scholarly journals Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations

2018 ◽  
Vol 67 (5) ◽  
pp. 800-820 ◽  
Author(s):  
Paul Bastide ◽  
Claudia Solís-Lemus ◽  
Ricardo Kriebel ◽  
K William Sparks ◽  
Cécile Ané
Keyword(s):  
Phylogenetic Signal ◽  
Statistical Tests ◽  
Recursive Algorithm ◽  
Species Traits ◽  
Comparative Methods ◽  
Hybrid Vigor ◽  
Phylogenetic Networks ◽  
Phylogenetic Comparative Methods ◽  
Data Set ◽  
Phylogenetic Regression

Abstract The goal of phylogenetic comparative methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species’ traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel’s $\lambda$ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a data set of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.

scholarly journals Phylogenetic comparative methods on phylogenetic networks with reticulations

2017 ◽  
Author(s):  
Paul Bastide ◽  
Claudia Solís-Lemus ◽  
Ricardo Kriebel ◽  
K. William Sparks ◽  
Cécile Ané
Keyword(s):  
Phylogenetic Signal ◽  
Statistical Tests ◽  
Recursive Algorithm ◽  
Natural Extension ◽  
Weighted Average ◽  
Comparative Methods ◽  
Hybrid Vigor ◽  
Phylogenetic Networks ◽  
Phylogenetic Comparative Methods ◽  
Phylogenetic Regression

AbstractThe goal of Phylogenetic Comparative Methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species’ traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. One natural extension of the BM is to use a weighted average model for the trait of a hybrid, at a reticulation point. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel’s λ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts, and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios, and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a dataset of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.

Typological profile of the Transeurasian languages from a quantitative perspective

2020 ◽  
pp. 144-160
Author(s):  
Nataliia Hübler
Keyword(s):  
Phylogenetic Signal ◽  
Structural Features ◽  
Comparative Methods ◽  
Phylogenetic Comparative Methods ◽  
Data Set ◽  
Bayesian Tree ◽  
Language History

This chapter provides an overview of the typological features of the Transeurasian (Turkic, Mongolic, Tungusic, Japonic, Koreanic) languages, including brief descriptions of the phonology and morphosyntax of these languages. Through the application of phylogenetic comparative methods, a set of structural features with a high phylogenetic signal is delimited. These features can be assumed to be genealogically stable. The trees achieved by Bayesian tree-sampling based on all 226 features are compared with those derived via the 97 structural features with a high phylogenetic signal and the conclusion reached is that the data set with presumably stable structural features does not provide a tree that is compatible with the language history assumed by classical historical linguists. Neither the full nor the reduced feature set provides a reliable internal classification of the Turkic, Mongolic, Tungusic, and Japonic language families.

scholarly journals Somewhere I Belong: Phylogenetic Comparative Methods and Machine Learning to Investigate the Evolution of a Species-Rich Lineage of Parasites

2021 ◽  
Author(s):  
Armando Jairo Cruz-Laufer ◽  
Antoine Pariselle ◽  
Michiel W. P. Jorissen ◽  
Fidel Muterezi Bukinga ◽  
Anwar Al Assadi ◽  
...  
Keyword(s):  
Host Range ◽  
Phylogenetic Signal ◽  
Comparative Methods ◽  
Support Vector ◽  
Phylogenetic Comparative Methods ◽  
Ecological Data ◽  
Metazoan Parasites ◽  
Size Correction ◽  
Data Deficient ◽  
Attachment Organ

Metazoan parasites encompass a significant portion of the global biodiversity. Their relevance for environmental and human health calls for a better understanding as parasite macroevolution remains mostly understudied. Yet limited molecular, phenotypic, and ecological data have so far discouraged complex analyses of evolutionary mechanisms and encouraged the use of data discretisation and body-size correction. In this case study, we aim to highlight the limitations of these methods and propose new methods optimised for small datasets. We apply multivariate phylogenetic comparative methods (PCMs) and statistical classification using support vector machines (SVMs) to a data-deficient host-parasite system. We use continuous morphometric and host range data currently widely inferred from a species-rich lineage of parasites (Cichlidogyrus incl. Scutogyrus - Platyhelminthes: Monogenea, Dactylogyridae) infecting cichlid fishes. For PCMs, we modelled the attachment organ and host range evolution using the data of 135 species and an updated multi-marker (28S and 18S rDNA, ITS1, COI mtDNA) phylogenetic reconstruction of 58/137 described species. Through a cluster analysis, SVM-based classification, and taxonomic literature survey, we infered the systematic informativeness of discretised and continuous characters. We demonstrate that an update to character coding and size-correction techniques is required as some techniques mask phylogenetic signals but remain useful for characterising species groups of Cichlidogyrus. Regarding the attachment organ evolution, PCMs suggest a pattern associated with genetic drift. Yet host and environmental parameters might put this structure under stabilising selection as indicated by a limited morphological variation. This contradiction, the absence of a phylogenetic signal and multicollinearity in most measurements, a moderate 73% accordance rate of taxonomic approach and SVMs, and a low phylogenetic informativeness of reproductive organ data suggest an overall limited systematic value of the measurements included in most species characterisations. We conclude that PCMs and SVM-based approaches are suitable tools to investigate the character evolution of data-deficient taxa.

scholarly journals phylogenize: correcting for phylogeny reveals genes associated with microbial distributions

2018 ◽  
Author(s):  
Patrick H. Bradley ◽  
Katherine S. Pollard
Keyword(s):  
Community Composition ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Comparative Methods ◽  
Shotgun Sequencing ◽  
Phylogenetic Comparative Methods ◽  
Sequencing Data ◽  
Link Type ◽  
Phylogenetic Regression ◽  
Project Data

AbstractSummaryPhylogenetic comparative methods are powerful but presently under-utilized ways to identify microbial genes underlying differences in community composition. These methods help to identify functionally important genes because they test for associations beyond those expected when related microbes occupy similar environments. We present phylogenize, a pipeline with web, QIIME2, and R interfaces that allows researchers to perform phylogenetic regression on 16S amplicon and shotgun sequencing data and to visualize results. phylogenize applies broadly to both host-associated and environmental microbiomes. Using Human Microbiome Project and Earth Microbiome Project data, we show that phylogenize draws similar conclusions from 16S versus shotgun sequencing and reveals both known and candidate pathways associated with host colonization.Availabilityphylogenize is available at https://phylogenize.org and https://bitbucket.org/pbradz/[email protected]

scholarly journals Realistic scenarios of missing taxa in phylogenetic comparative methods and their effects on model selection and parameter estimation

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7917 ◽  
Author(s):  
Rafael S. Marcondes
Keyword(s):  
Parameter Estimation ◽  
Model Selection ◽  
Phylogenetic Signal ◽  
Comparative Methods ◽  
Phylogenetic Comparative Methods ◽  
Trait Evolution ◽  
Continuous Trait ◽  
Starting Point ◽  
Almost All ◽  
Future Work

Model-based analyses of continuous trait evolution enable rich evolutionary insight. These analyses require a phylogenetic tree and a vector of trait values for the tree’s terminal taxa, but rarely do a tree and dataset include all taxa within a clade. Because the probability that a taxon is included in a dataset depends on ecological traits that have phylogenetic signal, missing taxa in real datasets should be expected to be phylogenetically clumped or correlated to the modelled trait. I examined whether those types of missing taxa represent a problem for model selection and parameter estimation. I simulated univariate traits under a suite of Brownian Motion and Ornstein-Uhlenbeck models, and assessed the performance of model selection and parameter estimation under absent, random, clumped or correlated missing taxa. I found that those analyses perform well under almost all scenarios, including situations with very sparsely sampled phylogenies. The only notable biases I detected were in parameter estimation under a very high percentage (90%) of correlated missing taxa. My results offer a degree of reassurance for studies of continuous trait evolution with missing taxa, but the problem of missing taxa in phylogenetic comparative methods still demands much further investigation. The framework I have described here might provide a starting point for future work.

scholarly journals Adaptation, phylogeny, and covariance in milk macronutrient composition

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8085
Author(s):  
Gregory E. Blomquist
Keyword(s):  
Life History ◽  
Natural History ◽  
Mixed Model ◽  
Phylogenetic Signal ◽  
Maternal Diet ◽  
Milk Composition ◽  
Nonparametric Tests ◽  
Comparative Methods ◽  
Phylogenetic Comparative Methods ◽  
Macronutrient Composition

Background Milk is a complicated chemical mixture often studied through macronutrient concentrations of fat, protein, and sugar. There is a long-standing natural history tradition describing interspecific diversity in these concentrations. However, recent work has shown little influence of ecological or life history variables on them, aside from maternal diet effects, along with a strong phylogenetic signal. Methods I used multivariate phylogenetic comparative methods to revisit the ecological and life history correlates of milk macronutrient composition and elaborate on the nature of the phylogenetic signal using the phylogenetic mixed model. I also identified clades with distinctive milks through nonparametric tests (KSI) and PhylogeneticEM evolutionary modeling. Results In addition to the previously reported diet effects, I found increasingly aquatic mammals have milk that this is lower in sugar and higher in fat. Phylogenteic heritabilities for each concentration were high and phylogenetic correlations were moderate to strong indicating coevolution among the concentrations. Primates and pinnipeds had the most outstanding milks according to KSI and PhylogeneticEM, with perissodactyls and marsupials as other noteworthy clades with distinct selection regimes. Discussion Mammalian milks are diverse but often characteristic of certain higher taxa. This complicates identifying the ecological and life history correlates of milk composition using common phylogenetic comparative methods because those traits are also conservative and clade-specific. Novel methods, careful assessment of data quality and hypotheses, and a “phylogenetic natural history” perspective provide alternatives to these traditional tools.

scholarly journals Statistically rigorous calculations do not support common input and long-term synchronization of motor-unit firings

2014 ◽  
Vol 112 (11) ◽  
pp. 2729-2744 ◽  
Author(s):  
Carlo J. De Luca ◽  
Joshua C. Kline
Keyword(s):  
Motor Unit ◽  
Statistical Tests ◽  
Vastus Lateralis ◽  
Common Input ◽  
Data Set ◽  
Order Of Magnitude ◽  
Score Method ◽  
Surface Electromyographic Signal ◽  
Measure Synchronization

Over the past four decades, various methods have been implemented to measure synchronization of motor-unit firings. In this work, we provide evidence that prior reports of the existence of universal common inputs to all motoneurons and the presence of long-term synchronization are misleading, because they did not use sufficiently rigorous statistical tests to detect synchronization. We developed a statistically based method (SigMax) for computing synchronization and tested it with data from 17,736 motor-unit pairs containing 1,035,225 firing instances from the first dorsal interosseous and vastus lateralis muscles—a data set one order of magnitude greater than that reported in previous studies. Only firing data, obtained from surface electromyographic signal decomposition with >95% accuracy, were used in the study. The data were not subjectively selected in any manner. Because of the size of our data set and the statistical rigor inherent to SigMax, we have confidence that the synchronization values that we calculated provide an improved estimate of physiologically driven synchronization. Compared with three other commonly used techniques, ours revealed three types of discrepancies that result from failing to use sufficient statistical tests necessary to detect synchronization. 1) On average, the z-score method falsely detected synchronization at 16 separate latencies in each motor-unit pair. 2) The cumulative sum method missed one out of every four synchronization identifications found by SigMax. 3) The common input assumption method identified synchronization from 100% of motor-unit pairs studied. SigMax revealed that only 50% of motor-unit pairs actually manifested synchronization.

Sign in / Sign up

Export Citation Format

Share Document