Population genomics reveals how 5 ka of human occupancy led the Lima leaf-toed gecko (Phyllodactylus sentosus) to the brink of extinction

Small species with high home fidelity, high ecological specialization or low vagility are particularly prone to suffer from habitat modification and fragmentation. The Lima leaf-toed gecko (Phyllodactylus sentosus) is a critically endangered Peruvian species that shelters mostly in pre-Incan archeol...

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Autores principales: Arana, Alejandra, Esteves, Juan, Ramírez, Rina, Galetti, Pedro M., Pérez Z., José, Ramirez, Jorge L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10611785/
https://www.ncbi.nlm.nih.gov/pubmed/37891335
http://dx.doi.org/10.1038/s41598-023-45715-x
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author Arana, Alejandra
Esteves, Juan
Ramírez, Rina
Galetti, Pedro M.
Pérez Z., José
Ramirez, Jorge L.
author_facet Arana, Alejandra
Esteves, Juan
Ramírez, Rina
Galetti, Pedro M.
Pérez Z., José
Ramirez, Jorge L.
author_sort Arana, Alejandra
collection PubMed
description Small species with high home fidelity, high ecological specialization or low vagility are particularly prone to suffer from habitat modification and fragmentation. The Lima leaf-toed gecko (Phyllodactylus sentosus) is a critically endangered Peruvian species that shelters mostly in pre-Incan archeological areas called huacas, where the original environmental conditions are maintained. We used genotyping by sequencing to understand the population genomic history of P. sentosus. We found low genetic diversity (He 0.0406–0.134 and nucleotide diversity 0.0812–0.145) and deviations of the observed heterozygosity relative to the expected heterozygosity in some populations (F(is) − 0.0202 to 0.0187). In all analyses, a clear population structuring was observed that cannot be explained by isolation by distance alone. Also, low levels of historical gene flow were observed between most populations, which decreased as shown in contemporary migration rate analysis. Demographic inference suggests these populations experienced bottleneck events during the last 5 ka. These results indicate that habitat modification since pre-Incan civilizations severely affected these populations, which currently face even more drastic urbanization threats. Finally, our predictions show that this species could become extinct in a decade without further intervention, which calls for urgent conservation actions being undertaken.
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spelling pubmed-106117852023-10-29 Population genomics reveals how 5 ka of human occupancy led the Lima leaf-toed gecko (Phyllodactylus sentosus) to the brink of extinction Arana, Alejandra Esteves, Juan Ramírez, Rina Galetti, Pedro M. Pérez Z., José Ramirez, Jorge L. Sci Rep Article Small species with high home fidelity, high ecological specialization or low vagility are particularly prone to suffer from habitat modification and fragmentation. The Lima leaf-toed gecko (Phyllodactylus sentosus) is a critically endangered Peruvian species that shelters mostly in pre-Incan archeological areas called huacas, where the original environmental conditions are maintained. We used genotyping by sequencing to understand the population genomic history of P. sentosus. We found low genetic diversity (He 0.0406–0.134 and nucleotide diversity 0.0812–0.145) and deviations of the observed heterozygosity relative to the expected heterozygosity in some populations (F(is) − 0.0202 to 0.0187). In all analyses, a clear population structuring was observed that cannot be explained by isolation by distance alone. Also, low levels of historical gene flow were observed between most populations, which decreased as shown in contemporary migration rate analysis. Demographic inference suggests these populations experienced bottleneck events during the last 5 ka. These results indicate that habitat modification since pre-Incan civilizations severely affected these populations, which currently face even more drastic urbanization threats. Finally, our predictions show that this species could become extinct in a decade without further intervention, which calls for urgent conservation actions being undertaken. Nature Publishing Group UK 2023-10-27 /pmc/articles/PMC10611785/ /pubmed/37891335 http://dx.doi.org/10.1038/s41598-023-45715-x Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Arana, Alejandra
Esteves, Juan
Ramírez, Rina
Galetti, Pedro M.
Pérez Z., José
Ramirez, Jorge L.
Population genomics reveals how 5 ka of human occupancy led the Lima leaf-toed gecko (Phyllodactylus sentosus) to the brink of extinction
title Population genomics reveals how 5 ka of human occupancy led the Lima leaf-toed gecko (Phyllodactylus sentosus) to the brink of extinction
title_full Population genomics reveals how 5 ka of human occupancy led the Lima leaf-toed gecko (Phyllodactylus sentosus) to the brink of extinction
title_fullStr Population genomics reveals how 5 ka of human occupancy led the Lima leaf-toed gecko (Phyllodactylus sentosus) to the brink of extinction
title_full_unstemmed Population genomics reveals how 5 ka of human occupancy led the Lima leaf-toed gecko (Phyllodactylus sentosus) to the brink of extinction
title_short Population genomics reveals how 5 ka of human occupancy led the Lima leaf-toed gecko (Phyllodactylus sentosus) to the brink of extinction
title_sort population genomics reveals how 5 ka of human occupancy led the lima leaf-toed gecko (phyllodactylus sentosus) to the brink of extinction
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10611785/
https://www.ncbi.nlm.nih.gov/pubmed/37891335
http://dx.doi.org/10.1038/s41598-023-45715-x
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