Nov 13, 2009

Bayesian inference of species trees from multilocus data

Molecular Biology and Evolution
Joseph Heled, Alexei J Drummond

Abstract

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...Continue Reading

  • References35
  • Citations880

References

  • References35
  • Citations880

Citations

Mentioned in this Paper

In Silico
Phylogeny
Sorting - Cell Movement
Organism
Monte Carlo Method
Cistron
Bayesian Prediction
Genetic Polymorphism
Evolution, Molecular
Anatomy, Regional

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