A novel unbiased test for molecular convergent evolution and discoveries in echolocating, aquatic and high-altitude mammals

Marcovitz, Amir; Turakhia, Yatish; Gloudemans, Michael J.; Braun, Benjamin; Chen, Heidi I.; Bejerano, Gill

doi:10.1101/170985

Cited by 7 publications

(7 citation statements)

References 41 publications

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“…We have not attempted to work at the level of entire gene sequences or even functional groups of genes, whereby the evidence obtained at the level of individual sites would be used collectively over the entire gene length or over several genes with a particular function to classify a gene or group of genes as convergent or not. However, other works have developed methods to work above the level of single sites ( Chabrol et al., 2017 ; Marcovitz et al., 2017 ), and our method is compatible with these. Both these approaches detect convergent substitutions that fit the definition of Zhang and Kumar (1997) and Foote et al.…”

Section: Discussionmentioning

confidence: 99%

“…For instance, PCOC has not been designed to deal with convergent relaxations of selection, which may contribute false positives. To filter out candidate genes that may be under convergent relaxations of selection, Marcovitz et al. (2017) used the numbers of divergent substitutions, that is, substitutions to different amino acids in the convergent species.…”

Section: Discussionmentioning

confidence: 99%

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Accurate Detection of Convergent Amino-Acid Evolution with PCOC

Rey

Guéguen

Sémon

et al. 2018

Molecular Biology and Evolution

122

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In the history of life, some phenotypes have been acquired several times independently, through convergent evolution. Recently, lots of genome-scale studies have been devoted to identify nucleotides or amino acids that changed in a convergent manner when the convergent phenotypes evolved. These efforts have had mixed results, probably because of differences in the detection methods, and because of conceptual differences about the definition of a convergent substitution. Some methods contend that substitutions are convergent only if they occur on all branches where the phenotype changed toward the exact same state at a given nucleotide or amino acid position. Others are much looser in their requirements and define a convergent substitution as one that leads the site at which they occur to prefer a phylogeny in which species with the convergent phenotype group together. Here, we suggest to look for convergent shifts in amino acid preferences instead of convergent substitutions to the exact same amino acid. We define as convergent shifts substitutions that occur on all branches where the phenotype changed and such that they correspond to a change in the type of amino acid preferred at this position. We implement the corresponding model into a method named PCOC. We show on simulations that PCOC better recovers convergent shifts than existing methods in terms of sensitivity and specificity. We test it on a plant protein alignment where convergent evolution has been studied in detail and find that our method recovers several previously identified convergent substitutions and proposes credible new candidates.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Accurate Detection of Convergent Amino-Acid Evolution with PCOC

Rey

Guéguen

Sémon

et al. 2018

Molecular Biology and Evolution

122

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“…For example, a recent method, "CLIME" Li et al 2018), uses a Bayesian approach similar in spirit to our model to cluster phylogenetic profiles of proteins to identify functionally related proteins. Jointly modeling a group of functionally related genomic regions in different species will provide more comprehensive insight of the evolutionary history and functional interaction of regulatory regions (Marcovitz et al 2017).…”

Section: Discussionmentioning

confidence: 99%

Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees

Sackton

Edwards

et al. 2018

Preprint

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Conservation of DNA sequence over evolutionary time is a strong indicator of function, and gain or loss of sequence conservation can be used to infer changes in function across a phylogeny. Changes in evolutionary rates on particular lineages in a phylogeny can indicate shared functional shifts, and thus can be used to detect genomic correlates of phenotypic convergence. However, existing methods do not allow easy detection of patterns of rate variation, which causes challenges for detecting convergent rate shifts or other complex evolutionary scenarios. Here we introduce PhyloAcc, a new Bayesian method to model substitution rate changes in conserved elements across a phylogeny. The method assumes several categories of substitution rate for each branch on the phylogenetic tree, estimates substitution rates per category, and detects changes of substitution rate as the posterior probability of a category switch. Simulations show that PhyloAcc can detect genomic regions with rate shifts in multiple target species better than previous methods and has a higher accuracy of reconstructing complex patterns of substitution rate changes than prevalent Bayesian relaxed clock models. We demonstrate the utility of PhyloAcc in two classic examples of convergent phenotypes: loss of flight in birds and the transition to marine life in mammals. In each case, our approach reveals numerous examples of conserved non-exonic elements with accelerations specific to the phenotypically convergent lineages. Our method is widely applicable to any set of conserved elements where multiple rate changes are expected on a phylogeny.

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“…Molecular convergence in protein evolution: Many recent studies of convergence have focused on protein or codon alignments to identify amino acid positions that have convergently changed in species that share a convergent trait [63][64][65]. In some circumstances, conflicting placement of convergent phenotypes between gene trees and species tree can be used to identify potential genomic convergence [66,67].…”

Section: Genomics Of Convergencementioning

confidence: 99%

Integrating natural history-derived phenomics with comparative genomics to study the genetic architecture of convergent evolution

Grayson

et al. 2019

Preprint

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Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part due to the advent of genomic techniques.However, the current 'genomics gold rush' in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep 'vertical', natural history knowledge with 'horizontal' knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa.

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A novel unbiased test for molecular convergent evolution and discoveries in echolocating, aquatic and high-altitude mammals

Cited by 7 publications

References 41 publications

Accurate Detection of Convergent Amino-Acid Evolution with PCOC

Accurate Detection of Convergent Amino-Acid Evolution with PCOC

Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees

Integrating natural history-derived phenomics with comparative genomics to study the genetic architecture of convergent evolution

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