Bayesian inference of species trees from multilocus data
Open accessAbstract
Until recently, it has been common practice for a phylogenetic analysis to use a single gene sequence from a single individual organism as a proxy for an entire species. With technological advances, it is now becoming more common to collect data sets containing multiple gene loci and multiple individuals per species. These data sets often reveal the need to directly model intraspecies polymorphism and incomplete lineage sorting in phylogenetic estimation procedures. For a single species, coalescent theory is widely used in contemporary population genetics to model intraspecific gene trees. Here, we present a Bayesian Markov chain Monte Carlo method for the multispecies coalescent. Our method coestimates multiple gene trees embedded in a shared species tree along with the effective population size of both extant and ancestral species. The inference is made possible by multilocus data from multiple individuals per species. Using a multiindividual data set and a series of simulations of rapid species radiations, we demonstrate the efficacy of our new method. These simulations give some insight into the behavior of the method as a function of sampled individuals, sampled loci, and sequence length. Finally, we compare our new method to both an existing method (BEST 2.2) with similar goals and the supermatrix (concatenation) method. We demonstrate that both BEST and our method have much better estimation accuracy for species tree topology than concatenation, and our method outperforms BEST in divergence time and population size estimation.
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Bayesian multispecies coalescent models like *BEAST and starBEAST2 consider gene tree variations and can give more accurate estimate of per-species substitution rates.
“Bayesian multispecies coalescent models like *BEAST and starBEAST2 consider gene tree variations and can give more accurate estimate of per-species substitution rates (Heled and Drummond 2010; Ogilvie et al. 2017).”
From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Heled and Drummond 2010
The Introduction and Comparison with BEST section say that *BEAST jointly estimates multiple gene trees under a multispecies coalescent model, supporting the gene-tree-variation part of the claim. In Results, “Estimation of Relative Substitution Rates for Different Loci” reports estimates of rates across loci, not more accurate estimates of per-species substitution rates. This source describes *BEAST; it does not assess starBEAST2. (LLM, conf=0.90)
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- Authors
- Heled, J., & Drummond, A. J.
- Affiliations
- University of Auckland (NZ)
- Corresponding author
- Heled, J.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-11-11
- Volume
- 27
- Issue
- 3
- Pages
- 570-580
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC2822290
- OpenAlex
- W2107608009
- Cited by
- 2,453
- References
- 4
- Citations by year
- 2026: 30 · 2025: 49 · 2024: 64 · 2023: 69 · 2022: 115 · 2021: 127 · 2020: 169 · 2019: 158 · 2018: 210 · 2017: 249 · 2016: 234 · 2015: 208 · 2014: 256 · 2013: 223 · 2012: 157
- FWCI
- 36.37
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Molecular Biology and Evolution (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- ResearchSpace (University of Auckland) (submittedVersion, cc-by)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- species tree estimation, multispecies coalescent, multilocus data, Bayesian phylogenetics, incomplete lineage sorting, effective population size, species radiation, Best, divergence time estimation
- MeSH terms
- Algorithms, Bayes Theorem, Computer Simulation, Genes, Models, Genetic, Monte Carlo Method, Phylogeny, Species Specificity, Evolution, Molecular
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