ASTRAL: genome-scale coalescent-based species tree estimation

Abstract

Motivation: Species trees provide insight into basic biology, including the mechanisms of evolution and how it modifies biomolecular function and structure, biodiversity and co-evolution between genes and species. Yet, gene trees often differ from species trees, creating challenges to species tree estimation. One of the most frequent causes for conflicting topologies between gene trees and species trees is incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent. While many methods have been developed to estimate species trees from multiple genes, some which have statistical guarantees under the multi-species coalescent model, existing methods are too computationally intensive for use with genome-scale analyses or have been shown to have poor accuracy under some realistic conditions.Results: We present ASTRAL, a fast method for estimating species trees from multiple genes. ASTRAL is statistically consistent, can run on datasets with thousands of genes and has outstanding accuracy—improving on MP-EST and the population tree from BUCKy, two statistically consistent leading coalescent-based methods. ASTRAL is often more accurate than concatenation using maximum likelihood, except when ILS levels are low or there are too few gene trees.Availability and implementation: ASTRAL is available in open source form at https://github.com/smirarab/ASTRAL/. Datasets studied in this article are available at http://www.cs.utexas.edu/users/phylo/datasets/astral.Contact: warnow@illinois.eduSupplementary information: Supplementary data are available at Bioinformatics online.

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

“…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.…”

Mammal madness: is the mammal tree of life not yet resolved?

“…However, fully parametric coalescent models such as *BEAST [79] and BEST [80], which co-estimate gene trees and the species tree [81], cannot be applied to large datasets because they are massively computationally intensive [19]. As such, shortcut coalescence methods such as STEAC, STAR [76], MP-EST [54] and ASTRAL [82], which carry out separate estimation of gene trees and the species tree, have been applied to large mammalian datasets [7,21] (table 3). Criticisms aimed at recent applications of these shortcut methods to the placental tree have focused on inappropriate coalescent-gene (c-gene) size and high levels of gene tree reconstruction error [10].…”

Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a MediterraneanCampanula(Campanulaceae) clade

“…2014). The 130 ML gene trees (best trees) inferred using RA × ML were used as input, and local posterior probabilities were estimated to provide support for relationships.…”