Relationships between gene trees and species trees.

TLDR

Gene trees often disagree with species trees, largely due to ancestral genetic polymorphism. The study evaluates the probability that a gene tree matches the species tree under neutral mutation assumptions. The probability is calculated as a function of Ti = ti/(2N) using one allele per species, and increasing it requires sampling many independent loci. If any Ti < 1, the probability of concordance drops below 1.0 and cannot be markedly improved by sampling more alleles per locus.

Abstract

It is well known that a phylogenetic tree (gene tree) constructed from DNA sequences for a genetic locus does not necessarily agree with the tree that represents the actual evolutionary pathway of the species involved (species tree). One of the important factors that cause this difference is genetic polymorphism in the ancestral species. Under the assumption of neutral mutations, this problem can be studied by evaluating the probability (P) that a gene tree has the same topology as that of the species tree. When one gene (allele) is used from each of the species involved, the probability can be expressed as a simple function of Ti = ti/(2N), where ti is the evolutionary time measured in generations for the ith internodal branch of the species tree and N is the effective population size. When any of the Ti's is less than 1, the probability P becomes considerably less than 1.0. This probability cannot be substantially increased by increasing the number of alleles sampled from a locus. To increase the probability, one has to use DNA sequences from many different loci that have evolved independently of each other.