Integrative methods reveal multiple drivers of diversification in rice paddy snakes
Abstract Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hy...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-03-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-024-54744-z |
| _version_ | 1797259360343162880 |
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| author | Justin M. Bernstein Harold K. Voris Bryan L. Stuart Daryl R. Karns Jimmy A. McGuire Djoko T. Iskandar Awal Riyanto Camilo A. Calderón-Acevedo Rafe M. Brown Marcelo Gehara J. Angel Soto-Centeno Sara Ruane |
| author_facet | Justin M. Bernstein Harold K. Voris Bryan L. Stuart Daryl R. Karns Jimmy A. McGuire Djoko T. Iskandar Awal Riyanto Camilo A. Calderón-Acevedo Rafe M. Brown Marcelo Gehara J. Angel Soto-Centeno Sara Ruane |
| author_sort | Justin M. Bernstein |
| collection | DOAJ |
| description | Abstract Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae: Hypsiscopus), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis that Hypsiscopus diversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggest Hypsiscopus diversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species of Hypsiscopus, indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets. |
| first_indexed | 2024-04-24T23:08:11Z |
| format | Article |
| id | doaj.art-76ba8989103f47959ad86945c35e995e |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-24T23:08:11Z |
| publishDate | 2024-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-76ba8989103f47959ad86945c35e995e2024-03-17T12:23:35ZengNature PortfolioScientific Reports2045-23222024-03-0114111510.1038/s41598-024-54744-zIntegrative methods reveal multiple drivers of diversification in rice paddy snakesJustin M. Bernstein0Harold K. Voris1Bryan L. Stuart2Daryl R. Karns3Jimmy A. McGuire4Djoko T. Iskandar5Awal Riyanto6Camilo A. Calderón-Acevedo7Rafe M. Brown8Marcelo Gehara9J. Angel Soto-Centeno10Sara Ruane11Center for Genomics, University of KansasLife Sciences Section, Negaunee Integrative Research Center, Field MuseumSection of Research and Collections, North Carolina Museum of Natural SciencesBiology Department, Hanover CollegeMuseum of Vertebrate Zoology and Department of Integrative Biology, University of CaliforniaSchool of Life Sciences and Technology, Institut Teknologi BandungMuseum Zoologicum Bogoriense, Research Center for Biology, National Research and Innovation Agency of Indonesia (BRIN)State University of New York: College of Environmental Science and ForestryDepartment of Ecology and Evolutionary Biology and Biodiversity Institute, University of KansasDepartment of Earth and Environmental Science, Rutgers University-NewarkDepartment of Earth and Environmental Science, Rutgers University-NewarkLife Sciences Section, Negaunee Integrative Research Center, Field MuseumAbstract Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae: Hypsiscopus), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis that Hypsiscopus diversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggest Hypsiscopus diversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species of Hypsiscopus, indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets.https://doi.org/10.1038/s41598-024-54744-z |
| spellingShingle | Justin M. Bernstein Harold K. Voris Bryan L. Stuart Daryl R. Karns Jimmy A. McGuire Djoko T. Iskandar Awal Riyanto Camilo A. Calderón-Acevedo Rafe M. Brown Marcelo Gehara J. Angel Soto-Centeno Sara Ruane Integrative methods reveal multiple drivers of diversification in rice paddy snakes Scientific Reports |
| title | Integrative methods reveal multiple drivers of diversification in rice paddy snakes |
| title_full | Integrative methods reveal multiple drivers of diversification in rice paddy snakes |
| title_fullStr | Integrative methods reveal multiple drivers of diversification in rice paddy snakes |
| title_full_unstemmed | Integrative methods reveal multiple drivers of diversification in rice paddy snakes |
| title_short | Integrative methods reveal multiple drivers of diversification in rice paddy snakes |
| title_sort | integrative methods reveal multiple drivers of diversification in rice paddy snakes |
| url | https://doi.org/10.1038/s41598-024-54744-z |
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