hemiplasy

Copetti D, Búrquez A, Bustamante E, Charboneau JLM, Childs KL, Eguiarte LE, Lee S, LIiu TL, McMahon MM, Whiteman NK, Wing RA, Wojciechowski MF & Sanderson MJ 2018 Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti. PNAS 114:12003-12008.

  • homoplasy can be elevated in genomes because individual loci may have independent evolutionary histories different from the species history
  • discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting
  • 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves
  • the high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits
  • we focus on the genomes of cacti and assess the degree to which apparent homoplasy among these species is elevated due to discordance between gene trees and the species tree
  • an important but recently recognized contributor to molecular homoplasy is “hemiplasy” (18, 19), originally defined as the apparent multiple origin of a character state on the inferred species tree arising when an inferred gene tree (with no homoplasy) is discordant with that species tree
  • a slight generalization of this definition is needed to account for characters with homoplasy on both trees (Fig. 1, Lower Right)
  • a character (site) exhibits hemiplasy if the inferred number of character state changes on the species tree is strictly greater than on the gene tree, which occurs only if the two trees are discordant
  • we partitioned the homoplastic amino acid sites in genes on the species tree into three parts:
  • the fraction arising from homoplasy on concordant gene trees (Fig. 1, Upper Right)
  • the fraction arising solely from gene trees with less homoplasy than the species tree but that are discordant with the species tree (hemiplasy: Fig. 1, Lower Left)
  • the small fraction that arises from homoplasy on discordant gene trees that is equally homoplastic on the species tree (which as yet has no term defined: Fig. 1, Lower Right)
  • hemiplasy accounts for 58–63% of all apparent homoplasy