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

Liu, Liangliang; Yu, Lili; Edwards, Scott V.

doi:10.1186/1471-2148-10-302

Cited by 592 publications

(602 citation statements)

References 68 publications

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“…When a high level of gene tree heterogeneity occurs in multilocus sequence data, theory and simulations have predicted that concatenation methods can yield misleading results (5,6). By contrast, more recently developed coalescence-based methods estimate a species phylogeny from a collection of gene trees, an approach that allows different genes to have different topologies (4,(7)(8)(9)(10). Simulations and theory have shown that coalescent methods can produce accurate phylogenies from multilocus sequence data that are subject to incomplete lineage sorting (ILS), a major cause of gene tree heterogeneity (4,(7)(8)(9)(10).…”

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confidence: 99%

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

Song

Liu

Edwards

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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428

774

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The reconstruction of the Tree of Life has relied almost entirely on concatenation methods, which do not accommodate gene tree heterogeneity, a property that simulations and theory have identified as a likely cause of incongruent phylogenies. However, this incongruence has not yet been demonstrated in empirical studies. Several key relationships among eutherian mammals remain controversial and conflicting among previous studies, including the root of eutherian tree and the relationships within Euarchontoglires and Laurasiatheria. Both Bayesian and maximum-likelihood analysis of genome-wide data of 447 nuclear genes from 37 species show that concatenation methods indeed yield strong incongruence in the phylogeny of eutherian mammals, as revealed by subsampling analyses of loci and taxa, which produced strongly conflicting topologies. In contrast, the coalescent methods, which accommodate gene tree heterogeneity, yield a phylogeny that is robust to variable gene and taxon sampling and is congruent with geographic data. The data also demonstrate that incomplete lineage sorting, a major source of gene tree heterogeneity, is relevant to deep-level phylogenies, such as those among eutherian mammals. Our results firmly place the eutherian root between Atlantogenata and Boreoeutheria and support ungulate polyphyly and a sister-group relationship between Scandentia and Primates. This study demonstrates that the incongruence introduced by concatenation methods is a major cause of long-standing uncertainty in the phylogeny of eutherian mammals, and the same may apply to other clades. Our analyses suggest that such incongruence can be resolved using phylogenomic data and coalescent methods that deal explicitly with gene tree heterogeneity.

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confidence: 99%

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

Song

Liu

Edwards

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

428

774

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“…For the 273 loci, we created 100 multilocus bootstraps (Seo, 2008) that resample both loci within the dataset and bases within a locus. We used three methods of species tree inference: (1) accurate species tree algorithm (ASTRAL; Mirarab et al., 2014), (2) maximum pseudo‐likelihood of estimating species trees (MP‐EST; Liu, Yu, & Edwards, 2010), and (3) species trees from average ranks of coalescence (STAR; Liu et al., 2009). In these analyses, the A. sagrei sample designated the outgroup.…”

Section: Methodsmentioning

confidence: 99%

Diversification in wild populations of the model organism Anolis carolinensis: A genome‐wide phylogeographic investigation

Manthey¹,

Tollis

Lemmon

et al. 2016

Ecology and Evolution

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The green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary history in association with morphological, physiological, or reproductive biology studies among sampling localities and necessitate increased effort to resolve evolutionary relationships among natural populations. Here, we used anchored hybrid enrichment of hundreds of genetic markers across the genome of A. carolinensis and identified five strongly supported phylogeographic groups. Using multiple analyses, we produced a fully resolved species tree, investigated relative support for each lineage across all gene trees, and identified mito‐nuclear discordance when comparing our results to previous studies. We found fixed differences in only one clade—southern Florida restricted to the Everglades region—while most polymorphisms were shared between lineages. The southern Florida group likely diverged from other populations during the Pliocene, with all other diversification during the Pleistocene. Multiple lines of support, including phylogenetic relationships, a latitudinal gradient in genetic diversity, and relatively more stable long‐term population sizes in southern phylogeographic groups, indicate that diversification in A. carolinensis occurred northward from southern Florida.

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“…Individual gene trees were estimated using maximum likelihood using the program RAxML [31]. Because gene tree discordance potentially can prevent recovery of the species tree with concatenated data [32], we used maximum pseudo-likelihood estimates of species trees (MP-EST) [33] to estimate the species tree from the set of gene trees. MP-EST has been shown to be statistically consistent in estimating the species tree even in the anomaly zone, and is computationally efficient for a moderate number of taxa, as in this study [33].…”

Section: Methodsmentioning

confidence: 99%

Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds

2012

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The origin and timing of the diversification of modern birds remains controversial, primarily because phylogenetic relationships are incompletely resolved and uncertainty persists in molecular estimates of lineage ages. Here, we present a species tree for the major palaeognath lineages using 27 nuclear genes and 27 archaic retroposon insertions. We show that rheas are sister to the kiwis, emu and cassowaries, and confirm ratite paraphyly because tinamous are sister to moas. Divergence dating using 10 genes with broader taxon sampling, including emu, cassowary, ostrich, five kiwis, two rheas, three tinamous, three extinct moas and 15 neognath lineages, suggests that three vicariant events and possibly two dispersals are required to explain their historical biogeography. The age of crown group birds was estimated at 131 Ma (95% highest posterior density 122-138 Ma), similar to previous molecular estimates. Problems associated with gene tree discordance and incomplete lineage sorting in birds will require much larger gene sets to increase species tree accuracy and improve error in divergence times. The relatively rapid branching within neoaves pre-dates the extinction of dinosaurs, suggesting that the genesis of the radiation within this diverse clade of birds was not in response to the Cretaceous-Paleogene extinction event.

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

Cited by 592 publications

References 68 publications

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

Diversification in wild populations of the model organism Anolis carolinensis: A genome‐wide phylogeographic investigation

Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds

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