Bayesian inference of species trees from multilocus data
| Item Type |
Journal Article |
| Author |
Joseph Heled |
| Author |
Alexei J Drummond |
| URL |
http://www.ncbi.nlm.nih.gov/pubmed/19906793
|
| Publication |
Molecular Biology and Evolution |
| ISSN |
1537-1719 |
| Date |
Nov 20, 2009 |
| Extra |
| Journal Abbr |
Mol. Biol. Evol |
| DOI |
10.1093/molbev/msp274 |
| Accessed |
2009-12-30 14:27:05 |
| Library Catalog |
NCBI PubMed |
| 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 MCMC method for the multispecies coalescent. Our method co-estimates 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 multi-locus data from multiple individuals per species. Using a multi-individual 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) 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. |
| Title |
Bayesian inference of species trees from multilocus data |
| Date Added |
2009-12-30 09:27 |
| Date Modified |
2009-12-30 09:27 |