Coalescent methods for estimating species trees from phylogenomic data

Liu, Liang; Wu, Shaoyuan; Yu, Lili

doi:10.1111/jse.12160

Cited by 87 publications

(92 citation statements)

References 66 publications

(75 reference statements)

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“…We know gene‐tree incongruence exists in our work and that of others (reviewed in Gatesy & Springer, ). Coalescent‐based methods for resolving species trees may account for heterogeneous gene trees and hold promise for phylogenomic data sets, even in the face of deep coalescence, incomplete lineage sorting, and mutation (see Liu et al, for a nice review of coalescent methods). Other approaches to handling gene tree discordance have been proposed, e.g., statistical binning of loci prior to gene tree estimation (Mirarab et al, ).…”

Section: Gene Tree Discordancementioning

confidence: 99%

The Compositae Tree of Life in the age of phylogenomics

Mandel

Barker

Bayer

et al. 2017

J of Sytematics Evolution

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Comprising more than 25 000 species, the Sunflower Family (Compositae or Asteraceae) is the largest family of flowering plants. Many of its lineages have experienced recent and rapid radiations, and the family has a deep and widespread history of large-scale gene duplications and polyploidy. Many of the most important evolutionary questions about the family's diversity remain unanswered due to poor resolution and lack of support for major nodes of the phylogeny. Our group has employed a phylogenomics approach using Hyb-Seq that includes sequencing 1000 low-copy number nuclear markers, plus partial plastomes for large numbers of species. Here we discuss our progress to date and present two phylogenies comprising nine subfamilies and 25 tribes using concatenated and coalescence-based analyses. We discuss future plans for incorporating high-quality reference genomes and transcriptomes to advance systematic and evolutionary studies in the Compositae. While we have made great strides toward developing tools for employing phylogenomics and resolving relationships within Compositae, much work remains. Recently formed global partnerships will work to solve the unanswered evolutionary questions for this megafamily.

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Section: Gene Tree Discordancementioning

confidence: 99%

The Compositae Tree of Life in the age of phylogenomics

Mandel

Barker

Bayer

et al. 2017

J of Sytematics Evolution

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“…Certain supertree methods incorporate the multi species coalescent model to estimate the species tree from a set of heterogeneous gene trees (Knowles, 2009). The multispecies coalescent model extends the classical coalescent (Kingman, 1980) to multiple populations and describes gene trees as indepen dent random variables generated from the coalescence process occurring along lineages of the species tree (Liu et al, 2015). A number of coalescent based methods have been developed to esti mate the species tree from multigene sequence data, including Bayesian (e.g., BUCKy, Ane et al, 2007; BEAST, Drummond et al, 2012) and likelihood approaches (e.g., STEM, Kubatko et al, 2009;STELLS, Wu, 2012).…”

Section: Introductionmentioning

confidence: 99%

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

Ottenburghs

Megens

Kraus

et al. 2016

Molecular Phylogenetics and Evolution

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a b s t r a c tPhylogenetic incongruence can be caused by analytical shortcomings or can be the result of biological processes, such as hybridization, incomplete lineage sorting and gene duplication. Differentiation between these causes of incongruence is essential to unravel complex speciation and diversification events. The phylogeny of the True Geese (tribe Anserini, Anatidae, Anseriformes) was, until now, con tentious, i.e., the phylogenetic relationships and the timing of divergence between the different goose species could not be fully resolved. We sequenced nineteen goose genomes (representing seventeen spe cies of which three subspecies of the Brent Goose, Branta bernicla) and used an exon based phylogenomic approach (41,736 exons, representing 5887 genes) to unravel the evolutionary history of this bird group. We thereby provide general guidance on the combination of whole genome evolutionary analyses and analytical tools for such cases where previous attempts to resolve the phylogenetic history of several taxa could not be unravelled. Identical topologies were obtained using either a concatenation (based upon an alignment of 6,630,626 base pairs) or a coalescent based consensus method. Two major lineages, corre sponding to the genera Anser and Branta, were strongly supported. Within the Branta lineage, the White cheeked Geese form a well supported sub lineage that is sister to the Red breasted Goose (Branta ruficol lis). In addition, two main clades of Anser species could be identified, the White Geese and the Grey Geese. The results from the consensus method suggest that the diversification of the genus Anser is heavily influ enced by rapid speciation and by hybridization, which may explain the failure of previous studies to resolve the phylogenetic relationships within this genus. The majority of speciation events took place in the late Pliocene and early Pleistocene (between 4 and 2 million years ago), conceivably driven by a global cooling trend that led to the establishment of a circumpolar tundra belt and the emergence of tem perate grasslands. Our approach will be a fruitful strategy for resolving many other complex evolutionary histories at the level of genera, species, and subspecies.

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“…Such incongruence can be caused by analytical shortcomings (Rokas et al 2003, Davalos et al 2012 or can be the result of biological processes, such as horizontal gene transfer, hybridization, incomplete lineage sorting, and gene duplication (Pamilo and Nei 1988, Maddison 1997, Degnan and Rosenberg 2009). Several methods have been developed to estimate a species tree from a collection of discordant gene trees (Delsuc et al 2005, Degnan and Rosenberg 2009, Liu et al 2015. The construction of a species tree from several discordant gene trees is based on the assumption that the underlying evolutionary process is tree-like.…”

mentioning

confidence: 99%