ArticleMolecular biology and evolution2012
Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis.
Article in Molecular biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 326 papers.
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326 citing papers in PubMed.
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- Estimating Waiting Distances between Genealogy Changes under a Multi-Species Extension of the Sequentially Markov Coalescent.Systematic biology · 2026Article
- Species Diversification in the Sky Islands of Southwestern China Revealed by Genomic, Introgression, and Demographic Analyses of Asian Shrew Moles.Systematic biology · 2026Article
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- Impact of Data Error on Phylogenetic Network Inference from Gene Trees Under the Multispecies Network Coalescent.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The Impact of Pleistocene Glacial Cycles on the Evolutionary Diversification of the Arctic-Alpine Silene acaulis Species Complex.Molecular ecology · 2026Article
- Morphological and genomic data from Belgian naturalised populations reinstate the enigmaticPhytoKeys · 2026Article
- Integrative Taxonomy Clarifies the Taxonomic Status of the Morphologically Intermediate Form BetweenInsects · 2025Article
- Global species delimitation of smooth-shelled blue mussels in the Mytilus edulis complex.Scientific reports · 2025Article
- Phylogenomics of Marine Angelfishes: Diagnosing Sources of Systematic Discordance for an Iconic Reef Fish Family (F: Pomacanthidae).Systematic biology · 2025Article
- Genomic Signatures in Maned Three-Toed Sloths From Ancient to Recent Environmental Changes in Brazil's Threatened Atlantic Forest.Molecular ecology · 2025Article
266 more citing papers are in PubMed but not listed here.
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5 authors.
Funding
Abstract
The multispecies coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. However, practical applications of the multispecies coalescent model are limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms, and we have implemented it in SNAPP, a Markov chain Monte Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism loci in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove).
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