scholarly journals Phylogenetic Comparative Methods and the Evolution of Multivariate Phenotypes

2019 ◽  
Vol 50 (1) ◽  
pp. 405-425 ◽  
Author(s):  
Dean C. Adams ◽  
Michael L. Collyer
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary Biology ◽  
Generalized Least Squares ◽  
Comparative Methods ◽  
High Dimensional ◽  
Phenotypic Integration ◽  
Phylogenetic Comparative Methods ◽  
Evolutionary Trends ◽  
Phenotype Space ◽  
Multivariate Phenotypes

Evolutionary biology is multivariate, and advances in phylogenetic comparative methods for multivariate phenotypes have surged to accommodate this fact. Evolutionary trends in multivariate phenotypes are derived from distances and directions between species in a multivariate phenotype space. For these patterns to be interpretable, phenotypes should be characterized by traits in commensurate units and scale. Visualizing such trends, as is achieved with phylomorphospaces, should continue to play a prominent role in macroevolutionary analyses. Evaluating phylogenetic generalized least squares (PGLS) models (e.g., phylogenetic analysis of variance and regression) is valuable, but using parametric procedures is limited to only a few phenotypic variables. In contrast, nonparametric, permutation-based PGLS methods provide a flexible alternative and are thus preferred for high-dimensional multivariate phenotypes. Permutation-based methods for evaluating covariation within multivariate phenotypes are also well established and can test evolutionary trends in phenotypic integration. However, comparing evolutionary rates and modes in multivariate phenotypes remains an important area of future development.

scholarly journals Diachronic change in Indo-European motion event encoding

2014 ◽  
Vol 4 (1) ◽  
pp. 40-83 ◽  
Author(s):  
Annemarie Verkerk
Keyword(s):  
Evolutionary Biology ◽  
Comparative Methods ◽  
Comparative Data ◽  
Historical Change ◽  
Phylogenetic Comparative Methods ◽  
Diachronic Change ◽  
Motion Event ◽  
The World ◽  
Historical Comparative ◽  
Made In

There are many different syntactic constructions that languages can use to encode motion events. In recent decades, great advances have been made in the description and study of these syntactic constructions from languages spoken around the world (Talmy 1985, 1991, Slobin 1996, 2004). However, relatively little attention has been paid to historical change in these systems (exceptions are Vincent 1999, Dufresne, Dupuis & Tremblay 2003, Kopecka 2006 and Peyraube 2006). In this article, diachronic change of motion event encoding systems in Indo-European is investigated using the available historical–comparative data and phylogenetic comparative methods adopted from evolutionary biology. It is argued that Proto-Indo-European was not satellite-framed, as suggested by Talmy (2007) and Acedo Matellán and Mateu (2008), but had a mixed motion event encoding system, as is suggested by the available historical–comparative data.

scholarly journals Special care is needed in applying phylogenetic comparative methods to gene trees with speciation and duplication nodes

2019 ◽  
Author(s):  
Tina Begum ◽  
Marc Robinson-Rechavi
Keyword(s):  
Functional Genomics ◽  
Gene Function ◽  
Evolutionary Biology ◽  
Tissue Specificity ◽  
Comparative Methods ◽  
Pairwise Comparisons ◽  
Phylogenetic Comparative Methods ◽  
Gene Trees ◽  
Time Calibration ◽  
Branch Lengths

AbstractHow gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, since genes, like species, are phylogenetically related. Phylogenetic comparative methods should allow to correct for this, but they depend on strong assumptions, including unbiased tree estimates relative to the hypothesis being tested. Such methods have recently been used to test the “ortholog conjecture”, the hypothesis that functional evolution is faster in paralogs than in orthologs. Whereas pairwise comparisons of tissue specificity (τ) provided support for the ortholog conjecture, phylogenetic independent contrasts did not. Our reanalysis on the same gene trees identified problems with the time calibration of duplication nodes. We find that the gene trees used suffer from important biases, due to the inclusion of trees with no duplication nodes, to the relative age of speciations and duplications, to systematic differences in branch lengths, and to non-Brownian motion of tissue-specificity on many trees. We find that incorrect implementation of phylogenetic method in empirical gene trees with duplications can be problematic. Controlling for biases allows to successfully use phylogenetic methods to study the evolution of gene function, and provides some support for the ortholog conjecture using three different phylogenetic approaches.

scholarly journals Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes

2020 ◽  
Author(s):  
Tina Begum ◽  
Marc Robinson-Rechavi
Keyword(s):  
Functional Genomics ◽  
Gene Function ◽  
Evolutionary Biology ◽  
Tissue Specificity ◽  
Comparative Methods ◽  
Pairwise Comparisons ◽  
Phylogenetic Comparative Methods ◽  
Gene Trees ◽  
Time Calibration ◽  
Branch Lengths

Abstract How gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, as genes, like species, are phylogenetically related. Phylogenetic comparative methods should be used to correct for this, but they depend on strong assumptions, including unbiased tree estimates relative to the hypothesis being tested. Such methods have recently been used to test the “ortholog conjecture,” the hypothesis that functional evolution is faster in paralogs than in orthologs. Although pairwise comparisons of tissue specificity (τ) provided support for the ortholog conjecture, phylogenetic independent contrasts did not. Our reanalysis on the same gene trees identified problems with the time calibration of duplication nodes. We find that the gene trees used suffer from important biases, due to the inclusion of trees with no duplication nodes, to the relative age of speciations and duplications, to systematic differences in branch lengths, and to non-Brownian motion of tissue specificity on many trees. We find that incorrect implementation of phylogenetic method in empirical gene trees with duplications can be problematic. Controlling for biases allows successful use of phylogenetic methods to study the evolution of gene function and provides some support for the ortholog conjecture using three different phylogenetic approaches.

The evolutionary trends of grammatical gender in Indo-Aryan languages

2020 ◽  
pp. 1-30
Author(s):  
Marc Allassonnière-Tang ◽  
Michael Dunn
Keyword(s):  
Historical Linguistic ◽  
Evolutionary Dynamics ◽  
Grammatical Gender ◽  
Comparative Methods ◽  
Phylogenetic Comparative Methods ◽  
Evolutionary Trends ◽  
Personal Pronouns ◽  
Demonstrative Pronouns ◽  
Feature Values ◽  
Prior Analysis

Abstract This paper infers the processes of development and change of grammatical gender in Indo-Aryan languages using phylogenetic comparative methods. 48 Indo-Aryan languages are coded based on 44 presence-absence features relating to gender marking on the verbs, adjectives, personal pronouns, demonstrative pronouns, and possessive pronouns. A Bayesian Reverse Jump Hyper Prior analysis, which infers the evolutionary dynamics of changes between feature values, gives results that are consistent with historical linguistic and typological studies on gender systems in Indo-Aryan languages and predicts the evolutionary trends of the features included in the dataset.

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