ArticleMolecular biology and evolution2017
StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates.
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143 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity.International journal of molecular sciences · 2019Pooled it
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- Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.Genome biology and evolution · 2025Article
- Beyond Level-1: Identifiability of a Class of Galled Tree-Child Networks.Bulletin of mathematical biology · 2025Article
- Leveraging Weighted Quartet Distributions for Enhanced Species Tree Inference from Genome-Wide Data.Genome biology and evolution · 2025Article
- Phylogenetic networks empower biodiversity research.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Integrating genome-wide traits and multi-loci phylogeny to investigate orchid evolution-A case study on Pleurothallidinae.The Plant journal : for cell and molecular biology · 2025Article
- Evolution is coupled with branching across many granularities of life.Proceedings. Biological sciences · 2025Article
- Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia.Systematic biology · 2025Article
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- Resolving Acuticulata (Metridioidea: Enthemonae: Actiniaria), a clade containing many invasive species of sea anemones.PloS one · 2025Article
83 more citing papers are in PubMed but not listed here.
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Abstract
Fully Bayesian multispecies coalescent (MSC) methods like *BEAST estimate species trees from multiple sequence alignments. Today thousands of genes can be sequenced for a given study, but using that many genes with *BEAST is intractably slow. An alternative is to use heuristic methods which compromise accuracy or completeness in return for speed. A common heuristic is concatenation, which assumes that the evolutionary history of each gene tree is identical to the species tree. This is an inconsistent estimator of species tree topology, a worse estimator of divergence times, and induces spurious substitution rate variation when incomplete lineage sorting is present. Another class of heuristics directly motivated by the MSC avoids many of the pitfalls of concatenation but cannot be used to estimate divergence times. To enable fuller use of available data and more accurate inference of species tree topologies, divergence times, and substitution rates, we have developed a new version of *BEAST called StarBEAST2. To improve convergence rates we add analytical integration of population sizes, novel MCMC operators and other optimizations. Computational performance improved by 13.5× and 13.8× respectively when analyzing two empirical data sets, and an average of 33.1× across 30 simulated data sets. To enable accurate estimates of per-species substitution rates, we introduce species tree relaxed clocks, and show that StarBEAST2 is a more powerful and robust estimator of rate variation than concatenation. StarBEAST2 is available through the BEAUTi package manager in BEAST 2.4 and above.
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