Email updates

Keep up to date with the latest news and content from BMC Evolutionary Biology and BioMed Central.

Open Access Highly Accessed Methodology article

Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling

David Gerard1, H Lisle Gibbs2 and Laura Kubatko12*

Author Affiliations

1 Department of Statistics, The Ohio State University, Columbus, OH 43210, USA

2 Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus OH 43210, USA

For all author emails, please log on.

BMC Evolutionary Biology 2011, 11:291  doi:10.1186/1471-2148-11-291

Published: 6 October 2011



A well-known characteristic of multi-locus data is that each locus has its own phylogenetic history which may differ substantially from the overall phylogenetic history of the species. Although the possibility that this arises through incomplete lineage sorting is often incorporated in models for the species-level phylogeny, it is much less common for hybridization to also be formally included in such models.


We have modified the evolutionary model of Meng and Kubatko (2009) to incorporate intraspecific sampling of multiple individuals for estimation of speciation times and times of hybridization events for testing for hybridization in the presence of incomplete lineage sorting. We have also utilized a more efficient algorithm for obtaining our estimates. Using simulations, we demonstrate that our approach performs well under conditions motivated by an empirical data set for Sistrurus rattlesnakes where putative hybridization has occurred. We further demonstrate that the method is able to accurately detect the signature of hybridization in the data, while this signal may be obscured when other species-tree inference methods that ignore hybridization are used.


Our approach is shown to be powerful in detecting hybridization when it is present. When applied to the Sistrurus data, we find no evidence of hybridization; instead, it appears that putative hybrid snakes in Missouri are most likely pure S. catenatus tergeminus in origin, which has significant conservation implications.