Accurate Detection of Convergent Amino-Acid Evolution with PCOC

Abstract

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.

Detecting convergent adaptive amino acid evolution

“…The low sensitivity of Identical and msd is expected as those methods can only detect convergent substitutions to a particular amino acid, not to an amino acid profile. Overall, these results are qualitatively congruent with previously published simulations obtained with simpler settings and fewer methods (17) . However, the precisions and sensitivities observed here are much worse than those reported in (17) , because simulations do not use the Profile Change with One Change model, which enforces substitutions on transition branches.…”

“…Example B shows a profile change, whereby 2 different amino acids, Q and Y, have good fitness in the convergent case. All methods but the Identical may detect such changes, although this depends on how different the ancestral and the convergent profiles are (17) . Example C is similar to Example B except that some substitutions occurred after the phenotype has changed (type 2 substitutions), not simultaneously with the phenotype change.…”

Unmatched level of molecular convergence among deeply divergent complex multicellular fungi

“…We also examined the extent of convergence in amino acid sites among CM Agarico-and Pezizomycotina, using approaches that incorporate null models ( 50 ) proposed in response to previous criticisms of published cases ( 51 – 53 ). We found 129 families in which convergent shifts in amino acid preference are significantly enriched relative to control analyses (Fig.…”

“…In order to gain insights into amino acid convergence between the Agaricomycotina and Pezizomycotina, we followed Rey et al’s approach ( 50 ) to identify convergent shifts in amino acid preference at a given site. Convergence is defined not only as changes to identical amino acids from different ancestral states, but also as changes to amino acids with similar biochemical properties (referred to as convergent shifts in amino acid composition).…”

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

“…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].…”