scholarly journals The impact of rate heterogeneity on inference of phylogenetic models of trait evolution

2016 ◽  
Vol 29 (12) ◽  
pp. 2502-2518 ◽  
Author(s):  
A. M. Chira ◽  
G. H. Thomas
Keyword(s):  
Rate Heterogeneity ◽  
Trait Evolution ◽  
The Impact ◽  
Phylogenetic Models

scholarly journals No latitudinal gradients in tempo or mode of morphological evolution in birds

2020 ◽  
Author(s):  
J. Drury ◽  
J. Clavel ◽  
J.A. Tobias ◽  
J. Rolland ◽  
C. Sheard ◽  
...  
Keyword(s):  
Species Interactions ◽  
Morphological Evolution ◽  
Latitudinal Gradients ◽  
Phenotypic Evolution ◽  
Trait Evolution ◽  
Trait Divergence ◽  
Diversity Gradient ◽  
The Tropics ◽  
The Impact ◽  
Phylogenetic Models

AbstractThe latitudinal diversity gradient is one of the most striking patterns in nature yet its implications for morphological evolution are poorly understood. In particular, it has been proposed that an increased intensity of species interactions in tropical biota may either promote or constrain trait evolution, but which of these outcomes predominates remains uncertain. Here, we develop tools for fitting phylogenetic models of phenotypic evolution in which the impact of species interactions can vary across lineages. Deploying these models on a global avian trait dataset to explore differences in trait divergence between tropical and temperate lineages, we find that the effect of latitude on the mode and tempo of morphological evolution is weak and clade- or trait-dependent. Our results indicate that species interactions do not disproportionately impact morphological evolution in tropical bird families and question the validity and universality of previously reported patterns of slower trait evolution in the tropics.

scholarly journals Tempo and mode of morphological evolution are decoupled from latitude in birds

PLoS Biology ◽  
2021 ◽  
Vol 19 (8) ◽  
pp. e3001270
Author(s):  
Jonathan P. Drury ◽  
Julien Clavel ◽  
Joseph A. Tobias ◽  
Jonathan Rolland ◽  
Catherine Sheard ◽  
...  
Keyword(s):  
Species Interactions ◽  
Morphological Evolution ◽  
Phenotypic Evolution ◽  
Trait Evolution ◽  
Trait Divergence ◽  
Latitudinal Diversity Gradient ◽  
Diversity Gradient ◽  
The Tropics ◽  
The Impact ◽  
Phylogenetic Models

The latitudinal diversity gradient is one of the most striking patterns in nature, yet its implications for morphological evolution are poorly understood. In particular, it has been proposed that an increased intensity of species interactions in tropical biota may either promote or constrain trait evolution, but which of these outcomes predominates remains uncertain. Here, we develop tools for fitting phylogenetic models of phenotypic evolution in which the impact of species interactions—namely, competition—can vary across lineages. Deploying these models on a global avian trait dataset to explore differences in trait divergence between tropical and temperate lineages, we find that the effect of latitude on the mode and tempo of morphological evolution is weak and clade- or trait dependent. Our results indicate that species interactions do not disproportionately impact morphological evolution in tropical bird families and question the validity of previously reported patterns of slower trait evolution in the tropics.

scholarly journals A chromosome level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution.

2020 ◽  
Author(s):  
Wesley Warren ◽  
Tyler Boggs ◽  
Richard Borowsky ◽  
Brian Carlson ◽  
Estephany Ferrufino ◽  
...  
Keyword(s):  
Complex Traits ◽  
Fish Genome ◽  
Trait Evolution ◽  
Protein Coding ◽  
Astyanax Mexicanus ◽  
Eye Size ◽  
Genome Wide ◽  
Trait Locus ◽  
The Impact ◽  
Chromosome Level

Abstract Identifying the genetic factors that underlie complex traits is central to understanding the mechanistic underpinnings of evolution. In nature, adaptation to severe environmental change, such as encountered following colonization of caves, has dramatically altered genomes of species over varied time spans. Genomic sequencing approaches have identified mutations associated with troglomorphic trait evolution, but the functional impacts of these mutations remain poorly understood. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, and also inhabits at least 30 different caves in the region. Cave-dwelling A. mexicanus morphs are well adapted to subterranean life and many populations appear to have evolved troglomorphic traits independently, while the surface-dwelling populations can be used as a proxy for the ancestral form. Here we present a high-resolution, chromosome-level surface fish genome, enabling the first genome-wide comparison between surface fish and cavefish populations. Using this resource, we performed quantitative trait locus (QTL) mapping analyses for pigmentation and eye size and found new candidate genes for eye loss such as dusp26. We used CRISPR gene editing in A. mexicanus to confirm the essential role of a gene within an eye size QTL, rx3, in eye formation. We also generated the first genome-wide evaluation of deletion variability that includes an analysis of the impact on protein-coding genes across cavefish populations to gain insight into this potential source of cave adaptation. The new surface fish genome reference now provides a more complete resource for comparative, functional, developmental and genetic studies of drastic trait differences within a species.

scholarly journals The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates

2018 ◽  
Author(s):  
Brice A. J. Sarver ◽  
Matthew W. Pennell ◽  
Joseph W. Brown ◽  
Sara Keeble ◽  
Kayla M. Hardwick ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Substitution Rate ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Parameter Estimates ◽  
Molecular Clocks ◽  
Estimation Of Parameters ◽  
Rate Heterogeneity ◽  
Diversification Rates ◽  
The Impact

AbstractComparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. However, the effect that the selection of these priors has on the inference of comparative parameters has not been thoroughly investigated. Such uncertainty may systematically bias phylogenetic reconstruction and, subsequently, parameter estimation. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we use BEAST to simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation rates and extinction rates) from these trees. When substitution rate heterogeneity is large, parameter estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate.

scholarly journals Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)

2020 ◽  
Author(s):  
Tamara Spasojevic ◽  
Gavin R Broad ◽  
Ilari E Sääksjärvi ◽  
Martin Schwarz ◽  
Masato Ito ◽  
...  
Keyword(s):  
Evolutionary Rate ◽  
Total Evidence ◽  
Morphological Data ◽  
Phylogenetic Study ◽  
Phylogenetic Distance ◽  
Rate Heterogeneity ◽  
The Family ◽  
The Impact ◽  
Age Estimates

Abstract Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information, but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artefact that might be detrimental for total-evidence dating: “bare-branch attraction”, namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought, but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information.

scholarly journals Macroevolutionary analysis of discrete traits with rate heterogeneity

2020 ◽  
Author(s):  
Michael C. Grundler ◽  
Daniel L. Rabosky
Keyword(s):  
New World ◽  
Evolutionary Rate ◽  
Simulated Data ◽  
Data Sets ◽  
Rate Heterogeneity ◽  
Trait Evolution ◽  
Discrete Traits ◽  
Simulated Data Sets ◽  
Dramatic Variation ◽  
Ancestral Character States

AbstractOrganismal traits show dramatic variation in phylogenetic patterns of origin and loss across the Tree of Life. Understanding the causes and consequences of this variation depends critically on accounting for heterogeneity in rates of trait evolution among lineages. Here, we describe a method for modeling among-lineage evolutionary rate heterogeneity in a trait with two discrete states. The method assumes that the present-day distribution of a binary trait is shaped by a mixture of stochastic processes in which the rate of evolution varies among lineages in a phylogeny. The number and location of rate changes, which we refer to as rate-shift events, are inferred automatically from the data. Simulations reveal that the method accurately reconstructs rates of trait evolution and ancestral character states even when simulated data violate model assumptions. We apply the method to an empirical dataset of mimetic coloration in snakes and find elevated rates of trait evolution in two clades of harmless snakes that are broadly sympatric with dangerously venomous New World coral snakes, recapitulating an earlier analysis of the same dataset. Although the method performed well on many simulated data sets, we caution that overall power for inferring heterogeneous dynamics of single binary traits is low.

scholarly journals A chromosome level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution

2020 ◽  
Author(s):  
Wesley C. Warren ◽  
Tyler E. Boggs ◽  
Richard Borowsky ◽  
Brian M. Carlson ◽  
Estephany Ferrufino ◽  
...  
Keyword(s):  
Complex Traits ◽  
Fish Genome ◽  
Trait Evolution ◽  
Protein Coding ◽  
Astyanax Mexicanus ◽  
Eye Size ◽  
Genome Wide ◽  
Trait Locus ◽  
The Impact ◽  
Chromosome Level

AbstractIdentifying the genetic factors that underlie complex traits is central to understanding the mechanistic underpinnings of evolution. In nature, adaptation to severe environmental change, such as encountered following colonization of caves, has dramatically altered genomes of species over varied time spans. Genomic sequencing approaches have identified mutations associated with troglomorphic trait evolution, but the functional impacts of these mutations remain poorly understood. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, and also inhabits at least 30 different caves in the region. Cave-dwelling A. mexicanus morphs are well adapted to subterranean life and many populations appear to have evolved troglomorphic traits independently, while the surface-dwelling populations can be used as a proxy for the ancestral form. Here we present a high-resolution, chromosome-level surface fish genome, enabling the first genome-wide comparison between surface fish and cavefish populations. Using this resource, we performed quantitative trait locus (QTL) mapping analyses for pigmentation and eye size and found new candidate genes for eye loss such as dusp26. We used CRISPR gene editing in A. mexicanus to confirm the essential role of a gene within an eye size QTL, rx3, in eye formation. We also generated the first genome-wide evaluation of deletion variability that includes an analysis of the impact on protein-coding genes across cavefish populations to gain insight into this potential source of cave adaptation. The new surface fish genome reference now provides a more complete resource for comparative, functional, developmental and genetic studies of drastic trait differences within a species.

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