hemiplasy

Avice JC & Robinson TJ 2008 Hemiplasy: a new term in the lexicon of phylogenetics. Syst Biol 57:503-507.

  • hemiplasy is a bona fide form of homology (allelic orthology in this case) that nonetheless can give the illusion of homoplasy in an organismal tree
  • gene genealogies can in principle differ in basic topology from the overall population tree or species tree of which they are a part, if for no other reason than stochastic lineage sorting across successive evolutionary nodes in an organismal phylogeny
  • the current molecular phylogenetic paradigm still reconstructs gene trees to represent the species tree
  • we suggest the word hemiplasy
  • the responsible lineage sorting processes have homoplasy-like consequences
  • the character states themselves are genuinely homologous and apomorphic
  • its evolutionary etiology is fully distinct from homoplasy
  • we suggest the following formal definition of hemiplasy:
  • the topological discordance between a gene tree and a species tree attributable to lineage sorting of genetic polymorphisms that were retained across successive nodes in a species tree
  • other evolutionary processes are also capable of producing homoplasy-free discordances between gene trees and species phylogenies
  • for example, particular alleles can leak across species boundaries via hybridization and introgression
  • for epistemological clarity we recommend that the term hemiplasy not include these additional (and well appreciated) generators of phylogenetic discordance between gene trees and species trees but instead be confined to discordances that arise from idiosyncratic lineage sorting per se
  • hemiplasy is not a synonym for lineage sorting
  • it is a consequence of lineage sorting
  • hemiplasy is not the exclusive outcome of lineage sorting
  • it is usually a minority outcome compared to the larger number of hemiplasy-free gene trees that normally are expected to comprise a typical species tree
  • adoption of the word hemiplasy should contribute to the injection of oft-neglected "population thinking" into phylogenetic assessments and thereby provide another incremental step toward unifying the traditionally disparate fields of phylogenetic biology and population genetics