Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in Pleistocene refugia followed by human-influenced dispersal
Cacao (Theobroma cacao L.) is indigenous to the Amazon basin, but is generally believed to have been domesticated in Mesoamerica for the production of chocolate beverage. However, cacao’s distribution of genetic diversity in South America is also likely to reflect pre-Columbian human influences that...
| Main Authors: | , , , , , |
|---|---|
| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Public Library of Science
2012
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/35815 |
| _version_ | 1855533486747680768 |
|---|---|
| author | Thomas, E. Zonneveld, M. van Loo, J. Hodgkin, T. Galluzzi, Gea Etten, Jacob van |
| author_browse | Etten, Jacob van Galluzzi, Gea Hodgkin, T. Loo, J. Thomas, E. Zonneveld, M. van |
| author_facet | Thomas, E. Zonneveld, M. van Loo, J. Hodgkin, T. Galluzzi, Gea Etten, Jacob van |
| author_sort | Thomas, E. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Cacao (Theobroma cacao L.) is indigenous to the Amazon basin, but is generally believed to have been domesticated in Mesoamerica for the production of chocolate beverage. However, cacao’s distribution of genetic diversity in South America is also likely to reflect pre-Columbian human influences that were superimposed on natural processes of genetic differentiation. Here we present the results of a spatial analysis of the intra-specific diversity of cacao in Latin America, drawing on a dataset of 939 cacao trees genotypically characterized by means of 96 SSR markers. To assess continental diversity patterns we performed grid-based calculations of allelic richness, Shannon diversity and Nei gene diversity, and distinguished different spatially coherent genetic groups by means of cluster analysis. The highest levels of genetic diversity were observed in the Upper Amazon areas from southern Peru to the Ecuadorian Amazon and the border areas between Colombia, Peru and Brazil. On the assumption that the last glaciation (22,000–13,000 BP) had the greatest pre-human impact on the current distribution and diversity of cacao, we modeled the species’ Pleistocene niche suitability and overlaid this with present-day diversity maps. The results suggest that cacao was already widely distributed in the Western Amazon before the onset of glaciation. During glaciations, cacao populations were likely to have been restricted to several refugia where they probably underwent genetic differentiation, resulting in a number of genetic clusters which are representative for, or closest related to, the original wild cacao populations. The analyses also suggested that genetic differentiation and geographical distribution of a number of other clusters seem to have been significantly affected by processes of human management and accompanying genetic bottlenecks. We discuss the implications of these results for future germplasm collection and in situ, on farm and ex situ conservation of cacao. |
| format | Journal Article |
| id | CGSpace35815 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2012 |
| publishDateRange | 2012 |
| publishDateSort | 2012 |
| publisher | Public Library of Science |
| publisherStr | Public Library of Science |
| record_format | dspace |
| spelling | CGSpace358152025-11-12T05:45:26Z Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in Pleistocene refugia followed by human-influenced dispersal Thomas, E. Zonneveld, M. van Loo, J. Hodgkin, T. Galluzzi, Gea Etten, Jacob van germplasm germplasm conservation human behaviour spatial distribution theobroma cacao Cacao (Theobroma cacao L.) is indigenous to the Amazon basin, but is generally believed to have been domesticated in Mesoamerica for the production of chocolate beverage. However, cacao’s distribution of genetic diversity in South America is also likely to reflect pre-Columbian human influences that were superimposed on natural processes of genetic differentiation. Here we present the results of a spatial analysis of the intra-specific diversity of cacao in Latin America, drawing on a dataset of 939 cacao trees genotypically characterized by means of 96 SSR markers. To assess continental diversity patterns we performed grid-based calculations of allelic richness, Shannon diversity and Nei gene diversity, and distinguished different spatially coherent genetic groups by means of cluster analysis. The highest levels of genetic diversity were observed in the Upper Amazon areas from southern Peru to the Ecuadorian Amazon and the border areas between Colombia, Peru and Brazil. On the assumption that the last glaciation (22,000–13,000 BP) had the greatest pre-human impact on the current distribution and diversity of cacao, we modeled the species’ Pleistocene niche suitability and overlaid this with present-day diversity maps. The results suggest that cacao was already widely distributed in the Western Amazon before the onset of glaciation. During glaciations, cacao populations were likely to have been restricted to several refugia where they probably underwent genetic differentiation, resulting in a number of genetic clusters which are representative for, or closest related to, the original wild cacao populations. The analyses also suggested that genetic differentiation and geographical distribution of a number of other clusters seem to have been significantly affected by processes of human management and accompanying genetic bottlenecks. We discuss the implications of these results for future germplasm collection and in situ, on farm and ex situ conservation of cacao. 2012 2014-06-10T09:06:25Z 2014-06-10T09:06:25Z Journal Article https://hdl.handle.net/10568/35815 en Open Access application/pdf Public Library of Science Thomas, E.; van Zonneveld, M.; Loo, J.; Hodgkin, T.; Galluzzi, G.; van Etten, J. -2012-Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in Pleistocene refugia followed by human-influenced dispersal-PLos ONE 7(10)-e47676 |
| spellingShingle | germplasm germplasm conservation human behaviour spatial distribution theobroma cacao Thomas, E. Zonneveld, M. van Loo, J. Hodgkin, T. Galluzzi, Gea Etten, Jacob van Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in Pleistocene refugia followed by human-influenced dispersal |
| title | Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in Pleistocene refugia followed by human-influenced dispersal |
| title_full | Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in Pleistocene refugia followed by human-influenced dispersal |
| title_fullStr | Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in Pleistocene refugia followed by human-influenced dispersal |
| title_full_unstemmed | Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in Pleistocene refugia followed by human-influenced dispersal |
| title_short | Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in Pleistocene refugia followed by human-influenced dispersal |
| title_sort | present spatial diversity patterns of theobroma cacao l in the neotropics reflect genetic differentiation in pleistocene refugia followed by human influenced dispersal |
| topic | germplasm germplasm conservation human behaviour spatial distribution theobroma cacao |
| url | https://hdl.handle.net/10568/35815 |
| work_keys_str_mv | AT thomase presentspatialdiversitypatternsoftheobromacacaolintheneotropicsreflectgeneticdifferentiationinpleistocenerefugiafollowedbyhumaninfluenceddispersal AT zonneveldmvan presentspatialdiversitypatternsoftheobromacacaolintheneotropicsreflectgeneticdifferentiationinpleistocenerefugiafollowedbyhumaninfluenceddispersal AT looj presentspatialdiversitypatternsoftheobromacacaolintheneotropicsreflectgeneticdifferentiationinpleistocenerefugiafollowedbyhumaninfluenceddispersal AT hodgkint presentspatialdiversitypatternsoftheobromacacaolintheneotropicsreflectgeneticdifferentiationinpleistocenerefugiafollowedbyhumaninfluenceddispersal AT galluzzigea presentspatialdiversitypatternsoftheobromacacaolintheneotropicsreflectgeneticdifferentiationinpleistocenerefugiafollowedbyhumaninfluenceddispersal AT ettenjacobvan presentspatialdiversitypatternsoftheobromacacaolintheneotropicsreflectgeneticdifferentiationinpleistocenerefugiafollowedbyhumaninfluenceddispersal |