Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model

Abstract

The multispecies coalescent (MSC) model provides a compelling framework for building phylogenetic trees from multilocus DNA sequence data. The pure MSC is best thought of as a special case of so-called "multispecies network coalescent" models, in which gene flow is allowed among branches of the tree, whereas MSC methods assume there is no gene flow between diverging species. Early implementations of the MSC, such as "parsimony" or "democratic vote" approaches to combining information from multiple gene trees, as well as concatenation, in which DNA sequences from multiple gene trees are combined into a single "supergene," were quickly shown to be inconsistent in some regions of tree space, in so far as they converged on the incorrect species tree as more gene trees and sequence data were accumulated. The anomaly zone, a region of tree space in which the most frequent gene tree is different from the species tree, is one such region where many so-called "coalescent" methods are inconsistent. Second-generation implementations of the MSC employed Bayesian or likelihood models; these are consistent in all regions of gene tree space, but Bayesian methods in particular are incapable of handling the large phylogenomic data sets currently available. Two-step methods, such as MP-EST and ASTRAL, in which gene trees are first estimated and then combined to estimate an overarching species tree, are currently popular in part because they can handle large phylogenomic data sets. These methods are consistent in the anomaly zone but can sometimes provide inappropriate measures of tree support or apportion error and signal in the data inappropriately. MP-EST in particular employs a likelihood model which can be conveniently manipulated to perform statistical tests of competing species trees, incorporating the likelihood of the collected gene trees on each species tree in a likelihood ratio test. Such tests provide a useful alternative to the multilocus bootstrap, which only indirectly tests the appropriateness of competing species trees. We illustrate these tests and implementations of the MSC with examples and suggest that MSC methods are a useful class of models effectively using information from multiple loci to build phylogenetic trees.

Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships

“…We supplied unconstrained gene trees from our summary coalescence analyses to MP-EST and constrained the species tree topologies but allowed the branch lengths to be optimized to best fit the data presented by the gene trees. We modified the test2.sptree function of phybase (provided in Data Supplement , ) to enable all three subfamily arrangements to be compared as described in Liu et al (2019) . Likelihood ratio test statistics ( t ) were calculated between pairs of alternative trees and we generated a distribution of the test statistic by bootstrap sampling gene trees 100 times to estimate the null distribution for t and provide a measure of statistical significance ( p- value).…”

Terraces in Gene Tree Reconciliation-Based Species Tree Inference

“…Copetti et al 2017). For the latter, however, there are a variety of model based and discrete algorithm approaches to inference (Liu et al 2019), whereas our results are most directly relevant to the simple method of minimizing the deep coalescence score (Maddison 1997; Ma et al 2001; Zhang 2011; Nakhleh 2013). However, we expect that the general idea of terraces will likely extend to certain model based methods of species tree inference by analogy with how it extends to likelihood based inference from multi-locus sequence alignments (Sanderson et al 2011, 2015).…”

“…Different regions of the genome can have different phylogenetic histories, and these “gene trees” can also differ from the species tree in which they are imbedded (Bravo et al 2019; Liu et al 2019). The framework of gene tree “reconciliation” provides an analytically rich and empirically powerful toolkit to understand this mosaic of histories and to infer species trees from discordant gene trees (Goodman et al 1979; Page 1994).…”

Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils

“…This composition of 37 genes and a control region is well-conserved in the bilaterian animals ( Bernt et al, 2012 ), though there are rare deviations from this general pattern. In beetles, they involve gene order reversal and presumably deletion of tRNA genes ( Timmermans & Vogler, 2012 ; Liu et al, 2019 ) and in rare cases rearrangements of PCGs genes, e.g., in Iberobaenia sp. (Iberobaemidae) ( Andujar et al, 2016 ) and Omus cazieri (Carabidae) ( López-López & Vogler, 2017 ).…”

“…Most seriously, gene trees may differ from species trees due to hybridization and incomplete lineage sorting ( Edwards, 2009 ; Maddison, 1997 ). Since mitochondrial genes are linked and behave as a single marker, a multispecies coalescent approach ( Liu et al, 2016 ) potentially solving these issues cannot be taken. However, facing millions of species (most of them arthropods) that need an improved phylogenetic placement, mitogenomes are our first choice.…”