Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

Davidson, Ruth; Vachaspati, Pranjal; Mirarab, Siavash; Warnow, Tandy

doi:10.1101/023168

Cited by 24 publications

(28 citation statements)

References 63 publications

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“…While a discussion of the associated challenges of concatenation and MSC methods is well beyond the scope of this work, a strong consensus exists in the literature in favor of using MSC methods to study shallow evolutionary relationships. More specifically, simulations suggest that MSC methods are better than concatenation methods in recovering highly accurate species relationships under ILS levels (Edwards et al, ; Degnan & Rosenberg, ; Davidson, Vachaspati, Mirarab, & Warnow, ; Mirarab, Bayzid, & Warnow, ). The latter approach may then be especially important for taxa that underwent relatively rapid divergence, such as Callithrix , and possess a recent tree root and associated shallow species trees usually typified by higher levels of ILS (Degnan & Rosenberg, ).…”

Section: Discussionmentioning

confidence: 99%

Phylogeny of the jacchus group of Callithrix marmosets based on complete mitochondrial genomes

Malukiewicz

Hepp

Guschanski

et al. 2016

American J Phys Anthropol

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Callithrix nuclear and mtDNA phylogenies frequently result in polytomies and paraphyly. Here, we present a well-supported phylogenetic tree based on mitochondrial genome sequences, which facilitates the understanding of the divergence of the jacchus marmosets. Our results demonstrate how mitochondrial genomes can enrich Callithrix phylogenetic studies by alleviating some of the difficulties faced by previous mtDNA studies and allow formulation of hypotheses to test further under larger genomic-scale analyses.

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Section: Discussionmentioning

confidence: 99%

Phylogeny of the jacchus group of Callithrix marmosets based on complete mitochondrial genomes

Malukiewicz

Hepp

Guschanski

et al. 2016

American J Phys Anthropol

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“…Liu et al [56] examined the effect of HGT on the pseudolikelihood method MP-EST and predicted that, mathematically, species tree branch lengths may be biased by HGT but that topologies were fairly robust. Davidson et al [108] found that quartetbased methods, such as ASTRAL-II, were fairly robust to HGT in the presence of ILS. Removal of genes suspected to be transferred via HGT prior to species tree analysis would be warranted; however, some methods to detect such events rely both on having the true species tree already in hand and also on the absence of other mechanisms causing gene tree discordance [109][110][111][112].…”

Section: Horizontal Gene Transfermentioning

confidence: 99%

Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model

Liu

Anderson²,

Pearl

et al. 2019

Methods in Molecular Biology

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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.

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“…The gene trees with the highest likelihoods from the RaxML analyses on each locus were combined and used as the input for analysis in ASTRAL-II. This method finds the tree that maximizes the number of induced quartet trees in the set of gene trees that are shared by the species tree and has shown to be accurate, even in the presence of incomplete lineage sorting and horizontal gene transfer (Chou et al, 2015;Davidson et al, 2015). We used the heuristic search and multi-locus bootstrapping functions for phylogenetic reconstruction.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Methodological congruence in phylogenomic analyses with morphological support for teiid lizards (Sauria: Teiidae)

Tucker

Colli

Giugliano

et al. 2016

Molecular Phylogenetics and Evolution

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A well-known issue in phylogenetics is discordance among gene trees, species trees, morphology, and other data types. Gene-tree discordance is often caused by incomplete lineage sorting, lateral gene transfer, and gene duplication. Multispecies-coalescent methods can account for incomplete lineage sorting and are believed by many to be more accurate than concatenation. However, simulation studies and empirical data have demonstrated that concatenation and species tree methods often recover similar topologies. We use three popular methods of phylogenetic reconstruction (one concatenation, two species tree) to evaluate relationships within Teiidae. These lizards are distributed across the United States to Argentina and the West Indies, and their classification has been controversial due to incomplete sampling and the discordance among various character types (chromosomes, DNA, musculature, osteology, etc.) used to reconstruct phylogenetic relationships. Recent morphological and molecular analyses of the group resurrected three genera and created five new genera to resolve non-monophyly in three historically ill-defined genera: Ameiva, Cnemidophorus, and Tupinambis. Here, we assess the phylogenetic relationships of the Teiidae using "next-generation" anchored-phylogenomics sequencing. Our final alignment includes 316 loci (488,656bp DNA) for 244 individuals (56 species of teiids, representing all currently recognized genera) and all three methods (ExaML, MP-EST, and ASTRAL-II) recovered essentially identical topologies. Our results are basically in agreement with recent results from morphology and smaller molecular datasets, showing support for monophyly of the eight new genera. Interestingly, even with hundreds of loci, the relationships among some genera in Tupinambinae remain ambiguous (i.e. low nodal support for the position of Salvator and Dracaena).

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Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

Cited by 24 publications

References 63 publications

Phylogeny of the jacchus group of Callithrix marmosets based on complete mitochondrial genomes

Phylogeny of the jacchus group of Callithrix marmosets based on complete mitochondrial genomes

Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model

Methodological congruence in phylogenomic analyses with morphological support for teiid lizards (Sauria: Teiidae)

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