Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling
<p>Abstract</p> <p>Background</p> <p>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 throug...
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| Format: | Article |
| Language: | English |
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BMC
2011-10-01
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| Series: | BMC Evolutionary Biology |
| Online Access: | http://www.biomedcentral.com/1471-2148/11/291 |
| _version_ | 1818978529305427968 |
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| author | Gibbs H Lisle Gerard David Kubatko Laura |
| author_facet | Gibbs H Lisle Gerard David Kubatko Laura |
| author_sort | Gibbs H Lisle |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>Sistrurus </it>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.</p> <p>Conclusions</p> <p>Our approach is shown to be powerful in detecting hybridization when it is present. When applied to the <it>Sistrurus </it>data, we find no evidence of hybridization; instead, it appears that putative hybrid snakes in Missouri are most likely pure <it>S. catenatus tergeminus </it>in origin, which has significant conservation implications.</p> |
| first_indexed | 2024-12-20T16:45:05Z |
| format | Article |
| id | doaj.art-9931ac22286f43ef95671b9aaa7f25b5 |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-20T16:45:05Z |
| publishDate | 2011-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-9931ac22286f43ef95671b9aaa7f25b52022-12-21T19:32:57ZengBMCBMC Evolutionary Biology1471-21482011-10-0111129110.1186/1471-2148-11-291Estimating hybridization in the presence of coalescence using phylogenetic intraspecific samplingGibbs H LisleGerard DavidKubatko Laura<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>Sistrurus </it>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.</p> <p>Conclusions</p> <p>Our approach is shown to be powerful in detecting hybridization when it is present. When applied to the <it>Sistrurus </it>data, we find no evidence of hybridization; instead, it appears that putative hybrid snakes in Missouri are most likely pure <it>S. catenatus tergeminus </it>in origin, which has significant conservation implications.</p>http://www.biomedcentral.com/1471-2148/11/291 |
| spellingShingle | Gibbs H Lisle Gerard David Kubatko Laura Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling BMC Evolutionary Biology |
| title | Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling |
| title_full | Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling |
| title_fullStr | Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling |
| title_full_unstemmed | Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling |
| title_short | Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling |
| title_sort | estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling |
| url | http://www.biomedcentral.com/1471-2148/11/291 |
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