Abstract
Waddell, P. J., and S. Shelley. 2003. Evaluating placental interordinal phylogenies with novel sequences including RAG1, γ -fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models. Mol. Phylogenet. Evol. 28:197–224. Waters, P. D., G. Dobigny, P. J. Waddell, and T. J. Robinson. 2007. Evolutionary history of LINE-1 in the major clades of placental mammals. PLoS ONE 2:e158. Wible, J. R., G. W. Rougier, M. J. Novacek, and R. J. Asher. 2007. Cretaceous eutherians and Laurasian origin for placental mammals near the K/T boundary. Nature 447:1003–1006.
Highlights
Homoplasy is a well-appreciated form of phylogenetic noise that systematists strive to identify and avoid when reconstructing species phylogenies
Hennig introduced the critical distinction between shared ancestral homology and shared derived homology, noting that only the latter is indicative of monophyly within an organismal phylogeny
DNA sequence homology in a multigene family can be due either to paralogy or to orthology
Summary
Homoplasy (trait similarity due to evolutionary convergence, parallelism, or character reversals) is a well-appreciated form of phylogenetic noise that systematists strive to identify and avoid when reconstructing species phylogenies. Phylogenetic jargon is already extensive and important because words such as homoplasy, synapomorphy, and orthology capture and convey sophisticated evolutionary concepts that otherwise might remain opaque or underappreciated. In this spirit, here we formally define a new term—hemiplasy—for how the well-known phenomenon of idiosyncratic lineage sorting can lead to fundamental discordances between gene trees and organismal (species) trees. No other word or simple phrase currently exists to encapsulate the phenomenon that we will define under the suggested term
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