Abstract
An important challenge for phylogenetic studies of closely related species is the existence of deep coalescence and gene tree heterogeneity. However, their effects can vary between species and they are often neglected in phylogenetic analyses. In addition, a practical problem in the reconstruction of shallow phylogenies is to determine the most efficient set of DNA markers for a reliable estimation. To address these questions, we conducted a multilocus simulation study using empirical values of nucleotide diversity and substitution rates obtained from a wide range of mammals and evaluated the performance of both gene tree and species tree approaches to recover the known speciation times and topological relationships. We first show that deep coalescence can be a serious problem, more than usually assumed, for the estimation of speciation times in mammals using traditional gene trees. Furthermore, we tested the performance of different sets of DNA markers in the determination of species trees using a coalescent approach. Although the best estimates of speciation times were obtained, as expected, with the use of an increasing number of nuclear loci, our results show that similar estimations can be obtained with a much lower number of genes and the incorporation of a mitochondrial marker, with its high information content. Thus, the use of the combined information of both nuclear and mitochondrial markers in a species tree framework is the most efficient option to estimate recent speciation times and, consequently, the underlying species tree.
Highlights
Resolution of the phylogenetic relationships among organisms, at or above the species level, has usually been performed using mitochondrial DNA genes [1]
In conditions with the highest population sizes the measured mitochondrial DNA (mtDNA) divergence is 2.7 Myr on average for a simulated species split of 1 Myr, meaning that there is an amount of discordance (d) in the estimated time of 170%
For the shallowest divergences (0.5 Myr), d reaches 300% for a single mitochondrial gene. These values are in agreement with those predicted by coalescence theory, indicating that genealogical discordance is the major cause of these errors
Summary
Resolution of the phylogenetic relationships among organisms, at or above the species level, has usually been performed using mitochondrial DNA (mtDNA) genes [1]. In spite of the advantages of mtDNA, the use of a single marker in phylogenetics has a critical limitation: it allows obtaining only one particular genealogy among all possible ones compatible with the true populations or species tree [2,3]. The probability of observing discordant gene trees depends on Ne and the branch lengths of the species tree. The discordance among gene trees can occur in topology and in branch lengths [9] This source of heterogeneity is always present since different genes are likely to coalesce at different times. This will produce different gene trees (with different branch lengths) even if the topologies are identical. In the last few years, phylogenetics focused on the species tree, rather than on individual gene trees, has received considerable attention since these new methods take into account the coalescence of genes to construct species trees and to estimate reliable split times and demographic parameters [2,3,9,10,11]
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