hemiplasy
Mendes FK, Fuentes-González JA, Schraiber JG & Hahn MW 2018 A multispecies coalescent model for quantitative traits. eLife 7:e36482.
- the development of models incorporating discordance in order to deal with trait evolution have lagged behind those estimating species trees
- one way that gene tree discordance can affect inferences about trait evolution is by increasing the risk of hemiplasy
- hemiplasy is the production of a homoplasy-like pattern by a non-homoplastic event
- a character-state transition has occurred on a discordant gene tree
- hemiplasy can cause apparent substitution rate variation, can spuriously increase the detection of positive selection in coding sequences, and can lead to artefactual signals of convergence
- the manner in which genealogical discordance might affect studies of complex trait evolution is still not well understood
- a reasonable hypothesis is that gene tree discordance should only be problematic for traits controlled by a small number of loci, but not for those controlled by many loci
- traditional phylogenetic models such as BM do not consider the variation that exists in ancestral populations prior to speciation
- traditional models (BM or otherwise) do not allow for shared trait variation along branches that do not exist in the species tree
- the magnitude of the effect of hemiplasy on phylogenetic inferences is consistently proportional to the observed levels of gene tree discordance in a data set
- the number [of?] loci underlying a quantitative trait does not matter to the expected trends from such inferences
