Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis

Mol Biol Evol. 2012 Aug;29(8):1917-32. doi: 10.1093/molbev/mss086. Epub 2012 Mar 14.


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).

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Alleles*
  • Amplified Fragment Length Polymorphism Analysis
  • Computer Simulation
  • Databases, Genetic
  • Digitalis / genetics*
  • Genes, Plant / genetics*
  • Genetic Markers
  • Likelihood Functions
  • New Zealand
  • Phylogeny*
  • Species Specificity


  • Genetic Markers