Relationships between gene trees and species trees.

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.

Impact of long‐term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages

“…Irrespective of the variation in effective population sizes inputted, the distribution of mismatch gene trees followed the MSC model. Therefore, as population sizes increased, all three possible gene tree topologies tended to be equally likely, exactly as expected by the standard equations for three species rooted by an outgroup (Pamilo & Nei, 1988). We thus suggest that ancestral demographic dynamics fail to adequately explain our results for NP.…”

“…The same is true for hominids. For instance, using the equation of theoretical probability of a topological match between gene trees and the species tree (Pamilo & Nei, 1988), this internode interval varied from 0.03 to 0.19 coalescent units in NP and 0.09 to 0.57 in hominids. These values contrasted with previous estimates of ~0.3 for NP (Schrago et al., 2014) and ~1.1 coalescent units for hominids (Hobolth et al., 2007; Schrago, 2014a).…”

“…For instance, rooting with Pongo , if (( Homo , Pan ), Gorilla ) is the species tree, the frequencies of mismatch gene tree topologies, that is, (( Gorilla , Pan ), Homo ) and (( Homo , Gorilla ), Pan ), are expected to be equivalent under complete independence of gene loci (Pamilo & Nei, 1988). If chromosomal shuffling is an issue for MSC analysis of NP, we hypothesized that differences between the frequencies of mismatch topologies (i.e., frequency imbalance) would decrease with decreasing fragment length, because the shorter the fragments, the higher their probability of containing nucleotide sites sharing the same evolutionary history, thus behaving closely to MSC expectations.…”

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

“…Consider an arbitrary rooted triple $R{T}_j{}^{S^{*}}$= AB|C in the species tree and the length of the internal branch of $R{T}_j{}^{S^{*}}$ is B j . Let a, b, and c be the alleles sampled from species A, B, and C. Under coalescent, the probability that triple ab|c occurs in a gene tree randomly generated from species tree S * is $1-\left(2/3\right)e^{-B_j}$, whereas the probability is $\left(1/3\right)e^{-B_j}$ for triple ac|b or bc|a [41]. It indicates that the length B j of the internal branch of a species tree triple AB|C can be estimated by the proportion of gene trees containing triple ab|c.…”

Genetic Analysis of the Cytoplasmic Dynein Subunit Families

“…DYNC1H1 in humans, mouse, and rat). Relationships amongst dynein sequences of different species do not necessarily reflect the evolutionary relationships amongst species; see [208] and [209] for further details. Named clades are indicated in the right margins.…”