katharina T; Moulton, Vincent; Wu, Taoyang

2016-09-07

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of which is a generalization of the well-known nearest-neighbor interchange (NNI) operation on phylogenetic trees. We show that any unrooted phylogenetic network can be transformed into any other such network using only these operations. This generalizes the well-known fact that any phylogenetic tree can be transformed into any other such tree using only NNI operations. It also allows us to define a generalization of tree space and to define some new metrics on unrooted phylogenetic networks. To prove our main results, we employ some fascinating new connections between phylogenetic networks and cubic graphs that we have recently discovered. Our results should be useful in developing new strategies to search for optimal phylogenetic networks, a topic that has recently generated some interest in the literature, as well as for providing new ways to compare networks. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multiparametric Quantitative Ultrasound Imaging in Assessment of Chronic Kidney Disease.

PubMed

Gao, Jing; Perlman, Alan; Kalache, Safa; Berman, Nathaniel; Seshan, Surya; Salvatore, Steven; Smith, Lindsey; Wehrli, Natasha; Waldron, Levi; Kodali, Hanish; Chevalier, James

2017-11-01

To evaluate the value of multiparametric quantitative ultrasound imaging in assessing chronic kidney disease (CKD) using kidney biopsy pathologic findings as reference standards. We prospectively measured multiparametric quantitative ultrasound markers with grayscale, spectral Doppler, and acoustic radiation force impulse imaging in 25 patients with CKD before kidney biopsy and 10 healthy volunteers. Based on all pathologic (glomerulosclerosis, interstitial fibrosis/tubular atrophy, arteriosclerosis, and edema) scores, the patients with CKD were classified into mild (no grade 3 and <2 of grade 2) and moderate to severe (at least 2 of grade 2 or 1 of grade 3) CKD groups. Multiparametric quantitative ultrasound parameters included kidney length, cortical thickness, pixel intensity, parenchymal shear wave velocity, intrarenal artery peak systolic velocity (PSV), end-diastolic velocity (EDV), and resistive index. We tested the difference in quantitative ultrasound parameters among mild CKD, moderate to severe CKD, and healthy controls using analysis of variance, analyzed correlations of quantitative ultrasound parameters with pathologic scores and the estimated glomerular filtration rate (GFR) using Pearson correlation coefficients, and examined the diagnostic performance of quantitative ultrasound parameters in determining moderate CKD and an estimated GFR of less than 60 mL/min/1.73 m 2 using receiver operating characteristic curve analysis. There were significant differences in cortical thickness, pixel intensity, PSV, and EDV among the 3 groups (all P < .01). Among quantitative ultrasound parameters, the top areas under the receiver operating characteristic curves for PSV and EDV were 0.88 and 0.97, respectively, for determining pathologic moderate to severe CKD, and 0.76 and 0.86 for estimated GFR of less than 60 mL/min/1.73 m 2 . Moderate to good correlations were found for PSV, EDV, and pixel intensity with pathologic scores and estimated GFR. The

Tree phylogenetic diversity promotes host-parasitoid interactions.

PubMed

Staab, Michael; Bruelheide, Helge; Durka, Walter; Michalski, Stefan; Purschke, Oliver; Zhu, Chao-Dong; Klein, Alexandra-Maria

2016-07-13

Evidence from grassland experiments suggests that a plant community's phylogenetic diversity (PD) is a strong predictor of ecosystem processes, even stronger than species richness per se This has, however, never been extended to species-rich forests and host-parasitoid interactions. We used cavity-nesting Hymenoptera and their parasitoids collected in a subtropical forest as a model system to test whether hosts, parasitoids, and their interactions are influenced by tree PD and a comprehensive set of environmental variables, including tree species richness. Parasitism rate and parasitoid abundance were positively correlated with tree PD. All variables describing parasitoids decreased with elevation, and were, except parasitism rate, dependent on host abundance. Quantitative descriptors of host-parasitoid networks were independent of the environment. Our study indicates that host-parasitoid interactions in species-rich forests are related to the PD of the tree community, which influences parasitism rates through parasitoid abundance. We show that effects of tree community PD are much stronger than effects of tree species richness, can cascade to high trophic levels, and promote trophic interactions. As during habitat modification phylogenetic information is usually lost non-randomly, even species-rich habitats may not be able to continuously provide the ecosystem process parasitism if the evolutionarily most distinct plant lineages vanish. © 2016 The Author(s).

The Quantitative Reasoning for College Science (QuaRCS) Assessment: Emerging Themes from 5 Years of Data

NASA Astrophysics Data System (ADS)

Follette, Katherine; Dokter, Erin; Buxner, Sanlyn

2018-01-01

The Quantitative Reasoning for College Science (QuaRCS) Assessment is a validated assessment instrument that was designed to measure changes in students' quantitative reasoning skills, attitudes toward mathematics, and ability to accurately assess their own quantitative abilities. It has been administered to more than 5,000 students at a variety of institutions at the start and end of a semester of general education college science instruction. I will begin by briefly summarizing our published work surrounding validation of the instrument and identification of underlying attitudinal factors (composite variables identified via factor analysis) that predict 50% of the variation in students' scores on the assessment. I will then discuss more recent unpublished work, including: (1) Development and validation of an abbreviated version of the assessment (The QuaRCS Light), which results in marked improvements in students' ability to maintain a high effort level throughout the assessment and has broad implications for quantitative reasoning assessments in general, and (2) Our efforts to revise the attitudinal portion of the assessment to better assess math anxiety level, another key factor in student performance on numerical assessments.

Phylogenetic effective sample size.

PubMed

Bartoszek, Krzysztof

2016-10-21

In this paper I address the question-how large is a phylogenetic sample? I propose a definition of a phylogenetic effective sample size for Brownian motion and Ornstein-Uhlenbeck processes-the regression effective sample size. I discuss how mutual information can be used to define an effective sample size in the non-normal process case and compare these two definitions to an already present concept of effective sample size (the mean effective sample size). Through a simulation study I find that the AICc is robust if one corrects for the number of species or effective number of species. Lastly I discuss how the concept of the phylogenetic effective sample size can be useful for biodiversity quantification, identification of interesting clades and deciding on the importance of phylogenetic correlations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effectiveness of protected areas for vertebrates based on taxonomic and phylogenetic diversity.

PubMed

Quan, Qing; Che, Xianli; Wu, Yongjie; Wu, Yuchun; Zhang, Qiang; Zhang, Min; Zou, Fasheng

2018-04-01

Establishing protected areas is the primary goal and tool for preventing irreversible biodiversity loss. However, the effectiveness of protected areas that target specific species has been questioned for some time because targeting key species for conservation may impair the integral regional pool of species diversity and phylogenetic and functional diversity are seldom considered. We assessed the efficacy of protected areas in China for the conservation of phylogenetic diversity based on the ranges and phylogenies of 2279 terrestrial vertebrates. Phylogenetic and taxonomic diversity were strongly and positively correlated, and only 12.1-43.8% of priority conservation areas are currently protected. However, the patterns and coverage of phylogenetic diversity were affected when weighted by species richness. These results indicated that in China, protected areas targeting high species richness protected phylogenetic diversity well overall but failed to do so in some regions with more unique or threatened communities (e.g., coastal areas of eastern China, where severely threatened avian communities were less protected). Our results suggest that the current distribution of protected areas could be improved, although most protected areas protect both taxonomic and phylogenetic diversity. © 2017 Society for Conservation Biology.

A Format for Phylogenetic Placements

PubMed Central

Matsen, Frederick A.; Hoffman, Noah G.; Gallagher, Aaron; Stamatakis, Alexandros

2012-01-01

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g., short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format, which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement. PMID:22383988

A format for phylogenetic placements.

PubMed

Matsen, Frederick A; Hoffman, Noah G; Gallagher, Aaron; Stamatakis, Alexandros

2012-01-01

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g., short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format, which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.

Edge-related loss of tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest.

PubMed

Santos, Bráulio A; Arroyo-Rodríguez, Víctor; Moreno, Claudia E; Tabarelli, Marcelo

2010-09-08

Deforestation and forest fragmentation are known major causes of nonrandom extinction, but there is no information about their impact on the phylogenetic diversity of the remaining species assemblages. Using a large vegetation dataset from an old hyper-fragmented landscape in the Brazilian Atlantic rainforest we assess whether the local extirpation of tree species and functional impoverishment of tree assemblages reduce the phylogenetic diversity of the remaining tree assemblages. We detected a significant loss of tree phylogenetic diversity in forest edges, but not in core areas of small (<80 ha) forest fragments. This was attributed to a reduction of 11% in the average phylogenetic distance between any two randomly chosen individuals from forest edges; an increase of 17% in the average phylogenetic distance to closest non-conspecific relative for each individual in forest edges; and to the potential manifestation of late edge effects in the core areas of small forest remnants. We found no evidence supporting fragmentation-induced phylogenetic clustering or evenness. This could be explained by the low phylogenetic conservatism of key life-history traits corresponding to vulnerable species. Edge effects must be reduced to effectively protect tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest.

An integrated environmental modeling framework for performing quantitative microbial risk assessments

USDA-ARS?s Scientific Manuscript database

Standardized methods are often used to assess the likelihood of a human-health effect from exposure to a specified hazard, and inform opinions and decisions about risk management and communication. A Quantitative Microbial Risk Assessment (QMRA) is specifically adapted to detail potential human-heal...

General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters.

PubMed

Hadfield, J D; Nakagawa, S

2010-03-01

Although many of the statistical techniques used in comparative biology were originally developed in quantitative genetics, subsequent development of comparative techniques has progressed in relative isolation. Consequently, many of the new and planned developments in comparative analysis already have well-tested solutions in quantitative genetics. In this paper, we take three recent publications that develop phylogenetic meta-analysis, either implicitly or explicitly, and show how they can be considered as quantitative genetic models. We highlight some of the difficulties with the proposed solutions, and demonstrate that standard quantitative genetic theory and software offer solutions. We also show how results from Bayesian quantitative genetics can be used to create efficient Markov chain Monte Carlo algorithms for phylogenetic mixed models, thereby extending their generality to non-Gaussian data. Of particular utility is the development of multinomial models for analysing the evolution of discrete traits, and the development of multi-trait models in which traits can follow different distributions. Meta-analyses often include a nonrandom collection of species for which the full phylogenetic tree has only been partly resolved. Using missing data theory, we show how the presented models can be used to correct for nonrandom sampling and show how taxonomies and phylogenies can be combined to give a flexible framework with which to model dependence.

Hydrogen quantitative risk assessment workshop proceedings.

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

Groth, Katrina M.; Harris, Aaron P.

2013-09-01

The Quantitative Risk Assessment (QRA) Toolkit Introduction Workshop was held at Energetics on June 11-12. The workshop was co-hosted by Sandia National Laboratories (Sandia) and HySafe, the International Association for Hydrogen Safety. The objective of the workshop was twofold: (1) Present a hydrogen-specific methodology and toolkit (currently under development) for conducting QRA to support the development of codes and standards and safety assessments of hydrogen-fueled vehicles and fueling stations, and (2) Obtain feedback on the needs of early-stage users (hydrogen as well as potential leveraging for Compressed Natural Gas [CNG], and Liquefied Natural Gas [LNG]) and set priorities for %E2%80%9CVersionmore » 1%E2%80%9D of the toolkit in the context of the commercial evolution of hydrogen fuel cell electric vehicles (FCEV). The workshop consisted of an introduction and three technical sessions: Risk Informed Development and Approach; CNG/LNG Applications; and Introduction of a Hydrogen Specific QRA Toolkit.« less

The phylogenetic relationships of known mosquito (Diptera: Culicidae) mitogenomes.

PubMed

Chu, Hongliang; Li, Chunxiao; Guo, Xiaoxia; Zhang, Hengduan; Luo, Peng; Wu, Zhonghua; Wang, Gang; Zhao, Tongyan

2018-01-01

The known mosquito mitogenomes, containing a total of 34 species, which belong to five genera, were collected from GenBank, and the practicality and effectiveness of the variation in the complete mitochondrial DNA genome and portions of mitochondrial COI gene were assessed to reconstruct the phylogeny of mosquitoes. Phylogenetic trees were reconstructed on the basis of parsimony, maximum likelihood, and Bayesian (BI) methods. It is concluded that: (1) Both mitogenomes and COI gene support the monophly of following taxa: Subgenus Nyssorhynchus, Subgenus Cellia, Anopheles albitarsis complex, Anopheles gambiae complex, and Anopheles punctulatus group; (2) Genus Aedes is not monophyletic relative to Ochlerotatus vigilax; (3) The mitogenome results indicate a close relationship between Anopheles epiroticus and Anopheles gambiae complex, Anopheles dirus complex and Anopheles punctulatus group, respectively; (4) The Bayesian posterior probability (BPP) within phylogenetic tree reconstructed by mitogenomes is higher than COI tree. The results show that phylogenetic relationships reconstructed using the mitogenomes were more similar to those based on morphological data.

Molecular Phylogenetics: Concepts for a Newcomer.

PubMed

Ajawatanawong, Pravech

Molecular phylogenetics is the study of evolutionary relationships among organisms using molecular sequence data. The aim of this review is to introduce the important terminology and general concepts of tree reconstruction to biologists who lack a strong background in the field of molecular evolution. Some modern phylogenetic programs are easy to use because of their user-friendly interfaces, but understanding the phylogenetic algorithms and substitution models, which are based on advanced statistics, is still important for the analysis and interpretation without a guide. Briefly, there are five general steps in carrying out a phylogenetic analysis: (1) sequence data preparation, (2) sequence alignment, (3) choosing a phylogenetic reconstruction method, (4) identification of the best tree, and (5) evaluating the tree. Concepts in this review enable biologists to grasp the basic ideas behind phylogenetic analysis and also help provide a sound basis for discussions with expert phylogeneticists.

High-resolution phylogenetic microbial community profiling

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

Singer, Esther; Bushnell, Brian; Coleman-Derr, Devin

Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structuresmore » at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.« less

High-resolution phylogenetic microbial community profiling

DOE PAGES

Singer, Esther; Bushnell, Brian; Coleman-Derr, Devin; ...

2016-02-09

Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structuresmore » at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.« less

Assessment of phylogenetic relationship of rare plant species collected from Saudi Arabia using internal transcribed spacer sequences of nuclear ribosomal DNA.

PubMed

Al-Qurainy, F; Khan, S; Nadeem, M; Tarroum, M; Alaklabi, A

2013-03-11

The rare and endangered plants of any country are important genetic resources that often require urgent conservation measures. Assessment of phylogenetic relationships and evaluation of genetic diversity is very important prior to implementation of conservation strategies for saving rare and endangered plant species. We used internal transcribed spacer sequences of nuclear ribosomal DNA for the evaluation of sequence identity from the available taxa in the GenBank database by using the Basic Local Alignment Search Tool (BLAST). Two rare plant species viz, Heliotropium strigosum claded with H. pilosum (98% branch support) and Pancratium tortuosum claded with P. tenuifolium (61% branch support) clearly. However, some species, viz Scadoxus multiflorus, Commiphora myrrha and Senecio hadiensis showed close relationships with more than one species. We conclude that nuclear ribosomal internal transcribed spacer sequences are useful markers for phylogenetic study of these rare plant species in Saudi Arabia.

Encoding phylogenetic trees in terms of weighted quartets.

PubMed

Grünewald, Stefan; Huber, Katharina T; Moulton, Vincent; Semple, Charles

2008-04-01

One of the main problems in phylogenetics is to develop systematic methods for constructing evolutionary or phylogenetic trees. For a set of species X, an edge-weighted phylogenetic X-tree or phylogenetic tree is a (graph theoretical) tree with leaf set X and no degree 2 vertices, together with a map assigning a non-negative length to each edge of the tree. Within phylogenetics, several methods have been proposed for constructing such trees that work by trying to piece together quartet trees on X, i.e. phylogenetic trees each having four leaves in X. Hence, it is of interest to characterise when a collection of quartet trees corresponds to a (unique) phylogenetic tree. Recently, Dress and Erdös provided such a characterisation for binary phylogenetic trees, that is, phylogenetic trees all of whose internal vertices have degree 3. Here we provide a new characterisation for arbitrary phylogenetic trees.

Development and Assessment of Modules to Integrate Quantitative Skills in Introductory Biology Courses

ERIC Educational Resources Information Center

Hoffman, Kathleen; Leupen, Sarah; Dowell, Kathy; Kephart, Kerrie; Leips, Jeff

2016-01-01

Redesigning undergraduate biology courses to integrate quantitative reasoning and skill development is critical to prepare students for careers in modern medicine and scientific research. In this paper, we report on the development, implementation, and assessment of stand-alone modules that integrate quantitative reasoning into introductory…

An Assessment of Phylogenetic Tools for Analyzing the Interplay Between Interspecific Interactions and Phenotypic Evolution.

PubMed

Drury, J P; Grether, G F; Garland, T; Morlon, H

2018-05-01

Much ecological and evolutionary theory predicts that interspecific interactions often drive phenotypic diversification and that species phenotypes in turn influence species interactions. Several phylogenetic comparative methods have been developed to assess the importance of such processes in nature; however, the statistical properties of these methods have gone largely untested. Focusing mainly on scenarios of competition between closely-related species, we assess the performance of available comparative approaches for analyzing the interplay between interspecific interactions and species phenotypes. We find that many currently used statistical methods often fail to detect the impact of interspecific interactions on trait evolution, that sister-taxa analyses are particularly unreliable in general, and that recently developed process-based models have more satisfactory statistical properties. Methods for detecting predictors of species interactions are generally more reliable than methods for detecting character displacement. In weighing the strengths and weaknesses of different approaches, we hope to provide a clear guide for empiricists testing hypotheses about the reciprocal effect of interspecific interactions and species phenotypes and to inspire further development of process-based models.

Assessing the danger of self-sustained HIV epidemics in heterosexuals by population based phylogenetic cluster analysis

PubMed Central

Turk, Teja; Bachmann, Nadine; Kadelka, Claus; Böni, Jürg; Yerly, Sabine; Aubert, Vincent; Klimkait, Thomas; Battegay, Manuel; Bernasconi, Enos; Calmy, Alexandra; Cavassini, Matthias; Furrer, Hansjakob; Hoffmann, Matthias; Aubert, V; Battegay, M; Bernasconi, E; Böni, J; Braun, DL; Bucher, HC; Calmy, A; Cavassini, M; Ciuffi, A; Dollenmaier, G; Egger, M; Elzi, L; Fehr, J; Fellay, J; Furrer, H; Fux, CA; Günthard, HF; Haerry, D; Hasse, B; Hirsch, HH; Hoffmann, M; Hösli, I; Kahlert, C; Kaiser, L; Keiser, O; Klimkait, T; Kouyos, RD; Kovari, H; Ledergerber, B; Martinetti, G; Martinez de Tejada, B; Marzolini, C; Metzner, KJ; Müller, N; Nicca, D; Pantaleo, G; Paioni, P; Rauch, A; Rudin, C; Scherrer, AU; Schmid, P; Speck, R; Stöckle, M; Tarr, P; Trkola, A; Vernazza, P; Wandeler, G; Weber, R; Yerly, S

2017-01-01

Assessing the danger of transition of HIV transmission from a concentrated to a generalized epidemic is of major importance for public health. In this study, we develop a phylogeny-based statistical approach to address this question. As a case study, we use this to investigate the trends and determinants of HIV transmission among Swiss heterosexuals. We extract the corresponding transmission clusters from a phylogenetic tree. To capture the incomplete sampling, the delayed introduction of imported infections to Switzerland, and potential factors associated with basic reproductive number R0, we extend the branching process model to infer transmission parameters. Overall, the R0 is estimated to be 0.44 (95%-confidence interval 0.42—0.46) and it is decreasing by 11% per 10 years (4%—17%). Our findings indicate rather diminishing HIV transmission among Swiss heterosexuals far below the epidemic threshold. Generally, our approach allows to assess the danger of self-sustained epidemics from any viral sequence data. PMID:28895527

Inferring 'weak spots' in phylogenetic trees: application to mosasauroid nomenclature.

PubMed

Madzia, Daniel; Cau, Andrea

2017-01-01

Mosasauroid squamates represented the apex predators within the Late Cretaceous marine and occasionally also freshwater ecosystems. Proper understanding of the origin of their ecological adaptations or paleobiogeographic dispersals requires adequate knowledge of their phylogeny. The studies assessing the position of mosasauroids on the squamate evolutionary tree and their origins have long given conflicting results. The phylogenetic relationships within Mosasauroidea, however, have experienced only little changes throughout the last decades. Considering the substantial improvements in the development of phylogenetic methodology that have undergone in recent years, resulting, among others, in numerous alterations in the phylogenetic hypotheses of other fossil amniotes, we test the robustness in our understanding of mosasauroid beginnings and their evolutionary history. We re-examined a data set that results from modifications assembled in the course of the last 20 years and performed multiple parsimony analyses and Bayesian tip-dating analysis. Following the inferred topologies and the 'weak spots' in the phylogeny of mosasauroids, we revise the nomenclature of the 'traditionally' recognized mosasauroid clades, to acknowledge the overall weakness among branches and the alternative topologies suggested previously, and discuss several factors that might have an impact on the differing phylogenetic hypotheses and their statistical support.

Tree-Based Unrooted Phylogenetic Networks.

PubMed

Francis, A; Huber, K T; Moulton, V

2018-02-01

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph in which every vertex has degree 1 or 3 and whose leaf set is X. It is called a phylogenetic tree if the underlying graph is a tree. In this paper we consider properties of tree-based networks, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hybridization which are important factors in the evolution of many organisms.

Plant traits determine the phylogenetic structure of arbuscular mycorrhizal fungal communities.

PubMed

López-García, Álvaro; Varela-Cervero, Sara; Vasar, Martti; Öpik, Maarja; Barea, José M; Azcón-Aguilar, Concepción

2017-12-01

Functional diversity in ecosystems has traditionally been studied using aboveground plant traits. Despite the known effect of plant traits on the microbial community composition, their effects on the microbial functional diversity are only starting to be assessed. In this study, the phylogenetic structure of arbuscular mycorrhizal (AM) fungal communities associated with plant species differing in life cycle and growth form, that is, plant life forms, was determined to unravel the effect of plant traits on the functional diversity of this fungal group. The results of the 454 pyrosequencing showed that the AM fungal community composition differed across plant life forms and this effect was dependent on the soil collection date. Plants with ruderal characteristics tended to associate with phylogenetically clustered AM fungal communities. By contrast, plants with resource-conservative traits associated with phylogenetically overdispersed AM fungal communities. Additionally, the soil collected in different seasons yielded AM fungal communities with different phylogenetic dispersion. In summary, we found that the phylogenetic structure, and hence the functional diversity, of AM fungal communities is dependent on plant traits. This finding adds value to the use of plant traits for the evaluation of belowground ecosystem diversity, functions and processes. © 2017 John Wiley & Sons Ltd.

The dawn of open access to phylogenetic data.

PubMed

Magee, Andrew F; May, Michael R; Moore, Brian R

2014-01-01

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation--extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for [Formula: see text] of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Importantly, our survey spans recent policy initiatives and infrastructural changes; our analyses indicate that the positive impact of these community initiatives has been both dramatic and immediate. Although the results of our study indicate that the situation is dire, our findings also reveal tremendous recent progress in the sharing and preservation of phylogenetic data.

Nodal distances for rooted phylogenetic trees.

PubMed

Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente, Gabriel

2010-08-01

Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. For rooted phylogenetic trees, however, these vectors can only separate non-weighted binary trees, and therefore these dissimilarity measures are metrics only on this class of rooted phylogenetic trees. In this paper we overcome this problem, by splitting in a suitable way each path length between two taxa into two lengths. We prove that the resulting splitted path lengths matrices single out arbitrary rooted phylogenetic trees with nested taxa and arcs weighted in the set of positive real numbers. This allows the definition of metrics on this general class of rooted phylogenetic trees by comparing these matrices through metrics in spaces M(n)(R) of real-valued n x n matrices. We conclude this paper by establishing some basic facts about the metrics for non-weighted phylogenetic trees defined in this way using L(p) metrics on M(n)(R), with p [epsilon] R(>0).

Marine turtle mitogenome phylogenetics and evolution.

PubMed

Duchene, Sebastián; Frey, Amy; Alfaro-Núñez, Alonzo; Dutton, Peter H; Thomas P Gilbert, M; Morin, Phillip A

2012-10-01

The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1 Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution. Published by Elsevier Inc.

Phylogenetically resolving epidemiologic linkage

PubMed Central

Romero-Severson, Ethan O.; Bulla, Ingo; Leitner, Thomas

2016-01-01

Although the use of phylogenetic trees in epidemiological investigations has become commonplace, their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the true transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals’ HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. We confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results. PMID:26903617

Genetic toxicology at the crossroads-from qualitative hazard evaluation to quantitative risk assessment.

PubMed

White, Paul A; Johnson, George E

2016-05-01

Applied genetic toxicology is undergoing a transition from qualitative hazard identification to quantitative dose-response analysis and risk assessment. To facilitate this change, the Health and Environmental Sciences Institute (HESI) Genetic Toxicology Technical Committee (GTTC) sponsored a workshop held in Lancaster, UK on July 10-11, 2014. The event included invited speakers from several institutions and the contents was divided into three themes-1: Point-of-departure Metrics for Quantitative Dose-Response Analysis in Genetic Toxicology; 2: Measurement and Estimation of Exposures for Better Extrapolation to Humans and 3: The Use of Quantitative Approaches in Genetic Toxicology for human health risk assessment (HHRA). A host of pertinent issues were discussed relating to the use of in vitro and in vivo dose-response data, the development of methods for in vitro to in vivo extrapolation and approaches to use in vivo dose-response data to determine human exposure limits for regulatory evaluations and decision-making. This Special Issue, which was inspired by the workshop, contains a series of papers that collectively address topics related to the aforementioned themes. The Issue includes contributions that collectively evaluate, describe and discuss in silico, in vitro, in vivo and statistical approaches that are facilitating the shift from qualitative hazard evaluation to quantitative risk assessment. The use and application of the benchmark dose approach was a central theme in many of the workshop presentations and discussions, and the Special Issue includes several contributions that outline novel applications for the analysis and interpretation of genetic toxicity data. Although the contents of the Special Issue constitutes an important step towards the adoption of quantitative methods for regulatory assessment of genetic toxicity, formal acceptance of quantitative methods for HHRA and regulatory decision-making will require consensus regarding the

Preschool Temperament Assessment: A Quantitative Assessment of the Validity of Behavioral Style Questionnaire Data

ERIC Educational Resources Information Center

Huelsman, Timothy J.; Gagnon, Sandra Glover; Kidder-Ashley, Pamela; Griggs, Marissa Swaim

2014-01-01

Research Findings: Child temperament is an important construct, but its measurement has been marked by a number of weaknesses that have diminished the frequency with which it is assessed in practice. We address this problem by presenting the results of a quantitative construct validation study. We calculated validity indices by hypothesizing the…

SUNPLIN: simulation with uncertainty for phylogenetic investigations.

PubMed

Martins, Wellington S; Carmo, Welton C; Longo, Humberto J; Rosa, Thierson C; Rangel, Thiago F

2013-11-15

Phylogenetic comparative analyses usually rely on a single consensus phylogenetic tree in order to study evolutionary processes. However, most phylogenetic trees are incomplete with regard to species sampling, which may critically compromise analyses. Some approaches have been proposed to integrate non-molecular phylogenetic information into incomplete molecular phylogenies. An expanded tree approach consists of adding missing species to random locations within their clade. The information contained in the topology of the resulting expanded trees can be captured by the pairwise phylogenetic distance between species and stored in a matrix for further statistical analysis. Thus, the random expansion and processing of multiple phylogenetic trees can be used to estimate the phylogenetic uncertainty through a simulation procedure. Because of the computational burden required, unless this procedure is efficiently implemented, the analyses are of limited applicability. In this paper, we present efficient algorithms and implementations for randomly expanding and processing phylogenetic trees so that simulations involved in comparative phylogenetic analysis with uncertainty can be conducted in a reasonable time. We propose algorithms for both randomly expanding trees and calculating distance matrices. We made available the source code, which was written in the C++ language. The code may be used as a standalone program or as a shared object in the R system. The software can also be used as a web service through the link: http://purl.oclc.org/NET/sunplin/. We compare our implementations to similar solutions and show that significant performance gains can be obtained. Our results open up the possibility of accounting for phylogenetic uncertainty in evolutionary and ecological analyses of large datasets.

On Tree-Based Phylogenetic Networks.

PubMed

Zhang, Louxin

2016-07-01

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of taxa. This answers two problems posted by Francis and Steel recently. A byproduct is a computer program for generating random binary phylogenetic networks under the uniform distribution model.

76 FR 19311 - Update of the 2003 Interagency Quantitative Assessment of the Relative Risk to Public Health From...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-07

... the 2003 Interagency Quantitative Assessment of the Relative Risk to Public Health From Foodborne... quantitative targets established in ``Healthy People 2010.'' In 2005, FoodNet data showed 0.30 L. monocytogenes... 4). In 2003, FDA and FSIS published a quantitative assessment of the relative risk to public health...

Patterns of forest phylogenetic community structure across the United States and their possible forest health implications

Treesearch

Kevin M. Potter; Frank H. Koch

2014-01-01

The analysis of phylogenetic relationships among co-occurring tree species offers insights into the ecological organization of forest communities from an evolutionary perspective and, when employed regionally across thousands of plots, can assist in forest health assessment. Phylogenetic clustering of species, when species are more closely related than expected by...

Functional & phylogenetic diversity of copepod communities

NASA Astrophysics Data System (ADS)

Benedetti, F.; Ayata, S. D.; Blanco-Bercial, L.; Cornils, A.; Guilhaumon, F.

2016-02-01

The diversity of natural communities is classically estimated through species identification (taxonomic diversity) but can also be estimated from the ecological functions performed by the species (functional diversity), or from the phylogenetic relationships among them (phylogenetic diversity). Estimating functional diversity requires the definition of specific functional traits, i.e., phenotypic characteristics that impact fitness and are relevant to ecosystem functioning. Estimating phylogenetic diversity requires the description of phylogenetic relationships, for instance by using molecular tools. In the present study, we focused on the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. First, we implemented a specific trait database for the most commonly-sampled and abundant copepod species of the Mediterranean Sea. Our database includes 191 species, described by seven traits encompassing diverse ecological functions: minimal and maximal body length, trophic group, feeding type, spawning strategy, diel vertical migration and vertical habitat. Clustering analysis in the functional trait space revealed that Mediterranean copepods can be gathered into groups that have different ecological roles. Second, we reconstructed a phylogenetic tree using the available sequences of 18S rRNA. Our tree included 154 of the analyzed Mediterranean copepod species. We used these two datasets to describe the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. The replacement component (turn-over) and the species richness difference component (nestedness) of the beta diversity indices were identified. Finally, by comparing various and complementary aspects of plankton diversity (taxonomic, functional, and phylogenetic diversity) we were able to gain a better understanding of the relationships among the zooplankton community, biodiversity, ecosystem function, and environmental forcing.

treespace: Statistical exploration of landscapes of phylogenetic trees.

PubMed

Jombart, Thibaut; Kendall, Michelle; Almagro-Garcia, Jacob; Colijn, Caroline

2017-11-01

The increasing availability of large genomic data sets as well as the advent of Bayesian phylogenetics facilitates the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect meaningful biological processes as well as relevant statistical uncertainty, both of which can yield valuable insights in evolutionary studies. We introduce a new tool for investigating phylogenetic incongruence through the exploration of phylogenetic tree landscapes. Our approach, implemented in the R package treespace, combines tree metrics and multivariate analysis to provide low-dimensional representations of the topological variability in a set of trees, which can be used for identifying clusters of similar trees and group-specific consensus phylogenies. treespace also provides a user-friendly web interface for interactive data analysis and is integrated alongside existing standards for phylogenetics. It fills a gap in the current phylogenetics toolbox in R and will facilitate the investigation of phylogenetic results. © 2017 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

SUNPLIN: Simulation with Uncertainty for Phylogenetic Investigations

PubMed Central

2013-01-01

Background Phylogenetic comparative analyses usually rely on a single consensus phylogenetic tree in order to study evolutionary processes. However, most phylogenetic trees are incomplete with regard to species sampling, which may critically compromise analyses. Some approaches have been proposed to integrate non-molecular phylogenetic information into incomplete molecular phylogenies. An expanded tree approach consists of adding missing species to random locations within their clade. The information contained in the topology of the resulting expanded trees can be captured by the pairwise phylogenetic distance between species and stored in a matrix for further statistical analysis. Thus, the random expansion and processing of multiple phylogenetic trees can be used to estimate the phylogenetic uncertainty through a simulation procedure. Because of the computational burden required, unless this procedure is efficiently implemented, the analyses are of limited applicability. Results In this paper, we present efficient algorithms and implementations for randomly expanding and processing phylogenetic trees so that simulations involved in comparative phylogenetic analysis with uncertainty can be conducted in a reasonable time. We propose algorithms for both randomly expanding trees and calculating distance matrices. We made available the source code, which was written in the C++ language. The code may be used as a standalone program or as a shared object in the R system. The software can also be used as a web service through the link: http://purl.oclc.org/NET/sunplin/. Conclusion We compare our implementations to similar solutions and show that significant performance gains can be obtained. Our results open up the possibility of accounting for phylogenetic uncertainty in evolutionary and ecological analyses of large datasets. PMID:24229408

Status and future of Quantitative Microbiological Risk Assessment in China

PubMed Central

Dong, Q.L.; Barker, G.C.; Gorris, L.G.M.; Tian, M.S.; Song, X.Y.; Malakar, P.K.

2015-01-01

Since the implementation of the Food Safety Law of the People's Republic of China in 2009 use of Quantitative Microbiological Risk Assessment (QMRA) has increased. QMRA is used to assess the risk posed to consumers by pathogenic bacteria which cause the majority of foodborne outbreaks in China. This review analyses the progress of QMRA research in China from 2000 to 2013 and discusses 3 possible improvements for the future. These improvements include planning and scoping to initiate QMRA, effectiveness of microbial risk assessment utility for risk management decision making, and application of QMRA to establish appropriate Food Safety Objectives. PMID:26089594

Phylogenetically resolving epidemiologic linkage

DOE PAGES

Romero-Severson, Ethan O.; Bulla, Ingo; Leitner, Thomas

2016-02-22

The use of phylogenetic trees in epidemiological investigations has become commonplace, but their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the truemore » transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals’ HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. Moreover, we confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results.« less

Spatial patterns of phylogenetic diversity.

PubMed

Morlon, Hélène; Schwilk, Dylan W; Bryant, Jessica A; Marquet, Pablo A; Rebelo, Anthony G; Tauss, Catherine; Bohannan, Brendan J M; Green, Jessica L

2011-02-01

Ecologists and conservation biologists have historically used species-area and distance-decay relationships as tools to predict the spatial distribution of biodiversity and the impact of habitat loss on biodiversity. These tools treat each species as evolutionarily equivalent, yet the importance of species' evolutionary history in their ecology and conservation is becoming increasingly evident. Here, we provide theoretical predictions for phylogenetic analogues of the species-area and distance-decay relationships. We use a random model of community assembly and a spatially explicit flora dataset collected in four Mediterranean-type regions to provide theoretical predictions for the increase in phylogenetic diversity - the total phylogenetic branch-length separating a set of species - with increasing area and the decay in phylogenetic similarity with geographic separation. These developments may ultimately provide insights into the evolution and assembly of biological communities, and guide the selection of protected areas. © 2010 Blackwell Publishing Ltd/CNRS.

Multivariate Phylogenetic Comparative Methods: Evaluations, Comparisons, and Recommendations.

PubMed

Adams, Dean C; Collyer, Michael L

2018-01-01

pairwise composite likelihood methods should be avoided, whereas algebraic generalizations of the phylogenetic comparative toolkit provide a useful means of assessing macroevolutionary patterns in multivariate data. Finally, we discuss areas in which multivariate phylogenetic comparative methods are still in need of future development; namely highly multivariate Ornstein-Uhlenbeck models and approaches for multivariate evolutionary model comparisons. © The Author(s) 2017. Published by Oxford University Press on behalf of the Systematic Biology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Comparison of clinical semi-quantitative assessment of muscle fat infiltration with quantitative assessment using chemical shift-based water/fat separation in MR studies of the calf of post-menopausal women.

PubMed

Alizai, Hamza; Nardo, Lorenzo; Karampinos, Dimitrios C; Joseph, Gabby B; Yap, Samuel P; Baum, Thomas; Krug, Roland; Majumdar, Sharmila; Link, Thomas M

2012-07-01

The goal of this study was to compare the semi-quantitative Goutallier classification for fat infiltration with quantitative fat-fraction derived from a magnetic resonance imaging (MRI) chemical shift-based water/fat separation technique. Sixty-two women (age 61 ± 6 years), 27 of whom had diabetes, underwent MRI of the calf using a T1-weighted fast spin-echo sequence and a six-echo spoiled gradient-echo sequence at 3 T. Water/fat images and fat fraction maps were reconstructed using the IDEAL algorithm with T2* correction and a multi-peak model for the fat spectrum. Two radiologists scored fat infiltration on the T1-weighted images using the Goutallier classification in six muscle compartments. Spearman correlations between the Goutallier grades and the fat fraction were calculated; in addition, intra-observer and inter-observer agreement were calculated. A significant correlation between the clinical grading and the fat fraction values was found for all muscle compartments (P < 0.0001, R values ranging from 0.79 to 0.88). Goutallier grades 0-4 had a fat fraction ranging from 3.5 to 19%. Intra-observer and inter-observer agreement values of 0.83 and 0.81 were calculated for the semi-quantitative grading. Semi-quantitative grading of intramuscular fat and quantitative fat fraction were significantly correlated and both techniques had excellent reproducibility. However, the clinical grading was found to overestimate muscle fat. Fat infiltration of muscle commonly occurs in many metabolic and neuromuscular diseases. • Image-based semi-quantitative classifications for assessing fat infiltration are not well validated. • Quantitative MRI techniques provide an accurate assessment of muscle fat.

Phylogenetic overdispersion of plant species in southern Brazilian savannas.

PubMed

Silva, I A; Batalha, M A

2009-08-01

Ecological communities are the result of not only present ecological processes, such as competition among species and environmental filtering, but also past and continuing evolutionary processes. Based on these assumptions, we may infer mechanisms of contemporary coexistence from the phylogenetic relationships of the species in a community. We studied the phylogenetic structure of plant communities in four cerrado sites, in southeastern Brazil. We calculated two raw phylogenetic distances among the species sampled. We estimated the phylogenetic structure by comparing the observed phylogenetic distances to the distribution of phylogenetic distances in null communities. We obtained null communities by randomizing the phylogenetic relationships of the regional pool of species. We found a phylogenetic overdispersion of the cerrado species. Phylogenetic overdispersion has several explanations, depending on the phylogenetic history of traits and contemporary ecological interactions. However, based on coexistence models between grasses and trees, density-dependent ecological forces, and the evolutionary history of the cerrado flora, we argue that the phylogenetic overdispersion of cerrado species is predominantly due to competitive interactions, herbivores and pathogen attacks, and ecological speciation. Future studies will need to include information on the phylogenetic history of plant traits.

Short Course Introduction to Quantitative Mineral Resource Assessments

USGS Publications Warehouse

Singer, Donald A.

2007-01-01

This is an abbreviated text supplementing the content of three sets of slides used in a short course that has been presented by the author at several workshops. The slides should be viewed in the order of (1) Introduction and models, (2) Delineation and estimation, and (3) Combining estimates and summary. References cited in the slides are listed at the end of this text. The purpose of the three-part form of mineral resource assessments discussed in the accompanying slides is to make unbiased quantitative assessments in a format needed in decision-support systems so that consequences of alternative courses of action can be examined. The three-part form of mineral resource assessments was developed to assist policy makers evaluate the consequences of alternative courses of action with respect to land use and mineral-resource development. The audience for three-part assessments is a governmental or industrial policy maker, a manager of exploration, a planner of regional development, or similar decision-maker. Some of the tools and models presented here will be useful for selection of exploration sites, but that is a side benefit, not the goal. To provide unbiased information, we recommend the three-part form of mineral resource assessments where general locations of undiscovered deposits are delineated from a deposit type's geologic setting, frequency distributions of tonnages and grades of well-explored deposits serve as models of grades and tonnages of undiscovered deposits, and number of undiscovered deposits are estimated probabilistically by type. The internally consistent descriptive, grade and tonnage, deposit density, and economic models used in the design of the three-part form of assessments reduce the chances of biased estimates of the undiscovered resources. What and why quantitative resource assessments: The kind of assessment recommended here is founded in decision analysis in order to provide a framework for making decisions concerning mineral

Different relationships between temporal phylogenetic turnover and phylogenetic similarity and in two forests were detected by a new null model.

PubMed

Huang, Jian-Xiong; Zhang, Jian; Shen, Yong; Lian, Ju-yu; Cao, Hong-lin; Ye, Wan-hui; Wu, Lin-fang; Bin, Yue

2014-01-01

Ecologists have been monitoring community dynamics with the purpose of understanding the rates and causes of community change. However, there is a lack of monitoring of community dynamics from the perspective of phylogeny. We attempted to understand temporal phylogenetic turnover in a 50 ha tropical forest (Barro Colorado Island, BCI) and a 20 ha subtropical forest (Dinghushan in southern China, DHS). To obtain temporal phylogenetic turnover under random conditions, two null models were used. The first shuffled names of species that are widely used in community phylogenetic analyses. The second simulated demographic processes with careful consideration on the variation in dispersal ability among species and the variations in mortality both among species and among size classes. With the two models, we tested the relationships between temporal phylogenetic turnover and phylogenetic similarity at different spatial scales in the two forests. Results were more consistent with previous findings using the second null model suggesting that the second null model is more appropriate for our purposes. With the second null model, a significantly positive relationship was detected between phylogenetic turnover and phylogenetic similarity in BCI at a 10 m×10 m scale, potentially indicating phylogenetic density dependence. This relationship in DHS was significantly negative at three of five spatial scales. This could indicate abiotic filtering processes for community assembly. Using variation partitioning, we found phylogenetic similarity contributed to variation in temporal phylogenetic turnover in the DHS plot but not in BCI plot. The mechanisms for community assembly in BCI and DHS vary from phylogenetic perspective. Only the second null model detected this difference indicating the importance of choosing a proper null model.

Undergraduate Students’ Difficulties in Reading and Constructing Phylogenetic Tree

NASA Astrophysics Data System (ADS)

Sa'adah, S.; Tapilouw, F. S.; Hidayat, T.

2017-02-01

Representation is a very important communication tool to communicate scientific concepts. Biologists produce phylogenetic representation to express their understanding of evolutionary relationships. The phylogenetic tree is visual representation depict a hypothesis about the evolutionary relationship and widely used in the biological sciences. Phylogenetic tree currently growing for many disciplines in biology. Consequently, learning about phylogenetic tree become an important part of biological education and an interesting area for biology education research. However, research showed many students often struggle with interpreting the information that phylogenetic trees depict. The purpose of this study was to investigate undergraduate students’ difficulties in reading and constructing a phylogenetic tree. The method of this study is a descriptive method. In this study, we used questionnaires, interviews, multiple choice and open-ended questions, reflective journals and observations. The findings showed students experiencing difficulties, especially in constructing a phylogenetic tree. The students’ responds indicated that main reasons for difficulties in constructing a phylogenetic tree are difficult to placing taxa in a phylogenetic tree based on the data provided so that the phylogenetic tree constructed does not describe the actual evolutionary relationship (incorrect relatedness). Students also have difficulties in determining the sister group, character synapomorphy, autapomorphy from data provided (character table) and comparing among phylogenetic tree. According to them building the phylogenetic tree is more difficult than reading the phylogenetic tree. Finding this studies provide information to undergraduate instructor and students to overcome learning difficulties of reading and constructing phylogenetic tree.

Constructing phylogenetic trees using interacting pathways.

PubMed

Wan, Peng; Che, Dongsheng

2013-01-01

Phylogenetic trees are used to represent evolutionary relationships among biological species or organisms. The construction of phylogenetic trees is based on the similarities or differences of their physical or genetic features. Traditional approaches of constructing phylogenetic trees mainly focus on physical features. The recent advancement of high-throughput technologies has led to accumulation of huge amounts of biological data, which in turn changed the way of biological studies in various aspects. In this paper, we report our approach of building phylogenetic trees using the information of interacting pathways. We have applied hierarchical clustering on two domains of organisms-eukaryotes and prokaryotes. Our preliminary results have shown the effectiveness of using the interacting pathways in revealing evolutionary relationships.

The Evolutionary Ecology of Plant Disease: A Phylogenetic Perspective.

PubMed

Gilbert, Gregory S; Parker, Ingrid M

2016-08-04

An explicit phylogenetic perspective provides useful tools for phytopathology and plant disease ecology because the traits of both plants and microbes are shaped by their evolutionary histories. We present brief primers on phylogenetic signal and the analytical tools of phylogenetic ecology. We review the literature and find abundant evidence of phylogenetic signal in pathogens and plants for most traits involved in disease interactions. Plant nonhost resistance mechanisms and pathogen housekeeping functions are conserved at deeper phylogenetic levels, whereas molecular traits associated with rapid coevolutionary dynamics are more labile at branch tips. Horizontal gene transfer disrupts the phylogenetic signal for some microbial traits. Emergent traits, such as host range and disease severity, show clear phylogenetic signals. Therefore pathogen spread and disease impact are influenced by the phylogenetic structure of host assemblages. Phylogenetically rare species escape disease pressure. Phylogenetic tools could be used to develop predictive tools for phytosanitary risk analysis and reduce disease pressure in multispecies cropping systems.

Inferring Phylogenetic Networks Using PhyloNet.

PubMed

Wen, Dingqiao; Yu, Yun; Zhu, Jiafan; Nakhleh, Luay

2018-07-01

PhyloNet was released in 2008 as a software package for representing and analyzing phylogenetic networks. At the time of its release, the main functionalities in PhyloNet consisted of measures for comparing network topologies and a single heuristic for reconciling gene trees with a species tree. Since then, PhyloNet has grown significantly. The software package now includes a wide array of methods for inferring phylogenetic networks from data sets of unlinked loci while accounting for both reticulation (e.g., hybridization) and incomplete lineage sorting. In particular, PhyloNet now allows for maximum parsimony, maximum likelihood, and Bayesian inference of phylogenetic networks from gene tree estimates. Furthermore, Bayesian inference directly from sequence data (sequence alignments or biallelic markers) is implemented. Maximum parsimony is based on an extension of the "minimizing deep coalescences" criterion to phylogenetic networks, whereas maximum likelihood and Bayesian inference are based on the multispecies network coalescent. All methods allow for multiple individuals per species. As computing the likelihood of a phylogenetic network is computationally hard, PhyloNet allows for evaluation and inference of networks using a pseudolikelihood measure. PhyloNet summarizes the results of the various analyzes and generates phylogenetic networks in the extended Newick format that is readily viewable by existing visualization software.

Improving the Linkages between Air Pollution Epidemiology and Quantitative Risk Assessment

PubMed Central

Bell, Michelle L.; Walker, Katy; Hubbell, Bryan

2011-01-01

Background: Air pollution epidemiology plays an integral role in both identifying the hazards of air pollution as well as supplying the risk coefficients that are used in quantitative risk assessments. Evidence from both epidemiology and risk assessments has historically supported critical environmental policy decisions. The extent to which risk assessors can properly specify a quantitative risk assessment and characterize key sources of uncertainty depends in part on the availability, and clarity, of data and assumptions in the epidemiological studies. Objectives: We discuss the interests shared by air pollution epidemiology and risk assessment communities in ensuring that the findings of epidemiological studies are appropriately characterized and applied correctly in risk assessments. We highlight the key input parameters for risk assessments and consider how modest changes in the characterization of these data might enable more accurate risk assessments that better represent the findings of epidemiological studies. Discussion: We argue that more complete information regarding the methodological choices and input data used in epidemiological studies would support more accurate risk assessments—to the benefit of both disciplines. In particular, we suggest including additional details regarding air quality, demographic, and health data, as well as certain types of data-rich graphics. Conclusions: Relatively modest changes to the data reported in epidemiological studies will improve the quality of risk assessments and help prevent the misinterpretation and mischaracterization of the results of epidemiological studies. Such changes may also benefit epidemiologists undertaking meta-analyses. We suggest workshops as a way to improve the dialogue between the two communities. PMID:21816702

Phylogenetic classification of bony fishes.

PubMed

Betancur-R, Ricardo; Wiley, Edward O; Arratia, Gloria; Acero, Arturo; Bailly, Nicolas; Miya, Masaki; Lecointre, Guillaume; Ortí, Guillermo

2017-07-06

Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny ( www.deepfin.org ). We here update the first version of that classification by incorporating the most recent phylogenetic results. The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified. This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution

Assessing covariate balance when using the generalized propensity score with quantitative or continuous exposures.

PubMed

Austin, Peter C

2018-01-01

Propensity score methods are increasingly being used to estimate the effects of treatments and exposures when using observational data. The propensity score was initially developed for use with binary exposures (e.g., active treatment vs. control). The generalized propensity score is an extension of the propensity score for use with quantitative exposures (e.g., dose or quantity of medication, income, years of education). A crucial component of any propensity score analysis is that of balance assessment. This entails assessing the degree to which conditioning on the propensity score (via matching, weighting, or stratification) has balanced measured baseline covariates between exposure groups. Methods for balance assessment have been well described and are frequently implemented when using the propensity score with binary exposures. However, there is a paucity of information on how to assess baseline covariate balance when using the generalized propensity score. We describe how methods based on the standardized difference can be adapted for use with quantitative exposures when using the generalized propensity score. We also describe a method based on assessing the correlation between the quantitative exposure and each covariate in the sample when weighted using generalized propensity score -based weights. We conducted a series of Monte Carlo simulations to evaluate the performance of these methods. We also compared two different methods of estimating the generalized propensity score: ordinary least squared regression and the covariate balancing propensity score method. We illustrate the application of these methods using data on patients hospitalized with a heart attack with the quantitative exposure being creatinine level.

A Framework for General Education Assessment: Assessing Information Literacy and Quantitative Literacy with ePortfolios

ERIC Educational Resources Information Center

Hubert, David A.; Lewis, Kati J.

2014-01-01

This essay presents the findings of an authentic and holistic assessment, using a random sample of one hundred student General Education ePortfolios, of two of Salt Lake Community College's (SLCC) college-wide learning outcomes: quantitative literacy (QL) and information literacy (IL). Performed by four faculty from biology, humanities, and…

Computerized assessment of communication for cognitive stimulation for people with cognitive decline using spectral-distortion measures and phylogenetic inference.

PubMed

Pham, Tuan D; Oyama-Higa, Mayumi; Truong, Cong-Thang; Okamoto, Kazushi; Futaba, Terufumi; Kanemoto, Shigeru; Sugiyama, Masahide; Lampe, Lisa

2015-01-01

Therapeutic communication and interpersonal relationships in care homes can help people to improve their mental wellbeing. Assessment of the efficacy of these dynamic and complex processes are necessary for psychosocial planning and management. This paper presents a pilot application of photoplethysmography in synchronized physiological measurements of communications between the care-giver and people with dementia. Signal-based evaluations of the therapy can be carried out using the measures of spectral distortion and the inference of phylogenetic trees. The proposed computational models can be of assistance and cost-effectiveness in caring for and monitoring people with cognitive decline.

Computerized Assessment of Communication for Cognitive Stimulation for People with Cognitive Decline Using Spectral-Distortion Measures and Phylogenetic Inference

PubMed Central

Pham, Tuan D.; Oyama-Higa, Mayumi; Truong, Cong-Thang; Okamoto, Kazushi; Futaba, Terufumi; Kanemoto, Shigeru; Sugiyama, Masahide; Lampe, Lisa

2015-01-01

Therapeutic communication and interpersonal relationships in care homes can help people to improve their mental wellbeing. Assessment of the efficacy of these dynamic and complex processes are necessary for psychosocial planning and management. This paper presents a pilot application of photoplethysmography in synchronized physiological measurements of communications between the care-giver and people with dementia. Signal-based evaluations of the therapy can be carried out using the measures of spectral distortion and the inference of phylogenetic trees. The proposed computational models can be of assistance and cost-effectiveness in caring for and monitoring people with cognitive decline. PMID:25803586

The space of ultrametric phylogenetic trees.

PubMed

Gavryushkin, Alex; Drummond, Alexei J

2016-08-21

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data. Hence the question of statistical consistency of such methods is equivalent to the consistency of the summary of the sample. More generally, statistical consistency is ensured by the tree space used to analyse the sample. In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. For each of these parameterisations we introduce a natural metric space on ultrametric phylogenetic trees. We compare the introduced spaces with existing models of tree space and formulate several formal requirements that a metric space on phylogenetic trees must possess in order to be a satisfactory space for statistical analysis, and justify them. We show that only a few known constructions of the space of phylogenetic trees satisfy these requirements. However, our results suggest that these basic requirements are not enough to distinguish between the two metric spaces we introduce and that the choice between metric spaces requires additional properties to be considered. Particularly, that the summary tree minimising the square distance to the trees from the sample might be different for different parameterisations. This suggests that further fundamental insight is needed into the problem of statistical consistency of phylogenetic inference methods. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Characterization and assessment of an avian repetitive DNA sequence as an icterid phylogenetic marker.

PubMed

Quinn, J S; Guglich, E; Seutin, G; Lau, R; Marsolais, J; Parna, L; Boag, P T; White, B N

1992-02-01

The first tandemly repeated sequence examined in a passerine bird, a 431-bp PstI fragment named pMAT1, has been cloned from the genome of the brown-headed cowbird (Molothrus ater). The sequence represents about 5-10% of the genome (about 4 x 10(5) copies) and yields prominent ethidium bromide stained bands when genomic DNA cut with a variety of restriction enzymes is electrophoresed in agarose gels. A particularly striking ladder of fragments is apparent when the DNA is cut with HinfI, indicative of a tandem arrangement of the monomer. The cloned PstI monomer has been sequenced, revealing no internal repeated structure. There are sequences that hybridize with pMAT1 found in related nine-primaried oscines but not in more distantly related oscines, suboscines, or nonpasserine species. Little sequence similarity to tandemly repeated PstI cut sequences from the merlin (Falco columbarius), saurus crane (Grus antigone), or Puerto Rican parrot (Amazona vittata) or to HinfI digested sequence from the Toulouse goose (Anser anser) was detected. The isolated sequence was used as a probe to examine DNA samples of eight members of the tribe Icterini. This examination revealed phylogenetically informative characters. The repeat contains cutting sites from a number of restriction enzymes, which, if sufficiently polymorphic, would provide new phylogenetic characters. Sequences like these, conserved within a species, but variable between closely related species, may be very useful for phylogenetic studies of closely related taxa.

Undergraduate Students’ Initial Ability in Understanding Phylogenetic Tree

NASA Astrophysics Data System (ADS)

Sa'adah, S.; Hidayat, T.; Sudargo, Fransisca

2017-04-01

The Phylogenetic tree is a visual representation depicts a hypothesis about the evolutionary relationship among taxa. Evolutionary experts use this representation to evaluate the evidence for evolution. The phylogenetic tree is currently growing for many disciplines in biology. Consequently, learning about the phylogenetic tree has become an important part of biological education and an interesting area of biology education research. Skill to understanding and reasoning of the phylogenetic tree, (called tree thinking) is an important skill for biology students. However, research showed many students have difficulty in interpreting, constructing, and comparing among the phylogenetic tree, as well as experiencing a misconception in the understanding of the phylogenetic tree. Students are often not taught how to reason about evolutionary relationship depicted in the diagram. Students are also not provided with information about the underlying theory and process of phylogenetic. This study aims to investigate the initial ability of undergraduate students in understanding and reasoning of the phylogenetic tree. The research method is the descriptive method. Students are given multiple choice questions and an essay that representative by tree thinking elements. Each correct answer made percentages. Each student is also given questionnaires. The results showed that the undergraduate students’ initial ability in understanding and reasoning phylogenetic tree is low. Many students are not able to answer questions about the phylogenetic tree. Only 19 % undergraduate student who answered correctly on indicator evaluate the evolutionary relationship among taxa, 25% undergraduate student who answered correctly on indicator applying concepts of the clade, 17% undergraduate student who answered correctly on indicator determines the character evolution, and only a few undergraduate student who can construct the phylogenetic tree.

Improved Maximum Parsimony Models for Phylogenetic Networks.

PubMed

Van Iersel, Leo; Jones, Mark; Scornavacca, Celine

2018-05-01

Phylogenetic networks are well suited to represent evolutionary histories comprising reticulate evolution. Several methods aiming at reconstructing explicit phylogenetic networks have been developed in the last two decades. In this article, we propose a new definition of maximum parsimony for phylogenetic networks that permits to model biological scenarios that cannot be modeled by the definitions currently present in the literature (namely, the "hardwired" and "softwired" parsimony). Building on this new definition, we provide several algorithmic results that lay the foundations for new parsimony-based methods for phylogenetic network reconstruction.

Genomic Repeat Abundances Contain Phylogenetic Signal

PubMed Central

Dodsworth, Steven; Chase, Mark W.; Kelly, Laura J.; Leitch, Ilia J.; Macas, Jiří; Novák, Petr; Piednoël, Mathieu; Weiss-Schneeweiss, Hanna; Leitch, Andrew R.

2015-01-01

A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution. PMID:25261464

Probabilistic Graphical Model Representation in Phylogenetics

PubMed Central

Höhna, Sebastian; Heath, Tracy A.; Boussau, Bastien; Landis, Michael J.; Ronquist, Fredrik; Huelsenbeck, John P.

2014-01-01

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis–Hastings or Gibbs sampling of the posterior distribution. [Computation; graphical models; inference; modularization; statistical phylogenetics; tree plate.] PMID:24951559

Phylogenetic structure of arbuscular mycorrhizal fungal communities along an elevation gradient.

PubMed

Egan, Cameron P; Callaway, Ragan M; Hart, Miranda M; Pither, Jason; Klironomos, John

2017-04-01

Despite the importance of arbuscular mycorrhizal (AM) fungi within terrestrial ecosystems, we know little about how natural AM fungal communities are structured. To date, the majority of studies examining AM fungal community diversity have focused on single habitats with similar environmental conditions, with relatively few studies having assessed the diversity of AM fungi over large-scale environmental gradients. In this study, we characterized AM fungal communities in the soil along a high-elevation gradient in the North American Rocky Mountains. We focused on phylogenetic patterns of AM fungal communities to gain insight into how AM fungal communities are naturally assembled. We found that alpine AM fungal communities had lower phylogenetic diversity relative to lower elevation communities, as well as being more heterogeneous in composition than either treeline or subalpine communities. AM fungal communities were phylogenetically clustered at all elevations sampled, suggesting that environmental filtering, either selection by host plants or fungal niches, is the primary ecological process structuring communities along the gradient.

Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

PubMed Central

Tang, Cuong Q; Humphreys, Aelys M; Fontaneto, Diego; Barraclough, Timothy G; Paradis, Emmanuel

2014-01-01

Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses. PMID:25821577

Complete mitogenome of Asiatic lion resolves phylogenetic status within Panthera.

PubMed

Bagatharia, Snehal B; Joshi, Madhvi N; Pandya, Rohan V; Pandit, Aanal S; Patel, Riddhi P; Desai, Shivangi M; Sharma, Anu; Panchal, Omkar; Jasmani, Falguni P; Saxena, Akshay K

2013-08-23

The origin, evolution and speciation of the lion, has been subject of interest, debate and study. The present surviving lions of the genus Panthera comprise of eight sub-species inclusive of Asiatic lion Panthera leo persica of India's Gir forest. Except for the Asiatic lion, the other seven subspecies are found in different parts of Africa. There have been different opinions regarding the phylogenetic status of Panthera leo, as well as classifying lions of different geographic regions into subspecies and races. In the present study, mitogenome sequence of P. leo persica deduced, using Ion Torrent PGM to assess phylogeny and evolution which may play an increasingly important role in conservation biology. The mtDNA sequence of P. leo persica is 17,057 bp in length with 40.8% GC content. Annotation of mitogenome revealed total 37 genes, including 13 protein coding, 2 rRNA and 22 tRNA. Phylogenetic analysis based on whole mitogenome, suggests Panthera pardus as a neighbouring species to P. leo with species divergence at ~2.96 mya. This work presents first report on complete mitogenome of Panthera leo persica. It sheds light on the phylogenetic and evolutionary status within and across Felidae members. The result compared and evaluated with earlier reports of Felidae shows alteration of phylogenetic status and species evolution. This study may provide information on genetic diversity and population stability.

Complete mitogenome of asiatic lion resolves phylogenetic status within Panthera

PubMed Central

2013-01-01

Background The origin, evolution and speciation of the lion, has been subject of interest, debate and study. The present surviving lions of the genus Panthera comprise of eight sub-species inclusive of Asiatic lion Panthera leo persica of India's Gir forest. Except for the Asiatic lion, the other seven subspecies are found in different parts of Africa. There have been different opinions regarding the phylogenetic status of Panthera leo, as well as classifying lions of different geographic regions into subspecies and races. In the present study, mitogenome sequence of P. leo persica deduced, using Ion Torrent PGM to assess phylogeny and evolution which may play an increasingly important role in conservation biology. Results The mtDNA sequence of P. leo persica is 17,057 bp in length with 40.8% GC content. Annotation of mitogenome revealed total 37 genes, including 13 protein coding, 2 rRNA and 22 tRNA. Phylogenetic analysis based on whole mitogenome, suggests Panthera pardus as a neighbouring species to P. leo with species divergence at ~2.96 mya. Conclusion This work presents first report on complete mitogenome of Panthera leo persica. It sheds light on the phylogenetic and evolutionary status within and across Felidae members. The result compared and evaluated with earlier reports of Felidae shows alteration of phylogenetic status and species evolution. This study may provide information on genetic diversity and population stability. PMID:23968279

Assessing Quantitative Resistance against Leptosphaeria maculans (Phoma Stem Canker) in Brassica napus (Oilseed Rape) in Young Plants

PubMed Central

Huang, Yong-Ju; Qi, Aiming; King, Graham J.; Fitt, Bruce D. L.

2014-01-01

Quantitative resistance against Leptosphaeria maculans in Brassica napus is difficult to assess in young plants due to the long period of symptomless growth of the pathogen from the appearance of leaf lesions to the appearance of canker symptoms on the stem. By using doubled haploid (DH) lines A30 (susceptible) and C119 (with quantitative resistance), quantitative resistance against L. maculans was assessed in young plants in controlled environments at two stages: stage 1, growth of the pathogen along leaf veins/petioles towards the stem by leaf lamina inoculation; stage 2, growth in stem tissues to produce stem canker symptoms by leaf petiole inoculation. Two types of inoculum (ascospores; conidia) and three assessment methods (extent of visible necrosis; symptomless pathogen growth visualised using the GFP reporter gene; amount of pathogen DNA quantified by PCR) were used. In stage 1 assessments, significant differences were observed between lines A30 and C119 in area of leaf lesions, distance grown along veins/petioles assessed by visible necrosis or by viewing GFP and amount of L. maculans DNA in leaf petioles. In stage 2 assessments, significant differences were observed between lines A30 and C119 in severity of stem canker and amount of L. maculans DNA in stem tissues. GFP-labelled L. maculans spread more quickly from the stem cortex to the stem pith in A30 than in C119. Stem canker symptoms were produced more rapidly by using ascospore inoculum than by using conidial inoculum. These results suggest that quantitative resistance against L. maculans in B. napus can be assessed in young plants in controlled conditions. Development of methods to phenotype quantitative resistance against plant pathogens in young plants in controlled environments will help identification of stable quantitative resistance for control of crop diseases. PMID:24454767

A Consistent Phylogenetic Backbone for the Fungi

PubMed Central

Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt

2012-01-01

The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses. PMID:22114356

Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling.

PubMed

Sferra, Gabriella; Fratini, Federica; Ponzi, Marta; Pizzi, Elisabetta

2017-09-05

Elaboration of powerful methods to predict functional and/or physical protein-protein interactions from genome sequence is one of the main tasks in the post-genomic era. Phylogenetic profiling allows the prediction of protein-protein interactions at a whole genome level in both Prokaryotes and Eukaryotes. For this reason it is considered one of the most promising methods. Here, we propose an improvement of phylogenetic profiling that enables handling of large genomic datasets and infer global protein-protein interactions. This method uses the distance correlation as a new measure of phylogenetic profile similarity. We constructed robust reference sets and developed Phylo-dCor, a parallelized version of the algorithm for calculating the distance correlation that makes it applicable to large genomic data. Using Saccharomyces cerevisiae and Escherichia coli genome datasets, we showed that Phylo-dCor outperforms phylogenetic profiling methods previously described based on the mutual information and Pearson's correlation as measures of profile similarity. In this work, we constructed and assessed robust reference sets and propose the distance correlation as a measure for comparing phylogenetic profiles. To make it applicable to large genomic data, we developed Phylo-dCor, a parallelized version of the algorithm for calculating the distance correlation. Two R scripts that can be run on a wide range of machines are available upon request.

Phylogenetic assessment of filoviruses: how many lineages of Marburg virus?

PubMed Central

Peterson, A Townsend; Holder, Mark T

2012-01-01

Filoviruses have to date been considered as consisting of one diverse genus (Ebola viruses) and one undifferentiated genus (Marburg virus). We reconsider this idea by means of detailed phylogenetic analyses of sequence data available for the Filoviridae: using coalescent simulations, we ascertain that two Marburg isolates (termed the “RAVN” strain) represent a quite-distinct lineage that should be considered in studies of biogeography and host associations, and may merit recognition at the level of species. In contrast, filovirus isolates recently obtained from bat tissues are not distinct from previously known strains, and should be considered as drawn from the same population. Implications for understanding the transmission geography and host associations of these viruses are discussed. PMID:22957185

White-tailed deer are a biotic filter during community assembly, reducing species and phylogenetic diversity.

PubMed

Begley-Miller, Danielle R; Hipp, Andrew L; Brown, Bethany H; Hahn, Marlene; Rooney, Thomas P

2014-06-09

Community assembly entails a filtering process, where species found in a local community are those that can pass through environmental (abiotic) and biotic filters and successfully compete. Previous research has demonstrated the ability of white-tailed deer (Odocoileus virginianus) to reduce species diversity and favour browse-tolerant plant communities. In this study, we expand on our previous work by investigating deer as a possible biotic filter altering local plant community assembly. We used replicated 23-year-old deer exclosures to experimentally assess the effects of deer on species diversity (H'), richness (SR), phylogenetic community structure and phylogenetic diversity in paired browsed (control) and unbrowsed (exclosed) plots. Additionally, we developed a deer-browsing susceptibility index (DBSI) to assess the vulnerability of local species to deer. Deer browsing caused a 12 % reduction in H' and 17 % reduction in SR, consistent with previous studies. Furthermore, browsing reduced phylogenetic diversity by 63 %, causing significant phylogenetic clustering. Overall, graminoids were the least vulnerable to deer browsing based on DBSI calculations. These findings demonstrate that deer are a significant driver of plant community assembly due to their role as a selective browser, or more generally, as a biotic filter. This study highlights the importance of knowledge about the plant tree of life in assessing the effects of biotic filters on plant communities. Application of such knowledge has considerable potential to advance our understanding of plant community assembly. Published by Oxford University Press on behalf of the Annals of Botany Company.

Inferring ‘weak spots’ in phylogenetic trees: application to mosasauroid nomenclature

PubMed Central

2017-01-01

Mosasauroid squamates represented the apex predators within the Late Cretaceous marine and occasionally also freshwater ecosystems. Proper understanding of the origin of their ecological adaptations or paleobiogeographic dispersals requires adequate knowledge of their phylogeny. The studies assessing the position of mosasauroids on the squamate evolutionary tree and their origins have long given conflicting results. The phylogenetic relationships within Mosasauroidea, however, have experienced only little changes throughout the last decades. Considering the substantial improvements in the development of phylogenetic methodology that have undergone in recent years, resulting, among others, in numerous alterations in the phylogenetic hypotheses of other fossil amniotes, we test the robustness in our understanding of mosasauroid beginnings and their evolutionary history. We re-examined a data set that results from modifications assembled in the course of the last 20 years and performed multiple parsimony analyses and Bayesian tip-dating analysis. Following the inferred topologies and the ‘weak spots’ in the phylogeny of mosasauroids, we revise the nomenclature of the ‘traditionally’ recognized mosasauroid clades, to acknowledge the overall weakness among branches and the alternative topologies suggested previously, and discuss several factors that might have an impact on the differing phylogenetic hypotheses and their statistical support. PMID:28929018

Comparison study on qualitative and quantitative risk assessment methods for urban natural gas pipeline network.

PubMed

Han, Z Y; Weng, W G

2011-05-15

In this paper, a qualitative and a quantitative risk assessment methods for urban natural gas pipeline network are proposed. The qualitative method is comprised of an index system, which includes a causation index, an inherent risk index, a consequence index and their corresponding weights. The quantitative method consists of a probability assessment, a consequences analysis and a risk evaluation. The outcome of the qualitative method is a qualitative risk value, and for quantitative method the outcomes are individual risk and social risk. In comparison with previous research, the qualitative method proposed in this paper is particularly suitable for urban natural gas pipeline network, and the quantitative method takes different consequences of accidents into consideration, such as toxic gas diffusion, jet flame, fire ball combustion and UVCE. Two sample urban natural gas pipeline networks are used to demonstrate these two methods. It is indicated that both of the two methods can be applied to practical application, and the choice of the methods depends on the actual basic data of the gas pipelines and the precision requirements of risk assessment. Crown Copyright © 2011. Published by Elsevier B.V. All rights reserved.

Diagnostic accuracy of stress perfusion CMR in comparison with quantitative coronary angiography: fully quantitative, semiquantitative, and qualitative assessment.

PubMed

Mordini, Federico E; Haddad, Tariq; Hsu, Li-Yueh; Kellman, Peter; Lowrey, Tracy B; Aletras, Anthony H; Bandettini, W Patricia; Arai, Andrew E

2014-01-01

This study's primary objective was to determine the sensitivity, specificity, and accuracy of fully quantitative stress perfusion cardiac magnetic resonance (CMR) versus a reference standard of quantitative coronary angiography. We hypothesized that fully quantitative analysis of stress perfusion CMR would have high diagnostic accuracy for identifying significant coronary artery stenosis and exceed the accuracy of semiquantitative measures of perfusion and qualitative interpretation. Relatively few studies apply fully quantitative CMR perfusion measures to patients with coronary disease and comparisons to semiquantitative and qualitative methods are limited. Dual bolus dipyridamole stress perfusion CMR exams were performed in 67 patients with clinical indications for assessment of myocardial ischemia. Stress perfusion images alone were analyzed with a fully quantitative perfusion (QP) method and 3 semiquantitative methods including contrast enhancement ratio, upslope index, and upslope integral. Comprehensive exams (cine imaging, stress/rest perfusion, late gadolinium enhancement) were analyzed qualitatively with 2 methods including the Duke algorithm and standard clinical interpretation. A 70% or greater stenosis by quantitative coronary angiography was considered abnormal. The optimum diagnostic threshold for QP determined by receiver-operating characteristic curve occurred when endocardial flow decreased to <50% of mean epicardial flow, which yielded a sensitivity of 87% and specificity of 93%. The area under the curve for QP was 92%, which was superior to semiquantitative methods: contrast enhancement ratio: 78%; upslope index: 82%; and upslope integral: 75% (p = 0.011, p = 0.019, p = 0.004 vs. QP, respectively). Area under the curve for QP was also superior to qualitative methods: Duke algorithm: 70%; and clinical interpretation: 78% (p < 0.001 and p < 0.001 vs. QP, respectively). Fully quantitative stress perfusion CMR has high diagnostic accuracy for

[Phylogenetic analysis of closely related Leuconostoc citreum species based on partial housekeeping genes].

PubMed

Lv, Qiang; Chen, Ming; Xu, Haiyan; Song, Yuqin; Sun, Zhihong; Dan, Tong; Sun, Tiansong

2013-07-04

Using the 16S rRNA, dnaA, murC and pyrG gene sequences, we identified the phylogenetic relationship among closely related Leuconostoc citreum species. Seven Leu. citreum strains originally isolated from sourdough were characterized by PCR methods to amplify the dnaA, murC and pyrG gene sequences, which were determined to assess the suitability as phylogenetic markers. Then, we estimated the genetic distance and constructed the phylogenetic trees including 16S rRNA and above mentioned three housekeeping genes combining with published corresponding sequences. By comparing the phylogenetic trees, the topology of three housekeeping genes trees were consistent with that of 16S rRNA gene. The homology of closely related Leu. citreum species among dnaA, murC, pyrG and 16S rRNA gene sequences were different, ranged from75.5% to 97.2%, 50.2% to 99.7%, 65.0% to 99.8% and 98.5% 100%, respectively. The phylogenetic relationship of three housekeeping genes sequences were highly consistent with the results of 16S rRNA gene sequence, while the genetic distance of these housekeeping genes were extremely high than 16S rRNA gene. Consequently, the dnaA, murC and pyrG gene are suitable for classification and identification closely related Leu. citreum species.

Rearrangement moves on rooted phylogenetic networks

PubMed Central

Gambette, Philippe; van Iersel, Leo; Jones, Mark; Scornavacca, Celine

2017-01-01

Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based principles, and in a Bayesian context. Their basic components are rearrangement moves that specify all possible ways of generating alternative phylogenies from a given one, and whose fundamental property is to be able to transform, by repeated application, any phylogeny into any other phylogeny. Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network—that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. To fill this gap, we propose “horizontal” moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and “vertical” moves that ensure reachability between networks of different complexities. When applied to phylogenetic trees, our horizontal moves—named rNNI and rSPR—reduce to the best-known moves on rooted phylogenetic trees, nearest-neighbor interchange and rooted subtree pruning and regrafting. Besides a number of reachability results—separating the contributions of horizontal and vertical moves—we prove that rNNI moves are local versions of rSPR moves, and provide bounds on the sizes of the rNNI neighborhoods. The paper focuses on the most biologically meaningful versions of phylogenetic networks, where edges are oriented and reticulation events clearly identified. Moreover, our rearrangement moves are robust to the fact that networks with higher complexity usually allow a better fit with the data. Our goal is to provide a

Fourier transform inequalities for phylogenetic trees.

PubMed

Matsen, Frederick A

2009-01-01

Phylogenetic invariants are not the only constraints on site-pattern frequency vectors for phylogenetic trees. A mutation matrix, by its definition, is the exponential of a matrix with non-negative off-diagonal entries; this positivity requirement implies non-trivial constraints on the site-pattern frequency vectors. We call these additional constraints "edge-parameter inequalities". In this paper, we first motivate the edge-parameter inequalities by considering a pathological site-pattern frequency vector corresponding to a quartet tree with a negative internal edge. This site-pattern frequency vector nevertheless satisfies all of the constraints described up to now in the literature. We next describe two complete sets of edge-parameter inequalities for the group-based models; these constraints are square-free monomial inequalities in the Fourier transformed coordinates. These inequalities, along with the phylogenetic invariants, form a complete description of the set of site-pattern frequency vectors corresponding to bona fide trees. Said in mathematical language, this paper explicitly presents two finite lists of inequalities in Fourier coordinates of the form "monomial < or = 1", each list characterizing the phylogenetically relevant semialgebraic subsets of the phylogenetic varieties.

Novel quantitative assessment of metamorphopsia in maculopathy.

PubMed

Wiecek, Emily; Lashkari, Kameran; Dakin, Steven C; Bex, Peter

2014-11-18

Patients with macular disease often report experiencing metamorphopsia (visual distortion). Although typically measured with Amsler charts, more quantitative assessments of perceived distortion are desirable to effectively monitor the presence, progression, and remediation of visual impairment. Participants with binocular (n = 33) and monocular (n = 50) maculopathy across seven disease groups, and control participants (n = 10) with no identifiable retinal disease completed a modified Amsler grid assessment (presented on a computer screen with eye tracking to ensure fixation compliance) and two novel assessments to measure metamorphopsia in the central 5° of visual field. A total of 81% (67/83) of participants completed a hyperacuity task where they aligned eight dots in the shape of a square, and 64% (32/50) of participants with monocular distortion completed a spatial alignment task using dichoptic stimuli. Ten controls completed all tasks. Horizontal and vertical distortion magnitudes were calculated for each of the three assessments. Distortion magnitudes were significantly higher in patients than controls in all assessments. There was no significant difference in magnitude of distortion across different macular diseases. There were no significant correlations between overall magnitude of distortion among any of the three measures and no significant correlations in localized measures of distortion. Three alternative quantifications of monocular spatial distortion in the central visual field generated uncorrelated estimates of visual distortion. It is therefore unlikely that metamorphopsia is caused solely by retinal displacement, but instead involves additional top-down information, knowledge about the scene, and perhaps, cortical reorganization. Copyright 2015 The Association for Research in Vision and Ophthalmology, Inc.

Phylogenetic search through partial tree mixing

PubMed Central

2012-01-01

Background Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques. Results When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda Conclusions The use of Partial Tree Mixing in a partition based tree space allows the algorithm to quickly converge on near optimal tree regions. These regions can then be searched in a methodical way to determine the overall optimal phylogenetic solution. PMID:23320449

QUANTITATIVE CANCER RISK ASSESSMENT METHODOLOGY USING SHORT-TERM GENETIC BIOASSAYS: THE COMPARATIVE POTENCY METHOD

EPA Science Inventory

Quantitative risk assessment is fraught with many uncertainties. The validity of the assumptions underlying the methods employed are often difficult to test or validate. Cancer risk assessment has generally employed either human epidemiological data from relatively high occupatio...

Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions

PubMed Central

Giaro, Krzysztof

2017-01-01

Abstract Ability to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in the literature, the most commonly used seems to be the Robinson–Foulds distance. In this article, we define a new metric for rooted trees—the Matching Pair (MP) distance. The MP metric uses the concept of the minimum-weight perfect matching in a complete bipartite graph constructed from partitions of all pairs of leaves of the compared phylogenetic trees. We analyze the properties of the MP metric and present computational experiments showing its potential applicability in tasks related to finding the HGT events. PMID:28177699

Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions.

PubMed

Bogdanowicz, Damian; Giaro, Krzysztof

2017-05-01

Ability to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in the literature, the most commonly used seems to be the Robinson-Foulds distance. In this article, we define a new metric for rooted trees-the Matching Pair (MP) distance. The MP metric uses the concept of the minimum-weight perfect matching in a complete bipartite graph constructed from partitions of all pairs of leaves of the compared phylogenetic trees. We analyze the properties of the MP metric and present computational experiments showing its potential applicability in tasks related to finding the HGT events.

Estimating the Effective Sample Size of Tree Topologies from Bayesian Phylogenetic Analyses

PubMed Central

Lanfear, Robert; Hua, Xia; Warren, Dan L.

2016-01-01

Bayesian phylogenetic analyses estimate posterior distributions of phylogenetic tree topologies and other parameters using Markov chain Monte Carlo (MCMC) methods. Before making inferences from these distributions, it is important to assess their adequacy. To this end, the effective sample size (ESS) estimates how many truly independent samples of a given parameter the output of the MCMC represents. The ESS of a parameter is frequently much lower than the number of samples taken from the MCMC because sequential samples from the chain can be non-independent due to autocorrelation. Typically, phylogeneticists use a rule of thumb that the ESS of all parameters should be greater than 200. However, we have no method to calculate an ESS of tree topology samples, despite the fact that the tree topology is often the parameter of primary interest and is almost always central to the estimation of other parameters. That is, we lack a method to determine whether we have adequately sampled one of the most important parameters in our analyses. In this study, we address this problem by developing methods to estimate the ESS for tree topologies. We combine these methods with two new diagnostic plots for assessing posterior samples of tree topologies, and compare their performance on simulated and empirical data sets. Combined, the methods we present provide new ways to assess the mixing and convergence of phylogenetic tree topologies in Bayesian MCMC analyses. PMID:27435794

Phylogenetic diversity measures based on Hill numbers.

PubMed

Chao, Anne; Chiu, Chun-Huo; Jost, Lou

2010-11-27

We propose a parametric class of phylogenetic diversity (PD) measures that are sensitive to both species abundance and species taxonomic or phylogenetic distances. This work extends the conventional parametric species-neutral approach (based on 'effective number of species' or Hill numbers) to take into account species relatedness, and also generalizes the traditional phylogenetic approach (based on 'total phylogenetic length') to incorporate species abundances. The proposed measure quantifies 'the mean effective number of species' over any time interval of interest, or the 'effective number of maximally distinct lineages' over that time interval. The product of the measure and the interval length quantifies the 'branch diversity' of the phylogenetic tree during that interval. The new measures generalize and unify many existing measures and lead to a natural definition of taxonomic diversity as a special case. The replication principle (or doubling property), an important requirement for species-neutral diversity, is generalized to PD. The widely used Rao's quadratic entropy and the phylogenetic entropy do not satisfy this essential property, but a simple transformation converts each to our measures, which do satisfy the property. The proposed approach is applied to forest data for interpreting the effects of thinning.

Quantitative imaging biomarkers: a review of statistical methods for technical performance assessment.

PubMed

Raunig, David L; McShane, Lisa M; Pennello, Gene; Gatsonis, Constantine; Carson, Paul L; Voyvodic, James T; Wahl, Richard L; Kurland, Brenda F; Schwarz, Adam J; Gönen, Mithat; Zahlmann, Gudrun; Kondratovich, Marina V; O'Donnell, Kevin; Petrick, Nicholas; Cole, Patricia E; Garra, Brian; Sullivan, Daniel C

2015-02-01

Technological developments and greater rigor in the quantitative measurement of biological features in medical images have given rise to an increased interest in using quantitative imaging biomarkers to measure changes in these features. Critical to the performance of a quantitative imaging biomarker in preclinical or clinical settings are three primary metrology areas of interest: measurement linearity and bias, repeatability, and the ability to consistently reproduce equivalent results when conditions change, as would be expected in any clinical trial. Unfortunately, performance studies to date differ greatly in designs, analysis method, and metrics used to assess a quantitative imaging biomarker for clinical use. It is therefore difficult or not possible to integrate results from different studies or to use reported results to design studies. The Radiological Society of North America and the Quantitative Imaging Biomarker Alliance with technical, radiological, and statistical experts developed a set of technical performance analysis methods, metrics, and study designs that provide terminology, metrics, and methods consistent with widely accepted metrological standards. This document provides a consistent framework for the conduct and evaluation of quantitative imaging biomarker performance studies so that results from multiple studies can be compared, contrasted, or combined. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Quantitative Assessment of Breast Cosmetic Outcome After Whole-Breast Irradiation

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

Reddy, Jay P.; Lei, Xiudong; Huang, Sheng-Cheng

Purpose: To measure, by quantitative analysis of digital photographs, breast cosmetic outcome within the setting of a randomized trial of conventionally fractionated (CF) and hypofractionated (HF) whole-breast irradiation (WBI), to identify how quantitative cosmesis metrics were associated with patient- and physician-reported cosmesis and whether they differed by treatment arm. Methods and Materials: From 2011 to 2014, 287 women aged ≥40 with ductal carcinoma in situ or early invasive breast cancer were randomized to HF-WBI (42.56 Gy/16 fractions [fx] + 10-12.5 Gy/4-5 fx boost) or CF-WBI (50 Gy/25 fx + 10-14 Gy/5-7 fx). At 1 year after treatment we collected digital photographs, patient-reported cosmesis using the Breast Cancer Treatment and Outcomesmore » Scale, and physician-reported cosmesis using the Radiation Therapy Oncology Group scale. Six quantitative measures of breast symmetry, labeled M1-M6, were calculated from anteroposterior digital photographs. For each measure, values closer to 1 imply greater symmetry, and values closer to 0 imply greater asymmetry. Associations between M1-M6 and patient- and physician-reported cosmesis and treatment arm were evaluated using the Kruskal-Wallis test. Results: Among 245 evaluable patients, patient-reported cosmesis was strongly associated with M1 (vertical symmetry measure) (P<.01). Physician-reported cosmesis was similarly correlated with M1 (P<.01) and also with M2 (vertical symmetry, P=.01) and M4 (horizontal symmetry, P=.03). At 1 year after treatment, HF-WBI resulted in better values of M2 (P=.02) and M3 (P<.01) than CF-WBI; treatment arm was not significantly associated with M1, M4, M5, or M6 (P≥.12). Conclusions: Quantitative assessment of breast photographs reveals similar to improved cosmetic outcome with HF-WBI compared with CF-WBI 1 year after treatment. Assessing cosmetic outcome using these measures could be useful for future comparative effectiveness studies and outcome reporting.« less

Quantitative Assessment of Breast Cosmetic Outcome After Whole-Breast Irradiation.

PubMed

Reddy, Jay P; Lei, Xiudong; Huang, Sheng-Cheng; Nicklaus, Krista M; Fingeret, Michelle C; Shaitelman, Simona F; Hunt, Kelly K; Buchholz, Thomas A; Merchant, Fatima; Markey, Mia K; Smith, Benjamin D

2017-04-01

To measure, by quantitative analysis of digital photographs, breast cosmetic outcome within the setting of a randomized trial of conventionally fractionated (CF) and hypofractionated (HF) whole-breast irradiation (WBI), to identify how quantitative cosmesis metrics were associated with patient- and physician-reported cosmesis and whether they differed by treatment arm. From 2011 to 2014, 287 women aged ≥40 with ductal carcinoma in situ or early invasive breast cancer were randomized to HF-WBI (42.56 Gy/16 fractions [fx] + 10-12.5 Gy/4-5 fx boost) or CF-WBI (50 Gy/25 fx + 10-14 Gy/5-7 fx). At 1 year after treatment we collected digital photographs, patient-reported cosmesis using the Breast Cancer Treatment and Outcomes Scale, and physician-reported cosmesis using the Radiation Therapy Oncology Group scale. Six quantitative measures of breast symmetry, labeled M1-M6, were calculated from anteroposterior digital photographs. For each measure, values closer to 1 imply greater symmetry, and values closer to 0 imply greater asymmetry. Associations between M1-M6 and patient- and physician-reported cosmesis and treatment arm were evaluated using the Kruskal-Wallis test. Among 245 evaluable patients, patient-reported cosmesis was strongly associated with M1 (vertical symmetry measure) (P<.01). Physician-reported cosmesis was similarly correlated with M1 (P<.01) and also with M2 (vertical symmetry, P=.01) and M4 (horizontal symmetry, P=.03). At 1 year after treatment, HF-WBI resulted in better values of M2 (P=.02) and M3 (P<.01) than CF-WBI; treatment arm was not significantly associated with M1, M4, M5, or M6 (P≥.12). Quantitative assessment of breast photographs reveals similar to improved cosmetic outcome with HF-WBI compared with CF-WBI 1 year after treatment. Assessing cosmetic outcome using these measures could be useful for future comparative effectiveness studies and outcome reporting. Copyright © 2016 Elsevier Inc. All rights reserved.

A Quantitative Needs Assessment Technique for Cross-Cultural Work Adjustment Training.

ERIC Educational Resources Information Center

Selmer, Lyn

2000-01-01

A study of 67 Swedish expatriate bosses and 104 local Hong Kong middle managers tested a quantitative needs assessment technique measuring work values. Two-thirds of middle managers' work values were not correctly estimated by their bosses, especially instrumental values (pay, benefits, security, working hours and conditions), indicating a need…

Phylogenetic reconstruction and shell evolution of the Diplommatinidae (Gastropoda: Caenogastropoda).

PubMed

Webster, Nicole B; Van Dooren, Tom J M; Schilthuizen, Menno

2012-06-01

The fascinating and often unlikely shell shapes in the terrestrial micromollusc family Diplommatinidae (Gastropoda: Caenogastropoda) provide a particularly attractive set of multiple morphological traits to investigate evolutionary patterns of shape variation. Here, a molecular phylogenetic reconstruction, based on five genes and 2700 bp, was undertaken for this family, integrated with ancestral state reconstruction and phylogenetic PCA of discrete and quantitative traits, respectively. We found strong support for the Diplommatininae as a monophyletic group, separating the Cochlostomatidae into a separate family. Five main clades appear within the Diplommatininae, corresponding with both coiling direction and biogeographic patterns. A Belau clade (A) with highly diverse (but always sinistral) morphology comprised Hungerfordia, Palaina, and some Diplommatina. Arinia (dextral) and Opisthostoma (sinistroid) are sister groups in clade B. Clade C and D solely contain sinistral Diplommatina that are robust and little ornamented (clade C) or slender and sculptured (clade D). Clade E is dextral but biogeographically diverse with species from all sampled regions save the Caroline Islands. Adelopoma, Diplommatina, Palaina, and Hungerfordia require revision to allow taxonomy to reflect phylogeny, whereas Opisthostoma is clearly monophyletic. Ancestral state reconstruction suggests a sinistral origin for the Diplommatinidae, with three reversals to dextrality. Copyright © 2012 Elsevier Inc. All rights reserved.

Study on quantitative risk assessment model of the third party damage for natural gas pipelines based on fuzzy comprehensive assessment

NASA Astrophysics Data System (ADS)

Qiu, Zeyang; Liang, Wei; Wang, Xue; Lin, Yang; Zhang, Meng

2017-05-01

As an important part of national energy supply system, transmission pipelines for natural gas are possible to cause serious environmental pollution, life and property loss in case of accident. The third party damage is one of the most significant causes for natural gas pipeline system accidents, and it is very important to establish an effective quantitative risk assessment model of the third party damage for reducing the number of gas pipelines operation accidents. Against the third party damage accident has the characteristics such as diversity, complexity and uncertainty, this paper establishes a quantitative risk assessment model of the third party damage based on Analytic Hierarchy Process (AHP) and Fuzzy Comprehensive Evaluation (FCE). Firstly, risk sources of third party damage should be identified exactly, and the weight of factors could be determined via improved AHP, finally the importance of each factor is calculated by fuzzy comprehensive evaluation model. The results show that the quantitative risk assessment model is suitable for the third party damage of natural gas pipelines and improvement measures could be put forward to avoid accidents based on the importance of each factor.

Food Consumption and Handling Survey for Quantitative Microbiological Consumer Phase Risk Assessments.

PubMed

Chardon, Jurgen; Swart, Arno

2016-07-01

In the consumer phase of a typical quantitative microbiological risk assessment (QMRA), mathematical equations identify data gaps. To acquire useful data we designed a food consumption and food handling survey (2,226 respondents) for QMRA applications that is especially aimed at obtaining quantitative data. For a broad spectrum of food products, the survey covered the following topics: processing status at retail, consumer storage, preparation, and consumption. Questions were designed to facilitate distribution fitting. In the statistical analysis, special attention was given to the selection of the most adequate distribution to describe the data. Bootstrap procedures were used to describe uncertainty. The final result was a coherent quantitative consumer phase food survey and parameter estimates for food handling and consumption practices in The Netherlands, including variation over individuals and uncertainty estimates.

A quantitative microbial risk assessment for center pivot irrigation of dairy wastewaters

USDA-ARS?s Scientific Manuscript database

In the western United States where livestock wastewaters are commonly land applied, there are concerns over individuals being exposed to airborne pathogens. In response, a quantitative microbial risk assessment (QMRA) was performed to estimate infectious risks from inhaling pathogens aerosolized dur...

Continental monophyly of cichlid fishes and the phylogenetic position of Heterochromis multidens.

PubMed

Keck, Benjamin P; Hulsey, C Darrin

2014-04-01

The incredibly species-rich cichlid fish faunas of both the Neotropics and Africa are generally thought to be reciprocally monophyletic. However, the phylogenetic affinity of the African cichlid Heterochromis multidens is ambiguous, and this distinct lineage could make African cichlids paraphyletic. In past studies, Heterochromis has been variously suggested to be one of the earliest diverging lineages within either the Neotropical or the African cichlid radiations, and it has even been hypothesized to be the sister lineage to a clade containing all Neotropical and African cichlids. We examined the phylogenetic relationships among a representative sample of cichlids with a dataset of 29 nuclear loci to assess the support for the different hypotheses of the phylogenetic position of Heterochromis. Although individual gene trees in some instances supported alternative relationships, a majority of gene trees, integration of genes into species trees, and hypothesis testing of putative topologies all supported Heterochromis as belonging to the clade of African cichlids. Copyright © 2014 Elsevier Inc. All rights reserved.

Alpine cushion plants inhibit the loss of phylogenetic diversity in severe environments.

PubMed

Butterfield, B J; Cavieres, L A; Callaway, R M; Cook, B J; Kikvidze, Z; Lortie, C J; Michalet, R; Pugnaire, F I; Schöb, C; Xiao, S; Zaitchek, B; Anthelme, F; Björk, R G; Dickinson, K; Gavilán, R; Kanka, R; Maalouf, J-P; Noroozi, J; Parajuli, R; Phoenix, G K; Reid, A; Ridenour, W; Rixen, C; Wipf, S; Zhao, L; Brooker, R W

2013-04-01

Biotic interactions can shape phylogenetic community structure (PCS). However, we do not know how the asymmetric effects of foundation species on communities extend to effects on PCS. We assessed PCS of alpine plant communities around the world, both within cushion plant foundation species and adjacent open ground, and compared the effects of foundation species and climate on alpha (within-microsite), beta (between open and cushion) and gamma (open and cushion combined) PCS. In the open, alpha PCS shifted from highly related to distantly related with increasing potential productivity. However, we found no relationship between gamma PCS and climate, due to divergence in phylogenetic composition between cushion and open sub-communities in severe environments, as demonstrated by increasing phylo-beta diversity. Thus, foundation species functioned as micro-refugia by facilitating less stress-tolerant lineages in severe environments, erasing a global productivity - phylogenetic diversity relationship that would go undetected without accounting for this important biotic interaction. © 2013 Blackwell Publishing Ltd/CNRS.

Quantitative 3D breast magnetic resonance imaging fibroglandular tissue analysis and correlation with qualitative assessments: a feasibility study.

PubMed

Ha, Richard; Mema, Eralda; Guo, Xiaotao; Mango, Victoria; Desperito, Elise; Ha, Jason; Wynn, Ralph; Zhao, Binsheng

2016-04-01

The amount of fibroglandular tissue (FGT) has been linked to breast cancer risk based on mammographic density studies. Currently, the qualitative assessment of FGT on mammogram (MG) and magnetic resonance imaging (MRI) is prone to intra and inter-observer variability. The purpose of this study is to develop an objective quantitative FGT measurement tool for breast MRI that could provide significant clinical value. An IRB approved study was performed. Sixty breast MRI cases with qualitative assessment of mammographic breast density and MRI FGT were randomly selected for quantitative analysis from routine breast MRIs performed at our institution from 1/2013 to 12/2014. Blinded to the qualitative data, whole breast and FGT contours were delineated on T1-weighted pre contrast sagittal images using an in-house, proprietary segmentation algorithm which combines the region-based active contours and a level set approach. FGT (%) was calculated by: [segmented volume of FGT (mm(3))/(segmented volume of whole breast (mm(3))] ×100. Statistical correlation analysis was performed between quantified FGT (%) on MRI and qualitative assessments of mammographic breast density and MRI FGT. There was a significant positive correlation between quantitative MRI FGT assessment and qualitative MRI FGT (r=0.809, n=60, P<0.001) and mammographic density assessment (r=0.805, n=60, P<0.001). There was a significant correlation between qualitative MRI FGT assessment and mammographic density assessment (r=0.725, n=60, P<0.001). The four qualitative assessment categories of FGT correlated with the calculated mean quantitative FGT (%) of 4.61% (95% CI, 0-12.3%), 8.74% (7.3-10.2%), 18.1% (15.1-21.1%), 37.4% (29.5-45.3%). Quantitative measures of FGT (%) were computed with data derived from breast MRI and correlated significantly with conventional qualitative assessments. This quantitative technique may prove to be a valuable tool in clinical use by providing computer generated standardized

The Quantitative Reasoning for College Science (QuaRCS) Assessment in non-Astro 101 Courses

NASA Astrophysics Data System (ADS)

Kirkman, Thomas W.; Jensen, Ellen

2016-06-01

The innumeracy of American students and adults is a much lamented educational problem. The quantitative reasoning skills of college students may be particularly addressed and improved in "general education" science courses like Astro 101. Demonstrating improvement requires a standardized instrument. Among the non-proprietary instruments the Quantitative Literacy and Reasoning Assessment[1] (QRLA) and the Quantitative Reasoning for College Science (QuaRCS) Assessment[2] stand out.Follette et al. developed the QuaRCS in the context of Astro 101 at University of Arizona. We report on QuaRCS results in different contexts: pre-med physics and pre-nursing microbiology at a liberal arts college. We report on the mismatch between students' contemporaneous report of a question's difficulty and the actual probability of success. We report correlations between QuaRCS and other assessments of overall student performance in the class. We report differences in attitude towards mathematics in these two different but health-related student populations .[1] QLRA, Gaze et al., 2014, DOI: http://dx.doi.org/10.5038/1936-4660.7.2.4[2] QuaRCS, Follette, et al., 2015, DOI: http://dx.doi.org/10.5038/1936-4660.8.2.2

Phylogenetic impoverishment of plant communities following chronic human disturbances in the Brazilian Caatinga.

PubMed

Ribeiro, Elâine M S; Santos, Bráulio A; Arroyo-Rodríguez, Víctor; Tabarelli, Marcelo; Souza, Gustavo; Leal, Inara R

2016-06-01

Chronic disturbances, such as selective logging, firewood extraction and extensive grazing, may lead to the taxonomic and phylogenetic impoverishment of remaining old-growth forest communities worldwide; however, the empirical evidence on this topic is limited. We tested this hypothesis in the Caatinga vegetation--a seasonally dry tropical forest restricted to northeast Brazil. We sampled 11,653 individuals (adults, saplings, and seedlings) from 51 species in 29 plots distributed along a gradient of chronic disturbance. The gradient was assessed using a chronic disturbance index (CDI) based on five recognized indicators of chronic disturbances: proximity to urban center, houses and roads and the density of both people and livestock. We used linear models to test if mean effective number of lineages, mean phylogenetic distance and phylogenetic dispersion decreased with CDI and if such relationships differed among ontogenetic stages. As expected, the mean effective number of lineages and the mean phylogenetic distance were negatively related to CDI, and such diversity losses occurred irrespective of ontogeny. Yet the increase in phylogenetic clustering in more disturbed plots was only evident in seedlings and saplings, mostly because clades with more descendent taxa than expected by chance (e.g., Euphorbiaceae) thrived in more disturbed plots. This novel study indicates that chronic human disturbances are promoting the phylogenetic impoverishment of the irreplaceable woody flora of the Brazilian Caatinga forest. The highest impoverishment was observed in seedlings and saplings, indicating that if current chronic disturbances remain, they will result in increasingly poorer phylogenetically forests. This loss of evolutionary history will potentially limit the capacity of this ecosystem to respond to human disturbances (i.e., lower ecological resilience) and particularly their ability to adapt to rapid climatic changes in the region.

Understanding outbreaks of waterborne infectious disease: quantitative microbial risk assessment vs. epidemiology

USDA-ARS?s Scientific Manuscript database

Drinking water contaminated with microbial pathogens can cause outbreaks of infectious disease, and these outbreaks are traditionally studied using epidemiologic methods. Quantitative microbial risk assessment (QMRA) can predict – and therefore help prevent – such outbreaks, but it has never been r...

QUANTITATIVE ASSESSMENT OF CORAL DISEASES IN THE FLORIDA KEYS: STRATEGY AND METHODOLOGY

EPA Science Inventory

Most studies of coral disease have focused on the incidence of a single disease within a single location. Our overall objective is to use quantitative assessments to characterize annual patterns in the distribution and frequency of scleractinian and gorgonian coral diseases over ...

Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling.

PubMed

Ozer, Abdullah; Tome, Jacob M; Friedman, Robin C; Gheba, Dan; Schroth, Gary P; Lis, John T

2015-08-01

Because RNA-protein interactions have a central role in a wide array of biological processes, methods that enable a quantitative assessment of these interactions in a high-throughput manner are in great demand. Recently, we developed the high-throughput sequencing-RNA affinity profiling (HiTS-RAP) assay that couples sequencing on an Illumina GAIIx genome analyzer with the quantitative assessment of protein-RNA interactions. This assay is able to analyze interactions between one or possibly several proteins with millions of different RNAs in a single experiment. We have successfully used HiTS-RAP to analyze interactions of the EGFP and negative elongation factor subunit E (NELF-E) proteins with their corresponding canonical and mutant RNA aptamers. Here we provide a detailed protocol for HiTS-RAP that can be completed in about a month (8 d hands-on time). This includes the preparation and testing of recombinant proteins and DNA templates, clustering DNA templates on a flowcell, HiTS and protein binding with a GAIIx instrument, and finally data analysis. We also highlight aspects of HiTS-RAP that can be further improved and points of comparison between HiTS-RAP and two other recently developed methods, quantitative analysis of RNA on a massively parallel array (RNA-MaP) and RNA Bind-n-Seq (RBNS), for quantitative analysis of RNA-protein interactions.

Effects of Phylogenetic Tree Style on Student Comprehension

NASA Astrophysics Data System (ADS)

Dees, Jonathan Andrew

Phylogenetic trees are powerful tools of evolutionary biology that have become prominent across the life sciences. Consequently, learning to interpret and reason from phylogenetic trees is now an essential component of biology education. However, students often struggle to understand these diagrams, even after explicit instruction. One factor that has been observed to affect student understanding of phylogenetic trees is style (i.e., diagonal or bracket). The goal of this dissertation research was to systematically explore effects of style on student interpretations and construction of phylogenetic trees in the context of an introductory biology course. Before instruction, students were significantly more accurate with bracket phylogenetic trees for a variety of interpretation and construction tasks. Explicit instruction that balanced the use of diagonal and bracket phylogenetic trees mitigated some, but not all, style effects. After instruction, students were significantly more accurate for interpretation tasks involving taxa relatedness and construction exercises when using the bracket style. Based on this dissertation research and prior studies on style effects, I advocate for introductory biology instructors to use only the bracket style. Future research should examine causes of style effects and variables other than style to inform the development of research-based instruction that best supports student understanding of phylogenetic trees.

Automated Tracking of Quantitative Assessments of Tumor Burden in Clinical Trials1

PubMed Central

Rubin, Daniel L; Willrett, Debra; O'Connor, Martin J; Hage, Cleber; Kurtz, Camille; Moreira, Dilvan A

2014-01-01

There are two key challenges hindering effective use of quantitative assessment of imaging in cancer response assessment: 1) Radiologists usually describe the cancer lesions in imaging studies subjectively and sometimes ambiguously, and 2) it is difficult to repurpose imaging data, because lesion measurements are not recorded in a format that permits machine interpretation and interoperability. We have developed a freely available software platform on the basis of open standards, the electronic Physician Annotation Device (ePAD), to tackle these challenges in two ways. First, ePAD facilitates the radiologist in carrying out cancer lesion measurements as part of routine clinical trial image interpretation workflow. Second, ePAD records all image measurements and annotations in a data format that permits repurposing image data for analyses of alternative imaging biomarkers of treatment response. To determine the impact of ePAD on radiologist efficiency in quantitative assessment of imaging studies, a radiologist evaluated computed tomography (CT) imaging studies from 20 subjects having one baseline and three consecutive follow-up imaging studies with and without ePAD. The radiologist made measurements of target lesions in each imaging study using Response Evaluation Criteria in Solid Tumors 1.1 criteria, initially with the aid of ePAD, and then after a 30-day washout period, the exams were reread without ePAD. The mean total time required to review the images and summarize measurements of target lesions was 15% (P < .039) shorter using ePAD than without using this tool. In addition, it was possible to rapidly reanalyze the images to explore lesion cross-sectional area as an alternative imaging biomarker to linear measure. We conclude that ePAD appears promising to potentially improve reader efficiency for quantitative assessment of CT examinations, and it may enable discovery of future novel image-based biomarkers of cancer treatment response. PMID:24772204

Bayesian models for comparative analysis integrating phylogenetic uncertainty.

PubMed

de Villemereuil, Pierre; Wells, Jessie A; Edwards, Robert D; Blomberg, Simon P

2012-06-28

Uncertainty in comparative analyses can come from at least two sources: a) phylogenetic uncertainty in the tree topology or branch lengths, and b) uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow) and inflated significance in hypothesis testing (e.g. p-values will be too small). Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable. We developed models to directly incorporate phylogenetic uncertainty into a range of analyses that biologists commonly perform, using a Bayesian framework and Markov Chain Monte Carlo analyses. We demonstrate applications in linear regression, quantification of phylogenetic signal, and measurement error models. Phylogenetic uncertainty was incorporated by applying a prior distribution for the phylogeny, where this distribution consisted of the posterior tree sets from Bayesian phylogenetic tree estimation programs. The models were analysed using simulated data sets, and applied to a real data set on plant traits, from rainforest plant species in Northern Australia. Analyses were performed using the free and open source software OpenBUGS and JAGS. Incorporating phylogenetic uncertainty through an empirical prior distribution of trees leads to more precise estimation of regression model parameters than using a single consensus tree and enables a more realistic estimation of confidence intervals. In addition, models incorporating measurement errors and/or individual variation, in one or both variables, are easily formulated in the Bayesian framework. We show that BUGS is a useful, flexible general purpose tool for phylogenetic comparative analyses

Bayesian models for comparative analysis integrating phylogenetic uncertainty

PubMed Central

2012-01-01

Background Uncertainty in comparative analyses can come from at least two sources: a) phylogenetic uncertainty in the tree topology or branch lengths, and b) uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow) and inflated significance in hypothesis testing (e.g. p-values will be too small). Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable. Methods We developed models to directly incorporate phylogenetic uncertainty into a range of analyses that biologists commonly perform, using a Bayesian framework and Markov Chain Monte Carlo analyses. Results We demonstrate applications in linear regression, quantification of phylogenetic signal, and measurement error models. Phylogenetic uncertainty was incorporated by applying a prior distribution for the phylogeny, where this distribution consisted of the posterior tree sets from Bayesian phylogenetic tree estimation programs. The models were analysed using simulated data sets, and applied to a real data set on plant traits, from rainforest plant species in Northern Australia. Analyses were performed using the free and open source software OpenBUGS and JAGS. Conclusions Incorporating phylogenetic uncertainty through an empirical prior distribution of trees leads to more precise estimation of regression model parameters than using a single consensus tree and enables a more realistic estimation of confidence intervals. In addition, models incorporating measurement errors and/or individual variation, in one or both variables, are easily formulated in the Bayesian framework. We show that BUGS is a useful, flexible general purpose tool for

Open Reading Frame Phylogenetic Analysis on the Cloud

PubMed Central

2013-01-01

Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus. PMID:23671843

Quantitative motor assessment of muscular weakness in myasthenia gravis: a pilot study.

PubMed

Hoffmann, Sarah; Siedler, Jana; Brandt, Alexander U; Piper, Sophie K; Kohler, Siegfried; Sass, Christian; Paul, Friedemann; Reilmann, Ralf; Meisel, Andreas

2015-12-23

Muscular weakness in myasthenia gravis (MG) is commonly assessed using Quantitative Myasthenia Gravis Score (QMG). More objective and quantitative measures may complement the use of clinical scales and might detect subclinical affection of muscles. We hypothesized that muscular weakness in patients with MG can be quantified with the non-invasive Quantitative Motor (Q-Motor) test for Grip Force Assessment (QGFA) and Involuntary Movement Assessment (QIMA) and that pathological findings correlate with disease severity as measured by QMG. This was a cross-sectional pilot study investigating patients with confirmed diagnosis of MG. Data was compared to healthy controls (HC). Subjects were asked to lift a device (250 and 500 g) equipped with electromagnetic sensors that measured grip force (GF) and three-dimensional changes in position and orientation. These were used to calculate the position index (PI) and orientation index (OI) as measures for involuntary movements due to muscular weakness. Overall, 40 MG patients and 23 HC were included. PI and OI were significantly higher in MG patients for both weights in the dominant and non-dominant hand. Subgroup analysis revealed that patients with clinically ocular myasthenia gravis (OMG) also showed significantly higher values for PI and OI in both hands and for both weights. Disease severity correlates with QIMA performance in the non-dominant hand. Q-Motor tests and particularly QIMA may be useful objective tools for measuring motor impairment in MG and seem to detect subclinical generalized motor signs in patients with OMG. Q-Motor parameters might serve as sensitive endpoints for clinical trials in MG.

Assessment of fecal pollution sources in a small northern-plains watershed using PCR and phylogenetic analyses of Bacteroidetes 16S rRNA gene

USGS Publications Warehouse

Lamendella, R.; Domingo, J.W.S.; Oerther, D.B.; Vogel, J.R.; Stoeckel, D.M.

2007-01-01

We evaluated the efficacy, sensitivity, host-specificity, and spatial/temporal dynamics of human- and ruminant-specific 16S rRNA gene Bacteroidetes markers used to assess the sources of fecal pollution in a fecally impacted watershed. Phylogenetic analyses of 1271 fecal and environmental 16S rRNA gene clones were also performed to study the diversity of Bacteroidetes in this watershed. The host-specific assays indicated that ruminant feces were present in 28-54% of the water samples and in all sampling seasons, with increasing frequency in downstream sites. The human-targeted assays indicated that only 3-5% of the water samples were positive for human fecal signals, although a higher percentage of human-associated signals (19-24%) were detected in sediment samples. Phylogenetic analysis indicated that 57% of all water clones clustered with yet-to-be-cultured Bacteroidetes species associated with sequences obtained from ruminant feces, further supporting the prevalence of ruminant contamination in this watershed. However, since several clusters contained sequences from multiple sources, future studies need to consider the potential cosmopolitan nature of these bacterial populations when assessing fecal pollution sources using Bacteroidetes markers. Moreover, additional data is needed in order to understand the distribution of Bacteroidetes host-specific markers and their relationship to water quality regulatory standards. ?? 2006 Federation of European Microbiological Societies.

A comparative study of qualitative and quantitative methods for the assessment of adhesive remnant after bracket debonding.

PubMed

Cehreli, S Burcak; Polat-Ozsoy, Omur; Sar, Cagla; Cubukcu, H Evren; Cehreli, Zafer C

2012-04-01

The amount of the residual adhesive after bracket debonding is frequently assessed in a qualitative manner, utilizing the adhesive remnant index (ARI). This study aimed to investigate whether quantitative assessment of the adhesive remnant yields more precise results compared to qualitative methods utilizing the 4- and 5-point ARI scales. Twenty debonded brackets were selected. Evaluation and scoring of the adhesive remnant on bracket bases were made consecutively using: 1. qualitative assessment (visual scoring) and 2. quantitative measurement (image analysis) on digital photographs. Image analysis was made on scanning electron micrographs (SEM) and high-precision elemental maps of the adhesive remnant as determined by energy dispersed X-ray spectrometry. Evaluations were made in accordance with the original 4-point and the modified 5-point ARI scales. Intra-class correlation coefficients (ICCs) were calculated, and the data were evaluated using Friedman test followed by Wilcoxon signed ranks test with Bonferroni correction. ICC statistics indicated high levels of agreement for qualitative visual scoring among examiners. The 4-point ARI scale was compliant with the SEM assessments but indicated significantly less adhesive remnant compared to the results of quantitative elemental mapping. When the 5-point scale was used, both quantitative techniques yielded similar results with those obtained qualitatively. These results indicate that qualitative visual scoring using the ARI is capable of generating similar results with those assessed by quantitative image analysis techniques. In particular, visual scoring with the 5-point ARI scale can yield similar results with both the SEM analysis and elemental mapping.

Molecular cytogenetic characterisation and phylogenetic analysis of the seven cultivated Vigna species (Fabaceae).

PubMed

She, C-W; Jiang, X-H; Ou, L-J; Liu, J; Long, K-L; Zhang, L-H; Duan, W-T; Zhao, W; Hu, J-C

2015-01-01

The genomic organisation of the seven cultivated Vigna species, V. unguiculata, V. subterranea, V. angularis, V. umbellata, V. radiata, V. mungo and V. aconitifolia, was determined using sequential combined PI and DAPI (CPD) staining and dual-colour fluorescence in situ hybridisation (FISH) with 5S and 45S rDNA probes. For phylogenetic analyses, comparative genomic in situ hybridisation (cGISH) onto somatic chromosomes and sequence analysis of the internal transcribed spacer (ITS) of 45S rDNA were used. Quantitative karyotypes were established using chromosome measurements, fluorochrome bands and rDNA FISH signals. All species had symmetrical karyotypes composed of only metacentric or metacentric and submetacentric chromosomes. Distinct heterochromatin differentiation was revealed by CPD staining and DAPI counterstaining after FISH. The rDNA sites among all species differed in their number, location and size. cGISH of V. umbellata genomic DNA to the chromosomes of all species produced strong signals in all centromeric regions of V. umbellata and V. angularis, weak signals in all pericentromeric regions of V. aconitifolia, and CPD-banded proximal regions of V. mungo var. mungo. Molecular phylogenetic trees showed that V. angularis and V. umbellata were the closest relatives, and V. mungo and V. aconitifolia were relatively closely related; these species formed a group that was separated from another group comprising V. radiata, V. unguiculata ssp. sesquipedalis and V. subterranea. This result was consistent with the phylogenetic relationships inferred from the heterochromatin and cGISH patterns; thus, fluorochrome banding and cGISH are efficient tools for the phylogenetic analysis of Vigna species. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Phylogenetic incongruence in the Drosophila melanogaster species group

PubMed Central

Wong, Alex; Jensen, Jeffrey D.; Pool, John E.; Aquadro, Charles F.

2007-01-01

Drosophila melanogaster and its close relatives are used extensively in comparative biology. Despite the importance of phylogenetic information for such studies, relationships between some melanogaster species group members are unclear due to conflicting phylogenetic signals at different loci. In this study, we use twelve nuclear loci (eleven coding and one non-coding) to assess the degree of phylogenetic incongruence in this model system. We focus on two nodes: (1) The node joining the D. erecta-D. orena, D. melanogaster-D. simulans, and D. yakuba-D. teissieri lineages, and (2) The node joining the lineages leading to the melanogaster, takahashii, and eugracilis subgroups. We find limited evidence for incongruence at the first node; our data, as well as those of several previous studies, strongly support monophyly of a clade consisting of D. erecta-D. orena and D. yakuba-D. teissieri. By contrast, using likelihood based tests of congruence, we find robust evidence for topological incongruence at the second node. Different loci support different relationships among the melanogaster, takahashii and eugracilis subgroups, and the observed incongruence is not easily attributable to homoplasy, non-equilibrium base composition, or positive selection on a subset of loci. We argue that lineage sorting in the common ancestor of these three subgroups is the most plausible explanation for our observations. Such lineage sorting may lead to biased estimation of tree topology and evolutionary rates, and may confound inferences of positive selection. PMID:17071113

SERAPHIM: studying environmental rasters and phylogenetically informed movements.

PubMed

Dellicour, Simon; Rose, Rebecca; Faria, Nuno R; Lemey, Philippe; Pybus, Oliver G

2016-10-15

SERAPHIM ("Studying Environmental Rasters and PHylogenetically Informed Movements") is a suite of computational methods developed to study phylogenetic reconstructions of spatial movement in an environmental context. SERAPHIM extracts the spatio-temporal information contained in estimated phylogenetic trees and uses this information to calculate summary statistics of spatial spread and to visualize dispersal history. Most importantly, SERAPHIM enables users to study the impact of customized environmental variables on the spread of the study organism. Specifically, given an environmental raster, SERAPHIM computes environmental "weights" for each phylogeny branch, which represent the degree to which the environmental variable impedes (or facilitates) lineage movement. Correlations between movement duration and these environmental weights are then assessed, and the statistical significances of these correlations are evaluated using null distributions generated by a randomization procedure. SERAPHIM can be applied to any phylogeny whose nodes are annotated with spatial and temporal information. At present, such phylogenies are most often found in the field of emerging infectious diseases, but will become increasingly common in other biological disciplines as population genomic data grows. SERAPHIM 1.0 is freely available from http://evolve.zoo.ox.ac.uk/ R package, source code, example files, tutorials and a manual are also available from this website. simon.dellicour@kuleuven.be or oliver.pybus@zoo.ox.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Tetrapods on the EDGE: Overcoming data limitations to identify phylogenetic conservation priorities

PubMed Central

Gray, Claudia L.; Wearn, Oliver R.; Owen, Nisha R.

2018-01-01

The scale of the ongoing biodiversity crisis requires both effective conservation prioritisation and urgent action. As extinction is non-random across the tree of life, it is important to prioritise threatened species which represent large amounts of evolutionary history. The EDGE metric prioritises species based on their Evolutionary Distinctiveness (ED), which measures the relative contribution of a species to the total evolutionary history of their taxonomic group, and Global Endangerment (GE), or extinction risk. EDGE prioritisations rely on adequate phylogenetic and extinction risk data to generate meaningful priorities for conservation. However, comprehensive phylogenetic trees of large taxonomic groups are extremely rare and, even when available, become quickly out-of-date due to the rapid rate of species descriptions and taxonomic revisions. Thus, it is important that conservationists can use the available data to incorporate evolutionary history into conservation prioritisation. We compared published and new methods to estimate missing ED scores for species absent from a phylogenetic tree whilst simultaneously correcting the ED scores of their close taxonomic relatives. We found that following artificial removal of species from a phylogenetic tree, the new method provided the closest estimates of their “true” ED score, differing from the true ED score by an average of less than 1%, compared to the 31% and 38% difference of the previous methods. The previous methods also substantially under- and over-estimated scores as more species were artificially removed from a phylogenetic tree. We therefore used the new method to estimate ED scores for all tetrapods. From these scores we updated EDGE prioritisation rankings for all tetrapod species with IUCN Red List assessments, including the first EDGE prioritisation for reptiles. Further, we identified criteria to identify robust priority species in an effort to further inform conservation action whilst

Affordable, automatic quantitative fall risk assessment based on clinical balance scales and Kinect data.

PubMed

Colagiorgio, P; Romano, F; Sardi, F; Moraschini, M; Sozzi, A; Bejor, M; Ricevuti, G; Buizza, A; Ramat, S

2014-01-01

The problem of a correct fall risk assessment is becoming more and more critical with the ageing of the population. In spite of the available approaches allowing a quantitative analysis of the human movement control system's performance, the clinical assessment and diagnostic approach to fall risk assessment still relies mostly on non-quantitative exams, such as clinical scales. This work documents our current effort to develop a novel method to assess balance control abilities through a system implementing an automatic evaluation of exercises drawn from balance assessment scales. Our aim is to overcome the classical limits characterizing these scales i.e. limited granularity and inter-/intra-examiner reliability, to obtain objective scores and more detailed information allowing to predict fall risk. We used Microsoft Kinect to record subjects' movements while performing challenging exercises drawn from clinical balance scales. We then computed a set of parameters quantifying the execution of the exercises and fed them to a supervised classifier to perform a classification based on the clinical score. We obtained a good accuracy (~82%) and especially a high sensitivity (~83%).

Quantitative traits and diversification.

PubMed

FitzJohn, Richard G

2010-12-01

Quantitative traits have long been hypothesized to affect speciation and extinction rates. For example, smaller body size or increased specialization may be associated with increased rates of diversification. Here, I present a phylogenetic likelihood-based method (quantitative state speciation and extinction [QuaSSE]) that can be used to test such hypotheses using extant character distributions. This approach assumes that diversification follows a birth-death process where speciation and extinction rates may vary with one or more traits that evolve under a diffusion model. Speciation and extinction rates may be arbitrary functions of the character state, allowing much flexibility in testing models of trait-dependent diversification. I test the approach using simulated phylogenies and show that a known relationship between speciation and a quantitative character could be recovered in up to 80% of the cases on large trees (500 species). Consistent with other approaches, detecting shifts in diversification due to differences in extinction rates was harder than when due to differences in speciation rates. Finally, I demonstrate the application of QuaSSE to investigate the correlation between body size and diversification in primates, concluding that clade-specific differences in diversification may be more important than size-dependent diversification in shaping the patterns of diversity within this group.

Universal artifacts affect the branching of phylogenetic trees, not universal scaling laws.

PubMed

Altaba, Cristian R

2009-01-01

The superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny? In order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods. All methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors--uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts

Using integrated environmental modeling to automate a process-based Quantitative Microbial Risk Assessment

EPA Science Inventory

Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, an...

Methods of quantitative risk assessment: The case of the propellant supply system

NASA Astrophysics Data System (ADS)

Merz, H. A.; Bienz, A.

1984-08-01

As a consequence of the disastrous accident in Lapua (Finland) in 1976, where an explosion in a cartridge loading facility killed 40 and injured more than 70 persons, efforts were undertaken to examine and improve the safety of such installations. An ammunition factory in Switzerland considered the replacement of the manual supply of propellant hoppers by a new pneumatic supply system. This would reduce the maximum quantity of propellant in the hoppers to a level, where an accidental ignition would no longer lead to a detonation, and this would drastically limit the effects on persons. A quantitative risk assessment of the present and the planned supply system demonstrated that, in this particular case, the pneumatic supply system would not reduce the risk enough to justify the related costs. In addition, it could be shown that the safety of the existing system can be improved more effectively by other safety measures at considerably lower costs. Based on this practical example, the advantages of a strictly quantitative risk assessment for the safety planning in explosives factories are demonstrated. The methodological background of a risk assessment and the steps involved in the analysis are summarized. In addition, problems of quantification are discussed.

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

PubMed Central

Erickson, David L.; Jones, Frank A.; Swenson, Nathan G.; Pei, Nancai; Bourg, Norman A.; Chen, Wenna; Davies, Stuart J.; Ge, Xue-jun; Hao, Zhanqing; Howe, Robert W.; Huang, Chun-Lin; Larson, Andrew J.; Lum, Shawn K. Y.; Lutz, James A.; Ma, Keping; Meegaskumbura, Madhava; Mi, Xiangcheng; Parker, John D.; Fang-Sun, I.; Wright, S. Joseph; Wolf, Amy T.; Ye, W.; Xing, Dingliang; Zimmerman, Jess K.; Kress, W. John

2014-01-01

Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of

Use of Quantitative Microbial Risk Assessment to Improve Interpretation of a Recreational Water Epidemiological Study

EPA Science Inventory

We conducted a supplemental water quality monitoring study and quantitative microbial risk assessment (QMRA) to complement the United States Environmental Protection Agency’s (U.S. EPA) National Epidemiological and Environmental Assessment of Recreational Water study at Boquerón ...

[A quantitative risk assessment model of salmonella on carcass in poultry slaughterhouse].

PubMed

Zhang, Yu; Chen, Yuzhen; Hu, Chunguang; Zhang, Huaning; Bi, Zhenwang; Bi, Zhenqiang

2015-05-01

To construct a quantitative risk assessment model of salmonella on carcass in poultry slaughterhouse and to find out effective interventions to reduce salmonella contamination. We constructed a modular process risk model (MPRM) from evisceration to chilling in Excel Sheet using the data of the process parameters in poultry and the Salmomella concentration surveillance of Jinan in 2012. The MPRM was simulated by @ risk software. The concentration of salmonella on carcass after chilling was 1.96MPN/g which was calculated by model. The sensitive analysis indicated that the correlation coefficient of the concentration of salmonella after defeathering and in chilling pool were 0.84 and 0.34,which were the primary factors to the concentration of salmonella on carcass after chilling. The study provided a quantitative assessment model structure for salmonella on carcass in poultry slaughterhouse. The risk manager could control the contamination of salmonella on carcass after chilling by reducing the concentration of salmonella after defeathering and in chilling pool.

Modeling adaptive kernels from probabilistic phylogenetic trees.

PubMed

Nicotra, Luca; Micheli, Alessio

2009-01-01

Modeling phylogenetic interactions is an open issue in many computational biology problems. In the context of gene function prediction we introduce a class of kernels for structured data leveraging on a hierarchical probabilistic modeling of phylogeny among species. We derive three kernels belonging to this setting: a sufficient statistics kernel, a Fisher kernel, and a probability product kernel. The new kernels are used in the context of support vector machine learning. The kernels adaptivity is obtained through the estimation of the parameters of a tree structured model of evolution using as observed data phylogenetic profiles encoding the presence or absence of specific genes in a set of fully sequenced genomes. We report results obtained in the prediction of the functional class of the proteins of the budding yeast Saccharomyces cerevisae which favorably compare to a standard vector based kernel and to a non-adaptive tree kernel function. A further comparative analysis is performed in order to assess the impact of the different components of the proposed approach. We show that the key features of the proposed kernels are the adaptivity to the input domain and the ability to deal with structured data interpreted through a graphical model representation.

Visualizing Phylogenetic Treespace Using Cartographic Projections

NASA Astrophysics Data System (ADS)

Sundberg, Kenneth; Clement, Mark; Snell, Quinn

Phylogenetic analysis is becoming an increasingly important tool for biological research. Applications include epidemiological studies, drug development, and evolutionary analysis. Phylogenetic search is a known NP-Hard problem. The size of the data sets which can be analyzed is limited by the exponential growth in the number of trees that must be considered as the problem size increases. A better understanding of the problem space could lead to better methods, which in turn could lead to the feasible analysis of more data sets. We present a definition of phylogenetic tree space and a visualization of this space that shows significant exploitable structure. This structure can be used to develop search methods capable of handling much larger datasets.

Phylogenetic diversity of a microbialite reef in a cold alkaline freshwater lake.

PubMed

Chan, Olivia W; Bugler-Lacap, Donnabella C; Biddle, Jennifer F; Lim, Darlene S; McKay, Christopher P; Pointing, Stephen B

2014-06-01

A culture-independent multidomain survey of biodiversity in microbialite structures within the cold alkaline Pavilion Lake (British Columbia, Canada) revealed a largely homogenous community at depths from 10 to 30 m. Real-time quantitative PCR was used to demonstrate that bacteria comprised approximately 80%-95% of recoverable phylotypes. Archaeal phylotypes accounted for <5% of the community in microbialites exposed to the water column, while structures in sediment contact supported 4- to 5-fold higher archaeal abundance. Eukaryal phylotypes were rare and indicated common aquatic diatoms that were concluded not to be part of the microbialite community. Phylogenetic analysis of rRNA genes from clone libraries (N = 491) revealed that alphaproteobacterial phylotypes were most abundant. Cyanobacterial phylotypes were highly diverse but resolved into 4 dominant genera: Acaryochloris, Leptolyngbya, Microcoleus, and Pseudanabaena. Interestingly, microbialite cyanobacteria generally affiliated phylogenetically with aquatic and coral cyanobacterial groups rather than those from stromatolites. Other commonly encountered bacterial phylotypes were from members of the Acidobacteria, with relatively low abundance of the Betaproteobacteria, Chloroflexi, Nitrospirae, and Planctomycetes. Archaeal diversity (N = 53) was largely accounted for by Euryarchaeota, with most phylotypes affiliated with freshwater methanogenic taxa.

Visualizing phylogenetic tree landscapes.

PubMed

Wilgenbusch, James C; Huang, Wen; Gallivan, Kyle A

2017-02-02

Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D

Comprehensive, Quantitative Risk Assessment of CO{sub 2} Geologic Sequestration

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

Lepinski, James

2013-09-30

A Quantitative Failure Modes and Effects Analysis (QFMEA) was developed to conduct comprehensive, quantitative risk assessments on CO{sub 2} capture, transportation, and sequestration or use in deep saline aquifers, enhanced oil recovery operations, or enhanced coal bed methane operations. The model identifies and characterizes potential risks; identifies the likely failure modes, causes, effects and methods of detection; lists possible risk prevention and risk mitigation steps; estimates potential damage recovery costs, mitigation costs and costs savings resulting from mitigation; and ranks (prioritizes) risks according to the probability of failure, the severity of failure, the difficulty of early failure detection and themore » potential for fatalities. The QFMEA model generates the necessary information needed for effective project risk management. Diverse project information can be integrated into a concise, common format that allows comprehensive, quantitative analysis, by a cross-functional team of experts, to determine: What can possibly go wrong? How much will damage recovery cost? How can it be prevented or mitigated? What is the cost savings or benefit of prevention or mitigation? Which risks should be given highest priority for resolution? The QFMEA model can be tailored to specific projects and is applicable to new projects as well as mature projects. The model can be revised and updated as new information comes available. It accepts input from multiple sources, such as literature searches, site characterization, field data, computer simulations, analogues, process influence diagrams, probability density functions, financial analysis models, cost factors, and heuristic best practices manuals, and converts the information into a standardized format in an Excel spreadsheet. Process influence diagrams, geologic models, financial models, cost factors and an insurance schedule were developed to support the QFMEA model. Comprehensive, quantitative risk

Development and Assessment of Modules to Integrate Quantitative Skills in Introductory Biology Courses

PubMed Central

Hoffman, Kathleen; Leupen, Sarah; Dowell, Kathy; Kephart, Kerrie; Leips, Jeff

2016-01-01

Redesigning undergraduate biology courses to integrate quantitative reasoning and skill development is critical to prepare students for careers in modern medicine and scientific research. In this paper, we report on the development, implementation, and assessment of stand-alone modules that integrate quantitative reasoning into introductory biology courses. Modules are designed to improve skills in quantitative numeracy, interpreting data sets using visual tools, and making inferences about biological phenomena using mathematical/statistical models. We also examine demographic/background data that predict student improvement in these skills through exposure to these modules. We carried out pre/postassessment tests across four semesters and used student interviews in one semester to examine how students at different levels approached quantitative problems. We found that students improved in all skills in most semesters, although there was variation in the degree of improvement among skills from semester to semester. One demographic variable, transfer status, stood out as a major predictor of the degree to which students improved (transfer students achieved much lower gains every semester, despite the fact that pretest scores in each focus area were similar between transfer and nontransfer students). We propose that increased exposure to quantitative skill development in biology courses is effective at building competency in quantitative reasoning. PMID:27146161

Folding and unfolding phylogenetic trees and networks.

PubMed

Huber, Katharina T; Moulton, Vincent; Steel, Mike; Wu, Taoyang

2016-12-01

Phylogenetic networks are rooted, labelled directed acyclic graphswhich are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network N can be "unfolded" to obtain a MUL-tree U(N) and, conversely, a MUL-tree T can in certain circumstances be "folded" to obtain aphylogenetic network F(T) that exhibits T. In this paper, we study properties of the operations U and F in more detail. In particular, we introduce the class of stable networks, phylogenetic networks N for which F(U(N)) is isomorphic to N, characterise such networks, and show that they are related to the well-known class of tree-sibling networks. We also explore how the concept of displaying a tree in a network N can be related to displaying the tree in the MUL-tree U(N). To do this, we develop aphylogenetic analogue of graph fibrations. This allows us to view U(N) as the analogue of the universal cover of a digraph, and to establish a close connection between displaying trees in U(N) and reconciling phylogenetic trees with networks.

Assessment of Scientific Literacy: Development and Validation of the Quantitative Assessment of Socio-Scientific Reasoning (QuASSR)

ERIC Educational Resources Information Center

Romine, William L.; Sadler, Troy D.; Kinslow, Andrew T.

2017-01-01

We describe the development and validation of the Quantitative Assessment of Socio-scientific Reasoning (QuASSR) in a college context. The QuASSR contains 10 polytomous, two-tiered items crossed between two scenarios, and is based on theory suggesting a four-pronged structure for SSR (complexity, perspective taking, inquiry, and skepticism). In…

Worldwide Phylogenetic Relationship of Avian Poxviruses

PubMed Central

Foster, Jeffrey T.; Dán, Ádám; Ip, Hon S.; Egstad, Kristina F.; Parker, Patricia G.; Higashiguchi, Jenni M.; Skinner, Michael A.; Höfle, Ursula; Kreizinger, Zsuzsa; Dorrestein, Gerry M.; Solt, Szabolcs; Sós, Endre; Kim, Young Jun; Uhart, Marcela; Pereda, Ariel; González-Hein, Gisela; Hidalgo, Hector; Blanco, Juan-Manuel; Erdélyi, Károly

2013-01-01

Poxvirus infections have been found in 230 species of wild and domestic birds worldwide in both terrestrial and marine environments. This ubiquity raises the question of how infection has been transmitted and globally dispersed. We present a comprehensive global phylogeny of 111 novel poxvirus isolates in addition to all available sequences from GenBank. Phylogenetic analysis of the Avipoxvirus genus has traditionally relied on one gene region (4b core protein). In this study we expanded the analyses to include a second locus (DNA polymerase gene), allowing for a more robust phylogenetic framework, finer genetic resolution within specific groups, and the detection of potential recombination. Our phylogenetic results reveal several major features of avipoxvirus evolution and ecology and propose an updated avipoxvirus taxonomy, including three novel subclades. The characterization of poxviruses from 57 species of birds in this study extends the current knowledge of their host range and provides the first evidence of the phylogenetic effect of genetic recombination of avipoxviruses. The repeated occurrence of avian family or order-specific grouping within certain clades (e.g., starling poxvirus, falcon poxvirus, raptor poxvirus, etc.) indicates a marked role of host adaptation, while the sharing of poxvirus species within prey-predator systems emphasizes the capacity for cross-species infection and limited host adaptation. Our study provides a broad and comprehensive phylogenetic analysis of the Avipoxvirus genus, an ecologically and environmentally important viral group, to formulate a genome sequencing strategy that will clarify avipoxvirus taxonomy. PMID:23408635

Worldwide phylogenetic relationship of avian poxviruses

USGS Publications Warehouse

Gyuranecz, Miklós; Foster, Jeffrey T.; Dán, Ádám; Ip, Hon S.; Egstad, Kristina F.; Parker, Patricia G.; Higashiguchi, Jenni M.; Skinner, Michael A.; Höfle, Ursula; Kreizinger, Zsuzsa; Dorrestein, Gerry M.; Solt, Szabolcs; Sós, Endre; Kim, Young Jun; Uhart, Marcela; Pereda, Ariel; González-Hein, Gisela; Hidalgo, Hector; Blanco, Juan-Manuel; Erdélyi, Károly

2013-01-01

Poxvirus infections have been found in 230 species of wild and domestic birds worldwide in both terrestrial and marine environments. This ubiquity raises the question of how infection has been transmitted and globally dispersed. We present a comprehensive global phylogeny of 111 novel poxvirus isolates in addition to all available sequences from GenBank. Phylogenetic analysis of Avipoxvirus genus has traditionally relied on one gene region (4b core protein). In this study we have expanded the analyses to include a second locus (DNA polymerase gene), allowing for a more robust phylogenetic framework, finer genetic resolution within specific groups and the detection of potential recombination. Our phylogenetic results reveal several major features of avipoxvirus evolution and ecology and propose an updated avipoxvirus taxonomy, including three novel subclades. The characterization of poxviruses from 57 species of birds in this study extends the current knowledge of their host range and provides the first evidence of the phylogenetic effect of genetic recombination of avipoxviruses. The repeated occurrence of avian family or order-specific grouping within certain clades (e.g. starling poxvirus, falcon poxvirus, raptor poxvirus, etc.) indicates a marked role of host adaptation, while the sharing of poxvirus species within prey-predator systems emphasizes the capacity for cross-species infection and limited host adaptation. Our study provides a broad and comprehensive phylogenetic analysis of the Avipoxvirus genus, an ecologically and environmentally important viral group, to formulate a genome sequencing strategy that will clarify avipoxvirus taxonomy.

Quantitative risk assessment for skin sensitization: Success or failure?

PubMed

Kimber, Ian; Gerberick, G Frank; Basketter, David A

2017-02-01

Skin sensitization is unique in the world of toxicology. There is a combination of reliable, validated predictive test methods for identification of skin sensitizing chemicals, a clearly documented and transparent approach to risk assessment, and effective feedback from dermatology clinics around the world delivering evidence of the success or failure of the hazard identification/risk assessment/management process. Recent epidemics of contact allergy, particularly to preservatives, have raised questions of whether the safety/risk assessment process is working in an optimal manner (or indeed is working at all!). This review has as its focus skin sensitization quantitative risk assessment (QRA). The core toxicological principles of QRA are reviewed, and evidence of use and misuse examined. What becomes clear is that skin sensitization QRA will only function adequately if two essential criteria are met. The first is that QRA is applied rigourously, and the second is that potential exposure to the sensitizing substance is assessed adequately. This conclusion will come as no surprise to any toxicologist who appreciates the basic premise that "risk = hazard x exposure". Accordingly, use of skin sensitization QRA is encouraged, not least because the essential feedback from dermatology clinics can be used as a tool to refine QRA in situations where this risk assessment tool has not been properly used. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantitative analysis for peripheral vascularity assessment based on clinical photoacoustic and ultrasound images

NASA Astrophysics Data System (ADS)

Murakoshi, Dai; Hirota, Kazuhiro; Ishii, Hiroyasu; Hashimoto, Atsushi; Ebata, Tetsurou; Irisawa, Kaku; Wada, Takatsugu; Hayakawa, Toshiro; Itoh, Kenji; Ishihara, Miya

2018-02-01

Photoacoustic (PA) imaging technology is expected to be applied to clinical assessment for peripheral vascularity. We started a clinical evaluation with the prototype PA imaging system we recently developed. Prototype PA imaging system was composed with in-house Q-switched Alexandrite laser system which emits short-pulsed laser with 750 nm wavelength, handheld ultrasound transducer where illumination optics were integrated and signal processing for PA image reconstruction implemented in the clinical ultrasound (US) system. For the purpose of quantitative assessment of PA images, an image analyzing function has been developed and applied to clinical PA images. In this analyzing function, vascularity derived from PA signal intensity ranged for prescribed threshold was defined as a numerical index of vessel fulfillment and calculated for the prescribed region of interest (ROI). Skin surface was automatically detected by utilizing B-mode image acquired simultaneously with PA image. Skinsurface position is utilized to place the ROI objectively while avoiding unwanted signals such as artifacts which were imposed due to melanin pigment in the epidermal layer which absorbs laser emission and generates strong PA signals. Multiple images were available to support the scanned image set for 3D viewing. PA images for several fingers of patients with systemic sclerosis (SSc) were quantitatively assessed. Since the artifact region is trimmed off in PA images, the visibility of vessels with rather low PA signal intensity on the 3D projection image was enhanced and the reliability of the quantitative analysis was improved.

Using integrated environmental modeling to automate a process-based Quantitative Microbial Risk Assessment

USDA-ARS?s Scientific Manuscript database

Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, and human health effect...

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution

PubMed Central

Kendall, Michelle; Colijn, Caroline

2016-01-01

Evolutionary relationships are frequently described by phylogenetic trees, but a central barrier in many fields is the difficulty of interpreting data containing conflicting phylogenetic signals. We present a metric-based method for comparing trees which extracts distinct alternative evolutionary relationships embedded in data. We demonstrate detection and resolution of phylogenetic uncertainty in a recent study of anole lizards, leading to alternate hypotheses about their evolutionary relationships. We use our approach to compare trees derived from different genes of Ebolavirus and find that the VP30 gene has a distinct phylogenetic signature composed of three alternatives that differ in the deep branching structure. Key words: phylogenetics, evolution, tree metrics, genetics, sequencing. PMID:27343287

A phylogenetic perspective on species diversity, β-diversity and biogeography for the microbial world.

PubMed

Barberán, Albert; Casamayor, Emilio O

2014-12-01

There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high-altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High-altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies. © 2014 John Wiley & Sons Ltd.

Quantitative Approach to Collaborative Learning: Performance Prediction, Individual Assessment, and Group Composition

ERIC Educational Resources Information Center

Cen, Ling; Ruta, Dymitr; Powell, Leigh; Hirsch, Benjamin; Ng, Jason

2016-01-01

The benefits of collaborative learning, although widely reported, lack the quantitative rigor and detailed insight into the dynamics of interactions within the group, while individual contributions and their impacts on group members and their collaborative work remain hidden behind joint group assessment. To bridge this gap we intend to address…

High School Students’ Learning and Perceptions of Phylogenetics of Flowering Plants

PubMed Central

Landis, Jacob B.; Crippen, Kent J.

2014-01-01

Basic phylogenetics and associated “tree thinking” are often minimized or excluded in formal school curricula. Informal settings provide an opportunity to extend the K–12 school curriculum, introducing learners to new ideas, piquing interest in science, and fostering scientific literacy. Similarly, university researchers participating in science, technology, engineering, and mathematics (STEM) outreach activities increase awareness of college and career options and highlight interdisciplinary fields of science research and augment the science curriculum. To aid in this effort, we designed a 6-h module in which students utilized 12 flowering plant species to generate morphological and molecular phylogenies using biological techniques and bioinformatics tools. The phylogenetics module was implemented with 83 high school students during a weeklong university STEM immersion program and aimed to increase student understanding of phylogenetics and coevolution of plants and pollinators. Student response reflected positive engagement and learning gains as evidenced through content assessments, program evaluation surveys, and program artifacts. We present the results of the first year of implementation and discuss modifications for future use in our immersion programs as well as in multiple course settings at the high school and undergraduate levels. PMID:25452488

Quantitative Assessment of a Field-Based Course on Integrative Geology, Ecology and Cultural History

ERIC Educational Resources Information Center

Sheppard, Paul R.; Donaldson, Brad A.; Huckleberry, Gary

2010-01-01

A field-based course at the University of Arizona called Sense of Place (SOP) covers the geology, ecology and cultural history of the Tucson area. SOP was quantitatively assessed for pedagogical effectiveness. Students of the Spring 2008 course were given pre- and post-course word association surveys in order to assess awareness and comprehension…

Invasions but not extinctions change phylogenetic diversity of angiosperm assemblage on southeastern Pacific Oceanic islands

PubMed Central

2017-01-01

We assessed changes in phylogenetic diversity of angiosperm flora on six oceanic islands located in the southeastern Pacific Ocean, by comparing flora from two periods: the pre-European colonization of islands and current times. We hypothesize that, in the time between these periods, extinction of local plant species and addition of exotic plants modified phylogenetic-α-diversity at different levels (deeper and terminal phylogeny) and increased phylo-β-diversity among islands. Based on floristic studies, we assembled a phylogenetic tree from occurrence data that includes 921 species, of which 165 and 756 were native or exotic in origin, respectively. Then, we studied change in the phylo-α-diversity and phylo-β-diversity (1 –Phylosor) by comparing pre-European and current times. Despite extinction of 18 native angiosperm species, an increase in species richness and phylo-α-diversity was observed for all islands studied, attributed to introduction of exotic plants (between 6 to 477 species per island). We did not observe significant variation of mean phylogenetic distance (MPD), a measure of the ‘deeper’ phylogenetic diversity of assemblages (e.g., orders, families), suggesting that neither extinctions nor introductions altered phylogenetic structure of the angiosperms of these islands. In regard to phylo-β-diversity, we detected temporal turnover (variation in phylogenetic composition) between periods to flora (0.38 ± 0.11). However, when analyses were performed only considering native plants, we did not observe significant temporal turnover between periods (0.07 ± 0.06). These results indicate that introduction of exotic angiosperms has contributed more notably than extinctions to the configuration of plant assemblages and phylogenetic diversity on the studied islands. Because phylogenetic diversity is closely related to functional diversity (species trait variations and roles performed by organisms), our results suggests that the introduction of

Predicting rates of interspecific interaction from phylogenetic trees.

PubMed

Nuismer, Scott L; Harmon, Luke J

2015-01-01

Integrating phylogenetic information can potentially improve our ability to explain species' traits, patterns of community assembly, the network structure of communities, and ecosystem function. In this study, we use mathematical models to explore the ecological and evolutionary factors that modulate the explanatory power of phylogenetic information for communities of species that interact within a single trophic level. We find that phylogenetic relationships among species can influence trait evolution and rates of interaction among species, but only under particular models of species interaction. For example, when interactions within communities are mediated by a mechanism of phenotype matching, phylogenetic trees make specific predictions about trait evolution and rates of interaction. In contrast, if interactions within a community depend on a mechanism of phenotype differences, phylogenetic information has little, if any, predictive power for trait evolution and interaction rate. Together, these results make clear and testable predictions for when and how evolutionary history is expected to influence contemporary rates of species interaction. © 2014 John Wiley & Sons Ltd/CNRS.

Laser gingival retraction: a quantitative assessment.

PubMed

Krishna Ch, Vamsi; Gupta, Nidhi; Reddy, K Mahendranadh; Sekhar, N Chandra; Aditya, Venkata; Reddy, G V K Mohan

2013-08-01

Proper gingival retraction improves the prognosis of crowns and bridges with sub gingival finishlines.Use of lasers assists the operator to achieve proper retraction with good clinical results. The present study was intended to assess the amount of lateral gingival retraction achieved quantitatively by using diode lasers. Study was carried on 20 patients attended to a dental institution that underwent root canal treatment and indicated for fabrication of crowns. Gingival retraction was carried out on 20 teeth and elastomeric impressions were obtained. Models retrieved from the impressions were sectioned and the lateral distance between finish line and the marginal gingival was measured using tool makers microscope. Retraction was measured in mid buccal, mesio buccal and disto buccal regions. The values obtained were used to calculate the mean lateral retraction in microns. Mean retraction values of 399.5 μm, 445.5 μm and 422.5μm were obtained in mid buccal, mesio buccal and disto buccal regions respectively. Gingival Retraction achieved was closer to the thickness of sulcular epithelium and greater than the minimum required retraction of 200um.

Development of CD3 cell quantitation algorithms for renal allograft biopsy rejection assessment utilizing open source image analysis software.

PubMed

Moon, Andres; Smith, Geoffrey H; Kong, Jun; Rogers, Thomas E; Ellis, Carla L; Farris, Alton B Brad

2018-02-01

Renal allograft rejection diagnosis depends on assessment of parameters such as interstitial inflammation; however, studies have shown interobserver variability regarding interstitial inflammation assessment. Since automated image analysis quantitation can be reproducible, we devised customized analysis methods for CD3+ T-cell staining density as a measure of rejection severity and compared them with established commercial methods along with visual assessment. Renal biopsy CD3 immunohistochemistry slides (n = 45), including renal allografts with various degrees of acute cellular rejection (ACR) were scanned for whole slide images (WSIs). Inflammation was quantitated in the WSIs using pathologist visual assessment, commercial algorithms (Aperio nuclear algorithm for CD3+ cells/mm 2 and Aperio positive pixel count algorithm), and customized open source algorithms developed in ImageJ with thresholding/positive pixel counting (custom CD3+%) and identification of pixels fulfilling "maxima" criteria for CD3 expression (custom CD3+ cells/mm 2 ). Based on visual inspections of "markup" images, CD3 quantitation algorithms produced adequate accuracy. Additionally, CD3 quantitation algorithms correlated between each other and also with visual assessment in a statistically significant manner (r = 0.44 to 0.94, p = 0.003 to < 0.0001). Methods for assessing inflammation suggested a progression through the tubulointerstitial ACR grades, with statistically different results in borderline versus other ACR types, in all but the custom methods. Assessment of CD3-stained slides using various open source image analysis algorithms presents salient correlations with established methods of CD3 quantitation. These analysis techniques are promising and highly customizable, providing a form of on-slide "flow cytometry" that can facilitate additional diagnostic accuracy in tissue-based assessments.

Assessing the diversity, host-specificity and infection patterns of apicomplexan parasites in reptiles from Oman, Arabia.

PubMed

Maia, João P; Harris, D James; Carranza, Salvador; Goméz-Díaz, Elena

2016-11-01

Understanding the processes that shape parasite diversification, their distribution and abundance provides valuable information on the dynamics and evolution of disease. In this study, we assessed the diversity, distribution, host-specificity and infection patterns of apicomplexan parasites in amphibians and reptiles from Oman, Arabia. Using a quantitative PCR approach we detected three apicomplexan parasites (haemogregarines, lankesterellids and sarcocystids). A total of 13 haemogregarine haplotypes were identified, which fell into four main clades in a phylogenetic framework. Phylogenetic analysis of six new lankesterellid haplotypes revealed that these parasites were distinct from, but phylogenetically related to, known Lankesterella species and might represent new taxa. The percentage of infected hosts (prevalence) and the number of haemogregarines in the blood (parasitaemia) varied significantly between gecko species. We also found significant differences in parasitaemia between haemogregarine parasite lineages (defined by phylogenetic clustering of haplotypes), suggesting differences in host-parasite compatibility between these lineages. For Pristurus rupestris, we found significant differences in haemogregarine prevalence between geographical areas. Our results suggest that host ecology and host relatedness may influence haemogregarine distributions and, more generally, highlight the importance of screening wild hosts from remote regions to provide new insights into parasite diversity.

Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology.

PubMed

von Bergen, Martin; Jehmlich, Nico; Taubert, Martin; Vogt, Carsten; Bastida, Felipe; Herbst, Florian-Alexander; Schmidt, Frank; Richnow, Hans-Hermann; Seifert, Jana

2013-10-01

The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution.

PubMed

Kendall, Michelle; Colijn, Caroline

2016-10-01

Evolutionary relationships are frequently described by phylogenetic trees, but a central barrier in many fields is the difficulty of interpreting data containing conflicting phylogenetic signals. We present a metric-based method for comparing trees which extracts distinct alternative evolutionary relationships embedded in data. We demonstrate detection and resolution of phylogenetic uncertainty in a recent study of anole lizards, leading to alternate hypotheses about their evolutionary relationships. We use our approach to compare trees derived from different genes of Ebolavirus and find that the VP30 gene has a distinct phylogenetic signature composed of three alternatives that differ in the deep branching structure. phylogenetics, evolution, tree metrics, genetics, sequencing. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Quantitative assessment model for gastric cancer screening

PubMed Central

Chen, Kun; Yu, Wei-Ping; Song, Liang; Zhu, Yi-Min

2005-01-01

AIM: To set up a mathematic model for gastric cancer screening and to evaluate its function in mass screening for gastric cancer. METHODS: A case control study was carried on in 66 patients and 198 normal people, then the risk and protective factors of gastric cancer were determined, including heavy manual work, foods such as small yellow-fin tuna, dried small shrimps, squills, crabs, mothers suffering from gastric diseases, spouse alive, use of refrigerators and hot food, etc. According to some principles and methods of probability and fuzzy mathematics, a quantitative assessment model was established as follows: first, we selected some factors significant in statistics, and calculated weight coefficient for each one by two different methods; second, population space was divided into gastric cancer fuzzy subset and non gastric cancer fuzzy subset, then a mathematic model for each subset was established, we got a mathematic expression of attribute degree (AD). RESULTS: Based on the data of 63 patients and 693 normal people, AD of each subject was calculated. Considering the sensitivity and specificity, the thresholds of AD values calculated were configured with 0.20 and 0.17, respectively. According to these thresholds, the sensitivity and specificity of the quantitative model were about 69% and 63%. Moreover, statistical test showed that the identification outcomes of these two different calculation methods were identical (P>0.05). CONCLUSION: The validity of this method is satisfactory. It is convenient, feasible, economic and can be used to determine individual and population risks of gastric cancer. PMID:15655813

Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.

PubMed

Zaccaria, Simone; El-Kebir, Mohammed; Klau, Gunnar W; Raphael, Benjamin J

2018-04-16

Cancer is an evolutionary process driven by somatic mutations. This process can be represented as a phylogenetic tree. Constructing such a phylogenetic tree from genome sequencing data is a challenging task due to the many types of mutations in cancer and the fact that nearly all cancer sequencing is of a bulk tumor, measuring a superposition of somatic mutations present in different cells. We study the problem of reconstructing tumor phylogenies from copy-number aberrations (CNAs) measured in bulk-sequencing data. We introduce the Copy-Number Tree Mixture Deconvolution (CNTMD) problem, which aims to find the phylogenetic tree with the fewest number of CNAs that explain the copy-number data from multiple samples of a tumor. We design an algorithm for solving the CNTMD problem and apply the algorithm to both simulated and real data. On simulated data, we find that our algorithm outperforms existing approaches that either perform deconvolution/factorization of mixed tumor samples or build phylogenetic trees assuming homogeneous tumor samples. On real data, we analyze multiple samples from a prostate cancer patient, identifying clones within these samples and a phylogenetic tree that relates these clones and their differing proportions across samples. This phylogenetic tree provides a higher resolution view of copy-number evolution of this cancer than published analyses.

Refuting phylogenetic relationships

PubMed Central

Bucknam, James; Boucher, Yan; Bapteste, Eric

2006-01-01

Background Phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. This constitutes an important methodologic dimension not often taken into account. Here we address this dimension in the context of concatenation approaches to phylogeny. Results We discuss some of the limits of a methodology restricted to verificationism, the philosophy on which gene concatenation practices generally rely. As an alternative, we describe a software which identifies and focuses on impossible or refuted relationships, through a simple analysis of bootstrap bipartitions, followed by multivariate statistical analyses. We show how refuting phylogenetic relationships could in principle facilitate systematics. We also apply our method to the study of two complex phylogenies: the phylogeny of the archaea and the phylogeny of the core of genes shared by all life forms. While many groups are rejected, our results left open a possible proximity of N. equitans and the Methanopyrales, of the Archaea and the Cyanobacteria, and as well the possible grouping of the Methanobacteriales/Methanoccocales and Thermosplasmatales, of the Spirochaetes and the Actinobacteria and of the Proteobacteria and firmicutes. Conclusion It is sometimes easier (and preferable) to decide which species do not group together than which ones do. When possible topologies are limited, identifying local relationships that are rejected may be a useful alternative to classical concatenation approaches aiming to find a globally resolved tree on the basis of weak phylogenetic markers. Reviewers This article was reviewed by Mark Ragan, Eugene V Koonin and J Peter Gogarten. PMID:16956399

Standardizing evaluation of pQCT image quality in the presence of subject movement: qualitative versus quantitative assessment.

PubMed

Blew, Robert M; Lee, Vinson R; Farr, Joshua N; Schiferl, Daniel J; Going, Scott B

2014-02-01

Peripheral quantitative computed tomography (pQCT) is an essential tool for assessing bone parameters of the limbs, but subject movement and its impact on image quality remains a challenge to manage. The current approach to determine image viability is by visual inspection, but pQCT lacks a quantitative evaluation. Therefore, the aims of this study were to (1) examine the reliability of a qualitative visual inspection scale and (2) establish a quantitative motion assessment methodology. Scans were performed on 506 healthy girls (9-13 years) at diaphyseal regions of the femur and tibia. Scans were rated for movement independently by three technicians using a linear, nominal scale. Quantitatively, a ratio of movement to limb size (%Move) provided a measure of movement artifact. A repeat-scan subsample (n = 46) was examined to determine %Move's impact on bone parameters. Agreement between measurers was strong (intraclass correlation coefficient = 0.732 for tibia, 0.812 for femur), but greater variability was observed in scans rated 3 or 4, the delineation between repeat and no repeat. The quantitative approach found ≥95% of subjects had %Move <25 %. Comparison of initial and repeat scans by groups above and below 25% initial movement showed significant differences in the >25 % grouping. A pQCT visual inspection scale can be a reliable metric of image quality, but technicians may periodically mischaracterize subject motion. The presented quantitative methodology yields more consistent movement assessment and could unify procedure across laboratories. Data suggest a delineation of 25% movement for determining whether a diaphyseal scan is viable or requires repeat.

Standardizing Evaluation of pQCT Image Quality in the Presence of Subject Movement: Qualitative vs. Quantitative Assessment

PubMed Central

Blew, Robert M.; Lee, Vinson R.; Farr, Joshua N.; Schiferl, Daniel J.; Going, Scott B.

2013-01-01

Purpose Peripheral quantitative computed tomography (pQCT) is an essential tool for assessing bone parameters of the limbs, but subject movement and its impact on image quality remains a challenge to manage. The current approach to determine image viability is by visual inspection, but pQCT lacks a quantitative evaluation. Therefore, the aims of this study were to (1) examine the reliability of a qualitative visual inspection scale, and (2) establish a quantitative motion assessment methodology. Methods Scans were performed on 506 healthy girls (9–13yr) at diaphyseal regions of the femur and tibia. Scans were rated for movement independently by three technicians using a linear, nominal scale. Quantitatively, a ratio of movement to limb size (%Move) provided a measure of movement artifact. A repeat-scan subsample (n=46) was examined to determine %Move’s impact on bone parameters. Results Agreement between measurers was strong (ICC = .732 for tibia, .812 for femur), but greater variability was observed in scans rated 3 or 4, the delineation between repeat or no repeat. The quantitative approach found ≥95% of subjects had %Move <25%. Comparison of initial and repeat scans by groups above and below 25% initial movement, showed significant differences in the >25% grouping. Conclusions A pQCT visual inspection scale can be a reliable metric of image quality but technicians may periodically mischaracterize subject motion. The presented quantitative methodology yields more consistent movement assessment and could unify procedure across laboratories. Data suggest a delineation of 25% movement for determining whether a diaphyseal scan is viable or requires repeat. PMID:24077875

Quantitative Assessment of Arrhythmia Using Non-linear Approach: A Non-invasive Prognostic Tool

NASA Astrophysics Data System (ADS)

Chakraborty, Monisha; Ghosh, Dipak

2017-12-01

Accurate prognostic tool to identify severity of Arrhythmia is yet to be investigated, owing to the complexity of the ECG signal. In this paper, we have shown that quantitative assessment of Arrhythmia is possible using non-linear technique based on "Hurst Rescaled Range Analysis". Although the concept of applying "non-linearity" for studying various cardiac dysfunctions is not entirely new, the novel objective of this paper is to identify the severity of the disease, monitoring of different medicine and their dose, and also to assess the efficiency of different medicine. The approach presented in this work is simple which in turn will help doctors in efficient disease management. In this work, Arrhythmia ECG time series are collected from MIT-BIH database. Normal ECG time series are acquired using POLYPARA system. Both time series are analyzed in thelight of non-linear approach following the method "Rescaled Range Analysis". The quantitative parameter, "Fractal Dimension" (D) is obtained from both types of time series. The major finding is that Arrhythmia ECG poses lower values of D as compared to normal. Further, this information can be used to access the severity of Arrhythmia quantitatively, which is a new direction of prognosis as well as adequate software may be developed for the use of medical practice.

Quantitative Assessment of Arrhythmia Using Non-linear Approach: A Non-invasive Prognostic Tool

NASA Astrophysics Data System (ADS)

Chakraborty, Monisha; Ghosh, Dipak

2018-04-01

Accurate prognostic tool to identify severity of Arrhythmia is yet to be investigated, owing to the complexity of the ECG signal. In this paper, we have shown that quantitative assessment of Arrhythmia is possible using non-linear technique based on "Hurst Rescaled Range Analysis". Although the concept of applying "non-linearity" for studying various cardiac dysfunctions is not entirely new, the novel objective of this paper is to identify the severity of the disease, monitoring of different medicine and their dose, and also to assess the efficiency of different medicine. The approach presented in this work is simple which in turn will help doctors in efficient disease management. In this work, Arrhythmia ECG time series are collected from MIT-BIH database. Normal ECG time series are acquired using POLYPARA system. Both time series are analyzed in thelight of non-linear approach following the method "Rescaled Range Analysis". The quantitative parameter, "Fractal Dimension" (D) is obtained from both types of time series. The major finding is that Arrhythmia ECG poses lower values of D as compared to normal. Further, this information can be used to access the severity of Arrhythmia quantitatively, which is a new direction of prognosis as well as adequate software may be developed for the use of medical practice.

A novel iris transillumination grading scale allowing flexible assessment with quantitative image analysis and visual matching.

PubMed

Wang, Chen; Brancusi, Flavia; Valivullah, Zaheer M; Anderson, Michael G; Cunningham, Denise; Hedberg-Buenz, Adam; Power, Bradley; Simeonov, Dimitre; Gahl, William A; Zein, Wadih M; Adams, David R; Brooks, Brian

2018-01-01

To develop a sensitive scale of iris transillumination suitable for clinical and research use, with the capability of either quantitative analysis or visual matching of images. Iris transillumination photographic images were used from 70 study subjects with ocular or oculocutaneous albinism. Subjects represented a broad range of ocular pigmentation. A subset of images was subjected to image analysis and ranking by both expert and nonexpert reviewers. Quantitative ordering of images was compared with ordering by visual inspection. Images were binned to establish an 8-point scale. Ranking consistency was evaluated using the Kendall rank correlation coefficient (Kendall's tau). Visual ranking results were assessed using Kendall's coefficient of concordance (Kendall's W) analysis. There was a high degree of correlation among the image analysis, expert-based and non-expert-based image rankings. Pairwise comparisons of the quantitative ranking with each reviewer generated an average Kendall's tau of 0.83 ± 0.04 (SD). Inter-rater correlation was also high with Kendall's W of 0.96, 0.95, and 0.95 for nonexpert, expert, and all reviewers, respectively. The current standard for assessing iris transillumination is expert assessment of clinical exam findings. We adapted an image-analysis technique to generate quantitative transillumination values. Quantitative ranking was shown to be highly similar to a ranking produced by both expert and nonexpert reviewers. This finding suggests that the image characteristics used to quantify iris transillumination do not require expert interpretation. Inter-rater rankings were also highly similar, suggesting that varied methods of transillumination ranking are robust in terms of producing reproducible results.

Phylogenetic turnover along local environmental gradients in tropical forest communities.

PubMed

Baldeck, C A; Kembel, S W; Harms, K E; Yavitt, J B; John, R; Turner, B L; Madawala, S; Gunatilleke, N; Gunatilleke, S; Bunyavejchewin, S; Kiratiprayoon, S; Yaacob, A; Supardi, M N N; Valencia, R; Navarrete, H; Davies, S J; Chuyong, G B; Kenfack, D; Thomas, D W; Dalling, J W

2016-10-01

While the importance of local-scale habitat niches in shaping tree species turnover along environmental gradients in tropical forests is well appreciated, relatively little is known about the influence of phylogenetic signal in species' habitat niches in shaping local community structure. We used detailed maps of the soil resource and topographic variation within eight 24-50 ha tropical forest plots combined with species phylogenies created from the APG III phylogeny to examine how phylogenetic beta diversity (indicating the degree of phylogenetic similarity of two communities) was related to environmental gradients within tropical tree communities. Using distance-based redundancy analysis we found that phylogenetic beta diversity, expressed as either nearest neighbor distance or mean pairwise distance, was significantly related to both soil and topographic variation in all study sites. In general, more phylogenetic beta diversity within a forest plot was explained by environmental variables this was expressed as nearest neighbor distance versus mean pairwise distance (3.0-10.3 % and 0.4-8.8 % of variation explained among plots, respectively), and more variation was explained by soil resource variables than topographic variables using either phylogenetic beta diversity metric. We also found that patterns of phylogenetic beta diversity expressed as nearest neighbor distance were consistent with previously observed patterns of niche similarity among congeneric species pairs in these plots. These results indicate the importance of phylogenetic signal in local habitat niches in shaping the phylogenetic structure of tropical tree communities, especially at the level of close phylogenetic neighbors, where similarity in habitat niches is most strongly preserved.

Spatial phylogenetics of the native California flora.

PubMed

Thornhill, Andrew H; Baldwin, Bruce G; Freyman, William A; Nosratinia, Sonia; Kling, Matthew M; Morueta-Holme, Naia; Madsen, Thomas P; Ackerly, David D; Mishler, Brent D

2017-10-26

California is a world floristic biodiversity hotspot where the terms neo- and paleo-endemism were first applied. Using spatial phylogenetics, it is now possible to evaluate biodiversity from an evolutionary standpoint, including discovering significant areas of neo- and paleo-endemism, by combining spatial information from museum collections and DNA-based phylogenies. Here we used a distributional dataset of 1.39 million herbarium specimens, a phylogeny of 1083 operational taxonomic units (OTUs) and 9 genes, and a spatial randomization test to identify regions of significant phylogenetic diversity, relative phylogenetic diversity, and phylogenetic endemism (PE), as well as to conduct a categorical analysis of neo- and paleo-endemism (CANAPE). We found (1) extensive phylogenetic clustering in the South Coast Ranges, southern Great Valley, and deserts of California; (2) significant concentrations of short branches in the Mojave and Great Basin Deserts and the South Coast Ranges and long branches in the northern Great Valley, Sierra Nevada foothills, and the northwestern and southwestern parts of the state; (3) significant concentrations of paleo-endemism in Northwestern California, the northern Great Valley, and western Sonoran Desert, and neo-endemism in the White-Inyo Range, northern Mojave Desert, and southern Channel Islands. Multiple analyses were run to observe the effects on significance patterns of using different phylogenetic tree topologies (uncalibrated trees versus time-calibrated ultrametric trees) and using different representations of OTU ranges (herbarium specimen locations versus species distribution models). These analyses showed that examining the geographic distributions of branch lengths in a statistical framework adds a new dimension to California floristics that, in comparison with climatic data, helps to illuminate causes of endemism. In particular, the concentration of significant PE in more arid regions of California extends previous ideas

A Quantitative Approach to Assessing System Evolvability

NASA Technical Reports Server (NTRS)

Christian, John A., III

2004-01-01

When selecting a system from multiple candidates, the customer seeks the one that best meets his or her needs. Recently the desire for evolvable systems has become more important and engineers are striving to develop systems that accommodate this need. In response to this search for evolvability, we present a historical perspective on evolvability, propose a refined definition of evolvability, and develop a quantitative method for measuring this property. We address this quantitative methodology from both a theoretical and practical perspective. This quantitative model is then applied to the problem of evolving a lunar mission to a Mars mission as a case study.

Quantitative sonoelastography for the in vivo assessment of skeletal muscle viscoelasticity

NASA Astrophysics Data System (ADS)

Hoyt, Kenneth; Kneezel, Timothy; Castaneda, Benjamin; Parker, Kevin J.

2008-08-01

A novel quantitative sonoelastography technique for assessing the viscoelastic properties of skeletal muscle tissue was developed. Slowly propagating shear wave interference patterns (termed crawling waves) were generated using a two-source configuration vibrating normal to the surface. Theoretical models predict crawling wave displacement fields, which were validated through phantom studies. In experiments, a viscoelastic model was fit to dispersive shear wave speed sonoelastographic data using nonlinear least-squares techniques to determine frequency-independent shear modulus and viscosity estimates. Shear modulus estimates derived using the viscoelastic model were in agreement with that obtained by mechanical testing on phantom samples. Preliminary sonoelastographic data acquired in healthy human skeletal muscles confirm that high-quality quantitative elasticity data can be acquired in vivo. Studies on relaxed muscle indicate discernible differences in both shear modulus and viscosity estimates between different skeletal muscle groups. Investigations into the dynamic viscoelastic properties of (healthy) human skeletal muscles revealed that voluntarily contracted muscles exhibit considerable increases in both shear modulus and viscosity estimates as compared to the relaxed state. Overall, preliminary results are encouraging and quantitative sonoelastography may prove clinically feasible for in vivo characterization of the dynamic viscoelastic properties of human skeletal muscle.

Quantitative assessment of emphysema from whole lung CT scans: comparison with visual grading

NASA Astrophysics Data System (ADS)

Keller, Brad M.; Reeves, Anthony P.; Apanosovich, Tatiyana V.; Wang, Jianwei; Yankelevitz, David F.; Henschke, Claudia I.

2009-02-01

Emphysema is a disease of the lungs that destroys the alveolar air sacs and induces long-term respiratory dysfunction. CT scans allow for imaging of the anatomical basis of emphysema and for visual assessment by radiologists of the extent present in the lungs. Several measures have been introduced for the quantification of the extent of disease directly from CT data in order to add to the qualitative assessments made by radiologists. In this paper we compare emphysema index, mean lung density, histogram percentiles, and the fractal dimension to visual grade in order to evaluate the predictability of radiologist visual scoring of emphysema from low-dose CT scans through quantitative scores, in order to determine which measures can be useful as surrogates for visual assessment. All measures were computed over nine divisions of the lung field (whole lung, individual lungs, and upper/middle/lower thirds of each lung) for each of 148 low-dose, whole lung scans. In addition, a visual grade of each section was also given by an expert radiologist. One-way ANOVA and multinomial logistic regression were used to determine the ability of the measures to predict visual grade from quantitative score. We found that all measures were able to distinguish between normal and severe grades (p<0.01), and between mild/moderate and all other grades (p<0.05). However, no measure was able to distinguish between mild and moderate cases. Approximately 65% prediction accuracy was achieved from using quantitative score to predict visual grade, with 73% if mild and moderate cases are considered as a single class.

A Preliminary Quantitative Comparison of Vibratory Amplitude Using Rigid and Flexible Stroboscopic Assessment.

PubMed

Hosbach-Cannon, Carly J; Lowell, Soren Y; Kelley, Richard T; Colton, Raymond H

2016-07-01

The purpose of this study was to establish preliminary, quantitative data on amplitude of vibration during stroboscopic assessment in healthy speakers with normal voice characteristics. Amplitude of vocal fold vibration is a core physiological parameter used in diagnosing voice disorders, yet quantitative data are lacking to guide the determination of what constitutes normal vibratory amplitude. Eleven participants were assessed during sustained vowel production using rigid and flexible endoscopy with stroboscopy. Still images were extracted from digital recordings of a sustained /i/ produced at a comfortable pitch and loudness, with F0 controlled so that levels were within ±15% of each participant's comfortable mean level as determined from connected speech. Glottal width (GW), true vocal fold (TVF) length, and TVF width were measured from still frames representing the maximum open phase of the vibratory cycle. To control for anatomic and magnification differences across participants, GW was normalized to TVF length. GW as a ratio of TVF width was also computed for comparison with prior studies. Mean values and standard deviations were computed for the normalized measures. Paired t tests showed no significant differences between rigid and flexible endoscopy methods. Interrater and intrarater reliability values for raw measurements were found to be high (0.89-0.99). These preliminary quantitative data may be helpful in determining normality or abnormality of vocal fold vibration. Results indicate that quantified amplitude of vibration is similar between endoscopic methods, a clinically relevant finding for individuals performing and interpreting stroboscopic assessments. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

A quantitative model to assess Social Responsibility in Environmental Science and Technology.

PubMed

Valcárcel, M; Lucena, R

2014-01-01

The awareness of the impact of human activities in society and environment is known as "Social Responsibility" (SR). It has been a topic of growing interest in many enterprises since the fifties of the past Century, and its implementation/assessment is nowadays supported by international standards. There is a tendency to amplify its scope of application to other areas of the human activities, such as Research, Development and Innovation (R + D + I). In this paper, a model of quantitative assessment of Social Responsibility in Environmental Science and Technology (SR EST) is described in detail. This model is based on well established written standards as the EFQM Excellence model and the ISO 26000:2010 Guidance on SR. The definition of five hierarchies of indicators, the transformation of qualitative information into quantitative data and the dual procedure of self-evaluation and external evaluation are the milestones of the proposed model, which can be applied to Environmental Research Centres and institutions. In addition, a simplified model that facilitates its implementation is presented in the article. © 2013 Elsevier B.V. All rights reserved.

Towards an eco-phylogenetic framework for infectious disease ecology.

PubMed

Fountain-Jones, Nicholas M; Pearse, William D; Escobar, Luis E; Alba-Casals, Ana; Carver, Scott; Davies, T Jonathan; Kraberger, Simona; Papeş, Monica; Vandegrift, Kurt; Worsley-Tonks, Katherine; Craft, Meggan E

2018-05-01

Identifying patterns and drivers of infectious disease dynamics across multiple scales is a fundamental challenge for modern science. There is growing awareness that it is necessary to incorporate multi-host and/or multi-parasite interactions to understand and predict current and future disease threats better, and new tools are needed to help address this task. Eco-phylogenetics (phylogenetic community ecology) provides one avenue for exploring multi-host multi-parasite systems, yet the incorporation of eco-phylogenetic concepts and methods into studies of host pathogen dynamics has lagged behind. Eco-phylogenetics is a transformative approach that uses evolutionary history to infer present-day dynamics. Here, we present an eco-phylogenetic framework to reveal insights into parasite communities and infectious disease dynamics across spatial and temporal scales. We illustrate how eco-phylogenetic methods can help untangle the mechanisms of host-parasite dynamics from individual (e.g. co-infection) to landscape scales (e.g. parasite/host community structure). An improved ecological understanding of multi-host and multi-pathogen dynamics across scales will increase our ability to predict disease threats. © 2017 Cambridge Philosophical Society.

DOSIMETRY MODELING OF INHALED FORMALDEHYDE: BINNING NASAL FLUX PREDICTIONS FOR QUANTITATIVE RISK ASSESSMENT

EPA Science Inventory

Dosimetry Modeling of Inhaled Formaldehyde: Binning Nasal Flux Predictions for Quantitative Risk Assessment. Kimbell, J.S., Overton, J.H., Subramaniam, R.P., Schlosser, P.M., Morgan, K.T., Conolly, R.B., and Miller, F.J. (2001). Toxicol. Sci. 000, 000:000.

Interspecies e...

The Diaporthe sojae species complex: Phylogenetic re-assessment of pathogens associated with soybean, cucurbits and other field crops.

PubMed

Udayanga, Dhanushka; Castlebury, Lisa A; Rossman, Amy Y; Chukeatirote, Ekachai; Hyde, Kevin D

2015-05-01

Phytopathogenic species of Diaporthe are associated with a number of soybean diseases including seed decay, pod and stem blight and stem canker and lead to considerable crop production losses worldwide. Accurate morphological identification of the species that cause these diseases has been difficult. In this study, we determined the phylogenetic relationships and species boundaries of Diaporthe longicolla, Diaporthe phaseolorum, Diaporthe sojae and closely related taxa. Species boundaries for this complex were determined based on combined phylogenetic analysis of five gene regions: partial sequences of calmodulin (CAL), beta-tubulin (TUB), histone-3 (HIS), translation elongation factor 1-α (EF1-α), and the nuclear ribosomal internal transcribed spacers (ITS). Phylogenetic analyses revealed that this large complex of taxa is comprised of soybean pathogens as well as species associated with herbaceous field crops and weeds. Diaporthe arctii, Diaporthe batatas, D. phaseolorum and D. sojae are epitypified. The seed decay pathogen D. longicolla was determined to be distinct from D. sojae. D. phaseolorum, originally associated with stem and leaf blight of Lima bean, was not found to be associated with soybean. A new species, Diaporthe ueckerae on Cucumis melo, is introduced with description and illustrations. Published by Elsevier Ltd.

A standardized kit for automated quantitative assessment of candidate protein biomarkers in human plasma.

PubMed

Percy, Andrew J; Mohammed, Yassene; Yang, Juncong; Borchers, Christoph H

2015-12-01

An increasingly popular mass spectrometry-based quantitative approach for health-related research in the biomedical field involves the use of stable isotope-labeled standards (SIS) and multiple/selected reaction monitoring (MRM/SRM). To improve inter-laboratory precision and enable more widespread use of this 'absolute' quantitative technique in disease-biomarker assessment studies, methods must be standardized. Results/methodology: Using this MRM-with-SIS-peptide approach, we developed an automated method (encompassing sample preparation, processing and analysis) for quantifying 76 candidate protein markers (spanning >4 orders of magnitude in concentration) in neat human plasma. The assembled biomarker assessment kit - the 'BAK-76' - contains the essential materials (SIS mixes), methods (for acquisition and analysis), and tools (Qualis-SIS software) for performing biomarker discovery or verification studies in a rapid and standardized manner.

Quantitative Assessment of Parkinsonian Tremor Based on an Inertial Measurement Unit

PubMed Central

Dai, Houde; Zhang, Pengyue; Lueth, Tim C.

2015-01-01

Quantitative assessment of parkinsonian tremor based on inertial sensors can provide reliable feedback on the effect of medication. In this regard, the features of parkinsonian tremor and its unique properties such as motor fluctuations and dyskinesia are taken into account. Least-square-estimation models are used to assess the severities of rest, postural, and action tremors. In addition, a time-frequency signal analysis algorithm for tremor state detection was also included in the tremor assessment method. This inertial sensor-based method was verified through comparison with an electromagnetic motion tracking system. Seven Parkinson’s disease (PD) patients were tested using this tremor assessment system. The measured tremor amplitudes correlated well with the judgments of a neurologist (r = 0.98). The systematic analysis of sensor-based tremor quantification and the corresponding experiments could be of great help in monitoring the severity of parkinsonian tremor. PMID:26426020

Phylogenetic comparative methods complement discriminant function analysis in ecomorphology.

PubMed

Barr, W Andrew; Scott, Robert S

2014-04-01

In ecomorphology, Discriminant Function Analysis (DFA) has been used as evidence for the presence of functional links between morphometric variables and ecological categories. Here we conduct simulations of characters containing phylogenetic signal to explore the performance of DFA under a variety of conditions. Characters were simulated using a phylogeny of extant antelope species from known habitats. Characters were modeled with no biomechanical relationship to the habitat category; the only sources of variation were body mass, phylogenetic signal, or random "noise." DFA on the discriminability of habitat categories was performed using subsets of the simulated characters, and Phylogenetic Generalized Least Squares (PGLS) was performed for each character. Analyses were repeated with randomized habitat assignments. When simulated characters lacked phylogenetic signal and/or habitat assignments were random, <5.6% of DFAs and <8.26% of PGLS analyses were significant. When characters contained phylogenetic signal and actual habitats were used, 33.27 to 45.07% of DFAs and <13.09% of PGLS analyses were significant. False Discovery Rate (FDR) corrections for multiple PGLS analyses reduced the rate of significance to <4.64%. In all cases using actual habitats and characters with phylogenetic signal, correct classification rates of DFAs exceeded random chance. In simulations involving phylogenetic signal in both predictor variables and predicted categories, PGLS with FDR was rarely significant, while DFA often was. In short, DFA offered no indication that differences between categories might be explained by phylogenetic signal, while PGLS did. As such, PGLS provides a valuable tool for testing the functional hypotheses at the heart of ecomorphology. Copyright © 2013 Wiley Periodicals, Inc.

["Long-branch Attraction" artifact in phylogenetic reconstruction].

PubMed

Li, Yi-Wei; Yu, Li; Zhang, Ya-Ping

2007-06-01

Phylogenetic reconstruction among various organisms not only helps understand their evolutionary history but also reveal several fundamental evolutionary questions. Understanding of the evolutionary relationships among organisms establishes the foundation for the investigations of other biological disciplines. However, almost all the widely used phylogenetic methods have limitations which fail to eliminate systematic errors effectively, preventing the reconstruction of true organismal relationships. "Long-branch Attraction" (LBA) artifact is one of the most disturbing factors in phylogenetic reconstruction. In this review, the conception and analytic method as well as the avoidance strategy of LBA were summarized. In addition, several typical examples were provided. The approach to avoid and resolve LBA artifact has been discussed.

Understanding phylogenetic incongruence: lessons from phyllostomid bats

PubMed Central

Dávalos, Liliana M; Cirranello, Andrea L; Geisler, Jonathan H; Simmons, Nancy B

2012-01-01

All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive

Using Integrated Environmental Modeling to Automate a Process-Based Quantitative Microbial Risk Assessment (presentation)

EPA Science Inventory

Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, and...

Prioritizing Populations for Conservation Using Phylogenetic Networks

PubMed Central

Volkmann, Logan; Martyn, Iain; Moulton, Vincent; Spillner, Andreas; Mooers, Arne O.

2014-01-01

In the face of inevitable future losses to biodiversity, ranking species by conservation priority seems more than prudent. Setting conservation priorities within species (i.e., at the population level) may be critical as species ranges become fragmented and connectivity declines. However, existing approaches to prioritization (e.g., scoring organisms by their expected genetic contribution) are based on phylogenetic trees, which may be poor representations of differentiation below the species level. In this paper we extend evolutionary isolation indices used in conservation planning from phylogenetic trees to phylogenetic networks. Such networks better represent population differentiation, and our extension allows populations to be ranked in order of their expected contribution to the set. We illustrate the approach using data from two imperiled species: the spotted owl Strix occidentalis in North America and the mountain pygmy-possum Burramys parvus in Australia. Using previously published mitochondrial and microsatellite data, we construct phylogenetic networks and score each population by its relative genetic distinctiveness. In both cases, our phylogenetic networks capture the geographic structure of each species: geographically peripheral populations harbor less-redundant genetic information, increasing their conservation rankings. We note that our approach can be used with all conservation-relevant distances (e.g., those based on whole-genome, ecological, or adaptive variation) and suggest it be added to the assortment of tools available to wildlife managers for allocating effort among threatened populations. PMID:24586451

Genome-wide analysis of SINA family in plants and their phylogenetic relationships.

PubMed

Wang, Meng; Jin, Ying; Fu, Junjie; Zhu, Yun; Zheng, Jun; Hu, Jian; Wang, Guoying

2008-06-01

SINA genes in plants are part of a multigene family with 5 members in Arabidopsis thaliana, 10 members in Populus trichocarpa, 6 members in Oryza sativa, at least 6 members in Zea mays and at least 1 member in Physcomitrella patens. Six members in maize were confirmed by RT-PCR. All SINAs have one RING domain and one SINA domain. These two domains are highly conserved in plants. According to the motif organization and phylogenetic tree, SINA family members were divided into 2 groups. In addition, through semi-quantitative RT-PCR analysis of maize members and Digital Northern analysis of Arabidopsis and rice members, we found that the tissue expression patterns are more diverse in monocot than in Arabidopsis.

Phylogenetic structure of soil bacterial communities predicts ecosystem functioning.

PubMed

Pérez-Valera, Eduardo; Goberna, Marta; Verdú, Miguel

2015-05-01

Quantifying diversity with phylogeny-informed metrics helps understand the effects of diversity on ecosystem functioning (EF). The sign of these effects remains controversial because phylogenetic diversity and taxonomic identity may interactively influence EF. Positive relationships, traditionally attributed to complementarity effects, seem unimportant in natural soil bacterial communities. Negative relationships could be attributed to fitness differences leading to the overrepresentation of few productive clades, a mechanism recently invoked to assemble soil bacteria communities. We tested in two ecosystems contrasting in terms of environmental heterogeneity whether two metrics of phylogenetic community structure, a simpler measure of phylogenetic diversity (NRI) and a more complex metric incorporating taxonomic identity (PCPS), correctly predict microbially mediated EF. We show that the relationship between phylogenetic diversity and EF depends on the taxonomic identity of the main coexisting lineages. Phylogenetic diversity was negatively related to EF in soils where a marked fertility gradient exists and a single and productive clade (Proteobacteria) outcompete other clades in the most fertile plots. However, phylogenetic diversity was unrelated to EF in soils where the fertility gradient is less marked and Proteobacteria coexist with other abundant lineages. Including the taxonomic identity of bacterial lineages in metrics of phylogenetic community structure allows the prediction of EF in both ecosystems. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Characterizing the phylogenetic tree community structure of a protected tropical rain forest area in Cameroon.

PubMed

Manel, Stéphanie; Couvreur, Thomas L P; Munoz, François; Couteron, Pierre; Hardy, Olivier J; Sonké, Bonaventure

2014-01-01

Tropical rain forests, the richest terrestrial ecosystems in biodiversity on Earth are highly threatened by global changes. This paper aims to infer the mechanisms governing species tree assemblages by characterizing the phylogenetic structure of a tropical rain forest in a protected area of the Congo Basin, the Dja Faunal Reserve (Cameroon). We re-analyzed a dataset of 11538 individuals belonging to 372 taxa found along nine transects spanning five habitat types. We generated a dated phylogenetic tree including all sampled taxa to partition the phylogenetic diversity of the nine transects into alpha and beta components at the level of the transects and of the habitat types. The variation in phylogenetic composition among transects did not deviate from a random pattern at the scale of the Dja Faunal Reserve, probably due to a common history and weak environmental variation across the park. This lack of phylogenetic structure combined with an isolation-by-distance pattern of taxonomic diversity suggests that neutral dispersal limitation is a major driver of community assembly in the Dja. To assess any lack of sensitivity to the variation in habitat types, we restricted the analyses of transects to the terra firme primary forest and found results consistent with those of the whole dataset at the level of the transects. Additionally to previous analyses, we detected a weak but significant phylogenetic turnover among habitat types, suggesting that species sort in varying environments, even though it is not predominating on the overall phylogenetic structure. Finer analyses of clades indicated a signal of clustering for species from the Annonaceae family, while species from the Apocynaceae family indicated overdispersion. These results can contribute to the conservation of the park by improving our understanding of the processes dictating community assembly in these hyperdiverse but threatened regions of the world.

Characterizing the Phylogenetic Tree Community Structure of a Protected Tropical Rain Forest Area in Cameroon

PubMed Central

Munoz, François; Couteron, Pierre; Hardy, Olivier J.; Sonké, Bonaventure

2014-01-01

Tropical rain forests, the richest terrestrial ecosystems in biodiversity on Earth are highly threatened by global changes. This paper aims to infer the mechanisms governing species tree assemblages by characterizing the phylogenetic structure of a tropical rain forest in a protected area of the Congo Basin, the Dja Faunal Reserve (Cameroon). We re-analyzed a dataset of 11538 individuals belonging to 372 taxa found along nine transects spanning five habitat types. We generated a dated phylogenetic tree including all sampled taxa to partition the phylogenetic diversity of the nine transects into alpha and beta components at the level of the transects and of the habitat types. The variation in phylogenetic composition among transects did not deviate from a random pattern at the scale of the Dja Faunal Reserve, probably due to a common history and weak environmental variation across the park. This lack of phylogenetic structure combined with an isolation-by-distance pattern of taxonomic diversity suggests that neutral dispersal limitation is a major driver of community assembly in the Dja. To assess any lack of sensitivity to the variation in habitat types, we restricted the analyses of transects to the terra firme primary forest and found results consistent with those of the whole dataset at the level of the transects. Additionally to previous analyses, we detected a weak but significant phylogenetic turnover among habitat types, suggesting that species sort in varying environments, even though it is not predominating on the overall phylogenetic structure. Finer analyses of clades indicated a signal of clustering for species from the Annonaceae family, while species from the Apocynaceae family indicated overdispersion. These results can contribute to the conservation of the park by improving our understanding of the processes dictating community assembly in these hyperdiverse but threatened regions of the world. PMID:24936786

Quantitative assessment of paretic limb dexterity and interlimb coordination during bilateral arm rehabilitation training.

PubMed

Xu, Chang; Li, Siyi; Wang, Kui; Hou, Zengguang; Yu, Ningbo

2017-07-01

In neuro-rehabilitation after stroke, the conventional constrained induced movement therapy (CIMT) has been well-accepted. Existing bilateral trainings are mostly on mirrored symmetrical motion. However, complementary bilateral movements are dominantly involved in activities of daily living (ADLs), and functional bilateral therapies may bring better skill transfer from trainings to daily life. Neurophysiological evidence is also growing. In this work, we firstly introduce our bilateral arm training system realized with a haptic interface and a motion sensor, as well as the tasks that have been designed to train both the manipulation function of the paretic arm and coordination of bilateral upper limbs. Then, we propose quantitative measures for functional assessment of complementary bilateral training performance, including kinematic behavior indices, smoothness, submovement and bimanual coordination. After that, we describe the experiments with healthy subjects and the results with respect to these quantitative measures. Feasibility and sensitivity of the proposed indices were evaluated through comparison of unilateral and bilateral training outcomes. The proposed bilateral training system and tasks, as well as the quantitative measures, have been demonstrated effective for training and assessment of unilateral and bilateral arm functions.

Evolution of specialization: a phylogenetic study of host range in the red milkweed beetle (Tetraopes tetraophthalmus).

PubMed

Rasmann, Sergio; Agrawal, Anurag A

2011-06-01

Specialization is common in most lineages of insect herbivores, one of the most diverse groups of organisms on earth. To address how and why specialization is maintained over evolutionary time, we hypothesized that plant defense and other ecological attributes of potential host plants would predict the performance of a specialist root-feeding herbivore (the red milkweed beetle, Tetraopes tetraophthalmus). Using a comparative phylogenetic and functional trait approach, we assessed the determinants of insect host range across 18 species of Asclepias. Larval survivorship decreased with increasing phylogenetic distance from the true host, Asclepias syriaca, suggesting that adaptation to plant traits drives specialization. Among several root traits measured, only cardenolides (toxic defense chemicals) correlated with larval survival, and cardenolides also explained the phylogenetic distance effect in phylogenetically controlled multiple regression analyses. Additionally, milkweed species having a known association with other Tetraopes beetles were better hosts than species lacking Tetraopes herbivores, and milkweeds with specific leaf area values (a trait related to leaf function and habitat affiliation) similar to those of A. syriaca were better hosts than species having divergent values. We thus conclude that phylogenetic distance is an integrated measure of phenotypic and ecological attributes of Asclepias species, especially defensive cardenolides, which can be used to explain specialization and constraints on host shifts over evolutionary time.

A quantitative assessment of alkaptonuria: testing the reliability of two disease severity scoring systems.

PubMed

Cox, Trevor F; Ranganath, Lakshminarayan

2011-12-01

Alkaptonuria (AKU) is due to excessive homogentisic acid accumulation in body fluids due to lack of enzyme homogentisate dioxygenase leading in turn to varied clinical manifestations mainly by a process of conversion of HGA to a polymeric melanin-like pigment known as ochronosis. A potential treatment, a drug called nitisinone, to decrease formation of HGA is available. However, successful demonstration of its efficacy in modifying the natural history of AKU requires an effective quantitative assessment tool. We have described two potential tools that could be used to quantitate disease burden in AKU. One tool describes scoring the clinical features that includes clinical assessments, investigations and questionnaires in 15 patients with AKU. The second tool describes a scoring system that only includes items obtained from questionnaires used in 44 people with AKU. Statistical analyses were carried out on the two patient datasets to assess the AKU tools; these included the calculation of Chronbach's alpha, multidimensional scaling and simple linear regression analysis. The conclusion was that there was good evidence that the tools could be adopted as AKU assessment tools, but perhaps with further refinement before being used in the practical setting of a clinical trial.

Quantitative Assessment of In-solution Digestion Efficiency Identifies Optimal Protocols for Unbiased Protein Analysis*

PubMed Central

León, Ileana R.; Schwämmle, Veit; Jensen, Ole N.; Sprenger, Richard R.

2013-01-01

The majority of mass spectrometry-based protein quantification studies uses peptide-centric analytical methods and thus strongly relies on efficient and unbiased protein digestion protocols for sample preparation. We present a novel objective approach to assess protein digestion efficiency using a combination of qualitative and quantitative liquid chromatography-tandem MS methods and statistical data analysis. In contrast to previous studies we employed both standard qualitative as well as data-independent quantitative workflows to systematically assess trypsin digestion efficiency and bias using mitochondrial protein fractions. We evaluated nine trypsin-based digestion protocols, based on standard in-solution or on spin filter-aided digestion, including new optimized protocols. We investigated various reagents for protein solubilization and denaturation (dodecyl sulfate, deoxycholate, urea), several trypsin digestion conditions (buffer, RapiGest, deoxycholate, urea), and two methods for removal of detergents before analysis of peptides (acid precipitation or phase separation with ethyl acetate). Our data-independent quantitative liquid chromatography-tandem MS workflow quantified over 3700 distinct peptides with 96% completeness between all protocols and replicates, with an average 40% protein sequence coverage and an average of 11 peptides identified per protein. Systematic quantitative and statistical analysis of physicochemical parameters demonstrated that deoxycholate-assisted in-solution digestion combined with phase transfer allows for efficient, unbiased generation and recovery of peptides from all protein classes, including membrane proteins. This deoxycholate-assisted protocol was also optimal for spin filter-aided digestions as compared with existing methods. PMID:23792921

QUANTITATIVE ASSESSMENT OF INTEGRATED PHRENIC NERVE ACTIVITY

PubMed Central

Nichols, Nicole L.; Mitchell, Gordon S.

2016-01-01

Integrated electrical activity in the phrenic nerve is commonly used to assess within-animal changes in phrenic motor output. Because of concerns regarding the consistency of nerve recordings, activity is most often expressed as a percent change from baseline values. However, absolute values of nerve activity are necessary to assess the impact of neural injury or disease on phrenic motor output. To date, no systematic evaluations of the repeatability/reliability have been made among animals when phrenic recordings are performed by an experienced investigator using standardized methods. We performed a meta-analysis of studies reporting integrated phrenic nerve activity in many rat groups by the same experienced investigator; comparisons were made during baseline and maximal chemoreceptor stimulation in 14 wild-type Harlan and 14 Taconic Sprague Dawley groups, and in 3 pre-symptomatic and 11 end-stage SOD1G93A Taconic rat groups (an ALS model). Meta-analysis results indicate: 1) consistent measurements of integrated phrenic activity in each sub-strain of wild-type rats; 2) with bilateral nerve recordings, left-to-right integrated phrenic activity ratios are ~1.0; and 3) consistently reduced activity in end-stage SOD1G93A rats. Thus, with appropriate precautions, integrated phrenic nerve activity enables robust, quantitative comparisons among nerves or experimental groups, including differences caused by neuromuscular disease. PMID:26724605

Quantitative assessment of integrated phrenic nerve activity.

PubMed

Nichols, Nicole L; Mitchell, Gordon S

2016-06-01

Integrated electrical activity in the phrenic nerve is commonly used to assess within-animal changes in phrenic motor output. Because of concerns regarding the consistency of nerve recordings, activity is most often expressed as a percent change from baseline values. However, absolute values of nerve activity are necessary to assess the impact of neural injury or disease on phrenic motor output. To date, no systematic evaluations of the repeatability/reliability have been made among animals when phrenic recordings are performed by an experienced investigator using standardized methods. We performed a meta-analysis of studies reporting integrated phrenic nerve activity in many rat groups by the same experienced investigator; comparisons were made during baseline and maximal chemoreceptor stimulation in 14 wild-type Harlan and 14 Taconic Sprague Dawley groups, and in 3 pre-symptomatic and 11 end-stage SOD1(G93A) Taconic rat groups (an ALS model). Meta-analysis results indicate: (1) consistent measurements of integrated phrenic activity in each sub-strain of wild-type rats; (2) with bilateral nerve recordings, left-to-right integrated phrenic activity ratios are ∼1.0; and (3) consistently reduced activity in end-stage SOD1(G93A) rats. Thus, with appropriate precautions, integrated phrenic nerve activity enables robust, quantitative comparisons among nerves or experimental groups, including differences caused by neuromuscular disease. Copyright © 2015 Elsevier B.V. All rights reserved.

A program to compute the soft Robinson-Foulds distance between phylogenetic networks.

PubMed

Lu, Bingxin; Zhang, Louxin; Leong, Hon Wai

2017-03-14

Over the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic networks, phylogenetic trees and clusters serve as the basis for reconstruction and comparison of phylogenetic networks. To understand these relationships, two problems are raised: the tree containment problem, which asks whether a phylogenetic tree is displayed in a phylogenetic network, and the cluster containment problem, which asks whether a cluster is represented at a node in a phylogenetic network. Both the problems are NP-complete. A fast exponential-time algorithm for the cluster containment problem on arbitrary networks is developed and implemented in C. The resulting program is further extended into a computer program for fast computation of the Soft Robinson-Foulds distance between phylogenetic networks. Two computer programs are developed for facilitating reconstruction and validation of phylogenetic network models in evolutionary and comparative genomics. Our simulation tests indicated that they are fast enough for use in practice. Additionally, the distribution of the Soft Robinson-Foulds distance between phylogenetic networks is demonstrated to be unlikely normal by our simulation data.

Assessment of metabolic bone diseases by quantitative computed tomography

NASA Technical Reports Server (NTRS)

Richardson, M. L.; Genant, H. K.; Cann, C. E.; Ettinger, B.; Gordan, G. S.; Kolb, F. O.; Reiser, U. J.

1985-01-01

Advances in the radiologic sciences have permitted the development of numerous noninvasive techniques for measuring the mineral content of bone, with varying degrees of precision, accuracy, and sensitivity. The techniques of standard radiography, radiogrammetry, photodensitometry, Compton scattering, neutron activation analysis, single and dual photon absorptiometry, and quantitative computed tomography (QCT) are described and reviewed in depth. Results from previous cross-sectional and longitudinal QCT investigations are given. They then describe a current investigation in which they studied 269 subjects, including 173 normal women, 34 patients with hyperparathyroidism, 24 patients with steroid-induced osteoporosis, and 38 men with idiopathic osteoporosis. Spinal quantitative computed tomography, radiogrammetry, and single photon absorptiometry were performed, and a spinal fracture index was calculated on all patients. The authors found a disproportionate loss of spinal trabecular mineral compared to appendicular mineral in the men with idiopathic osteoporosis and the patients with steroid-induced osteoporosis. They observed roughly equivalent mineral loss in both the appendicular and axial regions in the hyperparathyroid patients. The appendicular cortical measurements correlated moderately well with each other but less well with spinal trabecular QCT. The spinal fracture index correlated well with QCT and less well with the appendicular measurements. Knowledge of appendicular cortical mineral status is important in its own right but is not a valid predictor of axial trabecular mineral status, which may be disproportionately decreased in certain diseases. Quantitative CT provides a reliable means of assessing the latter region of the skeleton, correlates well with the spinal fracture index (a semiquantitative measurement of end-organ failure), and offers the clinician a sensitive means of following the effects of therapy.

YBYRÁ facilitates comparison of large phylogenetic trees.

PubMed

Machado, Denis Jacob

2015-07-01

The number and size of tree topologies that are being compared by phylogenetic systematists is increasing due to technological advancements in high-throughput DNA sequencing. However, we still lack tools to facilitate comparison among phylogenetic trees with a large number of terminals. The "YBYRÁ" project integrates software solutions for data analysis in phylogenetics. It comprises tools for (1) topological distance calculation based on the number of shared splits or clades, (2) sensitivity analysis and automatic generation of sensitivity plots and (3) clade diagnoses based on different categories of synapomorphies. YBYRÁ also provides (4) an original framework to facilitate the search for potential rogue taxa based on how much they affect average matching split distances (using MSdist). YBYRÁ facilitates comparison of large phylogenetic trees and outperforms competing software in terms of usability and time efficiency, specially for large data sets. The programs that comprises this toolkit are written in Python, hence they do not require installation and have minimum dependencies. The entire project is available under an open-source licence at http://www.ib.usp.br/grant/anfibios/researchSoftware.html .

Patterns of Reproductive Isolation in Eucalyptus-A Phylogenetic Perspective.

PubMed

Larcombe, Matthew J; Holland, Barbara; Steane, Dorothy A; Jones, Rebecca C; Nicolle, Dean; Vaillancourt, René E; Potts, Brad M

2015-07-01

We assess phylogenetic patterns of hybridization in the speciose, ecologically and economically important genus Eucalyptus, in order to better understand the evolution of reproductive isolation. Eucalyptus globulus pollen was applied to 99 eucalypt species, mainly from the large commercially important subgenus, Symphyomyrtus. In the 64 species that produce seeds, hybrid compatibility was assessed at two stages, hybrid-production (at approximately 1 month) and hybrid-survival (at 9 months), and compared with phylogenies based on 8,350 genome-wide DArT (diversity arrays technology) markers. Model fitting was used to assess the relationship between compatibility and genetic distance, and whether or not the strength of incompatibility "snowballs" with divergence. There was a decline in compatibility with increasing genetic distance between species. Hybridization was common within two closely related clades (one including E. globulus), but rare between E. globulus and species in two phylogenetically distant clades. Of three alternative models tested (linear, slowdown, and snowball), we found consistent support for a snowball model, indicating that the strength of incompatibility accelerates relative to genetic distance. Although we can only speculate about the genetic basis of this pattern, it is consistent with a Dobzhansky-Muller-model prediction that incompatibilities should snowball with divergence due to negative epistasis. Different rates of compatibility decline in the hybrid-production and hybrid-survival measures suggest that early-acting postmating barriers developed first and are stronger than later-acting barriers. We estimated that complete reproductive isolation can take up to 21-31 My in Eucalyptus. Practical implications for hybrid eucalypt breeding and genetic risk assessment in Australia are discussed. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For

Disentangling the phylogenetic and ecological components of spider phenotypic variation.

PubMed

Gonçalves-Souza, Thiago; Diniz-Filho, José Alexandre Felizola; Romero, Gustavo Quevedo

2014-01-01

An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhabitat scale, although phylogenic signal is present in both scales. Taken together, these results suggest that whereas at the habitat scale selective colonization affect spider body size and shape, at fine scales both selective colonization and adaptive evolution determine spider body shape. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape. We also discussed the relevance in considering multiple scales when studying phylogenetic community structure.

Disentangling the Phylogenetic and Ecological Components of Spider Phenotypic Variation

PubMed Central

Gonçalves-Souza, Thiago; Diniz-Filho, José Alexandre Felizola; Romero, Gustavo Quevedo

2014-01-01

An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhabitat scale, although phylogenic signal is present in both scales. Taken together, these results suggest that whereas at the habitat scale selective colonization affect spider body size and shape, at fine scales both selective colonization and adaptive evolution determine spider body shape. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape. We also discussed the relevance in considering multiple scales when studying phylogenetic community structure. PMID:24651264

Comprehensive untargeted metabolomics of Lychnnophorinae subtribe (Asteraceae: Vernonieae) in a phylogenetic context.

PubMed

Martucci, Maria Elvira Poleti; Loeuille, Benoit; Pirani, José Rubens; Gobbo-Neto, Leonardo

2018-01-01

Members of the subtribe Lychnophorinae occur mostly within the Cerrado domain of the Brazilian Central Plateau. The relationships between its 11 genera, as well as between Lychnophorinae and other subtribes belonging to the tribe Vernonieae, have recently been investigated upon a phylogeny based on molecular and morphological data. We report the use of a comprehensive untargeted metabolomics approach, combining HPLC-MS and GC-MS data, followed by multivariate analyses aiming to assess the congruence between metabolomics data and the phylogenetic hypothesis, as well as its potential as a chemotaxonomic tool. We analyzed 78 species by UHPLC-MS and GC-MS in both positive and negative ionization modes. The metabolic profiles obtained for these species were treated in MetAlign and in MSClust and the matrices generated were used in SIMCA for hierarchical cluster analyses, principal component analyses and orthogonal partial least square discriminant analysis. The results showed that metabolomic analyses are mostly congruent with the phylogenetic hypothesis especially at lower taxonomic levels (Lychnophora or Eremanthus). Our results confirm that data generated using metabolomics provide evidence for chemotaxonomical studies, especially for phylogenetic inference of the Lychnophorinae subtribe and insight into the evolution of the secondary metabolites of this group.

Phylogenetic system and zoogeography of the Plecoptera.

PubMed

Zwick, P

2000-01-01

Information about the phylogenetic relationships of Plecoptera is summarized. The few characters supporting monophyly of the order are outlined. Several characters of possible significance for the search for the closest relatives of the stoneflies are discussed, but the sister-group of the order remains unknown. Numerous characters supporting the presently recognized phylogenetic system of Plecoptera are presented, alternative classifications are discussed, and suggestions for future studies are made. Notes on zoogeography are appended. The order as such is old (Permian fossils), but phylogenetic relationships and global distribution patterns suggest that evolution of the extant suborders started with the breakup of Pangaea. There is evidence of extensive recent speciation in all parts of the world.

Bayes` theorem and quantitative risk assessment

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

Kaplan, S.

1994-12-31

This paper argues that for a quantitative risk analysis (QRA) to be useful for public and private decision making, and for rallying the support necessary to implement those decisions, it is necessary that the QRA results be ``trustable.`` Trustable means that the results are based solidly and logically on all the relevant evidence available. This, in turn, means that the quantitative results must be derived from the evidence using Bayes` theorem. Thus, it argues that one should strive to make their QRAs more clearly and explicitly Bayesian, and in this way make them more ``evidence dependent`` than ``personality dependent.``

Phylogenetic groups among Klebsiella pneumoniae isolates from Brazil: relationship with antimicrobial resistance and origin.

PubMed

de Melo, Maíra Espíndola Silva; Cabral, Adriane Borges; Maciel, Maria Amélia Vieira; da Silveira, Vera Magalhães; de Souza Lopes, Ana Catarina

2011-05-01

The objectives of this study were to determine the distribution of phylogenetic groups among Klebsiella pneumoniae isolates from Recife, Brazil and to assess the relationship between the groups and the isolation sites and resistance profile. Ninety four isolates of K. pneumoniae from hospital or community infections and from normal microbiota were analyzed by gyrA PCR-RFLP, antibiotic susceptibility, and adonitol fermentation. The results revealed the distinction of three phylogenetic groups, as it has also been reported in Europe, showing that these clusters are highly conserved within K. pneumoniae. Group KpI was dominantly represented by hospital and community isolates while groups KpII and KpIII displayed mainly normal microbiota isolates. The resistance to third generation cephalosporins, aztreonam, imipenem, amoxicillin/clavulanic acid, and streptomycin was only observed in KpI. The percentage of resistance was higher in KpI, followed by KpII and KpIII. The differences in the distribution of K. pneumoniae phylogenetic groups observed in this study suggest distinctive clinical and epidemiological characteristics among the three groups, which is important to understand the epidemiology of infections caused by this organism. This is the first study in Brazil on K. pneumoniae isolates from normal microbiota and community infections regarding the distribution of phylogenetic groups based on the gyrA gene.

The problem and promise of scale dependency in community phylogenetics.

PubMed

Swenson, Nathan G; Enquist, Brian J; Pither, Jason; Thompson, Jill; Zimmerman, Jess K

2006-10-01

The problem of scale dependency is widespread in investigations of ecological communities. Null model investigations of community assembly exemplify the challenges involved because they typically include subjectively defined "regional species pools." The burgeoning field of community phylogenetics appears poised to face similar challenges. Our objective is to quantify the scope of the problem of scale dependency by comparing the phylogenetic structure of assemblages across contrasting geographic and taxonomic scales. We conduct phylogenetic analyses on communities within three tropical forests, and perform a sensitivity analysis with respect to two scaleable inputs: taxonomy and species pool size. We show that (1) estimates of phylogenetic overdispersion within local assemblages depend strongly on the taxonomic makeup of the local assemblage and (2) comparing the phylogenetic structure of a local assemblage to a species pool drawn from increasingly larger geographic scales results in an increased signal of phylogenetic clustering. We argue that, rather than posing a problem, "scale sensitivities" are likely to reveal general patterns of diversity that could help identify critical scales at which local or regional influences gain primacy for the structuring of communities. In this way, community phylogenetics promises to fill an important gap in community ecology and biogeography research.

Student Interpretations of Phylogenetic Trees in an Introductory Biology Course

PubMed Central

Dees, Jonathan; Niemi, Jarad; Montplaisir, Lisa

2014-01-01

Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa relatedness on phylogenetic trees, to measure the prevalence of correct taxa-relatedness interpretations, and to determine how student reasoning and correctness change in response to instruction and over time. Counting synapomorphies and nodes between taxa were the most common forms of incorrect reasoning, which presents a pedagogical dilemma concerning labeled synapomorphies on phylogenetic trees. Students also independently generated an alternative form of correct reasoning using monophyletic groups, the use of which decreased in popularity over time. Approximately half of all students were able to correctly interpret taxa relatedness on phylogenetic trees, and many memorized correct reasoning without understanding its application. Broad initial instruction that allowed students to generate inferences on their own contributed very little to phylogenetic tree understanding, while targeted instruction on evolutionary relationships improved understanding to some extent. Phylogenetic trees, which can directly affect student understanding of evolution, appear to offer introductory biology instructors a formidable pedagogical challenge. PMID:25452489

Landscape patterns in rainforest phylogenetic signal: isolated islands of refugia or structured continental distributions?

PubMed

Kooyman, Robert M; Rossetto, Maurizio; Sauquet, Hervé; Laffan, Shawn W

2013-01-01

Identify patterns of change in species distributions, diversity, concentrations of evolutionary history, and assembly of Australian rainforests. We used the distribution records of all known rainforest woody species in Australia across their full continental extent. These were analysed using measures of species richness, phylogenetic diversity (PD), phylogenetic endemism (PE) and phylogenetic structure (net relatedness index; NRI). Phylogenetic structure was assessed using both continental and regional species pools. To test the influence of growth-form, freestanding and climbing plants were analysed independently, and in combination. Species richness decreased along two generally orthogonal continental axes, corresponding with wet to seasonally dry and tropical to temperate habitats. The PE analyses identified four main areas of substantially restricted phylogenetic diversity, including parts of Cape York, Wet Tropics, Border Ranges, and Tasmania. The continental pool NRI results showed evenness (species less related than expected by chance) in groups of grid cells in coastally aligned areas of species rich tropical and sub-tropical rainforest, and in low diversity moist forest areas in the south-east of the Great Dividing Range and in Tasmania. Monsoon and drier vine forests, and moist forests inland from upland refugia showed phylogenetic clustering, reflecting lower diversity and more relatedness. Signals for evenness in Tasmania and clustering in northern monsoon forests weakened in analyses using regional species pools. For climbing plants, values for NRI by grid cell showed strong spatial structuring, with high diversity and PE concentrated in moist tropical and subtropical regions. Concentrations of rainforest evolutionary history (phylo-diversity) were patchily distributed within a continuum of species distributions. Contrasting with previous concepts of rainforest community distribution, our findings of continuous distributions and continental

Landscape Patterns in Rainforest Phylogenetic Signal: Isolated Islands of Refugia or Structured Continental Distributions?

PubMed Central

Kooyman, Robert M.; Rossetto, Maurizio; Sauquet, Hervé; Laffan, Shawn W.

2013-01-01

Objectives Identify patterns of change in species distributions, diversity, concentrations of evolutionary history, and assembly of Australian rainforests. Methods We used the distribution records of all known rainforest woody species in Australia across their full continental extent. These were analysed using measures of species richness, phylogenetic diversity (PD), phylogenetic endemism (PE) and phylogenetic structure (net relatedness index; NRI). Phylogenetic structure was assessed using both continental and regional species pools. To test the influence of growth-form, freestanding and climbing plants were analysed independently, and in combination. Results Species richness decreased along two generally orthogonal continental axes, corresponding with wet to seasonally dry and tropical to temperate habitats. The PE analyses identified four main areas of substantially restricted phylogenetic diversity, including parts of Cape York, Wet Tropics, Border Ranges, and Tasmania. The continental pool NRI results showed evenness (species less related than expected by chance) in groups of grid cells in coastally aligned areas of species rich tropical and sub-tropical rainforest, and in low diversity moist forest areas in the south-east of the Great Dividing Range and in Tasmania. Monsoon and drier vine forests, and moist forests inland from upland refugia showed phylogenetic clustering, reflecting lower diversity and more relatedness. Signals for evenness in Tasmania and clustering in northern monsoon forests weakened in analyses using regional species pools. For climbing plants, values for NRI by grid cell showed strong spatial structuring, with high diversity and PE concentrated in moist tropical and subtropical regions. Conclusions/Significance Concentrations of rainforest evolutionary history (phylo-diversity) were patchily distributed within a continuum of species distributions. Contrasting with previous concepts of rainforest community distribution, our findings of

Phylogenetic Analyses of Armillaria Reveal at Least 15 Phylogenetic Lineages in China, Seven of Which Are Associated with Cultivated Gastrodia elata

PubMed Central

Guo, Ting; Wang, Han Chen; Xue, Wan Qiu; Zhao, Jun; Yang, Zhu L.

2016-01-01

Fungal species of Armillaria, which can act as plant pathogens and/or symbionts of the Chinese traditional medicinal herb Gastrodia elata (“Tianma”), are ecologically and economically important and have consequently attracted the attention of mycologists. However, their taxonomy has been highly dependent on morphological characterization and mating tests. In this study, we phylogenetically analyzed Chinese Armillaria samples using the sequences of the internal transcribed spacer region, translation elongation factor-1 alpha gene and beta-tubulin gene. Our data revealed at least 15 phylogenetic lineages of Armillaria from China, of which seven were newly discovered and two were recorded from China for the first time. Fourteen Chinese biological species of Armillaria, which were previously defined based on mating tests, could be assigned to the 15 phylogenetic lineages identified herein. Seven of the 15 phylogenetic lineages were found to be disjunctively distributed in different continents of the Northern Hemisphere, while eight were revealed to be endemic to certain continents. In addition, we found that seven phylogenetic lineages of Armillaria were used for the cultivation of Tianma, only two of which had been recorded to be associated with Tianma previously. We also illustrated that G. elata f. glauca (“Brown Tianma”) and G. elata f. elata (“Red Tianma”), two cultivars of Tianma grown in different regions of China, form symbiotic relationships with different phylogenetic lineages of Armillaria. These findings should aid the development of Tianma cultivation in China. PMID:27138686

The application of quantitative risk assessment to microbial food safety risks.

PubMed

Jaykus, L A

1996-01-01

Regulatory programs and guidelines for the control of foodborne microbial agents have existed in the U.S. for nearly 100 years. However, increased awareness of the scope and magnitude of foodborne disease, as well as the emergence of previously unrecognized human pathogens transmitted via the foodborne route, have prompted regulatory officials to consider new and improved strategies to reduce the health risks associated with pathogenic microorganisms in foods. Implementation of these proposed strategies will involve definitive costs for a finite level of risk reduction. While regulatory decisions regarding the management of foodborne disease risk have traditionally been done with the aid of the scientific community, a formal conceptual framework for the evaluation of health risks from pathogenic microorganisms in foods is warranted. Quantitative risk assessment (QRA), which is formally defined as the technical assessment of the nature and magnitude of a risk caused by a hazard, provides such a framework. Reproducing microorganisms in foods present a particular challenge to QRA because both their introduction and numbers may be affected by numerous factors within the food chain, with all of these factors representing significant stages in food production, handling, and consumption, in a farm-to-table type of approach. The process of QRA entails four designated phases: (1) hazard identification, (2) exposure assessment, (3) dose-response assessment, and (4) risk characterization. Specific analytical tools are available to accomplish the analyses required for each phase of the QRA. The purpose of this paper is to provide a description of the conceptual framework for quantitative microbial risk assessment within the standard description provided by the National Academy of Sciences (NAS) paradigm. Each of the sequential steps in QRA are discussed in detail, providing information on current applications, tools for conducting the analyses, and methodological and/or data

Quantitative CMMI Assessment for Offshoring through the Analysis of Project Management Repositories

NASA Astrophysics Data System (ADS)

Sunetnanta, Thanwadee; Nobprapai, Ni-On; Gotel, Olly

The nature of distributed teams and the existence of multiple sites in offshore software development projects pose a challenging setting for software process improvement. Often, the improvement and appraisal of software processes is achieved through a turnkey solution where best practices are imposed or transferred from a company’s headquarters to its offshore units. In so doing, successful project health checks and monitoring for quality on software processes requires strong project management skills, well-built onshore-offshore coordination, and often needs regular onsite visits by software process improvement consultants from the headquarters’ team. This paper focuses on software process improvement as guided by the Capability Maturity Model Integration (CMMI) and proposes a model to evaluate the status of such improvement efforts in the context of distributed multi-site projects without some of this overhead. The paper discusses the application of quantitative CMMI assessment through the collection and analysis of project data gathered directly from project repositories to facilitate CMMI implementation and reduce the cost of such implementation for offshore-outsourced software development projects. We exemplify this approach to quantitative CMMI assessment through the analysis of project management data and discuss the future directions of this work in progress.

Climate-driven extinctions shape the phylogenetic structure of temperate tree floras.

PubMed

Eiserhardt, Wolf L; Borchsenius, Finn; Plum, Christoffer M; Ordonez, Alejandro; Svenning, Jens-Christian

2015-03-01

When taxa go extinct, unique evolutionary history is lost. If extinction is selective, and the intrinsic vulnerabilities of taxa show phylogenetic signal, more evolutionary history may be lost than expected under random extinction. Under what conditions this occurs is insufficiently known. We show that late Cenozoic climate change induced phylogenetically selective regional extinction of northern temperate trees because of phylogenetic signal in cold tolerance, leading to significantly and substantially larger than random losses of phylogenetic diversity (PD). The surviving floras in regions that experienced stronger extinction are phylogenetically more clustered, indicating that non-random losses of PD are of increasing concern with increasing extinction severity. Using simulations, we show that a simple threshold model of survival given a physiological trait with phylogenetic signal reproduces our findings. Our results send a strong warning that we may expect future assemblages to be phylogenetically and possibly functionally depauperate if anthropogenic climate change affects taxa similarly. © 2015 John Wiley & Sons Ltd/CNRS.

Increased phylogenetic resolution using target enrichment in Rubus

USDA-ARS?s Scientific Manuscript database

Phylogenetic analyses in Rubus L. have been challenging due to polyploidy, hybridization, and apomixis within the genus. Wide morphological diversity occurs within and between species, contributing to challenges at lower and higher systematic levels. Phylogenetic inferences to date have been based o...

Qualitative and quantitative approaches in the dose-response assessment of genotoxic carcinogens.

PubMed

Fukushima, Shoji; Gi, Min; Kakehashi, Anna; Wanibuchi, Hideki; Matsumoto, Michiharu

2016-05-01

Qualitative and quantitative approaches are important issues in field of carcinogenic risk assessment of the genotoxic carcinogens. Herein, we provide quantitative data on low-dose hepatocarcinogenicity studies for three genotoxic hepatocarcinogens: 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx), 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) and N-nitrosodiethylamine (DEN). Hepatocarcinogenicity was examined by quantitative analysis of glutathione S-transferase placental form (GST-P) positive foci, which are the preneoplastic lesions in rat hepatocarcinogenesis and the endpoint carcinogenic marker in the rat liver medium-term carcinogenicity bioassay. We also examined DNA damage and gene mutations which occurred through the initiation stage of carcinogenesis. For the establishment of points of departure (PoD) from which the cancer-related risk can be estimated, we analyzed the above events by quantitative no-observed-effect level and benchmark dose approaches. MeIQx at low doses induced formation of DNA-MeIQx adducts; somewhat higher doses caused elevation of 8-hydroxy-2'-deoxyquanosine levels; at still higher doses gene mutations occurred; and the highest dose induced formation of GST-P positive foci. These data indicate that early genotoxic events in the pathway to carcinogenesis showed the expected trend of lower PoDs for earlier events in the carcinogenic process. Similarly, only the highest dose of IQ caused an increase in the number of GST-P positive foci in the liver, while IQ-DNA adduct formation was observed with low doses. Moreover, treatment with DEN at low doses had no effect on development of GST-P positive foci in the liver. These data on PoDs for the markers contribute to understand whether genotoxic carcinogens have a threshold for their carcinogenicity. The most appropriate approach to use in low dose-response assessment must be approved on the basis of scientific judgment. © The Author 2015. Published by Oxford University Press on behalf of

Interpreting the universal phylogenetic tree

NASA Technical Reports Server (NTRS)

Woese, C. R.

2000-01-01

The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist.

Evolutionary tools for phytosanitary risk analysis: phylogenetic signal as a predictor of host range of plant pests and pathogens

PubMed Central

Gilbert, Gregory S; Magarey, Roger; Suiter, Karl; Webb, Campbell O

2012-01-01

Assessing risk from a novel pest or pathogen requires knowing which local plant species are susceptible. Empirical data on the local host range of novel pests are usually lacking, but we know that some pests are more likely to attack closely related plant species than species separated by greater evolutionary distance. We use the Global Pest and Disease Database, an internal database maintained by the United States Department of Agriculture Animal and Plant Health Inspection Service – Plant Protection and Quarantine Division (USDA APHIS-PPQ), to evaluate the strength of the phylogenetic signal in host range for nine major groups of plant pests and pathogens. Eight of nine groups showed significant phylogenetic signal in host range. Additionally, pests and pathogens with more known hosts attacked a phylogenetically broader range of hosts. This suggests that easily obtained data – the number of known hosts and the phylogenetic distance between known hosts and other species of interest – can be used to predict which plant species are likely to be susceptible to a particular pest. This can facilitate rapid assessment of risk from novel pests and pathogens when empirical host range data are not yet available and guide efficient collection of empirical data for risk evaluation. PMID:23346231

Evolutionary tools for phytosanitary risk analysis: phylogenetic signal as a predictor of host range of plant pests and pathogens.

PubMed

Gilbert, Gregory S; Magarey, Roger; Suiter, Karl; Webb, Campbell O

2012-12-01

Assessing risk from a novel pest or pathogen requires knowing which local plant species are susceptible. Empirical data on the local host range of novel pests are usually lacking, but we know that some pests are more likely to attack closely related plant species than species separated by greater evolutionary distance. We use the Global Pest and Disease Database, an internal database maintained by the United States Department of Agriculture Animal and Plant Health Inspection Service - Plant Protection and Quarantine Division (USDA APHIS-PPQ), to evaluate the strength of the phylogenetic signal in host range for nine major groups of plant pests and pathogens. Eight of nine groups showed significant phylogenetic signal in host range. Additionally, pests and pathogens with more known hosts attacked a phylogenetically broader range of hosts. This suggests that easily obtained data - the number of known hosts and the phylogenetic distance between known hosts and other species of interest - can be used to predict which plant species are likely to be susceptible to a particular pest. This can facilitate rapid assessment of risk from novel pests and pathogens when empirical host range data are not yet available and guide efficient collection of empirical data for risk evaluation.

Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses.

PubMed

Guillerme, Thomas; Cooper, Natalie

2016-05-01

Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies. © 2016 The Authors.

Quantitative Comparison Of Vesicular Glutamate Transporters in rat Deep Cerebellar Nuclei.

PubMed

Mao, Haian; Hamodeh, Salah; Sultan, Fahad

2018-04-15

The excitatory synapses of the rat deep cerebellar nuclei (DCN) were quantitatively analyzed by vesicular glutamate transporter 1 and 2 (vGluT1 and vGluT2) immunolabeling. We calculated the number and sizes of the labeled boutons and compared them between lateral/dentate nucleus (LN/DN), posterior interposed nucleus (PIN), anterior interposed nucleus (AIN), and medial nucleus (MN). The density of vGluT1+ boutons differs significantly within these nuclei. In contrast, the vGluT2+ bouton density is more similar between different nuclei. The phylogenetically newer DCN (LN/DN and PIN) have a 39% higher density of vGluT1+ boutons than the phylogenetically older DCN (AIN and MN). The volume of vGluT1+ boutons does not differ between the DCN, however the average volume of vGluT2+ boutons is larger in MN. In summary, our current results confirm and extend our previous findings showing that the increase in dendritic and axonal wiring in phylogenetically newer DCN is associated with an increase in vGluT1+ bouton density. Copyright © 2018 IBRO. Published by Elsevier Ltd. All rights reserved.

Phylogenetics beyond biology.

PubMed

Retzlaff, Nancy; Stadler, Peter F

2018-06-21

Evolutionary processes have been described not only in biology but also for a wide range of human cultural activities including languages and law. In contrast to the evolution of DNA or protein sequences, the detailed mechanisms giving rise to the observed evolution-like processes are not or only partially known. The absence of a mechanistic model of evolution implies that it remains unknown how the distances between different taxa have to be quantified. Considering distortions of metric distances, we first show that poor choices of the distance measure can lead to incorrect phylogenetic trees. Based on the well-known fact that phylogenetic inference requires additive metrics, we then show that the correct phylogeny can be computed from a distance matrix [Formula: see text] if there is a monotonic, subadditive function [Formula: see text] such that [Formula: see text] is additive. The required metric-preserving transformation [Formula: see text] can be computed as the solution of an optimization problem. This result shows that the problem of phylogeny reconstruction is well defined even if a detailed mechanistic model of the evolutionary process remains elusive.

An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology.

PubMed

Pennell, Matthew W; Harmon, Luke J

2013-06-01

Recent innovations in phylogenetic comparative methods (PCMs) have spurred a renaissance of research into the causes and consequences of large-scale patterns of biodiversity. In this paper, we review these advances. We also highlight the potential of comparative methods to integrate across fields and focus on three examples where such integration might be particularly valuable: quantitative genetics, community ecology, and paleobiology. We argue that PCMs will continue to be a key set of tools in evolutionary biology, shedding new light on how evolutionary processes have shaped patterns of biodiversity through deep time. © 2013 New York Academy of Sciences.

A quantitative method for risk assessment of agriculture due to climate change

NASA Astrophysics Data System (ADS)

Dong, Zhiqiang; Pan, Zhihua; An, Pingli; Zhang, Jingting; Zhang, Jun; Pan, Yuying; Huang, Lei; Zhao, Hui; Han, Guolin; Wu, Dong; Wang, Jialin; Fan, Dongliang; Gao, Lin; Pan, Xuebiao

2018-01-01

Climate change has greatly affected agriculture. Agriculture is facing increasing risks as its sensitivity and vulnerability to climate change. Scientific assessment of climate change-induced agricultural risks could help to actively deal with climate change and ensure food security. However, quantitative assessment of risk is a difficult issue. Here, based on the IPCC assessment reports, a quantitative method for risk assessment of agriculture due to climate change is proposed. Risk is described as the product of the degree of loss and its probability of occurrence. The degree of loss can be expressed by the yield change amplitude. The probability of occurrence can be calculated by the new concept of climate change effect-accumulated frequency (CCEAF). Specific steps of this assessment method are suggested. This method is determined feasible and practical by using the spring wheat in Wuchuan County of Inner Mongolia as a test example. The results show that the fluctuation of spring wheat yield increased with the warming and drying climatic trend in Wuchuan County. The maximum yield decrease and its probability were 3.5 and 64.6%, respectively, for the temperature maximum increase 88.3%, and its risk was 2.2%. The maximum yield decrease and its probability were 14.1 and 56.1%, respectively, for the precipitation maximum decrease 35.2%, and its risk was 7.9%. For the comprehensive impacts of temperature and precipitation, the maximum yield decrease and its probability were 17.6 and 53.4%, respectively, and its risk increased to 9.4%. If we do not adopt appropriate adaptation strategies, the degree of loss from the negative impacts of multiclimatic factors and its probability of occurrence will both increase accordingly, and the risk will also grow obviously.

The origin and evolution of tRNA inferred from phylogenetic analysis of structure.

PubMed

Sun, Feng-Jie; Caetano-Anollés, Gustavo

2008-01-01

The evolutionary history of the two structural and functional domains of tRNA is controversial but harbors the secrets of early translation and the genetic code. To explore the origin and evolution of tRNA, we reconstructed phylogenetic trees directly from molecular structure. Forty-two structural characters describing the geometry of 571 tRNAs and three statistical parameters describing thermodynamic and mechanical features of molecules quantitatively were used to derive phylogenetic trees of molecules and molecular substructures. Trees of molecules failed to group tRNA according to amino acid specificity and did not reveal the tripartite nature of life, probably due to loss of phylogenetic signal or because tRNA diversification predated organismal diversification. Trees of substructures derived from both structural and statistical characters support the origin of tRNA in the acceptor arm and the hypothesis that the top half domain composed of acceptor and pseudouridine (TPsiC) arms is more ancient than the bottom half domain composed of dihydrouridine (DHU) and anticodon arms. This constitutes the cornerstone of the genomic tag hypothesis that postulates tRNAs were ancient telomeres in the RNA world. The trees of substructures suggest a model for the evolution of the major functional and structural components of tRNA. In this model, short RNA hairpins with stems homologous to the acceptor arm of present day tRNAs were extended with regions homologous to TPsiC and anticodon arms. The DHU arm was then incorporated into the resulting three-stemmed structure to form a proto-cloverleaf structure. The variable region was the last structural addition to the molecular repertoire of evolving tRNA substructures.

Power law tails in phylogenetic systems.

PubMed

Qin, Chongli; Colwell, Lucy J

2018-01-23

Covariance analysis of protein sequence alignments uses coevolving pairs of sequence positions to predict features of protein structure and function. However, current methods ignore the phylogenetic relationships between sequences, potentially corrupting the identification of covarying positions. Here, we use random matrix theory to demonstrate the existence of a power law tail that distinguishes the spectrum of covariance caused by phylogeny from that caused by structural interactions. The power law is essentially independent of the phylogenetic tree topology, depending on just two parameters-the sequence length and the average branch length. We demonstrate that these power law tails are ubiquitous in the large protein sequence alignments used to predict contacts in 3D structure, as predicted by our theory. This suggests that to decouple phylogenetic effects from the interactions between sequence distal sites that control biological function, it is necessary to remove or down-weight the eigenvectors of the covariance matrix with largest eigenvalues. We confirm that truncating these eigenvectors improves contact prediction.

Promoting the safety performance of industrial radiography using a quantitative assessment system.

PubMed

Kardan, M R; Mianji, F A; Rastkhah, N; Babakhani, A; Azad, S Borhan

2006-12-01

The increasing number of industrial radiographers and their considerable occupational exposure has been one of the main concerns of the Iran Nuclear Regulatory Authority (INRA) in recent years. In 2002, a quantitative system of evaluating the safety performance of licensees and a complementary enforcement system was introduced by the National Radiation Protection Department (NRPD). Each parameter of the practice is given a weighting factor according to its importance to safety. Assessment of the licensees is done quantitatively by summing up their scores using prepared tables. Implementing this system of evaluation showed a considerable decrease in deficiencies in the various centres. Tables are updated regularly as a result of findings during the inspections. This system is used in addition to enforcement to promote safety performance and to increase the culture of safety in industrial radiography.

Determinants of plant community assembly in a mosaic of landscape units in central Amazonia: ecological and phylogenetic perspectives.

PubMed

Umaña, María Natalia; Norden, Natalia; Cano, Angela; Stevenson, Pablo R

2012-01-01

The Amazon harbours one of the richest ecosystems on Earth. Such diversity is likely to be promoted by plant specialization, associated with the occurrence of a mosaic of landscape units. Here, we integrate ecological and phylogenetic data at different spatial scales to assess the importance of habitat specialization in driving compositional and phylogenetic variation across the Amazonian forest. To do so, we evaluated patterns of floristic dissimilarity and phylogenetic turnover, habitat association and phylogenetic structure in three different landscape units occurring in terra firme (Hilly and Terrace) and flooded forests (Igapó). We established two 1-ha tree plots in each of these landscape units at the Caparú Biological Station, SW Colombia, and measured edaphic, topographic and light variables. At large spatial scales, terra firme forests exhibited higher levels of species diversity and phylodiversity than flooded forests. These two types of forests showed conspicuous differences in species and phylogenetic composition, suggesting that environmental sorting due to flood is important, and can go beyond the species level. At a local level, landscape units showed floristic divergence, driven both by geographical distance and by edaphic specialization. In terms of phylogenetic structure, Igapó forests showed phylogenetic clustering, whereas Hilly and Terrace forests showed phylogenetic evenness. Within plots, however, local communities did not show any particular trend. Overall, our findings suggest that flooded forests, characterized by stressful environments, impose limits to species occurrence, whereas terra firme forests, more environmentally heterogeneous, are likely to provide a wider range of ecological conditions and therefore to bear higher diversity. Thus, Amazonia should be considered as a mosaic of landscape units, where the strength of habitat association depends upon their environmental properties.

Determinants of Plant Community Assembly in a Mosaic of Landscape Units in Central Amazonia: Ecological and Phylogenetic Perspectives

PubMed Central

Umaña, María Natalia; Norden, Natalia; Cano, Ángela; Stevenson, Pablo R.

2012-01-01

The Amazon harbours one of the richest ecosystems on Earth. Such diversity is likely to be promoted by plant specialization, associated with the occurrence of a mosaic of landscape units. Here, we integrate ecological and phylogenetic data at different spatial scales to assess the importance of habitat specialization in driving compositional and phylogenetic variation across the Amazonian forest. To do so, we evaluated patterns of floristic dissimilarity and phylogenetic turnover, habitat association and phylogenetic structure in three different landscape units occurring in terra firme (Hilly and Terrace) and flooded forests (Igapó). We established two 1-ha tree plots in each of these landscape units at the Caparú Biological Station, SW Colombia, and measured edaphic, topographic and light variables. At large spatial scales, terra firme forests exhibited higher levels of species diversity and phylodiversity than flooded forests. These two types of forests showed conspicuous differences in species and phylogenetic composition, suggesting that environmental sorting due to flood is important, and can go beyond the species level. At a local level, landscape units showed floristic divergence, driven both by geographical distance and by edaphic specialization. In terms of phylogenetic structure, Igapó forests showed phylogenetic clustering, whereas Hilly and Terrace forests showed phylogenetic evenness. Within plots, however, local communities did not show any particular trend. Overall, our findings suggest that flooded forests, characterized by stressful environments, impose limits to species occurrence, whereas terra firme forests, more environmentally heterogeneous, are likely to provide a wider range of ecological conditions and therefore to bear higher diversity. Thus, Amazonia should be considered as a mosaic of landscape units, where the strength of habitat association depends upon their environmental properties. PMID:23028844

Phylogenetic tree construction based on 2D graphical representation

NASA Astrophysics Data System (ADS)

Liao, Bo; Shan, Xinzhou; Zhu, Wen; Li, Renfa

2006-04-01

A new approach based on the two-dimensional (2D) graphical representation of the whole genome sequence [Bo Liao, Chem. Phys. Lett., 401(2005) 196.] is proposed to analyze the phylogenetic relationships of genomes. The evolutionary distances are obtained through measuring the differences among the 2D curves. The fuzzy theory is used to construct phylogenetic tree. The phylogenetic relationships of H5N1 avian influenza virus illustrate the utility of our approach.

Contrasting biodiversity-ecosystem functioning relationships in phylogenetic and functional diversity.

PubMed

Steudel, Bastian; Hallmann, Christine; Lorenz, Maike; Abrahamczyk, Stefan; Prinz, Kathleen; Herrfurth, Cornelia; Feussner, Ivo; Martini, Johannes W R; Kessler, Michael

2016-10-01

It is well known that ecosystem functioning is positively influenced by biodiversity. Most biodiversity-ecosystem functioning experiments have measured biodiversity based on species richness or phylogenetic relationships. However, theoretical and empirical evidence suggests that ecosystem functioning should be more closely related to functional diversity than to species richness. We applied different metrics of biodiversity in an artificial biodiversity-ecosystem functioning experiment using 64 species of green microalgae in combinations of two to 16 species. We found that phylogenetic and functional diversity were positively correlated with biomass overyield, driven by their strong correlation with species richness. At low species richness, no significant correlation between overyield and functional and phylogenetic diversity was found. However, at high species richness (16 species), we found a positive relationship of overyield with functional diversity and a negative relationship with phylogenetic diversity. We show that negative phylogenetic diversity-ecosystem functioning relationships can result from interspecific growth inhibition. The opposing performances of facilitation (functional diversity) and inhibition (phylogenetic diversity) we observed at the 16 species level suggest that phylogenetic diversity is not always a good proxy for functional diversity and that results from experiments with low species numbers may underestimate negative species interactions. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Increased phylogenetic resolution within the ecologically important Rhizopogon subgenus Amylopogon using 10 anonymous nuclear loci.

PubMed

Dowie, Nicholas J; Grubisha, Lisa C; Burton, Brent A; Klooster, Matthew R; Miller, Steven L

2017-01-01

Rhizopogon species are ecologically significant ectomycorrhizal fungi in conifer ecosystems. The importance of this system merits the development and utilization of a more robust set of molecular markers specifically designed to evaluate their evolutionary ecology. Anonymous nuclear loci (ANL) were developed for R. subgenus Amylopogon. Members of this subgenus occur throughout the United States and are exclusive fungal symbionts associated with Pterospora andromedea, a threatened mycoheterotrophic plant endemic to disjunct eastern and western regions of North America. Candidate ANL were developed from 454 shotgun pyrosequencing and assessed for positive amplification across targeted species, sequencing success, and recovery of phylogenetically informative sites. Ten ANL were successfully developed and were subsequently used to sequence representative taxa, herbaria holotype and paratype specimens in R. subgenus Amylopogon. Phylogenetic reconstructions were performed on individual and concatenated data sets by Bayesian inference and maximum likelihood methods. Phylogenetic analyses of these 10 ANL were compared with a phylogeny traditionally constructed using the universal fungal barcode nuc rDNA ITS1-5.8S-ITS2 region (ITS). The resulting ANL phylogeny was consistent with most of the species designations delineated by ITS. However, the ANL phylogeny provided much greater phylogenetic resolution, yielding new evidence for cryptic species within previously defined species of R. subgenus Amylopogon. Additionally, the rooted ANL phylogeny provided an alternate topology to the ITS phylogeny, which inferred a novel set of evolutionary relationships not identified in prior phylogenetic studies.

A relative quantitative assessment of myocardial perfusion by first-pass technique: animal study

NASA Astrophysics Data System (ADS)

Chen, Jun; Zhang, Zhang; Yu, Xuefang; Zhou, Kenneth J.

2015-03-01

The purpose of this study is to quantitatively assess the myocardial perfusion by first-pass technique in swine model. Numerous techniques based on the analysis of Computed Tomography (CT) Hounsfield Unit (HU) density have emerged. Although these methods proposed to be able to assess haemodynamically significant coronary artery stenosis, their limitations are noticed. There are still needs to develop some new techniques. Experiments were performed upon five (5) closed-chest swine. Balloon catheters were placed into the coronary artery to simulate different degrees of luminal stenosis. Myocardial Blood Flow (MBF) was measured using color microsphere technique. Fractional Flow Reserve (FFR) was measured using pressure wire. CT examinations were performed twice during First-pass phase under adenosine-stress condition. CT HU Density (HUDCT) and CT HU Density Ratio (HUDRCT) were calculated using the acquired CT images. Our study presents that HUDRCT shows a good (y=0.07245+0.09963x, r2=0.898) correlation with MBF and FFR. In receiver operating characteristic (ROC) curve analyses, HUDRCT provides excellent diagnostic performance for the detection of significant ischemia during adenosine-stress as defined by FFR indicated by the value of Area Under the Curve (AUC) of 0.927. HUDRCT has the potential to be developed as a useful indicator of quantitative assessment of myocardial perfusion.

Estimating phylogenetic trees from genome-scale data.

PubMed

Liu, Liang; Xi, Zhenxiang; Wu, Shaoyuan; Davis, Charles C; Edwards, Scott V

2015-12-01

The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as "species tree" methods have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a single underlying species tree. Here we review theory and empirical examples that help clarify conflicts between species tree and concatenation methods, and misconceptions in the literature about the performance of species tree methods. Considering concatenation as a special case of the multispecies coalescent model helps explain differences in the behavior of the two methods on phylogenomic data sets. Recent work suggests that species tree methods are more robust than concatenation approaches to some of the classic challenges of phylogenetic analysis, including rapidly evolving sites in DNA sequences and long-branch attraction. We show that approaches, such as binning, designed to augment the signal in species tree analyses can distort the distribution of gene trees and are inconsistent. Computationally efficient species tree methods incorporating biological realism are a key to phylogenetic analysis of whole-genome data. © 2015 New York Academy of Sciences.

Quantifying MCMC exploration of phylogenetic tree space.

PubMed

Whidden, Chris; Matsen, Frederick A

2015-05-01

In order to gain an understanding of the effectiveness of phylogenetic Markov chain Monte Carlo (MCMC), it is important to understand how quickly the empirical distribution of the MCMC converges to the posterior distribution. In this article, we investigate this problem on phylogenetic tree topologies with a metric that is especially well suited to the task: the subtree prune-and-regraft (SPR) metric. This metric directly corresponds to the minimum number of MCMC rearrangements required to move between trees in common phylogenetic MCMC implementations. We develop a novel graph-based approach to analyze tree posteriors and find that the SPR metric is much more informative than simpler metrics that are unrelated to MCMC moves. In doing so, we show conclusively that topological peaks do occur in Bayesian phylogenetic posteriors from real data sets as sampled with standard MCMC approaches, investigate the efficiency of Metropolis-coupled MCMC (MCMCMC) in traversing the valleys between peaks, and show that conditional clade distribution (CCD) can have systematic problems when there are multiple peaks. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Climate Change Impacts on the Tree of Life: Changes in Phylogenetic Diversity Illustrated for Acropora Corals

PubMed Central

Faith, Daniel P.; Richards, Zoe T.

2012-01-01

The possible loss of whole branches from the tree of life is a dramatic, but under-studied, biological implication of climate change. The tree of life represents an evolutionary heritage providing both present and future benefits to humanity, often in unanticipated ways. Losses in this evolutionary (evo) life-support system represent losses in “evosystem” services, and are quantified using the phylogenetic diversity (PD) measure. High species-level biodiversity losses may or may not correspond to high PD losses. If climate change impacts are clumped on the phylogeny, then loss of deeper phylogenetic branches can mean disproportionately large PD loss for a given degree of species loss. Over time, successive species extinctions within a clade each may imply only a moderate loss of PD, until the last species within that clade goes extinct, and PD drops precipitously. Emerging methods of “phylogenetic risk analysis” address such phylogenetic tipping points by adjusting conservation priorities to better reflect risk of such worst-case losses. We have further developed and explored this approach for one of the most threatened taxonomic groups, corals. Based on a phylogenetic tree for the corals genus Acropora, we identify cases where worst-case PD losses may be avoided by designing risk-averse conservation priorities. We also propose spatial heterogeneity measures changes to assess possible changes in the geographic distribution of corals PD. PMID:24832524

The phylogenetic structure of plant-pollinator networks increases with habitat size and isolation.

PubMed

Aizen, Marcelo A; Gleiser, Gabriela; Sabatino, Malena; Gilarranz, Luis J; Bascompte, Jordi; Verdú, Miguel

2016-01-01

Similarity among species in traits related to ecological interactions is frequently associated with common ancestry. Thus, closely related species usually interact with ecologically similar partners, which can be reinforced by diverse co-evolutionary processes. The effect of habitat fragmentation on the phylogenetic signal in interspecific interactions and correspondence between plant and animal phylogenies is, however, unknown. Here, we address to what extent phylogenetic signal and co-phylogenetic congruence of plant-animal interactions depend on habitat size and isolation by analysing the phylogenetic structure of 12 pollination webs from isolated Pampean hills. Phylogenetic signal in interspecific interactions differed among webs, being stronger for flower-visiting insects than plants. Phylogenetic signal and overall co-phylogenetic congruence increased independently with hill size and isolation. We propose that habitat fragmentation would erode the phylogenetic structure of interaction webs. A decrease in phylogenetic signal and co-phylogenetic correspondence in plant-pollinator interactions could be associated with less reliable mutualism and erratic co-evolutionary change. © 2015 John Wiley & Sons Ltd/CNRS.

Quantitative Microbial Risk Assessment of Pharmaceutical Products.

PubMed

Eissa, Mostafa Essam

2017-01-01

Monitoring of microbiological quality in the pharmaceutical industry is an important criterion that is required to justify safe product release to the drug market. Good manufacturing practice and efficient control on bioburden level of product components are critical parameters that influence the microbiological cleanliness of medicinal products. However, because microbial dispersion through the samples follows Poisson distribution, the rate of detection of microbiologically defective samples lambda (λ) decreases when the number of defective units per batch decreases. When integrating a dose-response model of infection (P inf ) of a specific objectionable microbe with a contamination module, the overall probability of infection from a single batch of pharmaceutical product can be estimated. The combination of P inf with detectability chance of the test (P det ) will yield a value that could be used as a quantitative measure of the possibility of passing contaminated batch units of product with a certain load of a specific pathogen and infecting the final consumer without being detected in the firm. The simulation study can be used to assess the risk of contamination and infection from objectionable microorganisms for sterile and non-sterile products. LAY ABSTRACT: Microbial contamination of pharmaceutical products is a global problem that may lead to infection and possibly death. While reputable pharmaceutical companies strive to deliver microbiologically safe products, it would be helpful to apply an assessment system for the current risk associated with pharmaceutical batches delivered to the drug market. The current methodology may be helpful also in determining the degree of improvement or deterioration on the batch processing flow until reaching the final consumer. Moreover, the present system is flexible and can be applied to other industries such as food, cosmetics, or medical devices manufacturing and processing fields to assess the microbiological risk of

Phylogenetic lineages in Entomophthoromycota

USDA-ARS?s Scientific Manuscript database

Entomophthoromycota Humber is one of five major phylogenetic lineages among the former phylum Zygomycota. These early terrestrial fungi share evolutionarily ancestral characters such as coenocytic mycelium and gametangiogamy as a sexual process resulting in zygospore formation. Previous molecular st...

Phylogenetic context determines the role of competition in adaptive radiation

PubMed Central

Tan, Jiaqi; Slattery, Matthew R.; Yang, Xian; Jiang, Lin

2016-01-01

Understanding ecological mechanisms regulating the evolution of biodiversity is of much interest to ecologists and evolutionary biologists. Adaptive radiation constitutes an important evolutionary process that generates biodiversity. Competition has long been thought to influence adaptive radiation, but the directionality of its effect and associated mechanisms remain ambiguous. Here, we report a rigorous experimental test of the role of competition on adaptive radiation using the rapidly evolving bacterium Pseudomonas fluorescens SBW25 interacting with multiple bacterial species that differed in their phylogenetic distance to the diversifying bacterium. We showed that the inhibitive effect of competitors on the adaptive radiation of P. fluorescens decreased as their phylogenetic distance increased. To explain this phylogenetic dependency of adaptive radiation, we linked the phylogenetic distance between P. fluorescens and its competitors to their niche and competitive fitness differences. Competitive fitness differences, which showed weak phylogenetic signal, reduced P. fluorescens abundance and thus diversification, whereas phylogenetically conserved niche differences promoted diversification. These results demonstrate the context dependency of competitive effects on adaptive radiation, and highlight the importance of past evolutionary history for ongoing evolutionary processes. PMID:27335414

DendroPy: a Python library for phylogenetic computing.

PubMed

Sukumaran, Jeet; Holder, Mark T

2010-06-15

DendroPy is a cross-platform library for the Python programming language that provides for object-oriented reading, writing, simulation and manipulation of phylogenetic data, with an emphasis on phylogenetic tree operations. DendroPy uses a splits-hash mapping to perform rapid calculations of tree distances, similarities and shape under various metrics. It contains rich simulation routines to generate trees under a number of different phylogenetic and coalescent models. DendroPy's data simulation and manipulation facilities, in conjunction with its support of a broad range of phylogenetic data formats (NEXUS, Newick, PHYLIP, FASTA, NeXML, etc.), allow it to serve a useful role in various phyloinformatics and phylogeographic pipelines. The stable release of the library is available for download and automated installation through the Python Package Index site (http://pypi.python.org/pypi/DendroPy), while the active development source code repository is available to the public from GitHub (http://github.com/jeetsukumaran/DendroPy).

Phylogenetic and functional diversity in large carnivore assemblages

PubMed Central

Dalerum, F.

2013-01-01

Large terrestrial carnivores are important ecological components and prominent flagship species, but are often extinction prone owing to a combination of biological traits and high levels of human persecution. This study combines phylogenetic and functional diversity evaluations of global and continental large carnivore assemblages to provide a framework for conservation prioritization both between and within assemblages. Species-rich assemblages of large carnivores simultaneously had high phylogenetic and functional diversity, but species contributions to phylogenetic and functional diversity components were not positively correlated. The results further provide ecological justification for the largest carnivore species as a focus for conservation action, and suggests that range contraction is a likely cause of diminishing carnivore ecosystem function. This study highlights that preserving species-rich carnivore assemblages will capture both high phylogenetic and functional diversity, but that prioritizing species within assemblages will involve trade-offs between optimizing contemporary ecosystem function versus the evolutionary potential for future ecosystem performance. PMID:23576787

On the information content of discrete phylogenetic characters.

PubMed

Bordewich, Magnus; Deutschmann, Ina Maria; Fischer, Mareike; Kasbohm, Elisa; Semple, Charles; Steel, Mike

2017-12-16

Phylogenetic inference aims to reconstruct the evolutionary relationships of different species based on genetic (or other) data. Discrete characters are a particular type of data, which contain information on how the species should be grouped together. However, it has long been known that some characters contain more information than others. For instance, a character that assigns the same state to each species groups all of them together and so provides no insight into the relationships of the species considered. At the other extreme, a character that assigns a different state to each species also conveys no phylogenetic signal. In this manuscript, we study a natural combinatorial measure of the information content of an individual character and analyse properties of characters that provide the maximum phylogenetic information, particularly, the number of states such a character uses and how the different states have to be distributed among the species or taxa of the phylogenetic tree.

Quantitative assessment of risk reduction from hand washing with antibacterial soaps.

PubMed

Gibson, L L; Rose, J B; Haas, C N; Gerba, C P; Rusin, P A

2002-01-01

The Centers for Disease Control and Prevention have estimated that there are 3,713,000 cases of infectious disease associated with day care facilities each year. The objective of this study was to examine the risk reduction achieved from using different soap formulations after diaper changing using a microbial quantitative risk assessment approach. To achieve this, a probability of infection model and an exposure assessment based on micro-organism transfer were used to evaluate the efficacy of different soap formulations in reducing the probability of disease following hand contact with an enteric pathogen. Based on this model, it was determined that the probability of infection ranged from 24/100 to 91/100 for those changing diapers of babies with symptomatic shigellosis who used a control product (soap without an antibacterial ingredient), 22/100 to 91/100 for those who used an antibacterial soap (chlorohexadine 4%), and 15/100 to 90/100 for those who used a triclosan (1.5%) antibacterial soap. Those with asymptomatic shigellosis who used a non-antibacterial control soap had a risk between 49/100,000 and 53/100, those who used the 4% chlorohexadine-containing soap had a risk between 43/100,000 and 51/100, and for those who used a 1.5% triclosan soap had a risk between 21/100,000 and 43/100. The adequate washing of hands after diapering reduces risk and can be further reduced by a factor of 20% by the use of an antibacterial soap. Quantitative risk assessment is a valuable tool in the evaluation of household sanitizing agents and low risk outcomes.

Computer-Assisted Quantitative Assessment of Prostatic Calcifications in Patients with Chronic Prostatitis.

PubMed

Boltri, Matteo; Magri, Vittorio; Montanari, Emanuele; Perletti, Gianpaolo; Trinchieri, Alberto

2018-04-26

The aim of this study was the development of quantitative assessment of prostatic calcifications at prostatic ultrasound examination by the use of an image analyzer. A group of 82 patients was evaluated by medical history, physical, and transrectal ultrasound examination. Patients had a urethral swab, a 4-specimen study and culture of the seminal fluid. Patients were classified according to National Institute of Diabetes and Digestive and Kidney Diseases/National Institutes of Health. Subjective symptoms were scored by Chronic Prostatitis Symptom Index (CPSI) questionnaire. Ultrasound images were analyzed by the digital processing software Image J to quantitatively assess the presence of calcifications. Computer-assessed calcified areas were significantly higher in chronic bacterial prostatitis (n = 18; group II; 6.76 ± 8.09%) than in the chronic pelvic pain syndrome group IIIa (n = 26; 2.07 ± 1.01%) and IIIb (n = 38; 2.31 ± 2.18%). The area of calcification of the prostate was significantly related to the CPSI score for domains of micturition (r = 0.278, p = 0.023), Prostatic Specific Antigen values (r = 0341, p = 0.005), postvoiding residual urine (r = 0.262, p = 0.032), total prostate volume (r = 0.592, p = 0.000), and adenoma volume (r = 0.593; p = 0.000). The presence of calcifications is more frequently observed in patients with chronic bacterial prostatitis and is related to urinary symptoms. © 2018 S. Karger AG, Basel.

A Compressed Sensing-Based Wearable Sensor Network for Quantitative Assessment of Stroke Patients

PubMed Central

Yu, Lei; Xiong, Daxi; Guo, Liquan; Wang, Jiping

2016-01-01

Clinical rehabilitation assessment is an important part of the therapy process because it is the premise for prescribing suitable rehabilitation interventions. However, the commonly used assessment scales have the following two drawbacks: (1) they are susceptible to subjective factors; (2) they only have several rating levels and are influenced by a ceiling effect, making it impossible to exactly detect any further improvement in the movement. Meanwhile, energy constraints are a primary design consideration in wearable sensor network systems since they are often battery-operated. Traditionally, for wearable sensor network systems that follow the Shannon/Nyquist sampling theorem, there are many data that need to be sampled and transmitted. This paper proposes a novel wearable sensor network system to monitor and quantitatively assess the upper limb motion function, based on compressed sensing technology. With the sparse representation model, less data is transmitted to the computer than with traditional systems. The experimental results show that the accelerometer signals of Bobath handshake and shoulder touch exercises can be compressed, and the length of the compressed signal is less than 1/3 of the raw signal length. More importantly, the reconstruction errors have no influence on the predictive accuracy of the Brunnstrom stage classification model. It also indicated that the proposed system can not only reduce the amount of data during the sampling and transmission processes, but also, the reconstructed accelerometer signals can be used for quantitative assessment without any loss of useful information. PMID:26861337

A Compressed Sensing-Based Wearable Sensor Network for Quantitative Assessment of Stroke Patients.

PubMed

Yu, Lei; Xiong, Daxi; Guo, Liquan; Wang, Jiping

2016-02-05

Clinical rehabilitation assessment is an important part of the therapy process because it is the premise for prescribing suitable rehabilitation interventions. However, the commonly used assessment scales have the following two drawbacks: (1) they are susceptible to subjective factors; (2) they only have several rating levels and are influenced by a ceiling effect, making it impossible to exactly detect any further improvement in the movement. Meanwhile, energy constraints are a primary design consideration in wearable sensor network systems since they are often battery-operated. Traditionally, for wearable sensor network systems that follow the Shannon/Nyquist sampling theorem, there are many data that need to be sampled and transmitted. This paper proposes a novel wearable sensor network system to monitor and quantitatively assess the upper limb motion function, based on compressed sensing technology. With the sparse representation model, less data is transmitted to the computer than with traditional systems. The experimental results show that the accelerometer signals of Bobath handshake and shoulder touch exercises can be compressed, and the length of the compressed signal is less than 1/3 of the raw signal length. More importantly, the reconstruction errors have no influence on the predictive accuracy of the Brunnstrom stage classification model. It also indicated that the proposed system can not only reduce the amount of data during the sampling and transmission processes, but also, the reconstructed accelerometer signals can be used for quantitative assessment without any loss of useful information.

On the quirks of maximum parsimony and likelihood on phylogenetic networks.

PubMed

Bryant, Christopher; Fischer, Mareike; Linz, Simone; Semple, Charles

2017-03-21

Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe evolution accurately. For instance, processes like hybridization or lateral gene transfer that are commonplace in many groups of organisms and result in mosaic patterns of relationships cannot be represented by a single phylogenetic tree. This is why phylogenetic networks, which can display such events, are becoming of more and more interest in phylogenetic research. It is therefore necessary to extend concepts like maximum parsimony from phylogenetic trees to networks. Several suggestions for possible extensions can be found in recent literature, for instance the softwired and the hardwired parsimony concepts. In this paper, we analyze the so-called big parsimony problem under these two concepts, i.e. we investigate maximum parsimonious networks and analyze their properties. In particular, we show that finding a softwired maximum parsimony network is possible in polynomial time. We also show that the set of maximum parsimony networks for the hardwired definition always contains at least one phylogenetic tree. Lastly, we investigate some parallels of parsimony to different likelihood concepts on phylogenetic networks. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quantitative Imaging Biomarkers: A Review of Statistical Methods for Technical Performance Assessment

PubMed Central

2017-01-01

Technological developments and greater rigor in the quantitative measurement of biological features in medical images have given rise to an increased interest in using quantitative imaging biomarkers (QIBs) to measure changes in these features. Critical to the performance of a QIB in preclinical or clinical settings are three primary metrology areas of interest: measurement linearity and bias, repeatability, and the ability to consistently reproduce equivalent results when conditions change, as would be expected in any clinical trial. Unfortunately, performance studies to date differ greatly in designs, analysis method and metrics used to assess a QIB for clinical use. It is therefore, difficult or not possible to integrate results from different studies or to use reported results to design studies. The Radiological Society of North America (RSNA) and the Quantitative Imaging Biomarker Alliance (QIBA) with technical, radiological and statistical experts developed a set of technical performance analysis methods, metrics and study designs that provide terminology, metrics and methods consistent with widely accepted metrological standards. This document provides a consistent framework for the conduct and evaluation of QIB performance studies so that results from multiple studies can be compared, contrasted or combined. PMID:24919831

Characteristics of liver fibrosis with different etiologies using a fully quantitative fibrosis assessment tool.

PubMed

Wu, Q; Zhao, X; You, H

2017-05-18

This study aimed to test the diagnostic performance of a fully quantitative fibrosis assessment tool for liver fibrosis in patients with chronic hepatitis B (CHB), primary biliary cirrhosis (PBC) and non-alcoholic steatohepatitis (NASH). A total of 117 patients with liver fibrosis were included in this study, including 50 patients with CHB, 49 patients with PBC and 18 patients with NASH. All patients underwent liver biopsy (LB). Fibrosis stages were assessed by two experienced pathologists. Histopathological images of LB slices were processed by second harmonic generation (SHG)/two-photon excited fluorescence (TPEF) microscopy without staining, a system called qFibrosis (quantitative fibrosis) system. Altogether 101 quantitative features of the SHG/TPEF images were acquired. The parameters of aggregated collagen in portal, septal and fibrillar areas increased significantly with stages of liver fibrosis in PBC and CHB (P<0.05), but the same was not found for parameters of distributed collagen (P>0.05). There was a significant correlation between parameters of aggregated collagen in portal, septal and fibrillar areas and stages of liver fibrosis from CHB and PBC (P<0.05), but no correlation was found between the distributed collagen parameters and the stages of liver fibrosis from those patients (P>0.05). There was no significant correlation between NASH parameters and stages of fibrosis (P>0.05). For CHB and PBC patients, the highest correlation was between septal parameters and fibrosis stages, the second highest was between portal parameters and fibrosis stages and the lowest correlation was between fibrillar parameters and fibrosis stages. The correlation between the septal parameters of the PBC and stages is significantly higher than the parameters of the other two areas (P<0.05). The qFibrosis candidate parameters based on CHB were also applicable for quantitative analysis of liver fibrosis in PBC patients. Different parameters should be selected for liver

Characteristics of liver fibrosis with different etiologies using a fully quantitative fibrosis assessment tool

PubMed Central

Wu, Q.; Zhao, X.; You, H.

2017-01-01

This study aimed to test the diagnostic performance of a fully quantitative fibrosis assessment tool for liver fibrosis in patients with chronic hepatitis B (CHB), primary biliary cirrhosis (PBC) and non-alcoholic steatohepatitis (NASH). A total of 117 patients with liver fibrosis were included in this study, including 50 patients with CHB, 49 patients with PBC and 18 patients with NASH. All patients underwent liver biopsy (LB). Fibrosis stages were assessed by two experienced pathologists. Histopathological images of LB slices were processed by second harmonic generation (SHG)/two-photon excited fluorescence (TPEF) microscopy without staining, a system called qFibrosis (quantitative fibrosis) system. Altogether 101 quantitative features of the SHG/TPEF images were acquired. The parameters of aggregated collagen in portal, septal and fibrillar areas increased significantly with stages of liver fibrosis in PBC and CHB (P<0.05), but the same was not found for parameters of distributed collagen (P>0.05). There was a significant correlation between parameters of aggregated collagen in portal, septal and fibrillar areas and stages of liver fibrosis from CHB and PBC (P<0.05), but no correlation was found between the distributed collagen parameters and the stages of liver fibrosis from those patients (P>0.05). There was no significant correlation between NASH parameters and stages of fibrosis (P>0.05). For CHB and PBC patients, the highest correlation was between septal parameters and fibrosis stages, the second highest was between portal parameters and fibrosis stages and the lowest correlation was between fibrillar parameters and fibrosis stages. The correlation between the septal parameters of the PBC and stages is significantly higher than the parameters of the other two areas (P<0.05). The qFibrosis candidate parameters based on CHB were also applicable for quantitative analysis of liver fibrosis in PBC patients. Different parameters should be selected for liver

mcrA-Targeted Real-Time Quantitative PCR Method To Examine Methanogen Communities▿

PubMed Central

Steinberg, Lisa M.; Regan, John M.

2009-01-01

Methanogens are of great importance in carbon cycling and alternative energy production, but quantitation with culture-based methods is time-consuming and biased against methanogen groups that are difficult to cultivate in a laboratory. For these reasons, methanogens are typically studied through culture-independent molecular techniques. We developed a SYBR green I quantitative PCR (qPCR) assay to quantify total numbers of methyl coenzyme M reductase α-subunit (mcrA) genes. TaqMan probes were also designed to target nine different phylogenetic groups of methanogens in qPCR assays. Total mcrA and mcrA levels of different methanogen phylogenetic groups were determined from six samples: four samples from anaerobic digesters used to treat either primarily cow or pig manure and two aliquots from an acidic peat sample stored at 4°C or 20°C. Only members of the Methanosaetaceae, Methanosarcina, Methanobacteriaceae, and Methanocorpusculaceae and Fen cluster were detected in the environmental samples. The three samples obtained from cow manure digesters were dominated by members of the genus Methanosarcina, whereas the sample from the pig manure digester contained detectable levels of only members of the Methanobacteriaceae. The acidic peat samples were dominated by both Methanosarcina spp. and members of the Fen cluster. In two of the manure digester samples only one methanogen group was detected, but in both of the acidic peat samples and two of the manure digester samples, multiple methanogen groups were detected. The TaqMan qPCR assays were successfully able to determine the environmental abundance of different phylogenetic groups of methanogens, including several groups with few or no cultivated members. PMID:19447957

Environmental filtering of eudicot lineages underlies phylogenetic clustering in tropical South American flooded forests.

PubMed

Aldana, Ana M; Carlucci, Marcos B; Fine, Paul V A; Stevenson, Pablo R

2017-02-01

The phylogenetic community assembly approach has been used to elucidate the role of ecological and historical processes in shaping tropical tree communities. Recent studies have shown that stressful environments, such as seasonally dry, white-sand and flooded forests tend to be phylogenetically clustered, arguing for niche conservatism as the main driver for this pattern. Very few studies have attempted to identify the lineages that contribute to such assembly patterns. We aimed to improve our understanding of the assembly of flooded forest tree communities in Northern South America by asking the following questions: are seasonally flooded forests phylogenetically clustered? If so, which angiosperm lineages are over-represented in seasonally flooded forests? To assess our hypotheses, we investigated seasonally flooded and terra firme forests from the Magdalena, Orinoco and Amazon Basins, in Colombia. Our results show that, regardless of the river basin in which they are located, seasonally flooded forests of Northern South America tend to be phylogenetically clustered, which means that the more abundant taxa in these forests are more closely related to each other than expected by chance. Based on our alpha and beta phylodiversity analyses we interpret that eudicots are more likely to adapt to extreme environments such as seasonally flooded forests, which indicates the importance of environmental filtering in the assembly of the Neotropical flora.

Development and Assessment of Modules to Integrate Quantitative Skills in Introductory Biology Courses.

PubMed

Hoffman, Kathleen; Leupen, Sarah; Dowell, Kathy; Kephart, Kerrie; Leips, Jeff

2016-01-01

Redesigning undergraduate biology courses to integrate quantitative reasoning and skill development is critical to prepare students for careers in modern medicine and scientific research. In this paper, we report on the development, implementation, and assessment of stand-alone modules that integrate quantitative reasoning into introductory biology courses. Modules are designed to improve skills in quantitative numeracy, interpreting data sets using visual tools, and making inferences about biological phenomena using mathematical/statistical models. We also examine demographic/background data that predict student improvement in these skills through exposure to these modules. We carried out pre/postassessment tests across four semesters and used student interviews in one semester to examine how students at different levels approached quantitative problems. We found that students improved in all skills in most semesters, although there was variation in the degree of improvement among skills from semester to semester. One demographic variable, transfer status, stood out as a major predictor of the degree to which students improved (transfer students achieved much lower gains every semester, despite the fact that pretest scores in each focus area were similar between transfer and nontransfer students). We propose that increased exposure to quantitative skill development in biology courses is effective at building competency in quantitative reasoning. © 2016 K. Hoffman, S. Leupen, et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Reference charts for young stands — a quantitative methodology for assessing tree performance

Treesearch

Lance A. Vickers; David R. Larsen; Benjamin O. Knapp; John M. Kabrick; Daniel C. Dey

2017-01-01

Reference charts have long been used in the medical field for quantitative clinical assessment of juvenile development by plotting distribution quantiles for a selected attribute (e.g., height) against age for specified peer populations.We propose that early stand dynamics is an area of study that could benefit from the descriptions and analyses offered by similar...

Multilocus sequence analysis for assessment of phylogenetic diversity and biogeography in Thalassospira bacteria from diverse marine environments.

PubMed

Lai, Qiliang; Liu, Yang; Yuan, Jun; Du, Juan; Wang, Liping; Sun, Fengqin; Shao, Zongze

2014-01-01

Thalassospira bacteria are widespread and have been isolated from various marine environments. Less is known about their genetic diversity and biogeography, as well as their role in marine environments, many of them cannot be discriminated merely using the 16S rRNA gene. To address these issues, in this report, the phylogenetic analysis of 58 strains from seawater and deep sea sediments were carried out using the multilocus sequence analysis (MLSA) based on acsA, aroE, gyrB, mutL, rpoD and trpB genes, and the DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) based on genome sequences. The MLSA analysis demonstrated that the 58 strains were clearly separated into 15 lineages, corresponding to seven validly described species and eight potential novel species. The DDH and ANI values further confirmed the validity of the MLSA analysis and eight potential novel species. The MLSA interspecies gap of the genus Thalassospira was determined to be 96.16-97.12% sequence identity on the basis of the combined analyses of the DDH and MLSA, while the ANIm interspecies gap was 95.76-97.20% based on the in silico DDH analysis. Meanwhile, phylogenetic analyses showed that the Thalassospira bacteria exhibited distribution pattern to a certain degree according to geographic regions. Moreover, they clustered together according to the habitats depth. For short, the phylogenetic analyses and biogeography of the Thalassospira bacteria were systematically investigated for the first time. These results will be helpful to explore further their ecological role and adaptive evolution in marine environments.

Multilocus Sequence Analysis for Assessment of Phylogenetic Diversity and Biogeography in Thalassospira Bacteria from Diverse Marine Environments

PubMed Central

Yuan, Jun; Du, Juan; Wang, Liping; Sun, Fengqin; Shao, Zongze

2014-01-01

Thalassospira bacteria are widespread and have been isolated from various marine environments. Less is known about their genetic diversity and biogeography, as well as their role in marine environments, many of them cannot be discriminated merely using the 16S rRNA gene. To address these issues, in this report, the phylogenetic analysis of 58 strains from seawater and deep sea sediments were carried out using the multilocus sequence analysis (MLSA) based on acsA, aroE, gyrB, mutL, rpoD and trpB genes, and the DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) based on genome sequences. The MLSA analysis demonstrated that the 58 strains were clearly separated into 15 lineages, corresponding to seven validly described species and eight potential novel species. The DDH and ANI values further confirmed the validity of the MLSA analysis and eight potential novel species. The MLSA interspecies gap of the genus Thalassospira was determined to be 96.16–97.12% sequence identity on the basis of the combined analyses of the DDH and MLSA, while the ANIm interspecies gap was 95.76–97.20% based on the in silico DDH analysis. Meanwhile, phylogenetic analyses showed that the Thalassospira bacteria exhibited distribution pattern to a certain degree according to geographic regions. Moreover, they clustered together according to the habitats depth. For short, the phylogenetic analyses and biogeography of the Thalassospira bacteria were systematically investigated for the first time. These results will be helpful to explore further their ecological role and adaptive evolution in marine environments. PMID:25198177

Enumerating all maximal frequent subtrees in collections of phylogenetic trees.

PubMed

Deepak, Akshay; Fernández-Baca, David

2014-01-01

A common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant subset of the trees agree. One popular method to do so is through maximum agreement subtrees (MASTs). MASTs are also used, among other things, as a metric for comparing phylogenetic trees, computing congruence indices and to identify horizontal gene transfer events. We give algorithms and experimental results for two approaches to identify common patterns in a collection of phylogenetic trees, one based on agreement subtrees, called maximal agreement subtrees, the other on frequent subtrees, called maximal frequent subtrees. These approaches can return subtrees on larger sets of taxa than MASTs, and can reveal new common phylogenetic relationships not present in either MASTs or the majority rule tree (a popular consensus method). Our current implementation is available on the web at https://code.google.com/p/mfst-miner/. Our computational results confirm that maximal agreement subtrees and all maximal frequent subtrees can reveal a more complete phylogenetic picture of the common patterns in collections of phylogenetic trees than maximum agreement subtrees; they are also often more resolved than the majority rule tree. Further, our experiments show that enumerating maximal frequent subtrees is considerably more practical than enumerating ordinary (not necessarily maximal) frequent subtrees.

Phylogenetic evidence for cladogenetic polyploidization in land plants.

PubMed

Zhan, Shing H; Drori, Michal; Goldberg, Emma E; Otto, Sarah P; Mayrose, Itay

2016-07-01

Polyploidization is a common and recurring phenomenon in plants and is often thought to be a mechanism of "instant speciation". Whether polyploidization is associated with the formation of new species (cladogenesis) or simply occurs over time within a lineage (anagenesis), however, has never been assessed systematically. We tested this hypothesis using phylogenetic and karyotypic information from 235 plant genera (mostly angiosperms). We first constructed a large database of combined sequence and chromosome number data sets using an automated procedure. We then applied likelihood models (ClaSSE) that estimate the degree of synchronization between polyploidization and speciation events in maximum likelihood and Bayesian frameworks. Our maximum likelihood analysis indicated that 35 genera supported a model that includes cladogenetic transitions over a model with only anagenetic transitions, whereas three genera supported a model that incorporates anagenetic transitions over one with only cladogenetic transitions. Furthermore, the Bayesian analysis supported a preponderance of cladogenetic change in four genera but did not support a preponderance of anagenetic change in any genus. Overall, these phylogenetic analyses provide the first broad confirmation that polyploidization is temporally associated with speciation events, suggesting that it is indeed a major speciation mechanism in plants, at least in some genera. © 2016 Botanical Society of America.

PhyloExplorer: a web server to validate, explore and query phylogenetic trees

PubMed Central

Ranwez, Vincent; Clairon, Nicolas; Delsuc, Frédéric; Pourali, Saeed; Auberval, Nicolas; Diser, Sorel; Berry, Vincent

2009-01-01

Background Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or analyses such as supertree inference and tree comparisons. However, no tool is currently available to facilitate the management of tree collections providing, for instance: standardisation of taxon names among trees with respect to a reference taxonomy; selection of relevant subsets of trees or sub-trees according to a taxonomic query; or simply computation of descriptive statistics on the collection. Moreover, although several databases of phylogenetic trees exist, there is currently no easy way to find trees that are both relevant and complementary to a given collection of trees. Results We propose a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and identifying related trees in the TreeBASE database. Conclusion PhyloExplorer is a simple and interactive website implemented through underlying Python libraries and MySQL databases. It is available at: and the source code can be downloaded from: . PMID:19450253

Comprehensive untargeted metabolomics of Lychnnophorinae subtribe (Asteraceae: Vernonieae) in a phylogenetic context

PubMed Central

Martucci, Maria Elvira Poleti; Loeuille, Benoit; Pirani, José Rubens

2018-01-01

Members of the subtribe Lychnophorinae occur mostly within the Cerrado domain of the Brazilian Central Plateau. The relationships between its 11 genera, as well as between Lychnophorinae and other subtribes belonging to the tribe Vernonieae, have recently been investigated upon a phylogeny based on molecular and morphological data. We report the use of a comprehensive untargeted metabolomics approach, combining HPLC-MS and GC-MS data, followed by multivariate analyses aiming to assess the congruence between metabolomics data and the phylogenetic hypothesis, as well as its potential as a chemotaxonomic tool. We analyzed 78 species by UHPLC-MS and GC-MS in both positive and negative ionization modes. The metabolic profiles obtained for these species were treated in MetAlign and in MSClust and the matrices generated were used in SIMCA for hierarchical cluster analyses, principal component analyses and orthogonal partial least square discriminant analysis. The results showed that metabolomic analyses are mostly congruent with the phylogenetic hypothesis especially at lower taxonomic levels (Lychnophora or Eremanthus). Our results confirm that data generated using metabolomics provide evidence for chemotaxonomical studies, especially for phylogenetic inference of the Lychnophorinae subtribe and insight into the evolution of the secondary metabolites of this group. PMID:29324799

A cybertaxonomic revision of the new dung beetle tribe Parachoriini (Coleoptera: Scarabaeidae: Scarabaeinae) and its phylogenetic assessment using molecular and morphological data.

PubMed

Tarasov, Sergei

2017-10-03

Two Oriental dung beetle genera: Parachorius Harold, 1873 and Cassolus Sharp, 1875 have long had an ambiguous tribal position in Scarabaeinae (Coleoptera: Scarabaeidae), but have never been considered as closely related. A recently discovered species representing the morphological link between the two genera gave a hint to their possible close affiliation. To assess phylogenetic and taxonomic placement of these genera, I conducted phylogenetic analyses of global dung beetle samples using morphological (134 taxa, 232 characters) and molecular (551 terminals, 8 gene regions) data. Both morphological and molecular analyses strongly support the monophyly of Parachorius + Cassolus. This leads to the synonymy of Parachorius with Cassolus new synonymy, and resulted in the new generic concept for Parachorius. The isolated phylogenetic position of Parachorius and its morphological distinctiveness from all other known Scarabaeinae tribes suggest recognition of a new tribe, Parachoriini new tribe, to maintain the stability of tribal classification in dung beetles. Investigation of old and recent material of Parachorius revealed a large number of undescribed species and the need for a taxonomic revision of this genus. The revision of Parachorius, powered by the 3i cybertaxonomic tool, is presented in this study. The revised Parachorius is comprised of 19 species from the Oriental and southeastern Palaearctic Regions, of which seven are newly described (P. asymmetricus new species, P. bolavensis new species, P. longipenis new species, P. newthayerae new species, P. pseudojavanus new species, P. schuelkei new species, and P. solodovnikovi new species). Three species names in Parachorius are synonymized, namely, P. fungorum Kryzhanovsky & Medvedev, 1966 = P. krali Utsunomiya & Masumoto, 2001 new synonymy; P. thomsoni Harold, 1873 = P. lannathai Hanboonsong & Masumoto, 2001 new synonymy; and P. peninsularis (Arrow, 1907) = C. pongchaii Masumoto, 2001 new synonymy. Two species

Maximum parsimony, substitution model, and probability phylogenetic trees.

PubMed

Weng, J F; Thomas, D A; Mareels, I

2011-01-01

The problem of inferring phylogenies (phylogenetic trees) is one of the main problems in computational biology. There are three main methods for inferring phylogenies-Maximum Parsimony (MP), Distance Matrix (DM) and Maximum Likelihood (ML), of which the MP method is the most well-studied and popular method. In the MP method the optimization criterion is the number of substitutions of the nucleotides computed by the differences in the investigated nucleotide sequences. However, the MP method is often criticized as it only counts the substitutions observable at the current time and all the unobservable substitutions that really occur in the evolutionary history are omitted. In order to take into account the unobservable substitutions, some substitution models have been established and they are now widely used in the DM and ML methods but these substitution models cannot be used within the classical MP method. Recently the authors proposed a probability representation model for phylogenetic trees and the reconstructed trees in this model are called probability phylogenetic trees. One of the advantages of the probability representation model is that it can include a substitution model to infer phylogenetic trees based on the MP principle. In this paper we explain how to use a substitution model in the reconstruction of probability phylogenetic trees and show the advantage of this approach with examples.

An arctic community of symbiotic fungi assembled by long-distance dispersers: phylogenetic diversity of ectomycorrhizal basidiomycetes in Svalbard based on soil and sporocarp DNA

Treesearch

J. Geml; I. Timling; C.H. Robinson; N. Lennon; H.C. Nusbaum; C. Brochmann; M.E. Noordeloos; D.L. Taylor

2011-01-01

Current evidence from temperate studies suggests that ectomycorrhizal (ECM) fungi require overland routes for migration because of their obligate symbiotic associations with woody plants. Despite their key roles in arctic ecosystems, the phylogenetic diversity and phylogeography of arctic ECM fungi remains little known. Here we assess the phylogenetic diversity of ECM...

Phylogenetic inference under varying proportions of indel-induced alignment gaps

PubMed Central

Dwivedi, Bhakti; Gadagkar, Sudhindra R

2009-01-01

Background The effect of alignment gaps on phylogenetic accuracy has been the subject of numerous studies. In this study, we investigated the relationship between the total number of gapped sites and phylogenetic accuracy, when the gaps were introduced (by means of computer simulation) to reflect indel (insertion/deletion) events during the evolution of DNA sequences. The resulting (true) alignments were subjected to commonly used gap treatment and phylogenetic inference methods. Results (1) In general, there was a strong – almost deterministic – relationship between the amount of gap in the data and the level of phylogenetic accuracy when the alignments were very "gappy", (2) gaps resulting from deletions (as opposed to insertions) contributed more to the inaccuracy of phylogenetic inference, (3) the probabilistic methods (Bayesian, PhyML & "MLε, " a method implemented in DNAML in PHYLIP) performed better at most levels of gap percentage when compared to parsimony (MP) and distance (NJ) methods, with Bayesian analysis being clearly the best, (4) methods that treat gapped sites as missing data yielded less accurate trees when compared to those that attribute phylogenetic signal to the gapped sites (by coding them as binary character data – presence/absence, or as in the MLε method), and (5) in general, the accuracy of phylogenetic inference depended upon the amount of available data when the gaps resulted from mainly deletion events, and the amount of missing data when insertion events were equally likely to have caused the alignment gaps. Conclusion When gaps in an alignment are a consequence of indel events in the evolution of the sequences, the accuracy of phylogenetic analysis is likely to improve if: (1) alignment gaps are categorized as arising from insertion events or deletion events and then treated separately in the analysis, (2) the evolutionary signal provided by indels is harnessed in the phylogenetic analysis, and (3) methods that utilize the

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages

PubMed Central

Aguirre, Luis F.; Montaño-Centellas, Flavia A.; Gavilanez, M. Mercedes; Stevens, Richard D.

2016-01-01

Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.

PubMed

Aguirre, Luis F; Montaño-Centellas, Flavia A; Gavilanez, M Mercedes; Stevens, Richard D

2016-01-01

Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional

A Framework for Quantitative Assessment of Impacts Related to Energy and Mineral Resource Development

DOE PAGES

Haines, Seth S.; Diffendorfer, Jay E.; Balistrieri, Laurie; ...

2013-05-15

Natural resource planning at all scales demands methods for assessing the impacts of resource development and use, and in particular it requires standardized methods that yield robust and unbiased results. Building from existing probabilistic methods for assessing the volumes of energy and mineral resources, we provide an algorithm for consistent, reproducible, quantitative assessment of resource development impacts. The approach combines probabilistic input data with Monte Carlo statistical methods to determine probabilistic outputs that convey the uncertainties inherent in the data. For example, one can utilize our algorithm to combine data from a natural gas resource assessment with maps of sagemore » grouse leks and pinon-juniper woodlands in the same area to estimate possible future habitat impacts due to possible future gas development. As another example: one could combine geochemical data and maps of lynx habitat with data from a mineral deposit assessment in the same area to determine possible future mining impacts on water resources and lynx habitat. The approach can be applied to a broad range of positive and negative resource development impacts, such as water quantity or quality, economic benefits, or air quality, limited only by the availability of necessary input data and quantified relationships among geologic resources, development alternatives, and impacts. In conclusion, the framework enables quantitative evaluation of the trade-offs inherent in resource management decision-making, including cumulative impacts, to address societal concerns and policy aspects of resource development.« less

A framework for quantitative assessment of impacts related to energy and mineral resource development

USGS Publications Warehouse

Haines, Seth S.; Diffendorfer, James; Balistrieri, Laurie S.; Berger, Byron R.; Cook, Troy A.; Gautier, Donald L.; Gallegos, Tanya J.; Gerritsen, Margot; Graffy, Elisabeth; Hawkins, Sarah; Johnson, Kathleen; Macknick, Jordan; McMahon, Peter; Modde, Tim; Pierce, Brenda; Schuenemeyer, John H.; Semmens, Darius; Simon, Benjamin; Taylor, Jason; Walton-Day, Katherine

2013-01-01

Natural resource planning at all scales demands methods for assessing the impacts of resource development and use, and in particular it requires standardized methods that yield robust and unbiased results. Building from existing probabilistic methods for assessing the volumes of energy and mineral resources, we provide an algorithm for consistent, reproducible, quantitative assessment of resource development impacts. The approach combines probabilistic input data with Monte Carlo statistical methods to determine probabilistic outputs that convey the uncertainties inherent in the data. For example, one can utilize our algorithm to combine data from a natural gas resource assessment with maps of sage grouse leks and piñon-juniper woodlands in the same area to estimate possible future habitat impacts due to possible future gas development. As another example: one could combine geochemical data and maps of lynx habitat with data from a mineral deposit assessment in the same area to determine possible future mining impacts on water resources and lynx habitat. The approach can be applied to a broad range of positive and negative resource development impacts, such as water quantity or quality, economic benefits, or air quality, limited only by the availability of necessary input data and quantified relationships among geologic resources, development alternatives, and impacts. The framework enables quantitative evaluation of the trade-offs inherent in resource management decision-making, including cumulative impacts, to address societal concerns and policy aspects of resource development.

Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks.

PubMed

Pérez-Valera, Eduardo; Goberna, Marta; Faust, Karoline; Raes, Jeroen; García, Carlos; Verdú, Miguel

2017-01-01

Fire alters ecosystems by changing the composition and community structure of soil microbes. The phylogenetic structure of a community provides clues about its main assembling mechanisms. While environmental filtering tends to reduce the community phylogenetic diversity by selecting for functionally (and hence phylogenetically) similar species, processes like competitive exclusion by limiting similarity tend to increase it by preventing the coexistence of functionally (and phylogenetically) similar species. We used co-occurrence networks to detect co-presence (bacteria that co-occur) or exclusion (bacteria that do not co-occur) links indicative of the ecological interactions structuring the community. We propose that inspecting the phylogenetic structure of co-presence or exclusion links allows to detect the main processes simultaneously assembling the community. We monitored a soil bacterial community after an experimental fire and found that fire altered its composition, richness and phylogenetic diversity. Both co-presence and exclusion links were more phylogenetically related than expected by chance. We interpret such a phylogenetic clustering in co-presence links as a result of environmental filtering, while that in exclusion links reflects competitive exclusion by limiting similarity. This suggests that environmental filtering and limiting similarity operate simultaneously to assemble soil bacterial communities, widening the traditional view that only environmental filtering structures bacterial communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests.

PubMed

Posada, David; Buckley, Thomas R

2004-10-01

Model selection is a topic of special relevance in molecular phylogenetics that affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental concepts and techniques of model selection in the context of phylogenetics. We start by reviewing different aspects of the selection of substitution models in phylogenetics from a theoretical, philosophical and practical point of view, and summarize this comparison in table format. We argue that the most commonly implemented model selection approach, the hierarchical likelihood ratio test, is not the optimal strategy for model selection in phylogenetics, and that approaches like the Akaike Information Criterion (AIC) and Bayesian methods offer important advantages. In particular, the latter two methods are able to simultaneously compare multiple nested or nonnested models, assess model selection uncertainty, and allow for the estimation of phylogenies and model parameters using all available models (model-averaged inference or multimodel inference). We also describe how the relative importance of the different parameters included in substitution models can be depicted. To illustrate some of these points, we have applied AIC-based model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus(genus Carabus) ground beetles described by Sota and Vogler (2001).

Tanglegrams for rooted phylogenetic trees and networks

PubMed Central

Scornavacca, Celine; Zickmann, Franziska; Huson, Daniel H.

2011-01-01

Motivation: In systematic biology, one is often faced with the task of comparing different phylogenetic trees, in particular in multi-gene analysis or cospeciation studies. One approach is to use a tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines to connect matching taxa. There is an increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly represent reticulate events, such as horizontal gene transfer, hybridization or reassortment. Thus, the question arises how to define and compute a tanglegram for such networks. Results: In this article, we present the first formal definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach for computing one, called the NN-tanglegram method. We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets. For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets. Availability: The algorithm is implemented in our program Dendroscope 3, which is freely available from www.dendroscope.org. Contact: scornava@informatik.uni-tuebingen.de; huson@informatik.uni-tuebingen.de PMID:21685078

Quantitative Microbial Risk Assessment Tutorial: Installation of Software for Watershed Modeling in Support of QMRA

EPA Science Inventory

This tutorial provides instructions for accessing, retrieving, and downloading the following software to install on a host computer in support of Quantitative Microbial Risk Assessment (QMRA) modeling:• SDMProjectBuilder (which includes the Microbial Source Module as part...

An Assessment of the Quantitative Literacy of Undergraduate Students

ERIC Educational Resources Information Center

Wilkins, Jesse L. M.

2016-01-01

Quantitative literacy (QLT) represents an underlying higher-order construct that accounts for a person's willingness to engage in quantitative situations in everyday life. The purpose of this study is to retest the construct validity of a model of quantitative literacy (Wilkins, 2010). In this model, QLT represents a second-order factor that…

Integrating expert opinion with modelling for quantitative multi-hazard risk assessment in the Eastern Italian Alps

NASA Astrophysics Data System (ADS)

Chen, Lixia; van Westen, Cees J.; Hussin, Haydar; Ciurean, Roxana L.; Turkington, Thea; Chavarro-Rincon, Diana; Shrestha, Dhruba P.

2016-11-01

Extreme rainfall events are the main triggering causes for hydro-meteorological hazards in mountainous areas, where development is often constrained by the limited space suitable for construction. In these areas, hazard and risk assessments are fundamental for risk mitigation, especially for preventive planning, risk communication and emergency preparedness. Multi-hazard risk assessment in mountainous areas at local and regional scales remain a major challenge because of lack of data related to past events and causal factors, and the interactions between different types of hazards. The lack of data leads to a high level of uncertainty in the application of quantitative methods for hazard and risk assessment. Therefore, a systematic approach is required to combine these quantitative methods with expert-based assumptions and decisions. In this study, a quantitative multi-hazard risk assessment was carried out in the Fella River valley, prone to debris flows and flood in the north-eastern Italian Alps. The main steps include data collection and development of inventory maps, definition of hazard scenarios, hazard assessment in terms of temporal and spatial probability calculation and intensity modelling, elements-at-risk mapping, estimation of asset values and the number of people, physical vulnerability assessment, the generation of risk curves and annual risk calculation. To compare the risk for each type of hazard, risk curves were generated for debris flows, river floods and flash floods. Uncertainties were expressed as minimum, average and maximum values of temporal and spatial probability, replacement costs of assets, population numbers, and physical vulnerability. These result in minimum, average and maximum risk curves. To validate this approach, a back analysis was conducted using the extreme hydro-meteorological event that occurred in August 2003 in the Fella River valley. The results show a good performance when compared to the historical damage reports.

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

Enumerating all maximal frequent subtrees in collections of phylogenetic trees

PubMed Central

2014-01-01

Background A common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant subset of the trees agree. One popular method to do so is through maximum agreement subtrees (MASTs). MASTs are also used, among other things, as a metric for comparing phylogenetic trees, computing congruence indices and to identify horizontal gene transfer events. Results We give algorithms and experimental results for two approaches to identify common patterns in a collection of phylogenetic trees, one based on agreement subtrees, called maximal agreement subtrees, the other on frequent subtrees, called maximal frequent subtrees. These approaches can return subtrees on larger sets of taxa than MASTs, and can reveal new common phylogenetic relationships not present in either MASTs or the majority rule tree (a popular consensus method). Our current implementation is available on the web at https://code.google.com/p/mfst-miner/. Conclusions Our computational results confirm that maximal agreement subtrees and all maximal frequent subtrees can reveal a more complete phylogenetic picture of the common patterns in collections of phylogenetic trees than maximum agreement subtrees; they are also often more resolved than the majority rule tree. Further, our experiments show that enumerating maximal frequent subtrees is considerably more practical than enumerating ordinary (not necessarily maximal) frequent subtrees. PMID:25061474

Phylogenetic fields through time: temporal dynamics of geographical co-occurrence and phylogenetic structure within species ranges

PubMed Central

Carotenuto, Francesco; Diniz-Filho, José Alexandre F.

2016-01-01

Species co-occur with different sets of other species across their geographical distribution, which can be either closely or distantly related. Such co-occurrence patterns and their phylogenetic structure within individual species ranges represent what we call the species phylogenetic fields (PFs). These PFs allow investigation of the role of historical processes—speciation, extinction and dispersal—in shaping species co-occurrence patterns, in both extinct and extant species. Here, we investigate PFs of large mammalian species during the last 3 Myr, and how these correlate with trends in diversification rates. Using the fossil record, we evaluate species' distributional and co-occurrence patterns along with their phylogenetic structure. We apply a novel Bayesian framework on fossil occurrences to estimate diversification rates through time. Our findings highlight the effect of evolutionary processes and past climatic changes on species' distributions and co-occurrences. From the Late Pliocene to the Recent, mammal species seem to have responded in an individualistic manner to climate changes and diversification dynamics, co-occurring with different sets of species from different lineages across their geographical ranges. These findings stress the difficulty of forecasting potential effects of future climate changes on biodiversity. PMID:26977061

Phylogenetic fields through time: temporal dynamics of geographical co-occurrence and phylogenetic structure within species ranges.

PubMed

Villalobos, Fabricio; Carotenuto, Francesco; Raia, Pasquale; Diniz-Filho, José Alexandre F

2016-04-05

Species co-occur with different sets of other species across their geographical distribution, which can be either closely or distantly related. Such co-occurrence patterns and their phylogenetic structure within individual species ranges represent what we call the species phylogenetic fields (PFs). These PFs allow investigation of the role of historical processes--speciation, extinction and dispersal--in shaping species co-occurrence patterns, in both extinct and extant species. Here, we investigate PFs of large mammalian species during the last 3 Myr, and how these correlate with trends in diversification rates. Using the fossil record, we evaluate species' distributional and co-occurrence patterns along with their phylogenetic structure. We apply a novel Bayesian framework on fossil occurrences to estimate diversification rates through time. Our findings highlight the effect of evolutionary processes and past climatic changes on species' distributions and co-occurrences. From the Late Pliocene to the Recent, mammal species seem to have responded in an individualistic manner to climate changes and diversification dynamics, co-occurring with different sets of species from different lineages across their geographical ranges. These findings stress the difficulty of forecasting potential effects of future climate changes on biodiversity. © 2016 The Author(s).

Quantitative Assessment of Combination Antimicrobial Therapy against Multidrug-Resistant Acinetobacter baumannii▿

PubMed Central

Lim, Tze-Peng; Ledesma, Kimberly R.; Chang, Kai-Tai; Hou, Jing-Guo; Kwa, Andrea L.; Nikolaou, Michael; Quinn, John P.; Prince, Randall A.; Tam, Vincent H.

2008-01-01

Treatment of multidrug-resistant bacterial infections poses a therapeutic challenge to clinicians; combination therapy is often the only viable option for multidrug-resistant infections. A quantitative method was developed to assess the combined killing abilities of antimicrobial agents. Time-kill studies (TKS) were performed using a multidrug-resistant clinical isolate of Acinetobacter baumannii with escalating concentrations of cefepime (0 to 512 mg/liter), amikacin (0 to 256 mg/liter), and levofloxacin (0 to 64 mg/liter). The bacterial burden data in single and combined (two of the three agents with clinically achievable concentrations in serum) TKS at 24 h were mathematically modeled to provide an objective basis for comparing various antimicrobial agent combinations. Synergy and antagonism were defined as interaction indices of <1 and >1, respectively. A hollow-fiber infection model (HFIM) simulating various clinical (fluctuating concentrations over time) dosing exposures was used to selectively validate our quantitative assessment of the combined killing effect. Model fits in all single-agent TKS were satisfactory (r2 > 0.97). An enhanced combined overall killing effect was seen in the cefepime-amikacin combination (interactive index, 0.698; 95% confidence interval [CI], 0.675 to 0.722) and the cefepime-levofloxacin combination (interactive index, 0.929; 95% CI, 0.903 to 0.956), but no significant difference in the combined overall killing effect for the levofloxacin-amikacin combination was observed (interactive index, 0.994; 95% CI, 0.982 to 1.005). These assessments were consistent with observations in HFIM validation studies. Our method could be used to objectively rank the combined killing activities of two antimicrobial agents when used together against a multidrug-resistant A. baumannii isolate. It may offer better insights into the effectiveness of various antimicrobial combinations and warrants further investigations. PMID:18505848

Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods

PubMed Central

Aris-Brosou, Stéphane; Xia, Xuhua

2008-01-01

The reconstruction of phylogenies is becoming an increasingly simple activity. This is mainly due to two reasons: the democratization of computing power and the increased availability of sophisticated yet user-friendly software. This review describes some of the latest additions to the phylogenetic toolbox, along with some of their theoretical and practical limitations. It is shown that Bayesian methods are under heavy development, as they offer the possibility to solve a number of long-standing issues and to integrate several steps of the phylogenetic analyses into a single framework. Specific topics include not only phylogenetic reconstruction, but also the comparison of phylogenies, the detection of adaptive evolution, and the estimation of divergence times between species. PMID:18483574

MO-DE-303-03: Session on quantitative imaging for assessment of tumor response to radiation therapy

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

Bowen, S.

This session will focus on quantitative imaging for assessment of tumor response to radiation therapy. This is a technically challenging method to translate to practice in radiation therapy. In the new era of precision medicine, however, delivering the right treatment, to the right patient, and at the right time, can positively impact treatment choices and patient outcomes. Quantitative imaging provides the spatial sensitivity required by radiation therapy for precision medicine that is not available by other means. In this Joint ESTRO -AAPM Symposium, three leading-edge investigators will present specific motivations for quantitative imaging biomarkers in radiation therapy of esophageal, headmore » and neck, locally advanced non-small cell lung cancer, and hepatocellular carcinoma. Experiences with the use of dynamic contrast enhanced (DCE) MRI, diffusion- weighted (DW) MRI, PET/CT, and SPECT/CT will be presented. Issues covered will include: response prediction, dose-painting, timing between therapy and imaging, within-therapy biomarkers, confounding effects, normal tissue sparing, dose-response modeling, and association with clinical biomarkers and outcomes. Current information will be presented from investigational studies and clinical practice. Learning Objectives: Learn motivations for the use of quantitative imaging biomarkers for assessment of response to radiation therapy Review the potential areas of application in cancer therapy Examine the challenges for translation, including imaging confounds and paucity of evidence to date Compare exemplary examples of the current state of the art in DCE-MRI, DW-MRI, PET/CT and SPECT/CT imaging for assessment of response to radiation therapy Van der Heide: Research grants from the Dutch Cancer Society and the European Union (FP7) Bowen: RSNA Scholar grant.« less

Quantitative photoacoustic assessment of ex-vivo lymph nodes of colorectal cancer patients

NASA Astrophysics Data System (ADS)

Sampathkumar, Ashwin; Mamou, Jonathan; Saegusa-Beercroft, Emi; Chitnis, Parag V.; Machi, Junji; Feleppa, Ernest J.

2015-03-01

Staging of cancers and selection of appropriate treatment requires histological examination of multiple dissected lymph nodes (LNs) per patient, so that a staggering number of nodes require histopathological examination, and the finite resources of pathology facilities create a severe processing bottleneck. Histologically examining the entire 3D volume of every dissected node is not feasible, and therefore, only the central region of each node is examined histologically, which results in severe sampling limitations. In this work, we assess the feasibility of using quantitative photoacoustics (QPA) to overcome the limitations imposed by current procedures and eliminate the resulting under sampling in node assessments. QPA is emerging as a new hybrid modality that assesses tissue properties and classifies tissue type based on multiple estimates derived from spectrum analysis of photoacoustic (PA) radiofrequency (RF) data and from statistical analysis of envelope-signal data derived from the RF signals. Our study seeks to use QPA to distinguish cancerous from non-cancerous regions of dissected LNs and hence serve as a reliable means of imaging and detecting small but clinically significant cancerous foci that would be missed by current methods. Dissected lymph nodes were placed in a water bath and PA signals were generated using a wavelength-tunable (680-950 nm) laser. A 26-MHz, f-2 transducer was used to sense the PA signals. We present an overview of our experimental setup; provide a statistical analysis of multi-wavelength classification parameters (mid-band fit, slope, intercept) obtained from the PA signal spectrum generated in the LNs; and compare QPA performance with our established quantitative ultrasound (QUS) techniques in distinguishing metastatic from non-cancerous tissue in dissected LNs. QPA-QUS methods offer a novel general means of tissue typing and evaluation in a broad range of disease-assessment applications, e.g., cardiac, intravascular

Applying phylogenetic analysis to viral livestock diseases: moving beyond molecular typing.

PubMed

Olvera, Alex; Busquets, Núria; Cortey, Marti; de Deus, Nilsa; Ganges, Llilianne; Núñez, José Ignacio; Peralta, Bibiana; Toskano, Jennifer; Dolz, Roser

2010-05-01

Changes in livestock production systems in recent years have altered the presentation of many diseases resulting in the need for more sophisticated control measures. At the same time, new molecular assays have been developed to support the diagnosis of animal viral disease. Nucleotide sequences generated by these diagnostic techniques can be used in phylogenetic analysis to infer phenotypes by sequence homology and to perform molecular epidemiology studies. In this review, some key elements of phylogenetic analysis are highlighted, such as the selection of the appropriate neutral phylogenetic marker, the proper phylogenetic method and different techniques to test the reliability of the resulting tree. Examples are given of current and future applications of phylogenetic reconstructions in viral livestock diseases. Copyright 2009 Elsevier Ltd. All rights reserved.

Quantitative MRI assessments of white matter in children treated for acute lymphoblastic leukemia

NASA Astrophysics Data System (ADS)

Reddick, Wilburn E.; Glass, John O.; Helton, Kathleen J.; Li, Chin-Shang; Pui, Ching-Hon

2005-04-01

The purpose of this study was to use objective quantitative MR imaging methods to prospectively assess changes in the physiological structure of white matter during the temporal evolution of leukoencephalopathy (LE) in children treated for acute lymphoblastic leukemia. The longitudinal incidence, extent (proportion of white matter affect), and intensity (elevation of T1 and T2 relaxation rates) of LE was evaluated for 44 children. A combined imaging set consisting of T1, T2, PD, and FLAIR MR images and white matter, gray matter and CSF a priori maps from a spatially normalized atlas were analyzed with a neural network segmentation based on a Kohonen Self-Organizing Map (SOM). Quantitative T1 and T2 relaxation maps were generated using a nonlinear parametric optimization procedure to fit the corresponding multi-exponential models. A Cox proportional regression was performed to estimate the effect of intravenous methotrexate (IV-MTX) exposure on the development of LE followed by a generalized linear model to predict the probability of LE in new patients. Additional T-tests of independent samples were performed to assess differences in quantitative measures of extent and intensity at four different points in therapy. Higher doses and more courses of IV-MTX placed patients at a higher risk of developing LE and were associated with more intense changes affecting more of the white matter volume; many of the changes resolved after completion of therapy. The impact of these changes on neurocognitive functioning and quality of life in survivors remains to be determined.

QACD: A method for the quantitative assessment of compositional distribution in geologic materials

NASA Astrophysics Data System (ADS)

Loocke, M. P.; Lissenberg, J. C. J.; MacLeod, C. J.

2017-12-01

In order to fully understand the petrogenetic history of a rock, it is critical to obtain a thorough characterization of the chemical and textural relationships of its mineral constituents. Element mapping combines the microanalytical techniques that allow for the analysis of major- and minor elements at high spatial resolutions (e.g., electron microbeam analysis) with 2D mapping of samples in order to provide unprecedented detail regarding the growth histories and compositional distributions of minerals within a sample. We present a method for the acquisition and processing of large area X-ray element maps obtained by energy-dispersive X-ray spectrometer (EDS) to produce a quantitative assessment of compositional distribution (QACD) of mineral populations within geologic materials. By optimizing the conditions at which the EDS X-ray element maps are acquired, we are able to obtain full thin section quantitative element maps for most major elements in relatively short amounts of time. Such maps can be used to not only accurately identify all phases and calculate mineral modes for a sample (e.g., a petrographic thin section), but, critically, enable a complete quantitative assessment of their compositions. The QACD method has been incorporated into a python-based, easy-to-use graphical user interface (GUI) called Quack. The Quack software facilitates the generation of mineral modes, element and molar ratio maps and the quantification of full-sample compositional distributions. The open-source nature of the Quack software provides a versatile platform which can be easily adapted and modified to suit the needs of the user.

Quantitative assessment of building fire risk to life safety.

PubMed

Guanquan, Chu; Jinhua, Sun

2008-06-01

This article presents a quantitative risk assessment framework for evaluating fire risk to life safety. Fire risk is divided into two parts: probability and corresponding consequence of every fire scenario. The time-dependent event tree technique is used to analyze probable fire scenarios based on the effect of fire protection systems on fire spread and smoke movement. To obtain the variation of occurrence probability with time, Markov chain is combined with a time-dependent event tree for stochastic analysis on the occurrence probability of fire scenarios. To obtain consequences of every fire scenario, some uncertainties are considered in the risk analysis process. When calculating the onset time to untenable conditions, a range of fires are designed based on different fire growth rates, after which uncertainty of onset time to untenable conditions can be characterized by probability distribution. When calculating occupant evacuation time, occupant premovement time is considered as a probability distribution. Consequences of a fire scenario can be evaluated according to probability distribution of evacuation time and onset time of untenable conditions. Then, fire risk to life safety can be evaluated based on occurrence probability and consequences of every fire scenario. To express the risk assessment method in detail, a commercial building is presented as a case study. A discussion compares the assessment result of the case study with fire statistics.

Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals.

PubMed

Heydari, Mahdi; Marashi, Sayed-Amir; Tusserkani, Ruzbeh; Sadeghi, Mehdi

2014-10-01

One of the fundamental problems in bioinformatics is phylogenetic tree reconstruction, which can be used for classifying living organisms into different taxonomic clades. The classical approach to this problem is based on a marker such as 16S ribosomal RNA. Since evolutionary events like genomic rearrangements are not included in reconstructions of phylogenetic trees based on single genes, much effort has been made to find other characteristics for phylogenetic reconstruction in recent years. With the increasing availability of completely sequenced genomes, gene order can be considered as a new solution for this problem. In the present work, we applied maximal common intervals (MCIs) in two or more genomes to infer their distance and to reconstruct their evolutionary relationship. Additionally, measures based on uncommon segments (UCS's), i.e., those genomic segments which are not detected as part of any of the MCIs, are also used for phylogenetic tree reconstruction. We applied these two types of measures for reconstructing the phylogenetic tree of 63 prokaryotes with known COG (clusters of orthologous groups) families. Similarity between the MCI-based (resp. UCS-based) reconstructed phylogenetic trees and the phylogenetic tree obtained from NCBI taxonomy browser is as high as 93.1% (resp. 94.9%). We show that in the case of this diverse dataset of prokaryotes, tree reconstruction based on MCI and UCS outperforms most of the currently available methods based on gene orders, including breakpoint distance and DCJ. We additionally tested our new measures on a dataset of 13 closely-related bacteria from the genus Prochlorococcus. In this case, distances like rearrangement distance, breakpoint distance and DCJ proved to be useful, while our new measures are still appropriate for phylogenetic reconstruction. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

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.

Cnidarian phylogenetic relationships as revealed by mitogenomics.

PubMed

Kayal, Ehsan; Roure, Béatrice; Philippe, Hervé; Collins, Allen G; Lavrov, Dennis V

2013-01-09

Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia + Octocorallia) - cnidarians with a reproductive polyp and the absence of a medusa stage - and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) - cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia + Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae + Coronatae], Acraspeda [Cubozoa + Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that the shared morphological characters in

A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

PubMed

Bryant, Harold N; Cantino, Philip D

2002-02-01

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.

Sugar concentration in nectar: a quantitative metric of crop attractiveness for refined pollinator risk assessments.

PubMed

Knopper, Loren D; Dan, Tereza; Reisig, Dominic D; Johnson, Josephine D; Bowers, Lisa M

2016-10-01

Those involved with pollinator risk assessment know that agricultural crops vary in attractiveness to bees. Intuitively, this means that exposure to agricultural pesticides is likely greatest for attractive plants and lowest for unattractive plants. While crop attractiveness in the risk assessment process has been qualitatively remarked on by some authorities, absent is direction on how to refine the process with quantitative metrics of attractiveness. At a high level, attractiveness of crops to bees appears to depend on several key variables, including but not limited to: floral, olfactory, visual and tactile cues; seasonal availability; physical and behavioral characteristics of the bee; plant and nectar rewards. Notwithstanding the complexities and interactions among these variables, sugar content in nectar stands out as a suitable quantitative metric by which to refine pollinator risk assessments for attractiveness. Provided herein is a proposed way to use sugar nectar concentration to adjust the exposure parameter (with what is called a crop attractiveness factor) in the calculation of risk quotients in order to derive crop-specific tier I assessments. This Perspective is meant to invite discussion on incorporating such changes in the risk assessment process. © 2016 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. © 2016 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Dynamic and quantitative assessment of blood coagulation using optical coherence elastography

PubMed Central

Xu, Xiangqun; Zhu, Jiang; Chen, Zhongping

2016-01-01

Reliable clot diagnostic systems are needed for directing treatment in a broad spectrum of cardiovascular diseases and coagulopathy. Here, we report on non-contact measurement of elastic modulus for dynamic and quantitative assessment of whole blood coagulation using acoustic radiation force orthogonal excitation optical coherence elastography (ARFOE-OCE). In this system, acoustic radiation force (ARF) is produced by a remote ultrasonic transducer, and a shear wave induced by ARF excitation is detected by the optical coherence tomography (OCT) system. During porcine whole blood coagulation, changes in the elastic property of the clots increase the shear modulus of the sample, altering the propagating velocity of the shear wave. Consequently, dynamic blood coagulation status can be measured quantitatively by relating the velocity of the shear wave with clinically relevant coagulation metrics, including reaction time, clot formation kinetics and maximum shear modulus. The results show that the ARFOE-OCE is sensitive to the clot formation kinetics and can differentiate the elastic properties of the recalcified porcine whole blood, blood added with kaolin as an activator, and blood spiked with fibrinogen. PMID:27090437

Dynamic and quantitative assessment of blood coagulation using optical coherence elastography

NASA Astrophysics Data System (ADS)

Xu, Xiangqun; Zhu, Jiang; Chen, Zhongping

2016-04-01

Reliable clot diagnostic systems are needed for directing treatment in a broad spectrum of cardiovascular diseases and coagulopathy. Here, we report on non-contact measurement of elastic modulus for dynamic and quantitative assessment of whole blood coagulation using acoustic radiation force orthogonal excitation optical coherence elastography (ARFOE-OCE). In this system, acoustic radiation force (ARF) is produced by a remote ultrasonic transducer, and a shear wave induced by ARF excitation is detected by the optical coherence tomography (OCT) system. During porcine whole blood coagulation, changes in the elastic property of the clots increase the shear modulus of the sample, altering the propagating velocity of the shear wave. Consequently, dynamic blood coagulation status can be measured quantitatively by relating the velocity of the shear wave with clinically relevant coagulation metrics, including reaction time, clot formation kinetics and maximum shear modulus. The results show that the ARFOE-OCE is sensitive to the clot formation kinetics and can differentiate the elastic properties of the recalcified porcine whole blood, blood added with kaolin as an activator, and blood spiked with fibrinogen.

Semi-quantitative assessment of pulmonary perfusion in children using dynamic contrast-enhanced MRI

NASA Astrophysics Data System (ADS)

Fetita, Catalin; Thong, William E.; Ou, Phalla

2013-03-01

This paper addresses the study of semi-quantitative assessment of pulmonary perfusion acquired from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in a study population mainly composed of children with pulmonary malformations. The automatic analysis approach proposed is based on the indicator-dilution theory introduced in 1954. First, a robust method is developed to segment the pulmonary artery and the lungs from anatomical MRI data, exploiting 2D and 3D mathematical morphology operators. Second, the time-dependent contrast signal of the lung regions is deconvolved by the arterial input function for the assessment of the local hemodynamic system parameters, ie. mean transit time, pulmonary blood volume and pulmonary blood flow. The discrete deconvolution method implements here a truncated singular value decomposition (tSVD) method. Parametric images for the entire lungs are generated as additional elements for diagnosis and quantitative follow-up. The preliminary results attest the feasibility of perfusion quantification in pulmonary DCE-MRI and open an interesting alternative to scintigraphy for this type of evaluation, to be considered at least as a preliminary decision in the diagnostic due to the large availability of the technique and to the non-invasive aspects.

A phylogenetic blueprint for a modern whale.

PubMed

Gatesy, John; Geisler, Jonathan H; Chang, Joseph; Buell, Carl; Berta, Annalisa; Meredith, Robert W; Springer, Mark S; McGowen, Michael R

2013-02-01

The emergence of Cetacea in the Paleogene represents one of the most profound macroevolutionary transitions within Mammalia. The move from a terrestrial habitat to a committed aquatic lifestyle engendered wholesale changes in anatomy, physiology, and behavior. The results of this remarkable transformation are extant whales that include the largest, biggest brained, fastest swimming, loudest, deepest diving mammals, some of which can detect prey with a sophisticated echolocation system (Odontoceti - toothed whales), and others that batch feed using racks of baleen (Mysticeti - baleen whales). A broad-scale reconstruction of the evolutionary remodeling that culminated in extant cetaceans has not yet been based on integration of genomic and paleontological information. Here, we first place Cetacea relative to extant mammalian diversity, and assess the distribution of support among molecular datasets for relationships within Artiodactyla (even-toed ungulates, including Cetacea). We then merge trees derived from three large concatenations of molecular and fossil data to yield a composite hypothesis that encompasses many critical events in the evolutionary history of Cetacea. By combining diverse evidence, we infer a phylogenetic blueprint that outlines the stepwise evolutionary development of modern whales. This hypothesis represents a starting point for more detailed, comprehensive phylogenetic reconstructions in the future, and also highlights the synergistic interaction between modern (genomic) and traditional (morphological+paleontological) approaches that ultimately must be exploited to provide a rich understanding of evolutionary history across the entire tree of Life. Copyright © 2012 Elsevier Inc. All rights reserved.

Anatomic and Quantitative Temporal Bone CT for Preoperative Assessment of Branchio-Oto-Renal Syndrome.

PubMed

Ginat, D T; Ferro, L; Gluth, M B

2016-12-01

We describe the temporal bone computed tomography (CT) findings of an unusual case of branchio-oto-renal syndrome with ectopic ossicles that are partially located in the middle cranial fossa. We also describe quantitative temporal bone CT assessment pertaining to cochlear implantation in the setting of anomalous cochlear anatomy associated with this syndrome.

Phylogenetic support for the Tropical Niche Conservatism Hypothesis despite the absence of a clear latitudinal species richness gradient in Yunnan's woody flora

NASA Astrophysics Data System (ADS)

Tang, G.; Zhang, M. G.; Liu, C.; Zhou, Z.; Chen, W.; Slik, J. W. F.

2014-05-01

The Tropical Niche Conservatism Hypothesis (TCH) tries to explain the generally observed latitudinal gradient of increasing species diversity towards the tropics. To date, few studies have used phylogenetic approaches to assess its validity, even though such methods are especially suited to detect changes in niche structure. We test the TCH using modeled distributions of 1898 woody species in Yunnan Province (southwest China) in combination with a family level phylogeny. Unlike predicted, species richness and phylogenetic diversity did not show a latitudinal gradient, but identified two high diversity zones, one in Northwest and one in South Yunnan. Despite this, the underlying residual phylogenetic diversity showed a clear decline away from the tropics, while the species composition became progressingly more phylogenetically clustered towards the North. These latitudinal changes were strongly associated with more extreme temperature variability and declining precipitation and soil water availability, especially during the dry season. Our results suggests that the climatically more extreme conditions outside the tropics require adaptations for successful colonization, most likely related to the plant hydraulic system, that have been acquired by only a limited number of phylogenetically closely related plant lineages. We emphasize the importance of phylogenetic approaches for testing the TCH.

A generalized K statistic for estimating phylogenetic signal from shape and other high-dimensional multivariate data.

PubMed

Adams, Dean C

2014-09-01

Phylogenetic signal is the tendency for closely related species to display similar trait values due to their common ancestry. Several methods have been developed for quantifying phylogenetic signal in univariate traits and for sets of traits treated simultaneously, and the statistical properties of these approaches have been extensively studied. However, methods for assessing phylogenetic signal in high-dimensional multivariate traits like shape are less well developed, and their statistical performance is not well characterized. In this article, I describe a generalization of the K statistic of Blomberg et al. that is useful for quantifying and evaluating phylogenetic signal in highly dimensional multivariate data. The method (K(mult)) is found from the equivalency between statistical methods based on covariance matrices and those based on distance matrices. Using computer simulations based on Brownian motion, I demonstrate that the expected value of K(mult) remains at 1.0 as trait variation among species is increased or decreased, and as the number of trait dimensions is increased. By contrast, estimates of phylogenetic signal found with a squared-change parsimony procedure for multivariate data change with increasing trait variation among species and with increasing numbers of trait dimensions, confounding biological interpretations. I also evaluate the statistical performance of hypothesis testing procedures based on K(mult) and find that the method displays appropriate Type I error and high statistical power for detecting phylogenetic signal in high-dimensional data. Statistical properties of K(mult) were consistent for simulations using bifurcating and random phylogenies, for simulations using different numbers of species, for simulations that varied the number of trait dimensions, and for different underlying models of trait covariance structure. Overall these findings demonstrate that K(mult) provides a useful means of evaluating phylogenetic signal in high

Student interpretations of phylogenetic trees in an introductory biology course.

PubMed

Dees, Jonathan; Momsen, Jennifer L; Niemi, Jarad; Montplaisir, Lisa

2014-01-01

Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa relatedness on phylogenetic trees, to measure the prevalence of correct taxa-relatedness interpretations, and to determine how student reasoning and correctness change in response to instruction and over time. Counting synapomorphies and nodes between taxa were the most common forms of incorrect reasoning, which presents a pedagogical dilemma concerning labeled synapomorphies on phylogenetic trees. Students also independently generated an alternative form of correct reasoning using monophyletic groups, the use of which decreased in popularity over time. Approximately half of all students were able to correctly interpret taxa relatedness on phylogenetic trees, and many memorized correct reasoning without understanding its application. Broad initial instruction that allowed students to generate inferences on their own contributed very little to phylogenetic tree understanding, while targeted instruction on evolutionary relationships improved understanding to some extent. Phylogenetic trees, which can directly affect student understanding of evolution, appear to offer introductory biology instructors a formidable pedagogical challenge. © 2014 J. Dees et al. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

The importance of accounting for imperfect detection when estimating functional and phylogenetic community structure.

PubMed

Si, Xingfeng; Cadotte, Marc W; Zhao, Yuhao; Zhou, Haonan; Zeng, Di; Li, Jiaqi; Jin, Tinghao; Ren, Peng; Wang, Yanping; Ding, Ping; Tingley, Morgan W

2018-06-26

Incorporating imperfect detection when estimating species richness has become commonplace in the past decade. However, the question of how imperfect detection of species affects estimates of functional and phylogenetic community structure remains untested. We used long-term counts of breeding bird species that were detected at least once on islands in a land-bridge island system, and employed multi-species occupancy models to assess the effects of imperfect detection of species on estimates of bird diversity and community structure by incorporating species traits and phylogenies. Our results showed that taxonomic, functional, and phylogenetic diversity were all underestimated significantly as a result of species' imperfect detection, with taxonomic diversity showing the greatest bias. The functional and phylogenetic structure calculated from observed communities were both more clustered than those from the detection-corrected communities due to missed distinct species. The discrepancy between observed and estimated diversity differed according to the measure of biodiversity employed. Our study demonstrates the importance of accounting for species' imperfect detection in biodiversity studies, especially for functional and phylogenetic community ecology, and when attempting to infer community assembly processes. With datasets that allow for detection-corrected community structure, we can better estimate diversity and infer the underlying mechanisms that structure community assembly, and thus make reliable management decisions for the conservation of biodiversity. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Computational technique for stepwise quantitative assessment of equation correctness

NASA Astrophysics Data System (ADS)

Othman, Nuru'l Izzah; Bakar, Zainab Abu

2017-04-01

Many of the computer-aided mathematics assessment systems that are available today possess the capability to implement stepwise correctness checking of a working scheme for solving equations. The computational technique for assessing the correctness of each response in the scheme mainly involves checking the mathematical equivalence and providing qualitative feedback. This paper presents a technique, known as the Stepwise Correctness Checking and Scoring (SCCS) technique that checks the correctness of each equation in terms of structural equivalence and provides quantitative feedback. The technique, which is based on the Multiset framework, adapts certain techniques from textual information retrieval involving tokenization, document modelling and similarity evaluation. The performance of the SCCS technique was tested using worked solutions on solving linear algebraic equations in one variable. 350 working schemes comprising of 1385 responses were collected using a marking engine prototype, which has been developed based on the technique. The results show that both the automated analytical scores and the automated overall scores generated by the marking engine exhibit high percent agreement, high correlation and high degree of agreement with manual scores with small average absolute and mixed errors.

Using Genotype Abundance to Improve Phylogenetic Inference

PubMed Central

Mesin, Luka; Victora, Gabriel D; Minin, Vladimir N; Matsen, Frederick A

2018-01-01

Abstract Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in phylogenetic inference. In this article, we synthesize a stochastic process model with standard sequence-based phylogenetic optimality, and show that tree estimation is substantially improved by doing so. Our method is validated with extensive simulations and an experimental single-cell lineage tracing study of germinal center B cell receptor affinity maturation. PMID:29474671

Quantitative assessment of upper extremities motor function in multiple sclerosis.

PubMed

Daunoraviciene, Kristina; Ziziene, Jurgita; Griskevicius, Julius; Pauk, Jolanta; Ovcinikova, Agne; Kizlaitiene, Rasa; Kaubrys, Gintaras

2018-05-18

Upper extremity (UE) motor function deficits are commonly noted in multiple sclerosis (MS) patients and assessing it is challenging because of the lack of consensus regarding its definition. Instrumented biomechanical analysis of upper extremity movements can quantify coordination with different spatiotemporal measures and facilitate disability rating in MS patients. To identify objective quantitative parameters for more accurate evaluation of UE disability and relate it to existing clinical scores. Thirty-four MS patients and 24 healthy controls (CG) performed a finger-to-nose test as fast as possible and, in addition, clinical evaluation kinematic parameters of UE were measured by using inertial sensors. Generally, a higher disability score was associated with an increase of several temporal parameters, like slower task performance. The time taken to touch their nose was longer when the task was fulfilled with eyes closed. Time to peak angular velocity significantly changed in MS patients (EDSS > 5.0). The inter-joint coordination significantly decreases in MS patients (EDSS 3.0-5.5). Spatial parameters indicated that maximal ROM changes were in elbow flexion. Our findings have revealed that spatiotemporal parameters are related to the UE motor function and MS disability level. Moreover, they facilitate clinical rating by supporting clinical decisions with quantitative data.

Posterior Predictive Bayesian Phylogenetic Model Selection

PubMed Central

Lewis, Paul O.; Xie, Wangang; Chen, Ming-Hui; Fan, Yu; Kuo, Lynn

2014-01-01

We present two distinctly different posterior predictive approaches to Bayesian phylogenetic model selection and illustrate these methods using examples from green algal protein-coding cpDNA sequences and flowering plant rDNA sequences. The Gelfand–Ghosh (GG) approach allows dissection of an overall measure of model fit into components due to posterior predictive variance (GGp) and goodness-of-fit (GGg), which distinguishes this method from the posterior predictive P-value approach. The conditional predictive ordinate (CPO) method provides a site-specific measure of model fit useful for exploratory analyses and can be combined over sites yielding the log pseudomarginal likelihood (LPML) which is useful as an overall measure of model fit. CPO provides a useful cross-validation approach that is computationally efficient, requiring only a sample from the posterior distribution (no additional simulation is required). Both GG and CPO add new perspectives to Bayesian phylogenetic model selection based on the predictive abilities of models and complement the perspective provided by the marginal likelihood (including Bayes Factor comparisons) based solely on the fit of competing models to observed data. [Bayesian; conditional predictive ordinate; CPO; L-measure; LPML; model selection; phylogenetics; posterior predictive.] PMID:24193892

The quantitative assessment of epicardial fat distribution on human hearts: Implications for epicardial electrophysiology.

PubMed

Mattson, Alexander R; Soto, Mario J; Iaizzo, Paul A

2018-07-01

Epicardial electrophysiological procedures rely on dependable interfacing with the myocardial tissue. For example, epicardial pacing systems must generate sustainable chronic pacing capture, while epicardial ablations must effectively deliver energy to the target hyper-excitable myocytes. The human heart has a significant adipose layer which may impede epicardial procedures. The objective of this study was to quantitatively assess the relative location of epicardial adipose on the human heart, to define locations where epicardial therapies might be performed successfully. We studied perfusion-fixed human hearts (n = 105) in multiple isolated planes including: left ventricular margin, diaphragmatic surface, and anterior right ventricle. Relative adipose distribution was quantitatively assessed via planar images, using a custom-generated image analysis algorithm. In these specimens, 76.7 ± 13.8% of the left ventricular margin, 72.7 ± 11.3% of the diaphragmatic surface, and 92.1 ± 8.7% of the anterior right margin were covered with superficial epicardial adipose layers. Percent adipose coverage significantly increased with age (P < 0.001) and history of coronary artery disease (P < 0.05). No significant relationships were identified between relative percent adipose coverage and gender, body weight or height, BMI, history of hypertension, and/or history of congestive heart failure. Additionally, we describe two-dimensional probability distributions of epicardial adipose coverage for each of the three analysis planes. In this study, we detail the quantitative assessment and probabilistic mapping of the distribution of superficial epicardial adipose on the adult human heart. These findings have implications relative to performing epicardial procedures and/or designing procedures or tools to successfully perform such treatments. Clin. Anat. 31:661-666, 2018. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Phylogenetic approaches reveal biodiversity threats under climate change

NASA Astrophysics Data System (ADS)

González-Orozco, Carlos E.; Pollock, Laura J.; Thornhill, Andrew H.; Mishler, Brent D.; Knerr, Nunzio; Laffan, Shawn W.; Miller, Joseph T.; Rosauer, Dan F.; Faith, Daniel P.; Nipperess, David A.; Kujala, Heini; Linke, Simon; Butt, Nathalie; Külheim, Carsten; Crisp, Michael D.; Gruber, Bernd

2016-12-01

Predicting the consequences of climate change for biodiversity is critical to conservation efforts. Extensive range losses have been predicted for thousands of individual species, but less is known about how climate change might impact whole clades and landscape-scale patterns of biodiversity. Here, we show that climate change scenarios imply significant changes in phylogenetic diversity and phylogenetic endemism at a continental scale in Australia using the hyper-diverse clade of eucalypts. We predict that within the next 60 years the vast majority of species distributions (91%) across Australia will shrink in size (on average by 51%) and shift south on the basis of projected suitable climatic space. Geographic areas currently with high phylogenetic diversity and endemism are predicted to change substantially in future climate scenarios. Approximately 90% of the current areas with concentrations of palaeo-endemism (that is, places with old evolutionary diversity) are predicted to disappear or shift their location. These findings show that climate change threatens whole clades of the phylogenetic tree, and that the outlined approach can be used to forecast areas of biodiversity losses and continental-scale impacts of climate change.

Distance-Based Phylogenetic Methods Around a Polytomy.

PubMed

Davidson, Ruth; Sullivant, Seth

2014-01-01

Distance-based phylogenetic algorithms attempt to solve the NP-hard least-squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean space properly containing the space of all tree metrics as a polyhedral fan. Outputs of distance-based tree reconstruction algorithms such as UPGMA and neighbor-joining are points in the maximal cones in the fan. Tree metrics with polytomies lie at the intersections of maximal cones. A phylogenetic algorithm divides the space of all dissimilarity maps into regions based upon which combinatorial tree is reconstructed by the algorithm. Comparison of phylogenetic methods can be done by comparing the geometry of these regions. We use polyhedral geometry to compare the local nature of the subdivisions induced by least-squares phylogeny, UPGMA, and neighbor-joining when the true tree has a single polytomy with exactly four neighbors. Our results suggest that in some circumstances, UPGMA and neighbor-joining poorly match least-squares phylogeny.

Quantitative instruments used to assess children's sense of smell: a review article.

PubMed

Moura, Raissa Gomes Fonseca; Cunha, Daniele Andrade; Gomes, Ana Carolina de Lima Gusmão; Silva, Hilton Justino da

2014-01-01

To systematically gather from the literature available the quantitative instruments used to assess the sense of smell in studies carried out with children. The present study included a survey in the Pubmed and Bireme platforms and in the databases of MedLine, Lilacs, regional SciELO and Web of Science, followed by selection and critical analysis of the articles found and chosen. We selected original articles related to the topic in question, conducted only with children in Portuguese, English, and Spanish. We excluded studies addressing other phases of human development, exclusively or concurrently with the pediatric population; studies on animals; literature review articles; dissertations; book chapters; case study articles; and editorials. A book report protocol was created for this study, including the following information: author, department, year, location, population/sample, age, purpose of the study, methods, and main results. We found 8,451 articles by typing keywords and identifiers. Out of this total, 5,928 were excluded by the title, 2,366 by the abstract, and 123 after we read the full text. Thus, 34 articles were selected, of which 28 were repeated in the databases, totalizing 6 articles analyzed in this review. We observed a lack of standardization of the quantitative instruments used to assess children's sense of smell, with great variability in the methodology of the tests, which reduces the effectiveness and reliability of the results.

AFLP analysis of genetic diversity and phylogenetic relationships of Brassica oleracea in Ireland.

PubMed

El-Esawi, Mohamed A; Germaine, Kieran; Bourke, Paula; Malone, Renee

2016-01-01

Brassica oleracea L. is one of the most economically important vegetable crop species of the genus Brassica L. This species is threatened in Ireland, without any prior reported genetic studies. The use of this species is being very limited due to its imprecise phylogeny and uncompleted genetic characterisation. The main objective of this study was to assess the genetic diversity and phylogenetic relationships of a set of 25 Irish B. oleracea accessions using the powerful amplified fragment length polymorphism (AFLP) technique. A total of 471 fragments were scored across all the 11 AFLP primer sets used, out of which 423 (89.8%) were polymorphic and could differentiate the accessions analysed. The dendrogram showed that cauliflowers were more closely related to cabbages than kales were, and accessions of some cabbage types were distributed among different clusters within cabbage subgroups. Approximately 33.7% of the total genetic variation was found among accessions, and 66.3% of the variation resided within accessions. The total genetic diversity (HT) and the intra-accessional genetic diversity (HS) were 0.251 and 0.156, respectively. This high level of variation demonstrates that the Irish B. oleracea accessions studied should be managed and conserved for future utilisation and exploitation in food and agriculture. In conclusion, this study addressed important phylogenetic questions within this species, and provided a new insight into the inclusion of four accessions of cabbages and kales in future breeding programs for improving varieties. AFLP markers were efficient for assessing genetic diversity and phylogenetic relationships in Irish B. oleracea species. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

The power and pitfalls of HIV phylogenetics in public health.

PubMed

Brooks, James I; Sandstrom, Paul A

2013-07-25

Phylogenetics is the application of comparative studies of genetic sequences in order to infer evolutionary relationships among organisms. This tool can be used as a form of molecular epidemiology to enhance traditional population-level communicable disease surveillance. Phylogenetic study has resulted in new paradigms being created in the field of communicable diseases and this commentary aims to provide the reader with an explanation of how phylogenetics can be used in tracking infectious diseases. Special emphasis will be placed upon the application of phylogenetics as a tool to help elucidate HIV transmission patterns and the limitations to these methods when applied to forensic analysis. Understanding infectious disease epidemiology in order to prevent new transmissions is the sine qua non of public health. However, with increasing epidemiological resolution, there may be an associated potential loss of privacy to the individual. It is within this context that we aim to promote the discussion on how to use phylogenetics to achieve important public health goals, while at the same time protecting the rights of the individual.

Towards a general framework for predicting threat status of data-deficient species from phylogenetic, spatial and environmental information.

PubMed

Jetz, Walter; Freckleton, Robert P

2015-02-19

In taxon-wide assessments of threat status many species remain not included owing to lack of data. Here, we present a novel spatial-phylogenetic statistical framework that uses a small set of readily available or derivable characteristics, including phylogenetically imputed body mass and remotely sensed human encroachment, to provide initial baseline predictions of threat status for data-deficient species. Applied to assessed mammal species worldwide, the approach effectively identifies threatened species and predicts the geographical variation in threat. For the 483 data-deficient species, the models predict highly elevated threat, with 69% 'at-risk' species in this set, compared with 22% among assessed species. This results in 331 additional potentially threatened mammals, with elevated conservation importance in rodents, bats and shrews, and countries like Colombia, Sulawesi and the Philippines. These findings demonstrate the future potential for combining phylogenies and remotely sensed data with species distributions to identify species and regions of conservation concern. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Impact of tree priors in species delimitation and phylogenetics of the genus Oligoryzomys (Rodentia: Cricetidae).

PubMed

da Cruz, Marcos de O R; Weksler, Marcelo

2018-02-01

The use of genetic data and tree-based algorithms to delimit evolutionary lineages is becoming an important practice in taxonomic identification, especially in morphologically cryptic groups. The effects of different phylogenetic and/or coalescent models in the analyses of species delimitation, however, are not clear. In this paper, we assess the impact of different evolutionary priors in phylogenetic estimation, species delimitation, and molecular dating of the genus Oligoryzomys (Mammalia: Rodentia), a group with complex taxonomy and morphological cryptic species. Phylogenetic and coalescent analyses included 20 of the 24 recognized species of the genus, comprising of 416 Cytochrome b sequences, 26 Cytochrome c oxidase I sequences, and 27 Beta-Fibrinogen Intron 7 sequences. For species delimitation, we employed the General Mixed Yule Coalescent (GMYC) and Bayesian Poisson tree processes (bPTP) analyses, and contrasted 4 genealogical and phylogenetic models: Pure-birth (Yule), Constant Population Size Coalescent, Multiple Species Coalescent, and a mixed Yule-Coalescent model. GMYC analyses of trees from different genealogical models resulted in similar species delimitation and phylogenetic relationships, with incongruence restricted to areas of poor nodal support. bPTP results, however, significantly differed from GMYC for 5 taxa. Oligoryzomys early diversification was estimated to have occurred in the Early Pleistocene, between 0.7 and 2.6 MYA. The mixed Yule-Coalescent model, however, recovered younger dating estimates for Oligoryzomys diversification, and for the threshold for the speciation-coalescent horizon in GMYC. Eight of the 20 included Oligoryzomys species were identified as having two or more independent evolutionary units, indicating that current taxonomy of Oligoryzomys is still unsettled. Copyright © 2017 Elsevier Inc. All rights reserved.

Deciphering the enigma of undetected species, phylogenetic, and functional diversity based on Good-Turing theory.

PubMed

Chao, Anne; Chiu, Chun-Huo; Colwell, Robert K; Magnago, Luiz Fernando S; Chazdon, Robin L; Gotelli, Nicholas J

2017-11-01

Estimating the species, phylogenetic, and functional diversity of a community is challenging because rare species are often undetected, even with intensive sampling. The Good-Turing frequency formula, originally developed for cryptography, estimates in an ecological context the true frequencies of rare species in a single assemblage based on an incomplete sample of individuals. Until now, this formula has never been used to estimate undetected species, phylogenetic, and functional diversity. Here, we first generalize the Good-Turing formula to incomplete sampling of two assemblages. The original formula and its two-assemblage generalization provide a novel and unified approach to notation, terminology, and estimation of undetected biological diversity. For species richness, the Good-Turing framework offers an intuitive way to derive the non-parametric estimators of the undetected species richness in a single assemblage, and of the undetected species shared between two assemblages. For phylogenetic diversity, the unified approach leads to an estimator of the undetected Faith's phylogenetic diversity (PD, the total length of undetected branches of a phylogenetic tree connecting all species), as well as a new estimator of undetected PD shared between two phylogenetic trees. For functional diversity based on species traits, the unified approach yields a new estimator of undetected Walker et al.'s functional attribute diversity (FAD, the total species-pairwise functional distance) in a single assemblage, as well as a new estimator of undetected FAD shared between two assemblages. Although some of the resulting estimators have been previously published (but derived with traditional mathematical inequalities), all taxonomic, phylogenetic, and functional diversity estimators are now derived under the same framework. All the derived estimators are theoretically lower bounds of the corresponding undetected diversities; our approach reveals the sufficient conditions under

Microbial quality and phylogenetic diversity of fresh rainwater and tropical freshwater reservoir.

PubMed

Kaushik, Rajni; Balasubramanian, Rajasekhar; Dunstan, Hugh

2014-01-01

The impact of rainwater on the microbial quality of a tropical freshwater reservoir through atmospheric wet deposition of microorganisms was studied for the first time. Reservoir water samples were collected at four different sampling points and rainwater samples were collected in the immediate vicinity of the reservoir sites for a period of four months (January to April, 2012) during the Northeast monsoon period. Microbial quality of all fresh rainwater and reservoir water samples was assessed based on the counts for the microbial indicators: Escherichia coli (E. coli), total coliforms, and Enterococci along with total heterotrophic plate counts (HPC). The taxonomic richness and phylogenetic relationship of the freshwater reservoir with those of the fresh rainwater were also assessed using 16 S rRNA gene clone library construction. The levels of E. coli were found to be in the range of 0 CFU/100 mL-75 CFU/100 mL for the rainwater, and were 10-94 CFU/100 mL for the reservoir water. The sampling sites that were influenced by highway traffic emissions showed the maximum counts for all the bacterial indicators assessed. There was no significant increase in the bacterial abundances observed in the reservoir water immediately following rainfall. However, the composite fresh rainwater and reservoir water samples exhibited broad phylogenetic diversity, including sequences representing Betaproteobacteria, Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Lentisphaerae and Bacteriodetes. Members of the Betaproteobacteria group were the most dominant in both fresh rainwater and reservoir water, followed by Alphaproteobacteria, Sphingobacteria, Actinobacteria and Gammaproteobacteria.

Quantitative Assessment of Transportation Network Vulnerability with Dynamic Traffic Simulation Methods

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

Shekar, Venkateswaran; Fiondella, Lance; Chatterjee, Samrat

Transportation networks are critical to the social and economic function of nations. Given the continuing increase in the populations of cities throughout the world, the criticality of transportation infrastructure is expected to increase. Thus, it is ever more important to mitigate congestion as well as to assess the impact disruptions would have on individuals who depend on transportation for their work and livelihood. Moreover, several government organizations are responsible for ensuring transportation networks are available despite the constant threat of natural disasters and terrorist activities. Most of the previous transportation network vulnerability research has been performed in the context ofmore » static traffic models, many of which are formulated as traditional optimization problems. However, transportation networks are dynamic because their usage varies over time. Thus, more appropriate methods to characterize the vulnerability of transportation networks should consider their dynamic properties. This paper presents a quantitative approach to assess the vulnerability of a transportation network to disruptions with methods from traffic simulation. Our approach can prioritize the critical links over time and is generalizable to the case where both link and node disruptions are of concern. We illustrate the approach through a series of examples. Our results demonstrate that the approach provides quantitative insight into the time varying criticality of links. Such an approach could be used as the objective function of less traditional optimization methods that use simulation and other techniques to evaluate the relative utility of a particular network defense to reduce vulnerability and increase resilience.« less

A Universal Phylogenetic Tree.

ERIC Educational Resources Information Center

Offner, Susan

2001-01-01

Presents a universal phylogenetic tree suitable for use in high school and college-level biology classrooms. Illustrates the antiquity of life and that all life is related, even if it dates back 3.5 billion years. Reflects important evolutionary relationships and provides an exciting way to learn about the history of life. (SAH)

Phylogenetic Diversity and Metabolic Potential Revealed in a Glacier Ice Metagenome▿ †

PubMed Central

Simon, Carola; Wiezer, Arnim; Strittmatter, Axel W.; Daniel, Rolf

2009-01-01

The largest part of the Earth's microbial biomass is stored in cold environments, which represent almost untapped reservoirs of novel species, processes, and genes. In this study, the first metagenomic survey of the metabolic potential and phylogenetic diversity of a microbial assemblage present in glacial ice is presented. DNA was isolated from glacial ice of the Northern Schneeferner, Germany. Pyrosequencing of this DNA yielded 1,076,539 reads (239.7 Mbp). The phylogenetic composition of the prokaryotic community was assessed by evaluation of a pyrosequencing-derived data set and sequencing of 16S rRNA genes. The Proteobacteria (mainly Betaproteobacteria), Bacteroidetes, and Actinobacteria were the predominant phylogenetic groups. In addition, isolation of psychrophilic microorganisms was performed, and 13 different bacterial isolates were recovered. Analysis of the 16S rRNA gene sequences of the isolates revealed that all were affiliated to the predominant groups. As expected for microorganisms residing in a low-nutrient environment, a high metabolic versatility with respect to degradation of organic substrates was detected by analysis of the pyrosequencing-derived data set. The presence of autotrophic microorganisms was indicated by identification of genes typical for different ways of carbon fixation. In accordance with the results of the phylogenetic studies, in which mainly aerobic and facultative aerobic bacteria were detected, genes typical for central metabolism of aerobes were found. Nevertheless, the capability of growth under anaerobic conditions was indicated by genes involved in dissimilatory nitrate/nitrite reduction. Numerous characteristics for metabolic adaptations associated with a psychrophilic lifestyle, such as formation of cryoprotectants and maintenance of membrane fluidity by the incorporation of unsaturated fatty acids, were detected. Thus, analysis of the glacial metagenome provided insights into the microbial life in frozen habitats on

Phylogenetics of modern birds in the era of genomics

PubMed Central

Edwards, Scott V; Bryan Jennings, W; Shedlock, Andrew M

2005-01-01

In the 14 years since the first higher-level bird phylogenies based on DNA sequence data, avian phylogenetics has witnessed the advent and maturation of the genomics era, the completion of the chicken genome and a suite of technologies that promise to add considerably to the agenda of avian phylogenetics. In this review, we summarize current approaches and data characteristics of recent higher-level bird studies and suggest a number of as yet untested molecular and analytical approaches for the unfolding tree of life for birds. A variety of comparative genomics strategies, including adoption of objective quality scores for sequence data, analysis of contiguous DNA sequences provided by large-insert genomic libraries, and the systematic use of retroposon insertions and other rare genomic changes all promise an integrated phylogenetics that is solidly grounded in genome evolution. The avian genome is an excellent testing ground for such approaches because of the more balanced representation of single-copy and repetitive DNA regions than in mammals. Although comparative genomics has a number of obvious uses in avian phylogenetics, its application to large numbers of taxa poses a number of methodological and infrastructural challenges, and can be greatly facilitated by a ‘community genomics’ approach in which the modest sequencing throughputs of single PI laboratories are pooled to produce larger, complementary datasets. Although the polymerase chain reaction era of avian phylogenetics is far from complete, the comparative genomics era—with its ability to vastly increase the number and type of molecular characters and to provide a genomic context for these characters—will usher in a host of new perspectives and opportunities for integrating genome evolution and avian phylogenetics. PMID:16024355

Quantitative phase imaging for enhanced assessment of optomechanical cancer cell properties

NASA Astrophysics Data System (ADS)

Kastl, Lena; Kemper, Björn; Schnekenburger, Jürgen

2018-02-01

Optical cell stretching provides label-free investigations of cells by measuring their biomechanical properties based on deformability determination in a fiber optical two-beam trap. However, the stretching forces in this two-beam laser trap depend on the optical properties of the investigated specimen. Therefore, we characterized in parallel four cancer cell lines with varying degree of differentiation utilizing quantitative phase imaging (QPI) and optical cell stretching. The QPI data allowed enhanced assessment of the mechanical cell properties measured with the optical cell stretcher and demonstrates the high potential of cell phenotyping when both techniques are combined.

Investigation of the protein osteocalcin of Camelops hesternus: Sequence, structure and phylogenetic implications

NASA Astrophysics Data System (ADS)

Humpula, James F.; Ostrom, Peggy H.; Gandhi, Hasand; Strahler, John R.; Walker, Angela K.; Stafford, Thomas W.; Smith, James J.; Voorhies, Michael R.; George Corner, R.; Andrews, Phillip C.

2007-12-01

Ancient DNA sequences offer an extraordinary opportunity to unravel the evolutionary history of ancient organisms. Protein sequences offer another reservoir of genetic information that has recently become tractable through the application of mass spectrometric techniques. The extent to which ancient protein sequences resolve phylogenetic relationships, however, has not been explored. We determined the osteocalcin amino acid sequence from the bone of an extinct Camelid (21 ka, Camelops hesternus) excavated from Isleta Cave, New Mexico and three bones of extant camelids: bactrian camel ( Camelus bactrianus); dromedary camel ( Camelus dromedarius) and guanaco ( Llama guanacoe) for a diagenetic and phylogenetic assessment. There was no difference in sequence among the four taxa. Structural attributes observed in both modern and ancient osteocalcin include a post-translation modification, Hyp 9, deamidation of Gln 35 and Gln 39, and oxidation of Met 36. Carbamylation of the N-terminus in ancient osteocalcin may result in blockage and explain previous difficulties in sequencing ancient proteins via Edman degradation. A phylogenetic analysis using osteocalcin sequences of 25 vertebrate taxa was conducted to explore osteocalcin protein evolution and the utility of osteocalcin sequences for delineating phylogenetic relationships. The maximum likelihood tree closely reflected generally recognized taxonomic relationships. For example, maximum likelihood analysis recovered rodents, birds and, within hominins, the Homo-Pan-Gorilla trichotomy. Within Artiodactyla, character state analysis showed that a substitution of Pro 4 for His 4 defines the Capra-Ovis clade within Artiodactyla. Homoplasy in our analysis indicated that osteocalcin evolution is not a perfect indicator of species evolution. Limited sequence availability prevented assigning functional significance to sequence changes. Our preliminary analysis of osteocalcin evolution represents an initial step towards a

Functional and phylogenetic structure of island bird communities.

PubMed

Si, Xingfeng; Cadotte, Marc W; Zeng, Di; Baselga, Andrés; Zhao, Yuhao; Li, Jiaqi; Wu, Yiru; Wang, Siyu; Ding, Ping

2017-05-01

Biodiversity change in anthropogenically transformed habitats is often nonrandom, yet the nature and importance of the different mechanisms shaping community structure are unclear. Here, we extend the classic Theory of Island Biogeography (TIB) to account for nonrandom processes by incorporating species traits and phylogenetic relationships into a study of faunal relaxation following habitat loss and fragmentation. Two possible mechanisms can create nonrandom community patterns on fragment islands. First, small and isolated islands might consist of similar or closely related species because they are environmentally homogeneous or select for certain shared traits, such as dispersal ability. Alternatively, communities on small islands might contain more dissimilar or distantly related species than on large islands because limited space and resource availability result in greater competitive exclusion among species with high niche overlap. Breeding birds were surveyed on 36 islands and two mainland sites annually from 2010 to 2014 in the Thousand Island Lake region, China. We assessed community structure of breeding birds on these subtropical land-bridge islands by integrating species' trait and evolutionary distances. We additionally analysed habitat heterogeneity and variance in size ratios to distinguish biotic and abiotic processes of community assembly. Results showed that functional-phylogenetic diversity increased with island area, and decreased with isolation. Bird communities on the mainland were more diverse and generally less clustered than island bird communities and not different than randomly assembled communities. Bird communities on islands tend to be functionally similar and phylogenetically clustered, especially on small and isolated islands. The nonrandom decline in species diversity and change in bird community structure with island area and isolation, along with the relatively homogeneous habitats on small islands, support the environmental

Remotely Sensed Quantitative Drought Risk Assessment in Vulnerable Agroecosystems

NASA Astrophysics Data System (ADS)

Dalezios, N. R.; Blanta, A.; Spyropoulos, N. V.

2012-04-01

Hazard may be defined as a potential threat to humans and their welfare and risk (or consequence) as the probability of a hazard occurring and creating loss. Drought is considered as one of the major natural hazards with significant impact to agriculture, environment, economy and society. This paper deals with drought risk assessment, which the first step designed to find out what the problems are and comprises three distinct steps, namely risk identification, risk management which is not covered in this paper, there should be a fourth step to address the need for feedback and to take post-audits of all risk assessment exercises. In particular, quantitative drought risk assessment is attempted by using statistical methods. For the qualification of drought, the Reconnaissance Drought Index (RDI) is employed, which is a new index based on hydrometeorological parameters, such as precipitation and potential evapotranspiration. The remotely sensed estimation of RDI is based on NOA-AVHRR satellite data for a period of 20 years (1981-2001). The study area is Thessaly, central Greece, which is a drought-prone agricultural region characterized by vulnerable agriculture. Specifically, the undertaken drought risk assessment processes are specified as follows: 1. Risk identification: This step involves drought quantification and monitoring based on remotely sensed RDI and extraction of several features such as severity, duration, areal extent, onset and end time. Moreover, it involves a drought early warning system based on the above parameters. 2. Risk estimation: This step includes an analysis of drought severity, frequency and their relationships. 3. Risk evaluation: This step covers drought evaluation based on analysis of RDI images before and after each drought episode, which usually lasts one hydrological year (12month). The results of these three-step drought assessment processes are considered quite satisfactory in a drought-prone region such as Thessaly in central

Phylogenetic congruence between subtropical trees and their associated fungi.

PubMed

Liu, Xubing; Liang, Minxia; Etienne, Rampal S; Gilbert, Gregory S; Yu, Shixiao

2016-12-01

Recent studies have detected phylogenetic signals in pathogen-host networks for both soil-borne and leaf-infecting fungi, suggesting that pathogenic fungi may track or coevolve with their preferred hosts. However, a phylogenetically concordant relationship between multiple hosts and multiple fungi in has rarely been investigated. Using next-generation high-throughput DNA sequencing techniques, we analyzed fungal taxa associated with diseased leaves, rotten seeds, and infected seedlings of subtropical trees. We compared the topologies of the phylogenetic trees of the soil and foliar fungi based on the internal transcribed spacer (ITS) region with the phylogeny of host tree species based on matK , rbcL , atpB, and 5.8S genes. We identified 37 foliar and 103 soil pathogenic fungi belonging to the Ascomycota and Basidiomycota phyla and detected significantly nonrandom host-fungus combinations, which clustered on both the fungus phylogeny and the host phylogeny. The explicit evidence of congruent phylogenies between tree hosts and their potential fungal pathogens suggests either diffuse coevolution among the plant-fungal interaction networks or that the distribution of fungal species tracked spatially associated hosts with phylogenetically conserved traits and habitat preferences. Phylogenetic conservatism in plant-fungal interactions within a local community promotes host and parasite specificity, which is integral to the important role of fungi in promoting species coexistence and maintaining biodiversity of forest communities.

Turnover of plant lineages shapes herbivore phylogenetic beta diversity along ecological gradients.

PubMed

Pellissier, Loïc; Ndiribe, Charlotte; Dubuis, Anne; Pradervand, Jean-Nicolas; Salamin, Nicolas; Guisan, Antoine; Rasmann, Sergio

2013-05-01

Understanding drivers of biodiversity patterns is of prime importance in this era of severe environmental crisis. More diverse plant communities have been postulated to represent a larger functional trait-space, more likely to sustain a diverse assembly of herbivore species. Here, we expand this hypothesis to integrate environmental, functional and phylogenetic variation of plant communities as factors explaining the diversity of lepidopteran assemblages along elevation gradients in the Swiss Western Alps. According to expectations, we found that the association between butterflies and their host plants is highly phylogenetically structured. Multiple regression analyses showed the combined effect of climate, functional traits and phylogenetic diversity in structuring butterfly communities. Furthermore, we provide the first evidence that plant phylogenetic beta diversity is the major driver explaining butterfly phylogenetic beta diversity. Along ecological gradients, the bottom up control of herbivore diversity is thus driven by phylogenetically structured turnover of plant traits as well as environmental variables. © 2013 Blackwell Publishing Ltd/CNRS.

Diversity and phylogenetic relationships among Bartonella strains from Thai bats.

PubMed

McKee, Clifton D; Kosoy, Michael Y; Bai, Ying; Osikowicz, Lynn M; Franka, Richard; Gilbert, Amy T; Boonmar, Sumalee; Rupprecht, Charles E; Peruski, Leonard F

2017-01-01

Bartonellae are phylogenetically diverse, intracellular bacteria commonly found in mammals. Previous studies have demonstrated that bats have a high prevalence and diversity of Bartonella infections globally. Isolates (n = 42) were obtained from five bat species in four provinces of Thailand and analyzed using sequences of the citrate synthase gene (gltA). Sequences clustered into seven distinct genogroups; four of these genogroups displayed similarity with Bartonella spp. sequences from other bats in Southeast Asia, Africa, and Eastern Europe. Thirty of the isolates representing these seven genogroups were further characterized by sequencing four additional loci (ftsZ, nuoG, rpoB, and ITS) to clarify their evolutionary relationships with other Bartonella species and to assess patterns of diversity among strains. Among the seven genogroups, there were differences in the number of sequence variants, ranging from 1-5, and the amount of nucleotide divergence, ranging from 0.035-3.9%. Overall, these seven genogroups meet the criteria for distinction as novel Bartonella species, with sequence divergence among genogroups ranging from 6.4-15.8%. Evidence of intra- and intercontinental phylogenetic relationships and instances of homologous recombination among Bartonella genogroups in related bat species were found in Thai bats.

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

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

Quantitative assessment of Cerenkov luminescence for radioguided brain tumor resection surgery

NASA Astrophysics Data System (ADS)

Klein, Justin S.; Mitchell, Gregory S.; Cherry, Simon R.

2017-05-01

Cerenkov luminescence imaging (CLI) is a developing imaging modality that detects radiolabeled molecules via visible light emitted during the radioactive decay process. We used a Monte Carlo based computer simulation to quantitatively investigate CLI compared to direct detection of the ionizing radiation itself as an intraoperative imaging tool for assessment of brain tumor margins. Our brain tumor model consisted of a 1 mm spherical tumor remnant embedded up to 5 mm in depth below the surface of normal brain tissue. Tumor to background contrast ranging from 2:1 to 10:1 were considered. We quantified all decay signals (e±, gamma photon, Cerenkov photons) reaching the brain volume surface. CLI proved to be the most sensitive method for detecting the tumor volume in both imaging and non-imaging strategies as assessed by contrast-to-noise ratio and by receiver operating characteristic output of a channelized Hotelling observer.

Quantitative assessment of arm tremor in people with neurological disorders.

PubMed

Jeonghee Kim; Parnell, Claire; Wichmann, Thomas; DeWeerth, Stephen P

2016-08-01

Abnormal oscillatory movement (i.e. tremor) is usually evaluated with qualitative assessment by clinicians, and quantified with subjective scoring methods. These methods are often inaccurate. We utilized a quantitative and standardized task based on the Fitts' law to assess the performance of arm movement with tremor by controlling a gyration mouse on a computer. The experiment included the center-out tapping (COT) and rectangular track navigation (RTN) tasks. We report the results of a pilot study in which we collected the performance for healthy participants in whom tremor was simulated by imposing oscillatory movements to the arm with a vibration motor. We compared their movement speed and accuracy with and without the artificial "tremor." We found that the artificial tremor significantly affected the path efficiency for both tasks (COT: 56.8 vs. 46.2%, p <; 0.05; RTN: 94.2 vs. 67.4%, p <; 0.05), and we were able to distinguish the presence of tremor. From this result, we expect to quantify severity of tremor and the effectiveness therapy for tremor patients.

Cenozoic imprints on the phylogenetic structure of palm species assemblages worldwide.

PubMed

Kissling, W Daniel; Eiserhardt, Wolf L; Baker, William J; Borchsenius, Finn; Couvreur, Thomas L P; Balslev, Henrik; Svenning, Jens-Christian

2012-05-08

Despite long-standing interest in the origin and maintenance of species diversity, little is known about historical drivers of species assemblage structure at large spatiotemporal scales. Here, we use global species distribution data, a dated genus-level phylogeny, and paleo-reconstructions of biomes and climate to examine Cenozoic imprints on the phylogenetic structure of regional species assemblages of palms (Arecaceae), a species-rich plant family characteristic of tropical ecosystems. We find a strong imprint on phylogenetic clustering due to geographic isolation and in situ diversification, especially in the Neotropics and on islands with spectacular palm radiations (e.g., Madagascar, Hawaii, and Cuba). Phylogenetic overdispersion on mainlands and islands corresponds to biotic interchange areas. Differences in the degree of phylogenetic clustering among biogeographic realms are related to differential losses of tropical rainforests during the Cenozoic, but not to the cumulative area of tropical rainforest over geological time. A largely random phylogenetic assemblage structure in Africa coincides with severe losses of rainforest area, especially after the Miocene. More recent events also appear to be influential: phylogenetic clustering increases with increasing intensity of Quaternary glacial-interglacial climatic oscillations in South America and, to a lesser extent, Africa, indicating that specific clades perform better in climatically unstable regions. Our results suggest that continental isolation (in combination with limited long-distance dispersal) and changing climate and habitat loss throughout the Cenozoic have had strong impacts on the phylogenetic structure of regional species assemblages in the tropics.

Development of quantitative analysis method for stereotactic brain image: assessment of reduced accumulation in extent and severity using anatomical segmentation.

PubMed

Mizumura, Sunao; Kumita, Shin-ichiro; Cho, Keiichi; Ishihara, Makiko; Nakajo, Hidenobu; Toba, Masahiro; Kumazaki, Tatsuo

2003-06-01

Through visual assessment by three-dimensional (3D) brain image analysis methods using stereotactic brain coordinates system, such as three-dimensional stereotactic surface projections and statistical parametric mapping, it is difficult to quantitatively assess anatomical information and the range of extent of an abnormal region. In this study, we devised a method to quantitatively assess local abnormal findings by segmenting a brain map according to anatomical structure. Through quantitative local abnormality assessment using this method, we studied the characteristics of distribution of reduced blood flow in cases with dementia of the Alzheimer type (DAT). Using twenty-five cases with DAT (mean age, 68.9 years old), all of whom were diagnosed as probable Alzheimer's disease based on NINCDS-ADRDA, we collected I-123 iodoamphetamine SPECT data. A 3D brain map using the 3D-SSP program was compared with the data of 20 cases in the control group, who age-matched the subject cases. To study local abnormalities on the 3D images, we divided the whole brain into 24 segments based on anatomical classification. We assessed the extent of an abnormal region in each segment (rate of the coordinates with a Z-value that exceeds the threshold value, in all coordinates within a segment), and severity (average Z-value of the coordinates with a Z-value that exceeds the threshold value). This method clarified orientation and expansion of reduced accumulation, through classifying stereotactic brain coordinates according to the anatomical structure. This method was considered useful for quantitatively grasping distribution abnormalities in the brain and changes in abnormality distribution.

Cnidarian phylogenetic relationships as revealed by mitogenomics

PubMed Central

2013-01-01

Background Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia + Octocorallia) – cnidarians with a reproductive polyp and the absence of a medusa stage – and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) – cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. Results We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia + Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae + Coronatae], Acraspeda [Cubozoa + Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. Conclusions Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that

Efficient FPT Algorithms for (Strict) Compatibility of Unrooted Phylogenetic Trees.

PubMed

Baste, Julien; Paul, Christophe; Sau, Ignasi; Scornavacca, Celine

2017-04-01

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species X; these relationships are often depicted via a phylogenetic tree-a tree having its leaves labeled bijectively by elements of X and without degree-2 nodes-called the "species tree." One common approach for reconstructing a species tree consists in first constructing several phylogenetic trees from primary data (e.g., DNA sequences originating from some species in X), and then constructing a single phylogenetic tree maximizing the "concordance" with the input trees. The obtained tree is our estimation of the species tree and, when the input trees are defined on overlapping-but not identical-sets of labels, is called "supertree." In this paper, we focus on two problems that are central when combining phylogenetic trees into a supertree: the compatibility and the strict compatibility problems for unrooted phylogenetic trees. These problems are strongly related, respectively, to the notions of "containing as a minor" and "containing as a topological minor" in the graph community. Both problems are known to be fixed parameter tractable in the number of input trees k, by using their expressibility in monadic second-order logic and a reduction to graphs of bounded treewidth. Motivated by the fact that the dependency on k of these algorithms is prohibitively large, we give the first explicit dynamic programming algorithms for solving these problems, both running in time [Formula: see text], where n is the total size of the input.

PhySortR: a fast, flexible tool for sorting phylogenetic trees in R.

PubMed

Stephens, Timothy G; Bhattacharya, Debashish; Ragan, Mark A; Chan, Cheong Xin

2016-01-01

A frequent bottleneck in interpreting phylogenomic output is the need to screen often thousands of trees for features of interest, particularly robust clades of specific taxa, as evidence of monophyletic relationship and/or reticulated evolution. Here we present PhySortR, a fast, flexible R package for classifying phylogenetic trees. Unlike existing utilities, PhySortR allows for identification of both exclusive and non-exclusive clades uniting the target taxa based on tip labels (i.e., leaves) on a tree, with customisable options to assess clades within the context of the whole tree. Using simulated and empirical datasets, we demonstrate the potential and scalability of PhySortR in analysis of thousands of phylogenetic trees without a priori assumption of tree-rooting, and in yielding readily interpretable trees that unambiguously satisfy the query. PhySortR is a command-line tool that is freely available and easily automatable.

Evaluating variability and uncertainty separately in microbial quantitative risk assessment using two R packages.

PubMed

Pouillot, Régis; Delignette-Muller, Marie Laure

2010-09-01

Quantitative risk assessment has emerged as a valuable tool to enhance the scientific basis of regulatory decisions in the food safety domain. This article introduces the use of two new computing resources (R packages) specifically developed to help risk assessors in their projects. The first package, "fitdistrplus", gathers tools for choosing and fitting a parametric univariate distribution to a given dataset. The data may be continuous or discrete. Continuous data may be right-, left- or interval-censored as is frequently obtained with analytical methods, with the possibility of various censoring thresholds within the dataset. Bootstrap procedures then allow the assessor to evaluate and model the uncertainty around the parameters and to transfer this information into a quantitative risk assessment model. The second package, "mc2d", helps to build and study two dimensional (or second-order) Monte-Carlo simulations in which the estimation of variability and uncertainty in the risk estimates is separated. This package easily allows the transfer of separated variability and uncertainty along a chain of conditional mathematical and probabilistic models. The usefulness of these packages is illustrated through a risk assessment of hemolytic and uremic syndrome in children linked to the presence of Escherichia coli O157:H7 in ground beef. These R packages are freely available at the Comprehensive R Archive Network (cran.r-project.org). Copyright 2010 Elsevier B.V. All rights reserved.

Phylogenetic relationships among the North American cleomoids (Cleomaceae): a test of Iltis's reduction series.

PubMed

Riser, James P; Cardinal-McTeague, Warren M; Hall, Jocelyn C; Hahn, William J; Sytsma, Kenneth J; Roalson, Eric H

2013-10-01

A monophyletic group composed of five genera of the Cleomaceae represents an intriguing lineage with outstanding taxonomic and evolutionary questions. Generic boundaries are poorly defined, and historical hypotheses regarding the evolution of fruit type and phylogenetic relationships provide testable questions. This is the first detailed phylogenetic investigation of all 22 species in this group. We use this phylogenetic framework to assess generic monophyly and test Iltis's evolutionary "reduction series" hypothesis regarding phylogeny and fruit type/seed number. • Maximum likelihood and Bayesian analyses of four plastid intergenic spacer region sequences (rpl32-trnL, trnQ-rps16, ycf1-rps15, and psbA-trnH) and one nuclear (ITS) region were used to reconstruct phylogenetic relationships among the NA cleomoid species. Stochastic mapping and ancestral-state reconstruction were used to study the evolution of fruit type. • Both analyses recovered nearly identical phylogenies. Three of the currently recognized genera (Wislizenia, Carsonia, and Oxystylis) are monophyletic while two (Cleomella and Peritoma) are para- or polyphyletic. There was a single origin of the two-seeded schizocarp in the ancestor of the Oxystylis-Wislizenia clade and a secondary derivation of elongated capsule-type fruits in Peritoma from a truncated capsule state in Cleomella. • Our well-resolved phylogeny supports most of the current species circumscriptions but not current generic circumscriptions. Additionally, our results are inconsistent with Iltis's hypothesis of species with elongated many-seed fruits giving rise to species with truncated few-seeded fruits. Instead, we find support for the reversion to elongated multiseeded fruits from a truncate few-seeded ancestor in Peritoma.

Mammalian phylogenetic diversity-area relationships at a continental scale

PubMed Central

Mazel, Florent; Renaud, Julien; Guilhaumon, François; Mouillot, David; Gravel, Dominique; Thuiller, Wilfried

2015-01-01

In analogy to the species-area relationship (SAR), one of the few laws in Ecology, the phylogenetic diversity-area relationship (PDAR) describes the tendency of phylogenetic diversity (PD) to increase with area. Although investigating PDAR has the potential to unravel the underlying processes shaping assemblages across spatial scales and to predict PD loss through habitat reduction, it has been little investigated so far. Focusing on PD has noticeable advantages compared to species richness (SR) since PD also gives insights on processes such as speciation/extinction, assembly rules and ecosystem functioning. Here we investigate the universality and pervasiveness of the PDAR at continental scale using terrestrial mammals as study case. We define the relative robustness of PD (compared to SR) to habitat loss as the area between the standardized PDAR and standardized SAR (i.e. standardized by the diversity of the largest spatial window) divided by the area under the standardized SAR only. This metric quantifies the relative increase of PD robustness compared to SR robustness. We show that PD robustness is higher than SR robustness but that it varies among continents. We further use a null model approach to disentangle the relative effect of phylogenetic tree shape and non random spatial distribution of evolutionary history on the PDAR. We find that for most spatial scales and for all continents except Eurasia, PDARs are not different from expected by a model using only the observed SAR and the shape of the phylogenetic tree at continental scale. Interestingly, we detect a strong phylogenetic structure of the Eurasian PDAR that can be predicted by a model that specifically account for a finer biogeographical delineation of this continent. In conclusion, the relative robustness of PD to habitat loss compared to species richness is determined by the phylogenetic tree shape but also depends on the spatial structure of PD. PMID:26649401

Introduction of an automated user-independent quantitative volumetric magnetic resonance imaging breast density measurement system using the Dixon sequence: comparison with mammographic breast density assessment.

PubMed

Wengert, Georg Johannes; Helbich, Thomas H; Vogl, Wolf-Dieter; Baltzer, Pascal; Langs, Georg; Weber, Michael; Bogner, Wolfgang; Gruber, Stephan; Trattnig, Siegfried; Pinker, Katja

2015-02-01

The purposes of this study were to introduce and assess an automated user-independent quantitative volumetric (AUQV) breast density (BD) measurement system on the basis of magnetic resonance imaging (MRI) using the Dixon technique as well as to compare it with qualitative and quantitative mammographic (MG) BD measurements. Forty-three women with normal mammogram results (Breast Imaging Reporting and Data System 1) were included in this institutional review board-approved prospective study. All participants were subjected to BD assessment with MRI using the following sequence with the Dixon technique (echo time/echo time, 6 milliseconds/2.45 milliseconds/2.67 milliseconds; 1-mm isotropic; 3 minutes 38 seconds). To test the reproducibility, a second MRI after patient repositioning was performed. The AUQV magnetic resonance (MR) BD measurement system automatically calculated percentage (%) BD. The qualitative BD assessment was performed using the American College of Radiology Breast Imaging Reporting and Data System BD categories. Quantitative BD was estimated semiautomatically using the thresholding technique Cumulus4. Appropriate statistical tests were used to assess the agreement between the AUQV MR measurements and to compare them with qualitative and quantitative MG BD estimations. The AUQV MR BD measurements were successfully performed in all 43 women. There was a nearly perfect agreement of AUQV MR BD measurements between the 2 MR examinations for % BD (P < 0.001; intraclass correlation coefficient, 0.998) with no significant differences (P = 0.384). The AUQV MR BD measurements were significantly lower than quantitative and qualitative MG BD assessment (P < 0.001). The AUQV MR BD measurement system allows a fully automated, user-independent, robust, reproducible, as well as radiation- and compression-free volumetric quantitative BD assessment through different levels of BD. The AUQV MR BD measurements were significantly lower than the currently used qualitative

Assessing Student Status and Progress in Science Reasoning and Quantitative Literacy at a Very Large Undergraduate Institution

NASA Astrophysics Data System (ADS)

Donahue, Megan; Kaplan, J.; Ebert-May, D.; Ording, G.; Melfi, V.; Gilliland, D.; Sikorski, A.; Johnson, N.

2009-01-01

The typical large liberal-arts, tier-one research university requires all of its graduates to achieve some minimal standards of quantitative literacy and scientific reasoning skills. But how do we know what we are doing, as instructors and as a university, is working the way we think it should? At Michigan State University, a cross-disciplinary team of scientists, statisticians, and teacher education experts have begun a large-scale investigation about student mastery of quantitative and scientific skills, beginning with an assessment of 3,000 freshmen before they start their university careers. We will describe the process we used for developing and testing an instrument, for expanding faculty involvement and input on high-level goals. For this limited presentation, we will limit the discussion mainly to the scientific reasoning perspective, but we will briefly mention some intriguing observations regarding quantitative literacy as well. This project represents the beginning of long-term, longitudinal tracking of the progress of students at our institution. We will discuss preliminary results our 2008 assessment of incoming freshman at Michigan State, and where we plan to go from here. We acknowledge local support from the Quality Fund from the Office of the Provost at MSU. We also acknowledge the Center for Assessment at James Madison University and the NSF for their support at the very beginning of our work.

Quantitative assessment of 12-lead ECG synthesis using CAVIAR.

PubMed

Scherer, J A; Rubel, P; Fayn, J; Willems, J L

1992-01-01

The objective of this study is to assess the performance of patient-specific segment-specific (PSSS) synthesis in QRST complexes using CAVIAR, a new method of the serial comparison for electrocardiograms and vectorcardiograms. A collection of 250 multi-lead recordings from the Common Standards for Quantitative Electrocardiography (CSE) diagnostic pilot study is employed. QRS and ST-T segments are independently synthesized using the PSSS algorithm so that the mean-squared error between the original and estimated waveforms is minimized. CAVIAR compares the recorded and synthesized QRS and ST-T segments and calculates the mean-quadratic deviation as a measure of error. The results of this study indicate that estimated QRS complexes are good representatives of their recorded counterparts, and the integrity of the spatial information is maintained by the PSSS synthesis process. Analysis of the ST-T segments suggests that the deviations between recorded and synthesized waveforms are considerably greater than those associated with the QRS complexes. The poorer performance of the ST-T segments is attributed to magnitude normalization of the spatial loops, low-voltage passages, and noise interference. Using the mean-quadratic deviation and CAVIAR as methods of performance assessment, this study indicates that the PSSS-synthesis algorithm accurately maintains the signal information within the 12-lead electrocardiogram.

Co-Teaching in Middle School Classrooms: Quantitative Comparative Study of Special Education Student Assessment Performance

ERIC Educational Resources Information Center

Reese, De'borah Reese

2017-01-01

The purpose of this quantitative comparative study was to determine the existence or nonexistence of performance pass rate differences of special education middle school students on standardized assessments between pre and post co-teaching eras disaggregated by subject area and school. Co-teaching has altered classroom environments in many ways.…

Databases applicable to quantitative hazard/risk assessment-Towards a predictive systems toxicology

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

Waters, Michael; Jackson, Marcus

2008-11-15

The Workshop on The Power of Aggregated Toxicity Data addressed the requirement for distributed databases to support quantitative hazard and risk assessment. The authors have conceived and constructed with federal support several databases that have been used in hazard identification and risk assessment. The first of these databases, the EPA Gene-Tox Database was developed for the EPA Office of Toxic Substances by the Oak Ridge National Laboratory, and is currently hosted by the National Library of Medicine. This public resource is based on the collaborative evaluation, by government, academia, and industry, of short-term tests for the detection of mutagens andmore » presumptive carcinogens. The two-phased evaluation process resulted in more than 50 peer-reviewed publications on test system performance and a qualitative database on thousands of chemicals. Subsequently, the graphic and quantitative EPA/IARC Genetic Activity Profile (GAP) Database was developed in collaboration with the International Agency for Research on Cancer (IARC). A chemical database driven by consideration of the lowest effective dose, GAP has served IARC for many years in support of hazard classification of potential human carcinogens. The Toxicological Activity Profile (TAP) prototype database was patterned after GAP and utilized acute, subchronic, and chronic data from the Office of Air Quality Planning and Standards. TAP demonstrated the flexibility of the GAP format for air toxics, water pollutants and other environmental agents. The GAP format was also applied to developmental toxicants and was modified to represent quantitative results from the rodent carcinogen bioassay. More recently, the authors have constructed: 1) the NIEHS Genetic Alterations in Cancer (GAC) Database which quantifies specific mutations found in cancers induced by environmental agents, and 2) the NIEHS Chemical Effects in Biological Systems (CEBS) Knowledgebase that integrates genomic and other biological data

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.

High school students' learning and perceptions of phylogenetics of flowering plants.

PubMed

Bokor, Julie R; Landis, Jacob B; Crippen, Kent J

2014-01-01

Basic phylogenetics and associated "tree thinking" are often minimized or excluded in formal school curricula. Informal settings provide an opportunity to extend the K-12 school curriculum, introducing learners to new ideas, piquing interest in science, and fostering scientific literacy. Similarly, university researchers participating in science, technology, engineering, and mathematics (STEM) outreach activities increase awareness of college and career options and highlight interdisciplinary fields of science research and augment the science curriculum. To aid in this effort, we designed a 6-h module in which students utilized 12 flowering plant species to generate morphological and molecular phylogenies using biological techniques and bioinformatics tools. The phylogenetics module was implemented with 83 high school students during a weeklong university STEM immersion program and aimed to increase student understanding of phylogenetics and coevolution of plants and pollinators. Student response reflected positive engagement and learning gains as evidenced through content assessments, program evaluation surveys, and program artifacts. We present the results of the first year of implementation and discuss modifications for future use in our immersion programs as well as in multiple course settings at the high school and undergraduate levels. © 2014 J. R. Bokor et al. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Phylogenetic conservatism and trait correlates of spring phenological responses to climate change in northeast China.

PubMed

Du, Yanjun; Chen, Jingru; Willis, Charles G; Zhou, Zhiqiang; Liu, Tong; Dai, Wujun; Zhao, Yuan; Ma, Keping

2017-09-01

Climate change has resulted in major changes in plant phenology across the globe that includes leaf-out date and flowering time. The ability of species to respond to climate change, in part, depends on their response to climate as a phenological cue in general. Species that are not phenologically responsive may suffer in the face of continued climate change. Comparative studies of phenology have found phylogeny to be a reliable predictor of mean leaf-out date and flowering time at both the local and global scales. This is less true for flowering time response (i.e., the correlation between phenological timing and climate factors), while no study to date has explored whether the response of leaf-out date to climate factors exhibits phylogenetic signal. We used a 52-year observational phenological dataset for 52 woody species from the Forest Botanical Garden of Heilongjiang Province, China, to test phylogenetic signal in leaf-out date and flowering time, as well as, the response of these two phenological traits to both temperature and winter precipitation. Leaf-out date and flowering time were significantly responsive to temperature for most species, advancing, on average, 3.11 and 2.87 day/°C, respectively. Both leaf-out and flowering, and their responses to temperature exhibited significant phylogenetic signals. The response of leaf-out date to precipitation exhibited no phylogenetic signal, while flowering time response to precipitation did. Native species tended to have a weaker flowering response to temperature than non-native species. Earlier leaf-out species tended to have a greater response to winter precipitation. This study is the first to assess phylogenetic signal of leaf-out response to climate change, which suggests, that climate change has the potential to shape the plant communities, not only through flowering sensitivity, but also through leaf-out sensitivity.

Phylogenetic relationships among Maloideae species

USDA-ARS?s Scientific Manuscript database

The Maloideae is a highly diverse sub-family of the Rosaceae containing several agronomically important species (Malus sp. and Pyrus sp.) and their wild relatives. Previous phylogenetic work within the group has revealed extensive intergeneric hybridization and polyploidization. In order to develop...

Assessment of Intervertebral Disc Degeneration Based on Quantitative MRI Analysis: an in vivo study

PubMed Central

Grunert, Peter; Hudson, Katherine D.; Macielak, Michael R.; Aronowitz, Eric; Borde, Brandon H.; Alimi, Marjan; Njoku, Innocent; Ballon, Douglas; Tsiouris, Apostolos John; Bonassar, Lawrence J.; Härtl, Roger

2015-01-01

Study design Animal experimental study Objective To evaluate a novel quantitative imaging technique for assessing disc degeneration. Summary of Background Data T2-relaxation time (T2-RT) measurements have been used to quantitatively assess disc degeneration. T2 values correlate with the water content of inter vertebral disc tissue and thereby allow for the indirect measurement of nucleus pulposus (NP) hydration. Methods We developed an algorithm to subtract out MRI voxels not representing NP tissue based on T2-RT values. Filtered NP voxels were used to measure nuclear size by their amount and nuclear hydration by their mean T2-RT. This technique was applied to 24 rat-tail intervertebral discs’ (IVDs), which had been punctured with an 18-gauge needle according to different techniques to induce varying degrees of degeneration. NP voxel count and average T2-RT were used as parameters to assess the degeneration process at 1 and 3 months post puncture. NP voxel counts were evaluated against X-ray disc height measurements and qualitative MRI studies based on the Pfirrmann grading system. Tails were collected for histology to correlate NP voxel counts to histological disc degeneration grades and to NP cross-sectional area measurements. Results NP voxel count measurements showed strong correlations to qualitative MRI analyses (R2=0.79, p<0.0001), histological degeneration grades (R2=0.902, p<0.0001) and histological NP cross-sectional area measurements (R2=0.887, p<0.0001). In contrast to NP voxel counts, the mean T2-RT for each punctured group remained constant between months 1 and 3. The mean T2-RTs for the punctured groups did not show a statistically significant difference from those of healthy IVDs (63.55ms ±5.88ms month 1 and 62.61ms ±5.02ms) at either time point. Conclusion The NP voxel count proved to be a valid parameter to quantitatively assess disc degeneration in a needle puncture model. The mean NP T2-RT does not change significantly in needle

Cultural studies coupled with DNA based sequence analyses and its implication on pigmentation as a phylogenetic marker in Pestalotiopsis taxonomy.

PubMed

Liu, Ai-Rong; Chen, Shuang-Chen; Wu, Shang-Ying; Xu, Tong; Guo, Liang-Dong; Jeewon, Rajesh; Wei, Ji-Guang

2010-11-01

Previous phylogenetic studies based on DNA sequence data have partially resolved taxonomic relationships among Pestalotiopsis species. There are still some morphological characters whose phylogenetic significance have not been assessed properly due to limited taxon sampling, in particular the degree of pigmentation of median cells. In this study, the stability of pigmentation of median cells of conidia in Pestalotiopsis species was evaluated in subculture, and a molecular phylogenetic analysis was conducted on 45 strains belonging to 26 species in order to reappraise the pigmentation of median cells for its significance in the taxonomy of Pestalotiopsis. Phylogenetic relationships were inferred from nucleotide sequences in ITS regions (ITS1, 5.8S and ITS2) and β-tubulin 2 gene (tub2). The results showed that pigmentation of median cells was stable and it could be a key character in the taxonomy of Pestalotiopsis species. Instead of "concolorous" and "versicolor" proposed by Steyeart (1949), "brown to olivaceous" and "umber to fuliginous" are described and proposed in this paper. Copyright © 2010. Published by Elsevier Inc.

Keeping All the PIECES: Phylogenetically Informed Ex Situ Conservation of Endangered Species.

PubMed

Larkin, Daniel J; Jacobi, Sarah K; Hipp, Andrew L; Kramer, Andrea T

2016-01-01

Ex situ conservation in germplasm and living collections is a major focus of global plant conservation strategies. Prioritizing species for ex situ collection is a necessary component of this effort for which sound strategies are needed. Phylogenetic considerations can play an important role in prioritization. Collections that are more phylogenetically diverse are likely to encompass more ecological and trait variation, and thus provide stronger conservation insurance and richer resources for future restoration efforts. However, phylogenetic criteria need to be weighed against other, potentially competing objectives. We used ex situ collection and threat rank data for North American angiosperms to investigate gaps in ex situ coverage and phylogenetic diversity of collections and to develop a flexible framework for prioritizing species across multiple objectives. We found that ex situ coverage of 18,766 North American angiosperm taxa was low with respect to the most vulnerable taxa: just 43% of vulnerable to critically imperiled taxa were in ex situ collections, far short of a year-2020 goal of 75%. In addition, species held in ex situ collections were phylogenetically clustered (P < 0.001), i.e., collections comprised less phylogenetic diversity than would be expected had species been drawn at random. These patterns support incorporating phylogenetic considerations into ex situ prioritization in a manner balanced with other criteria, such as vulnerability. To meet this need, we present the 'PIECES' index (Phylogenetically Informed Ex situ Conservation of Endangered Species). PIECES integrates phylogenetic considerations into a flexible framework for prioritizing species across competing objectives using multi-criteria decision analysis. Applying PIECES to prioritizing ex situ conservation of North American angiosperms, we show strong return on investment across multiple objectives, some of which are negatively correlated with each other. A spreadsheet

Keeping All the PIECES: Phylogenetically Informed Ex Situ Conservation of Endangered Species

PubMed Central

Larkin, Daniel J.; Jacobi, Sarah K.; Hipp, Andrew L.; Kramer, Andrea T.

2016-01-01

Ex situ conservation in germplasm and living collections is a major focus of global plant conservation strategies. Prioritizing species for ex situ collection is a necessary component of this effort for which sound strategies are needed. Phylogenetic considerations can play an important role in prioritization. Collections that are more phylogenetically diverse are likely to encompass more ecological and trait variation, and thus provide stronger conservation insurance and richer resources for future restoration efforts. However, phylogenetic criteria need to be weighed against other, potentially competing objectives. We used ex situ collection and threat rank data for North American angiosperms to investigate gaps in ex situ coverage and phylogenetic diversity of collections and to develop a flexible framework for prioritizing species across multiple objectives. We found that ex situ coverage of 18,766 North American angiosperm taxa was low with respect to the most vulnerable taxa: just 43% of vulnerable to critically imperiled taxa were in ex situ collections, far short of a year-2020 goal of 75%. In addition, species held in ex situ collections were phylogenetically clustered (P < 0.001), i.e., collections comprised less phylogenetic diversity than would be expected had species been drawn at random. These patterns support incorporating phylogenetic considerations into ex situ prioritization in a manner balanced with other criteria, such as vulnerability. To meet this need, we present the ‘PIECES’ index (Phylogenetically Informed Ex situ Conservation of Endangered Species). PIECES integrates phylogenetic considerations into a flexible framework for prioritizing species across competing objectives using multi-criteria decision analysis. Applying PIECES to prioritizing ex situ conservation of North American angiosperms, we show strong return on investment across multiple objectives, some of which are negatively correlated with each other. A spreadsheet

Phylogenetic versus functional signals in the evolution of form-function relationships in terrestrial vision.

PubMed

Motani, Ryosuke; Schmitz, Lars

2011-08-01

Phylogeny is deeply pertinent to evolutionary studies. Traits that perform a body function are expected to be strongly influenced by physical "requirements" of the function. We investigated if such traits exhibit phylogenetic signals, and, if so, how phylogenetic noises bias quantification of form-function relationships. A form-function system that is strongly influenced by physics, namely the relationship between eye morphology and visual optics in amniotes, was used. We quantified the correlation between form (i.e., eye morphology) and function (i.e., ocular optics) while varying the level of phylogenetic bias removal through adjusting Pagel's λ. Ocular soft-tissue dimensions exhibited the highest correlation with ocular optics when 1% of phylogenetic bias expected from Brownian motion was removed (i.e., λ= 0.01); the value for hard-tissue data were 8%. A small degree of phylogenetic bias therefore exists in morphology despite of the stringent functional constraints. We also devised a phylogenetically informed discriminant analysis and recorded the effects of phylogenetic bias on this method using the same data. Use of proper λ values during phylogenetic bias removal improved misidentification rates in resulting classifications when prior probabilities were assumed to be equal. Even a small degree of phylogenetic bias affected the classification resulting from phylogenetically informed discriminant analysis. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Protocol for Standardizing High-to-Moderate Abundance Protein Biomarker Assessments Through an MRM-with-Standard-Peptides Quantitative Approach.

PubMed

Percy, Andrew J; Yang, Juncong; Chambers, Andrew G; Mohammed, Yassene; Miliotis, Tasso; Borchers, Christoph H

2016-01-01

Quantitative mass spectrometry (MS)-based approaches are emerging as a core technology for addressing health-related queries in systems biology and in the biomedical and clinical fields. In several 'omics disciplines (proteomics included), an approach centered on selected or multiple reaction monitoring (SRM or MRM)-MS with stable isotope-labeled standards (SIS), at the protein or peptide level, has emerged as the most precise technique for quantifying and screening putative analytes in biological samples. To enable the widespread use of MRM-based protein quantitation for disease biomarker assessment studies and its ultimate acceptance for clinical analysis, the technique must be standardized to facilitate precise and accurate protein quantitation. To that end, we have developed a number of kits for assessing method/platform performance, as well as for screening proposed candidate protein biomarkers in various human biofluids. Collectively, these kits utilize a bottom-up LC-MS methodology with SIS peptides as internal standards and quantify proteins using regression analysis of standard curves. This chapter details the methodology used to quantify 192 plasma proteins of high-to-moderate abundance (covers a 6 order of magnitude range from 31 mg/mL for albumin to 18 ng/mL for peroxidredoxin-2), and a 21-protein subset thereof. We also describe the application of this method to patient samples for biomarker discovery and verification studies. Additionally, we introduce our recently developed Qualis-SIS software, which is used to expedite the analysis and assessment of protein quantitation data in control and patient samples.

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data.

PubMed

Lee, Tae-Ho; Guo, Hui; Wang, Xiyin; Kim, Changsoo; Paterson, Andrew H

2014-02-26

Phylogenetic trees are widely used for genetic and evolutionary studies in various organisms. Advanced sequencing technology has dramatically enriched data available for constructing phylogenetic trees based on single nucleotide polymorphisms (SNPs). However, massive SNP data makes it difficult to perform reliable analysis, and there has been no ready-to-use pipeline to generate phylogenetic trees from these data. We developed a new pipeline, SNPhylo, to construct phylogenetic trees based on large SNP datasets. The pipeline may enable users to construct a phylogenetic tree from three representative SNP data file formats. In addition, in order to increase reliability of a tree, the pipeline has steps such as removing low quality data and considering linkage disequilibrium. A maximum likelihood method for the inference of phylogeny is also adopted in generation of a tree in our pipeline. Using SNPhylo, users can easily produce a reliable phylogenetic tree from a large SNP data file. Thus, this pipeline can help a researcher focus more on interpretation of the results of analysis of voluminous data sets, rather than manipulations necessary to accomplish the analysis.

Quantitative risk assessment of durable glass fibers.

PubMed

Fayerweather, William E; Eastes, Walter; Cereghini, Francesco; Hadley, John G

2002-06-01

This article presents a quantitative risk assessment for the theoretical lifetime cancer risk from the manufacture and use of relatively durable synthetic glass fibers. More specifically, we estimate levels of exposure to respirable fibers or fiberlike structures of E-glass and C-glass that, assuming a working lifetime exposure, pose a theoretical lifetime cancer risk of not more than 1 per 100,000. For comparability with other risk assessments we define these levels as nonsignificant exposures. Nonsignificant exposure levels are estimated from (a) the Institute of Occupational Medicine (IOM) chronic rat inhalation bioassay of durable E-glass microfibers, and (b) the Research Consulting Company (RCC) chronic inhalation bioassay of durable refractory ceramic fibers (RCF). Best estimates of nonsignificant E-glass exposure exceed 0.05-0.13 fibers (or shards) per cubic centimeter (cm3) when calculated from the multistage nonthreshold model. Best estimates of nonsignificant C-glass exposure exceed 0.27-0.6 fibers/cm3. Estimates of nonsignificant exposure increase markedly for E- and C-glass when non-linear models are applied and rapidly exceed 1 fiber/cm3. Controlling durable fiber exposures to an 8-h time-weighted average of 0.05 fibers/cm3 will assure that the additional theoretical lifetime risk from working lifetime exposures to these durable fibers or shards is kept below the 1 per 100,000 level. Measured airborne exposures to respirable, durable glass fibers (or shards) in glass fiber manufacturing and fabrication operations were compared with the nonsignificant exposure estimates described. Sampling results for B-sized respirable E-glass fibers at facilities that manufacture or fabricate small-diameter continuous-filament products, from those that manufacture respirable E-glass shards from PERG (process to efficiently recycle glass), from milled fiber operations, and from respirable C-glass shards from Flakeglass operations indicate very low median exposures of 0

Comparative Analysis of Begonia Plastid Genomes and Their Utility for Species-Level Phylogenetics

PubMed Central

Harrison, Nicola; Harrison, Richard J.

2016-01-01

Recent, rapid radiations make species-level phylogenetics difficult to resolve. We used a multiplexed, high-throughput sequencing approach to identify informative genomic regions to resolve phylogenetic relationships at low taxonomic levels in Begonia from a survey of sixteen species. A long-range PCR method was used to generate draft plastid genomes to provide a strong phylogenetic backbone, identify fast evolving regions and provide informative molecular markers for species-level phylogenetic studies in Begonia. PMID:27058864

Phylogenetic rooting using minimal ancestor deviation.

PubMed

Tria, Fernando Domingues Kümmel; Landan, Giddy; Dagan, Tal

2017-06-19

Ancestor-descendent relations play a cardinal role in evolutionary theory. Those relations are determined by rooting phylogenetic trees. Existing rooting methods are hampered by evolutionary rate heterogeneity or the unavailability of auxiliary phylogenetic information. Here we present a rooting approach, the minimal ancestor deviation (MAD) method, which accommodates heterotachy by using all pairwise topological and metric information in unrooted trees. We demonstrate the performance of the method, in comparison to existing rooting methods, by the analysis of phylogenies from eukaryotes and prokaryotes. MAD correctly recovers the known root of eukaryotes and uncovers evidence for the origin of cyanobacteria in the ocean. MAD is more robust and consistent than existing methods, provides measures of the root inference quality and is applicable to any tree with branch lengths.

Microbial Quality and Phylogenetic Diversity of Fresh Rainwater and Tropical Freshwater Reservoir

PubMed Central

Kaushik, Rajni; Balasubramanian, Rajasekhar; Dunstan, Hugh

2014-01-01

The impact of rainwater on the microbial quality of a tropical freshwater reservoir through atmospheric wet deposition of microorganisms was studied for the first time. Reservoir water samples were collected at four different sampling points and rainwater samples were collected in the immediate vicinity of the reservoir sites for a period of four months (January to April, 2012) during the Northeast monsoon period. Microbial quality of all fresh rainwater and reservoir water samples was assessed based on the counts for the microbial indicators: Escherichia coli (E. coli), total coliforms, and Enterococci along with total heterotrophic plate counts (HPC). The taxonomic richness and phylogenetic relationship of the freshwater reservoir with those of the fresh rainwater were also assessed using 16 S rRNA gene clone library construction. The levels of E. coli were found to be in the range of 0 CFU/100 mL – 75 CFU/100 mL for the rainwater, and were 10–94 CFU/100 mL for the reservoir water. The sampling sites that were influenced by highway traffic emissions showed the maximum counts for all the bacterial indicators assessed. There was no significant increase in the bacterial abundances observed in the reservoir water immediately following rainfall. However, the composite fresh rainwater and reservoir water samples exhibited broad phylogenetic diversity, including sequences representing Betaproteobacteria, Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Lentisphaerae and Bacteriodetes. Members of the Betaproteobacteria group were the most dominant in both fresh rainwater and reservoir water, followed by Alphaproteobacteria, Sphingobacteria, Actinobacteria and Gammaproteobacteria. PMID:24979573

Molecular identification and phylogenetic study of Demodex caprae.

PubMed

Zhao, Ya-E; Cheng, Juan; Hu, Li; Ma, Jun-Xian

2014-10-01

The DNA barcode has been widely used in species identification and phylogenetic analysis since 2003, but there have been no reports in Demodex. In this study, to obtain an appropriate DNA barcode for Demodex, molecular identification of Demodex caprae based on mitochondrial cox1 was conducted. Firstly, individual adults and eggs of D. caprae were obtained for genomic DNA (gDNA) extraction; Secondly, mitochondrial cox1 fragment was amplified, cloned, and sequenced; Thirdly, cox1 fragments of D. caprae were aligned with those of other Demodex retrieved from GenBank; Finally, the intra- and inter-specific divergences were computed and the phylogenetic trees were reconstructed to analyze phylogenetic relationship in Demodex. Results obtained from seven 429-bp fragments of D. caprae showed that sequence identities were above 99.1% among three adults and four eggs. The intraspecific divergences in D. caprae, Demodex folliculorum, Demodex brevis, and Demodex canis were 0.0-0.9, 0.5-0.9, 0.0-0.2, and 0.0-0.5%, respectively, while the interspecific divergences between D. caprae and D. folliculorum, D. canis, and D. brevis were 20.3-20.9, 21.8-23.0, and 25.0-25.3, respectively. The interspecific divergences were 10 times higher than intraspecific ones, indicating considerable barcoding gap. Furthermore, the phylogenetic trees showed that four Demodex species gathered separately, representing independent species; and Demodex folliculorum gathered with canine Demodex, D. caprae, and D. brevis in sequence. In conclusion, the selected 429-bp mitochondrial cox1 gene is an appropriate DNA barcode for molecular classification, identification, and phylogenetic analysis of Demodex. D. caprae is an independent species and D. folliculorum is closer to D. canis than to D. caprae or D. brevis.

Student Interpretations of Phylogenetic Trees in an Introductory Biology Course

ERIC Educational Resources Information Center

Dees, Jonathan; Momsen, Jennifer L.; Niemi, Jarad; Montplaisir, Lisa

2014-01-01

Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa…

Residual Isocyanates in Medical Devices and Products: A Qualitative and Quantitative Assessment

PubMed Central

Franklin, Gillian; Harari, Homero; Ahsan, Samavi; Bello, Dhimiter; Sterling, David A.; Nedrelow, Jonathan; Raynaud, Scott; Biswas, Swati; Liu, Youcheng

2016-01-01

We conducted a pilot qualitative and quantitative assessment of residual isocyanates and their potential initial exposures in neonates, as little is known about their contact effect. After a neonatal intensive care unit (NICU) stockroom inventory, polyurethane (PU) and PU foam (PUF) devices and products were qualitatively evaluated for residual isocyanates using Surface SWYPE™. Those containing isocyanates were quantitatively tested for methylene diphenyl diisocyanate (MDI) species, using UPLC-UV-MS/MS method. Ten of 37 products and devices tested, indicated both free and bound residual surface isocyanates; PU/PUF pieces contained aromatic isocyanates; one product contained aliphatic isocyanates. Overall, quantified mean MDI concentrations were low (4,4′-MDI = 0.52 to 140.1 pg/mg) and (2,4′-MDI = 0.01 to 4.48 pg/mg). The 4,4′-MDI species had the highest measured concentration (280 pg/mg). Commonly used medical devices/products contain low, but measurable concentrations of residual isocyanates. Quantifying other isocyanate species and neonatal skin exposure to isocyanates from these devices and products requires further investigation. PMID:27773989

Monitoring and quantitative assessment of tumor burden using in vivo bioluminescence imaging

NASA Astrophysics Data System (ADS)

Chen, Chia-Chi; Hwang, Jeng-Jong; Ting, Gann; Tseng, Yun-Long; Wang, Shyh-Jen; Whang-Peng, Jaqueline

2007-02-01

In vivo bioluminescence imaging (BLI) is a sensitive imaging modality that is rapid and accessible, and may comprise an ideal tool for evaluating tumor growth. In this study, the kinetic of tumor growth has been assessed in C26 colon carcinoma bearing BALB/c mouse model. The ability of BLI to noninvasively quantitate the growth of subcutaneous tumors transplanted with C26 cells genetically engineered to stably express firefly luciferase and herpes simplex virus type-1 thymidine kinase (C26/ tk-luc). A good correlation ( R2=0.998) of photon emission to the cell number was found in vitro. Tumor burden and tumor volume were monitored in vivo over time by quantitation of photon emission using Xenogen IVIS 50 and standard external caliper measurement, respectively. At various time intervals, tumor-bearing mice were imaged to determine the correlation of in vivo BLI to tumor volume. However, a correlation of BLI to tumor volume was observed when tumor volume was smaller than 1000 mm 3 ( R2=0.907). γ Scintigraphy combined with [ 131I]FIAU was another imaging modality used for verifying the previous results. In conclusion, this study showed that bioluminescence imaging is a powerful and quantitative tool for the direct assay to monitor tumor growth in vivo. The dual reporter genes transfected tumor-bearing animal model can be applied in the evaluation of the efficacy of new developed anti-cancer drugs.

A new algorithm to construct phylogenetic networks from trees.

PubMed

Wang, J

2014-03-06

Developing appropriate methods for constructing phylogenetic networks from tree sets is an important problem, and much research is currently being undertaken in this area. BIMLR is an algorithm that constructs phylogenetic networks from tree sets. The algorithm can construct a much simpler network than other available methods. Here, we introduce an improved version of the BIMLR algorithm, QuickCass. QuickCass changes the selection strategy of the labels of leaves below the reticulate nodes, i.e., the nodes with an indegree of at least 2 in BIMLR. We show that QuickCass can construct simpler phylogenetic networks than BIMLR. Furthermore, we show that QuickCass is a polynomial-time algorithm when the output network that is constructed by QuickCass is binary.

Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily.

PubMed

Lakshmi, Balasubramanian; Mishra, Madhulika; Srinivasan, Narayanaswamy; Archunan, Govindaraju

2015-01-01

Lipocalins constitute a superfamily of extracellular proteins that are found in all three kingdoms of life. Although very divergent in their sequences and functions, they show remarkable similarity in 3-D structures. Lipocalins bind and transport small hydrophobic molecules. Earlier sequence-based phylogenetic studies of lipocalins highlighted that they have a long evolutionary history. However the molecular and structural basis of their functional diversity is not completely understood. The main objective of the present study is to understand functional diversity of the lipocalins using a structure-based phylogenetic approach. The present study with 39 protein domains from the lipocalin superfamily suggests that the clusters of lipocalins obtained by structure-based phylogeny correspond well with the functional diversity. The detailed analysis on each of the clusters and sub-clusters reveals that the 39 lipocalin domains cluster based on their mode of ligand binding though the clustering was performed on the basis of gross domain structure. The outliers in the phylogenetic tree are often from single member families. Also structure-based phylogenetic approach has provided pointers to assign putative function for the domains of unknown function in lipocalin family. The approach employed in the present study can be used in the future for the functional identification of new lipocalin proteins and may be extended to other protein families where members show poor sequence similarity but high structural similarity.

Phylogenetic trees in bioinformatics

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

Burr, Tom L

2008-01-01

Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding themore » best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.« less

Quantitative Microbial Risk Assessment Tutorial Installation of Software for Watershed Modeling in Support of QMRA - Updated 2017

EPA Science Inventory

This tutorial provides instructions for accessing, retrieving, and downloading the following software to install on a host computer in support of Quantitative Microbial Risk Assessment (QMRA) modeling: • QMRA Installation • SDMProjectBuilder (which includes the Microbial ...

Hal: an automated pipeline for phylogenetic analyses of genomic data.

PubMed

Robbertse, Barbara; Yoder, Ryan J; Boyd, Alex; Reeves, John; Spatafora, Joseph W

2011-02-07

The rapid increase in genomic and genome-scale data is resulting in unprecedented levels of discrete sequence data available for phylogenetic analyses. Major analytical impasses exist, however, prior to analyzing these data with existing phylogenetic software. Obstacles include the management of large data sets without standardized naming conventions, identification and filtering of orthologous clusters of proteins or genes, and the assembly of alignments of orthologous sequence data into individual and concatenated super alignments. Here we report the production of an automated pipeline, Hal that produces multiple alignments and trees from genomic data. These alignments can be produced by a choice of four alignment programs and analyzed by a variety of phylogenetic programs. In short, the Hal pipeline connects the programs BLASTP, MCL, user specified alignment programs, GBlocks, ProtTest and user specified phylogenetic programs to produce species trees. The script is available at sourceforge (http://sourceforge.net/projects/bio-hal/). The results from an example analysis of Kingdom Fungi are briefly discussed.

Three-Dimensional Photography for Quantitative Assessment of Penile Volume-Loss Deformities in Peyronie's Disease.

PubMed

Margolin, Ezra J; Mlynarczyk, Carrie M; Mulhall, John P; Stember, Doron S; Stahl, Peter J

2017-06-01

Non-curvature penile deformities are prevalent and bothersome manifestations of Peyronie's disease (PD), but the quantitative metrics that are currently used to describe these deformities are inadequate and non-standardized, presenting a barrier to clinical research and patient care. To introduce erect penile volume (EPV) and percentage of erect penile volume loss (percent EPVL) as novel metrics that provide detailed quantitative information about non-curvature penile deformities and to study the feasibility and reliability of three-dimensional (3D) photography for measurement of quantitative penile parameters. We constructed seven penis models simulating deformities found in PD. The 3D photographs of each model were captured in triplicate by four observers using a 3D camera. Computer software was used to generate automated measurements of EPV, percent EPVL, penile length, minimum circumference, maximum circumference, and angle of curvature. The automated measurements were statistically compared with measurements obtained using water-displacement experiments, a tape measure, and a goniometer. Accuracy of 3D photography for average measurements of all parameters compared with manual measurements; inter-test, intra-observer, and inter-observer reliabilities of EPV and percent EPVL measurements as assessed by the intraclass correlation coefficient. The 3D images were captured in a median of 52 seconds (interquartile range = 45-61). On average, 3D photography was accurate to within 0.3% for measurement of penile length. It overestimated maximum and minimum circumferences by averages of 4.2% and 1.6%, respectively; overestimated EPV by an average of 7.1%; and underestimated percent EPVL by an average of 1.9%. All inter-test, inter-observer, and intra-observer intraclass correlation coefficients for EPV and percent EPVL measurements were greater than 0.75, reflective of excellent methodologic reliability. By providing highly descriptive and reliable measurements of

Phyx: phylogenetic tools for unix.

PubMed

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

2017-06-15

The ease with which phylogenomic data can be generated has drastically escalated the computational burden for even routine phylogenetic investigations. To address this, we present phyx : a collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects (alignments, trees and MCMC logs). Modelled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams that can be piped to quickly and easily form complex analytical pipelines. Because of the stream-centric paradigm, memory requirements are minimized (often only a single tree or sequence in memory at any instance), and hence phyx is capable of efficiently processing very large datasets. phyx runs on POSIX-compliant operating systems. Source code, installation instructions, documentation and example files are freely available under the GNU General Public License at https://github.com/FePhyFoFum/phyx. eebsmith@umich.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Phyx: phylogenetic tools for unix

PubMed Central

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

2017-01-01

Abstract Summary: The ease with which phylogenomic data can be generated has drastically escalated the computational burden for even routine phylogenetic investigations. To address this, we present phyx: a collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects (alignments, trees and MCMC logs). Modelled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams that can be piped to quickly and easily form complex analytical pipelines. Because of the stream-centric paradigm, memory requirements are minimized (often only a single tree or sequence in memory at any instance), and hence phyx is capable of efficiently processing very large datasets. Availability and Implementation: phyx runs on POSIX-compliant operating systems. Source code, installation instructions, documentation and example files are freely available under the GNU General Public License at https://github.com/FePhyFoFum/phyx Contact: eebsmith@umich.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28174903

Assessment of Overlap of Phylogenetic Transmission Clusters and Communities in Simple Sexual Contact Networks: Applications to HIV-1

PubMed Central

Villandre, Luc; Günthard, Huldrych F.; Kouyos, Roger; Stadler, Tanja

2016-01-01

Background Transmission patterns of sexually-transmitted infections (STIs) could relate to the structure of the underlying sexual contact network, whose features are therefore of interest to clinicians. Conventionally, we represent sexual contacts in a population with a graph, that can reveal the existence of communities. Phylogenetic methods help infer the history of an epidemic and incidentally, may help detecting communities. In particular, phylogenetic analyses of HIV-1 epidemics among men who have sex with men (MSM) have revealed the existence of large transmission clusters, possibly resulting from within-community transmissions. Past studies have explored the association between contact networks and phylogenies, including transmission clusters, producing conflicting conclusions about whether network features significantly affect observed transmission history. As far as we know however, none of them thoroughly investigated the role of communities, defined with respect to the network graph, in the observation of clusters. Methods The present study investigates, through simulations, community detection from phylogenies. We simulate a large number of epidemics over both unweighted and weighted, undirected random interconnected-islands networks, with islands corresponding to communities. We use weighting to modulate distance between islands. We translate each epidemic into a phylogeny, that lets us partition our samples of infected subjects into transmission clusters, based on several common definitions from the literature. We measure similarity between subjects’ island membership indices and transmission cluster membership indices with the adjusted Rand index. Results and Conclusion Analyses reveal modest mean correspondence between communities in graphs and phylogenetic transmission clusters. We conclude that common methods often have limited success in detecting contact network communities from phylogenies. The rarely-fulfilled requirement that network

Coalescent methods for estimating phylogenetic trees.

PubMed

Liu, Liang; Yu, Lili; Kubatko, Laura; Pearl, Dennis K; Edwards, Scott V

2009-10-01

We review recent models to estimate phylogenetic trees under the multispecies coalescent. Although the distinction between gene trees and species trees has come to the fore of phylogenetics, only recently have methods been developed that explicitly estimate species trees. Of the several factors that can cause gene tree heterogeneity and discordance with the species tree, deep coalescence due to random genetic drift in branches of the species tree has been modeled most thoroughly. Bayesian approaches to estimating species trees utilizes two likelihood functions, one of which has been widely used in traditional phylogenetics and involves the model of nucleotide substitution, and the second of which is less familiar to phylogeneticists and involves the probability distribution of gene trees given a species tree. Other recent parametric and nonparametric methods for estimating species trees involve parsimony criteria, summary statistics, supertree and consensus methods. Species tree approaches are an appropriate goal for systematics, appear to work well in some cases where concatenation can be misleading, and suggest that sampling many independent loci will be paramount. Such methods can also be challenging to implement because of the complexity of the models and computational time. In addition, further elaboration of the simplest of coalescent models will be required to incorporate commonly known issues such as deviation from the molecular clock, gene flow and other genetic forces.

Survey of Quantitative Research Metrics to Assess Pilot Performance in Upset Recovery

NASA Technical Reports Server (NTRS)

Le Vie, Lisa R.

2016-01-01

Accidents attributable to in-flight loss of control are the primary cause for fatal commercial jet accidents worldwide. The National Aeronautics and Space Administration (NASA) conducted a literature review to determine and identify the quantitative standards for assessing upset recovery performance. This review contains current recovery procedures for both military and commercial aviation and includes the metrics researchers use to assess aircraft recovery performance. Metrics include time to first input, recognition time and recovery time and whether that input was correct or incorrect. Other metrics included are: the state of the autopilot and autothrottle, control wheel/sidestick movement resulting in pitch and roll, and inputs to the throttle and rudder. In addition, airplane state measures, such as roll reversals, altitude loss/gain, maximum vertical speed, maximum/minimum air speed, maximum bank angle and maximum g loading are reviewed as well.

Phylogenetic impoverishment of Amazonian tree communities in an experimentally fragmented forest landscape.

PubMed

Santos, Bráulio A; Tabarelli, Marcelo; Melo, Felipe P L; Camargo, José L C; Andrade, Ana; Laurance, Susan G; Laurance, William F

2014-01-01

Amazonian rainforests sustain some of the richest tree communities on Earth, but their ecological and evolutionary responses to human threats remain poorly known. We used one of the largest experimental datasets currently available on tree dynamics in fragmented tropical forests and a recent phylogeny of angiosperms to test whether tree communities have lost phylogenetic diversity since their isolation about two decades previously. Our findings revealed an overall trend toward phylogenetic impoverishment across the experimentally fragmented landscape, irrespective of whether tree communities were in 1-ha, 10-ha, or 100-ha forest fragments, near forest edges, or in continuous forest. The magnitude of the phylogenetic diversity loss was low (<2% relative to before-fragmentation values) but widespread throughout the study landscape, occurring in 32 of 40 1-ha plots. Consistent with this loss in phylogenetic diversity, we observed a significant decrease of 50% in phylogenetic dispersion since forest isolation, irrespective of plot location. Analyses based on tree genera that have significantly increased (28 genera) or declined (31 genera) in abundance and basal area in the landscape revealed that increasing genera are more phylogenetically related than decreasing ones. Also, the loss of phylogenetic diversity was greater in tree communities where increasing genera proliferated and decreasing genera reduced their importance values, suggesting that this taxonomic replacement is partially underlying the phylogenetic impoverishment at the landscape scale. This finding has clear implications for the current debate about the role human-modified landscapes play in sustaining biodiversity persistence and key ecosystem services, such as carbon storage. Although the generalization of our findings to other fragmented tropical forests is uncertain, it could negatively affect ecosystem productivity and stability and have broader impacts on coevolved organisms.

Quantitative Microbial Risk Assessment and Infectious Disease Transmission Modeling of Waterborne Enteric Pathogens.

PubMed

Brouwer, Andrew F; Masters, Nina B; Eisenberg, Joseph N S

2018-04-20

Waterborne enteric pathogens remain a global health threat. Increasingly, quantitative microbial risk assessment (QMRA) and infectious disease transmission modeling (IDTM) are used to assess waterborne pathogen risks and evaluate mitigation. These modeling efforts, however, have largely been conducted independently for different purposes and in different settings. In this review, we examine the settings where each modeling strategy is employed. QMRA research has focused on food contamination and recreational water in high-income countries (HICs) and drinking water and wastewater in low- and middle-income countries (LMICs). IDTM research has focused on large outbreaks (predominately LMICs) and vaccine-preventable diseases (LMICs and HICs). Human ecology determines the niches that pathogens exploit, leading researchers to focus on different risk assessment research strategies in different settings. To enhance risk modeling, QMRA and IDTM approaches should be integrated to include dynamics of pathogens in the environment and pathogen transmission through populations.

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.

PubMed

Harris, J Kirk; Caporaso, J Gregory; Walker, Jeffrey J; Spear, John R; Gold, Nicholas J; Robertson, Charles E; Hugenholtz, Philip; Goodrich, Julia; McDonald, Daniel; Knights, Dan; Marshall, Paul; Tufo, Henry; Knight, Rob; Pace, Norman R

2013-01-01

The microbial mats of Guerrero Negro (GN), Baja California Sur, Mexico historically were considered a simple environment, dominated by cyanobacteria and sulfate-reducing bacteria. Culture-independent rRNA community profiling instead revealed these microbial mats as among the most phylogenetically diverse environments known. A preliminary molecular survey of the GN mat based on only ∼1500 small subunit rRNA gene sequences discovered several new phylum-level groups in the bacterial phylogenetic domain and many previously undetected lower-level taxa. We determined an additional ∼119,000 nearly full-length sequences and 28,000 >200 nucleotide 454 reads from a 10-layer depth profile of the GN mat. With this unprecedented coverage of long sequences from one environment, we confirm the mat is phylogenetically stratified, presumably corresponding to light and geochemical gradients throughout the depth of the mat. Previous shotgun metagenomic data from the same depth profile show the same stratified pattern and suggest that metagenome properties may be predictable from rRNA gene sequences. We verify previously identified novel lineages and identify new phylogenetic diversity at lower taxonomic levels, for example, thousands of operational taxonomic units at the family-genus levels differ considerably from known sequences. The new sequences populate parts of the bacterial phylogenetic tree that previously were poorly described, but indicate that any comprehensive survey of GN diversity has only begun. Finally, we show that taxonomic conclusions are generally congruent between Sanger and 454 sequencing technologies, with the taxonomic resolution achieved dependent on the abundance of reference sequences in the relevant region of the rRNA tree of life.

Dual phylogenetic origins of Nigerian lions (Panthera leo).

PubMed

Tende, Talatu; Bensch, Staffan; Ottosson, Ulf; Hansson, Bengt

2014-07-01

Lion fecal DNA extracts from four individuals each from Yankari Game Reserve and Kainji-Lake National Park (central northeast and west Nigeria, respectively) were Sanger-sequenced for the mitochondrial cytochrome b gene. The sequences were aligned against 61 lion reference sequences from other parts of Africa and India. The sequence data were analyzed further for the construction of phylogenetic trees using the maximum-likelihood approach to depict phylogenetic patterns of distribution among sequences. Our results show that Nigerian lions grouped together with lions from West and Central Africa. At the smaller geographical scale, lions from Kainji-Lake National Park in western Nigeria grouped with lions from Benin (located west of Nigeria), whereas lions from Yankari Game Reserve in central northeastern Nigeria grouped with the lion populations in Cameroon (located east of Nigeria). The finding that the two remaining lion populations in Nigeria have different phylogenetic origins is an important aspect to consider in future decisions regarding management and conservation of rapidly shrinking lion populations in West Africa.

Treetrimmer: a method for phylogenetic dataset size reduction.

PubMed

Maruyama, Shinichiro; Eveleigh, Robert J M; Archibald, John M

2013-04-12

With rapid advances in genome sequencing and bioinformatics, it is now possible to generate phylogenetic trees containing thousands of operational taxonomic units (OTUs) from a wide range of organisms. However, use of rigorous tree-building methods on such large datasets is prohibitive and manual 'pruning' of sequence alignments is time consuming and raises concerns over reproducibility. There is a need for bioinformatic tools with which to objectively carry out such pruning procedures. Here we present 'TreeTrimmer', a bioinformatics procedure that removes unnecessary redundancy in large phylogenetic datasets, alleviating the size effect on more rigorous downstream analyses. The method identifies and removes user-defined 'redundant' sequences, e.g., orthologous sequences from closely related organisms and 'recently' evolved lineage-specific paralogs. Representative OTUs are retained for more rigorous re-analysis. TreeTrimmer reduces the OTU density of phylogenetic trees without sacrificing taxonomic diversity while retaining the original tree topology, thereby speeding up downstream computer-intensive analyses, e.g., Bayesian and maximum likelihood tree reconstructions, in a reproducible fashion.

Phylogenetic Diversity in the Macromolecular Composition of Microalgae

PubMed Central

Finkel, Zoe V.; Follows, Mick J.; Liefer, Justin D.; Brown, Chris M.; Benner, Ina; Irwin, Andrew J.

2016-01-01

The elemental stoichiometry of microalgae reflects their underlying macromolecular composition and influences competitive interactions among species and their role in the food web and biogeochemistry. Here we provide a new estimate of the macromolecular composition of microalgae using a hierarchical Bayesian analysis of data compiled from the literature. The median macromolecular composition of nutrient-sufficient exponentially growing microalgae is 32.2% protein, 17.3% lipid, 15.0% carbohydrate, 17.3% ash, 5.7% RNA, 1.1% chlorophyll-a and 1.0% DNA as percent dry weight. Our analysis identifies significant phylogenetic differences in macromolecular composition undetected by previous studies due to small sample sizes and the large inherent variability in macromolecular pools. The phylogenetic differences in macromolecular composition lead to variations in carbon-to-nitrogen ratios that are consistent with independent observations. These phylogenetic differences in macromolecular and elemental composition reflect adaptations in cellular architecture and biochemistry; specifically in the cell wall, the light harvesting apparatus, and storage pools. PMID:27228080

Quantitative cervical vertebral maturation assessment in adolescents with normal occlusion: a mixed longitudinal study.

PubMed

Chen, Li-Li; Xu, Tian-Min; Jiang, Jiu-Hui; Zhang, Xing-Zhong; Lin, Jiu-Xiang

2008-12-01

The purpose of this study was to establish a quantitative cervical vertebral maturation (CVM) system for adolescents with normal occlusion. Mixed longitudinal data were used. The subjects included 87 children and adolescents from 8 to 18 years old with normal occlusion (32 boys, 55 girls) selected from 901 candidates. Sequential lateral cephalograms and hand-wrist films were taken once a year for 6 years. The lateral cephalograms of all subjects were divided into 11 maturation groups according to the Fishman skeletal maturity indicators. The morphologic characteristics of the second, third, and fourth cervical vertebrae at 11 developmental stages were measured and analyzed. Three characteristic parameters (H4/W4, AH3/PH3, @2) were selected to determine the classification of CVM. With 3 morphologic variables, the quantitative CVM system including 4 maturational stages was established. An equation that can accurately estimate the maturation of the cervical vertebrae was established: CVM stage=-4.13+3.57xH4/W4+4.07xAH3/PH3+0.03x@2. The quantitative CVM method is an efficient, objective, and relatively simple approach to assess the level of skeletal maturation during adolescence.

Stratification of co-evolving genomic groups using ranked phylogenetic profiles

PubMed Central

Freilich, Shiri; Goldovsky, Leon; Gottlieb, Assaf; Blanc, Eric; Tsoka, Sophia; Ouzounis, Christos A

2009-01-01

Background Previous methods of detecting the taxonomic origins of arbitrary sequence collections, with a significant impact to genome analysis and in particular metagenomics, have primarily focused on compositional features of genomes. The evolutionary patterns of phylogenetic distribution of genes or proteins, represented by phylogenetic profiles, provide an alternative approach for the detection of taxonomic origins, but typically suffer from low accuracy. Herein, we present rank-BLAST, a novel approach for the assignment of protein sequences into genomic groups of the same taxonomic origin, based on the ranking order of phylogenetic profiles of target genes or proteins across the reference database. Results The rank-BLAST approach is validated by computing the phylogenetic profiles of all sequences for five distinct microbial species of varying degrees of phylogenetic proximity, against a reference database of 243 fully sequenced genomes. The approach - a combination of sequence searches, statistical estimation and clustering - analyses the degree of sequence divergence between sets of protein sequences and allows the classification of protein sequences according to the species of origin with high accuracy, allowing taxonomic classification of 64% of the proteins studied. In most cases, a main cluster is detected, representing the corresponding species. Secondary, functionally distinct and species-specific clusters exhibit different patterns of phylogenetic distribution, thus flagging gene groups of interest. Detailed analyses of such cases are provided as examples. Conclusion Our results indicate that the rank-BLAST approach can capture the taxonomic origins of sequence collections in an accurate and efficient manner. The approach can be useful both for the analysis of genome evolution and the detection of species groups in metagenomics samples. PMID:19860884

New substitution models for rooting phylogenetic trees.

PubMed

Williams, Tom A; Heaps, Sarah E; Cherlin, Svetlana; Nye, Tom M W; Boys, Richard J; Embley, T Martin

2015-09-26

The root of a phylogenetic tree is fundamental to its biological interpretation, but standard substitution models do not provide any information on its position. Here, we describe two recently developed models that relax the usual assumptions of stationarity and reversibility, thereby facilitating root inference without the need for an outgroup. We compare the performance of these models on a classic test case for phylogenetic methods, before considering two highly topical questions in evolutionary biology: the deep structure of the tree of life and the root of the archaeal radiation. We show that all three alignments contain meaningful rooting information that can be harnessed by these new models, thus complementing and extending previous work based on outgroup rooting. In particular, our analyses exclude the root of the tree of life from the eukaryotes or Archaea, placing it on the bacterial stem or within the Bacteria. They also exclude the root of the archaeal radiation from several major clades, consistent with analyses using other rooting methods. Overall, our results demonstrate the utility of non-reversible and non-stationary models for rooting phylogenetic trees, and identify areas where further progress can be made. © 2015 The Authors.

Phylogenetic Invariants for Metazoan Mitochondrial Genome Evolution.

PubMed

Sankoff; Blanchette

1998-01-01

The method of phylogenetic invariants was developed to apply to aligned sequence data generated, according to a stochastic substitution model, for N species related through an unknown phylogenetic tree. The invariants are functions of the probabilities of the observable N-tuples, which are identically zero, over all choices of branch length, for some trees. Evaluating the invariants associated with all possible trees, using observed N-tuple frequencies over all sequence positions, enables us to rapidly infer the generating tree. An aspect of evolution at the genomic level much studied recently is the rearrangements of gene order along the chromosome from one species to another. Instead of the substitutions responsible for sequence evolution, we examine the non-local processes responsible for genome rearrangements such as inversion of arbitrarily long segments of chromosomes. By treating the potential adjacency of each possible pair of genes as a position", an appropriate substitution" model can be recognized as governing the rearrangement process, and a probabilistically principled phylogenetic inference can be set up. We calculate the invariants for this process for N=5, and apply them to mitochondrial genome data from coelomate metazoans, showing how they resolve key aspects of branching order.

Phylogenetic analysis of TCE-dechlorinating consortia enriched on a variety of electron donors.

PubMed

Freeborn, Ryan A; West, Kimberlee A; Bhupathiraju, Vishvesh K; Chauhan, Sadhana; Rahm, Brian G; Richardson, Ruth E; Alvarez-Cohen, Lisa

2005-11-01

Two rapidly fermented electron donors, lactate and methanol, and two slowly fermented electron donors, propionate and butyrate, were selected for enrichment studies to evaluate the characteristics of anaerobic microbial consortia that reductively dechlorinate TCE to ethene. Each electron donor enrichment subculture demonstrated the ability to dechlorinate TCE to ethene through several serial transfers. Microbial community analyses based upon 16S rDNA, including terminal restriction fragment length polymorphism (T-RFLP) and clone library/sequencing, were performed to assess major changes in microbial community structure associated with electron donors capable of stimulating reductive dechlorination. Results demonstrated that five phylogenic subgroups or genera of bacteria were present in all consortia, including Dehalococcoides sp., low G+C Gram-positives (mostly Clostridium and Eubacterium sp.), Bacteroides sp., Citrobacter sp., and delta Proteobacteria (mostly Desulfovibrio sp.). Phylogenetic association indicates that only minor shifts in the microbial community structure occurred between the four alternate electron donor enrichments and the parent consortium. Inconsistent detection of Dehalococcoides spp. in clone libraries and T-RFLP of enrichment subcultures was resolved using quantitative polymerase chain reaction (Q-PCR). Q-PCR with primers specific to Dehalococcoides 16S rDNA resulted in positive detection of this species in all enrichments. Our results suggest that TCE-dechlorinating consortia can be stably maintained on a variety of electron donors and that quantities of Dehalococcoides cells detected with Dehalococcoides specific 16S rDNA primer/probe sets do not necessarily correlate well with solvent degradation rates.

Zebrafish Caudal Fin Angiogenesis Assay—Advanced Quantitative Assessment Including 3-Way Correlative Microscopy

PubMed Central

Correa Shokiche, Carlos; Schaad, Laura; Triet, Ramona; Jazwinska, Anna; Tschanz, Stefan A.; Djonov, Valentin

2016-01-01

Background Researchers evaluating angiomodulating compounds as a part of scientific projects or pre-clinical studies are often confronted with limitations of applied animal models. The rough and insufficient early-stage compound assessment without reliable quantification of the vascular response counts, at least partially, to the low transition rate to clinics. Objective To establish an advanced, rapid and cost-effective angiogenesis assay for the precise and sensitive assessment of angiomodulating compounds using zebrafish caudal fin regeneration. It should provide information regarding the angiogenic mechanisms involved and should include qualitative and quantitative data of drug effects in a non-biased and time-efficient way. Approach & Results Basic vascular parameters (total regenerated area, vascular projection area, contour length, vessel area density) were extracted from in vivo fluorescence microscopy images using a stereological approach. Skeletonization of the vasculature by our custom-made software Skelios provided additional parameters including “graph energy” and “distance to farthest node”. The latter gave important insights into the complexity, connectivity and maturation status of the regenerating vascular network. The employment of a reference point (vascular parameters prior amputation) is unique for the model and crucial for a proper assessment. Additionally, the assay provides exceptional possibilities for correlative microscopy by combining in vivo-imaging and morphological investigation of the area of interest. The 3-way correlative microscopy links the dynamic changes in vivo with their structural substrate at the subcellular level. Conclusions The improved zebrafish fin regeneration model with advanced quantitative analysis and optional 3-way correlative morphology is a promising in vivo angiogenesis assay, well-suitable for basic research and preclinical investigations. PMID:26950851

Web-Based Phylogenetic Assignment Tool for Analysis of Terminal Restriction Fragment Length Polymorphism Profiles of Microbial Communities

PubMed Central

Kent, Angela D.; Smith, Dan J.; Benson, Barbara J.; Triplett, Eric W.

2003-01-01

Culture-independent DNA fingerprints are commonly used to assess the diversity of a microbial community. However, relating species composition to community profiles produced by community fingerprint methods is not straightforward. Terminal restriction fragment length polymorphism (T-RFLP) is a community fingerprint method in which phylogenetic assignments may be inferred from the terminal restriction fragment (T-RF) sizes through the use of web-based resources that predict T-RF sizes for known bacteria. The process quickly becomes computationally intensive due to the need to analyze profiles produced by multiple restriction digests and the complexity of profiles generated by natural microbial communities. A web-based tool is described here that rapidly generates phylogenetic assignments from submitted community T-RFLP profiles based on a database of fragments produced by known 16S rRNA gene sequences. Users have the option of submitting a customized database generated from unpublished sequences or from a gene other than the 16S rRNA gene. This phylogenetic assignment tool allows users to employ T-RFLP to simultaneously analyze microbial community diversity and species composition. An analysis of the variability of bacterial species composition throughout the water column in a humic lake was carried out to demonstrate the functionality of the phylogenetic assignment tool. This method was validated by comparing the results generated by this program with results from a 16S rRNA gene clone library. PMID:14602639

Phylogenetic analysis of the true water bugs (Insecta: Hemiptera: Heteroptera: Nepomorpha): evidence from mitochondrial genomes

PubMed Central

Hua, Jimeng; Li, Ming; Dong, Pengzhi; Cui, Ying; Xie, Qiang; Bu, Wenjun