Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites

Chifman, Julia; Kubatko, Laura

doi:10.1016/j.jtbi.2015.03.006

Cited by 243 publications

(245 citation statements)

References 34 publications

Supporting

Mentioning

245

Contrasting

Order By: Relevance

“…To obtain a species tree estimate that did not rely on prior inference of individual gene trees, we used SVDquartets4046, a method that analyzes quartets of species in a coalescent framework using singular value decomposition of the matrix of site pattern frequencies and then assembles a species tree from the quartets using a supertree method. This method was developed for analysis of unlinked single nucleotide polymorphism data, but extended to analysis of DNA sequences, especially large, multi-locus data sets.…”

Section: Methodsmentioning

confidence: 99%

Tectonic collision and uplift of Wallacea triggered the global songbird radiation

et al. 2016

View full text Add to dashboard Cite

Songbirds (oscine passerines) are the most species-rich and cosmopolitan bird group, comprising almost half of global avian diversity. Songbirds originated in Australia, but the evolutionary trajectory from a single species in an isolated continent to worldwide proliferation is poorly understood. Here, we combine the first comprehensive genome-scale DNA sequence data set for songbirds, fossil-based time calibrations, and geologically informed biogeographic reconstructions to provide a well-supported evolutionary hypothesis for the group. We show that songbird diversification began in the Oligocene, but accelerated in the early Miocene, at approximately half the age of most previous estimates. This burst of diversification occurred coincident with extensive island formation in Wallacea, which provided the first dispersal corridor out of Australia, and resulted in independent waves of songbird expansion through Asia to the rest of the globe. Our results reconcile songbird evolution with Earth history and link a major radiation of terrestrial biodiversity to early diversification within an isolated Australian continent.

show abstract

Section: Methodsmentioning

confidence: 99%

Tectonic collision and uplift of Wallacea triggered the global songbird radiation

et al. 2016

View full text Add to dashboard Cite

show abstract

“…In other words, when L / N, the estimate will converge in probability to the true species tree and true parameter values. Identifiability under commonly used substitution models has been discussed by Steel (2013) and Chifman and Kubatko (2015). The efficiency of the methods, while very important, appears intractable analytically.…”

Section: Full Likelihood Methods Of Species Tree Estimation Under Thementioning

confidence: 99%

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

2016

View full text Add to dashboard Cite

The multispecies coalescent (MSC) model has emerged as a powerful framework for inferring species phylogenies while accounting for ancestral polymorphism and gene tree-species tree conflict. A number of methods have been developed in the past few years to estimate the species tree under the MSC. The full likelihood methods (including maximum likelihood and Bayesian inference) average over the unknown gene trees and accommodate their uncertainties properly but involve intensive computation. The approximate or summary coalescent methods are computationally fast and are applicable to genomic datasets with thousands of loci, but do not make an efficient use of information in the multilocus data. Most of them take the two-step approach of reconstructing the gene trees for multiple loci by phylogenetic methods and then treating the estimated gene trees as observed data, without accounting for their uncertainties appropriately. In this article we review the statistical nature of the species tree estimation problem under the MSC, and explore the conceptual issues and challenges of species tree estimation by focusing mainly on simple cases of three or four closely related species. We use mathematical analysis and computer simulation to demonstrate that large differences in statistical performance may exist between the two classes of methods. We illustrate that several counterintuitive behaviors may occur with the summary methods but they are due to inefficient use of information in the data by summary methods and vanish when the data are analyzed using full-likelihood methods. These include (i) unidentifiability of parameters in the model, (ii) inconsistency in the so-called anomaly zone, (iii) singularity on the likelihood surface, and (iv) deterioration of performance upon addition of more data. We discuss the challenges and strategies of species tree inference for distantly related species when the molecular clock is violated, and highlight the need for improving the computational efficiency and model realism of the likelihood methods as well as the statistical efficiency of the summary methods.

show abstract

“…We also used two methods based on the multi-species coalescent model to infer the species phylogeny, SVDQuartets (Chifman and Kubatko 2015) and ASTRAL II (Mirarab et al 2014). SVDQuartets was performed by PAUP* version 4.0a150 using exhaustive quartet sampling and 1000 bootstrap replicates.…”

Section: Methodsmentioning

confidence: 99%

A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment

Maddison¹,

Evans²,

Hamilton³

et al. 2017

View full text Add to dashboard Cite

We present the first genome-wide molecular phylogeny of jumping spiders (Araneae: Salticidae), inferred from Anchored Hybrid Enrichment (AHE) sequence data. From 12 outgroups plus 34 salticid taxa representing all but one subfamily and most major groups recognized in previous work, we obtained 447 loci totalling 96,946 aligned nucleotide sites. Our analyses using concatenated likelihood, parsimony, and coalescent methods (ASTRAL and SVDQuartets) strongly confirm most previous results, resolving as monophyletic the Spartaeinae, Salticinae (with the hisponines sister), Salticoida, Amycoida, Saltafresia, and Simonida. The agoriines, previously difficult to place beyond subfamily, are finally placed confidently within the saltafresians as relatives of the chrysillines and hasariines. Relationships among the baviines, astioids, marpissoids, and saltafresians remain uncertain, though our analyses tentatively conclude the first three form a clade together. Deep relationships, among the seven subfamilies, appear to be largely resolved, with spartaeines, lyssomanines, and asemoneines forming a clade. In most analyses, Onomastus (representing the onomastines) is strongly supported as sister to the hisponines plus salticines. Overall, the much-improved resolution of many deep relationships despite a relatively sparse taxon sample suggests AHE is a promising technique for salticid phylogenetics.

show abstract

Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites

Cited by 243 publications

References 34 publications

Tectonic collision and uplift of Wallacea triggered the global songbird radiation

Tectonic collision and uplift of Wallacea triggered the global songbird radiation

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment

Contact Info

Product

Resources

About