Transcriptomic genotyping elucidates the population structure and demographic history of the endangered poison frog Oophaga vicentei (Anura: Dendrobatidae)

<h4>Background</h4>Amphibians are among the most vulnerable vertebrates, with 41% of assessed species at risk of extinction. The genus Oophaga has most of its species currently listed as threatened by the IUCN. Oophaga vicentei, an endangered species endemic to central Panama, is facing strong pressures from habitat fragmentation and mining. Despite its threat status, little is known about its population structure and size. Reduced representation approaches are cost efficient alternative to obtain genome-wide estimates of genetic diversity in non-model species. We herein genotyped thousands of exonic SNPs using RNA-seq data to uncover the genetic structure and effective population size of O. vicentei.<h4>Results</h4>Population structure analyses revealed two main genetic clusters: a West group (formed by individuals of Calovébora, La Empalizada, and Loma Grande) and an East group with individuals from La Ceiba. A further subdivision of the West cluster was apparent on the PCA with two localities (Calobévora, La Empalizada) splitting from the other Loma Grande. The La Ceiba locality was genetically the most divergent from the rest, with Calovébora and La Empalizada being the most similar. Effective population size of O. vicentei peaked around the Last Interglacial period and declined after the Last Glacial Maximum, with the locality La Ceiba showing the most pronounced decline towards present time.<h4>Conclusions</h4>The significant amount of data we obtained validates the applicability of mRNA sequences to elucidate the population structure and demography of a species. Our results reveal strong genetic structure in O. vicentei, with the two main population clusters showing significant differences in their most recent demographic history. These findings provide a genomic baseline for conservation strategies, emphasizing the need to protect all known populations of this endangered species.