Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets

Genes
Mark S Springer, John Gatesy

Abstract

coalescence methods have emerged as a popular alternative for inferring species trees with large genomic datasets, because these methods explicitly account for incomplete lineage sorting. However, statistical consistency of summary coalescence methods is not guaranteed unless several model assumptions are true, including the critical assumption that recombination occurs freely among but not within coalescence genes (c-genes), which are the fundamental units of analysis for these methods. Each c-gene has a single branching history, and large sets of these independent gene histories should be the input for genome-scale coalescence estimates of phylogeny. By contrast, numerous studies have reported the results of coalescence analyses in which complete protein-coding sequences are treated as c-genes even though exons for these loci can span more than a megabase of DNA. Empirical estimates of recombination breakpoints suggest that c-genes may be much shorter, especially when large clades with many species are the focus of analysis. Although this idea has been challenged recently in the literature, the inverse relationship between c-gene size and increased taxon sampling in a dataset-the 'recombination ratchet'-is a fundamental prope...Continue Reading

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Citations

Mar 7, 2019·Proceedings. Biological Sciences·Thomas J D HallidayAnjali Goswami
Dec 19, 2019·Frontiers in Genetics·Mark S SpringerWilliam J Murphy
Nov 25, 2020·Annual Review of Animal Biosciences·William J MurphyMark S Springer
Feb 6, 2021·Molecular Phylogenetics and Evolution·Mark P Simmons, John Gatesy
Oct 16, 2018·Molecular Phylogenetics and Evolution·Ryan A TamashiroRebecca T Kimball
Nov 6, 2018·Molecular Phylogenetics and Evolution·Mark P SimmonsJohn Gatesy

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Software Mentioned

FGT
MP
CoalHMM
OrthoMaM
II
RDP
ASTRAL
GENECONV
SiScan
STAR

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