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During the second third of last century, the Orinoco Crocodile (Crocodylus intermedius) underwent a hunting process driven by the demand from the North American, European, and Japanese leather industry, resulting in a sharp decline of its populations. Currently, only two known remaining populations of this Critically Endangered species persist in the Colombian Orinoquía: in the Guayabero-Duda-Lozada and the Cravo Norte-Ele-Lipa River Systems. The latter has been the only population subject of study, including recent surveys and local conservation initiatives such as egg and hatchling ranching. Despite suggestions for population recovery based on the observed increase in clutches in the area, information regarding its genetic status has been pending assessment. This research aims to provide a genetic characterization of this remaining population and to evaluate the diversity recovered during a period of the egg ranching initiative. For this purpose, we utilized variable molecular markers, specifically 17 microsatellite loci, nuclear DNA. Despite revealing intermediate levels of genetic diversity, we identified an effective population size of 11.5-17, well below the minimum values proposed for short-term subsistence. While no evidence of inbreeding was found, it is acknowledged as a potential risk based on the population's history. Additionally, we detected a historical bottleneck possibly influenced by arid periods affecting the region since the Pleistocene. While the evaluated population presents a unique opportunity for C. intermedius conservation, it also exposes a high risk of entering the extinction vortex. The primary action to be taken is to support the egg and hatchling ranching program, which successfully recovered most of the genetic diversity present in the population., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Castillo-Rodríguez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Kinosternon is the most speciose genus of extant turtles, with 22 currently recognized species, distributed across large parts of the Americas. Most species have small distributions, but K. leucostomum and K. scorpioides range from Mexico to South America. Previous studies have found discordance between mitochondrial and nuclear phylogenies in some kinosternid groups, with the current taxonomy following the nuclear-based results. Herein, based on extended molecular, geographic, and taxonomic sampling, we explore the phylogeographic structure and taxonomic limits for K. leucostomum and the K. scorpioides group and present a fossil-calibrated nuclear time tree for Kinosternon. Our results reveal contrasting differentiation patterns for the K. scorpioides group and K. leucostomum, despite overlapping distributions. Kinosternon leucostomum shows only shallow geographic divergence, whereas the K. scorpioides group is polyphyletic with up to 10 distinct taxa, some of them undescribed. We support the elevation of K. s. albogulare and K. s. cruentatum to species level. Given the deep divergence within the genus Kinosternon, we propose the recognition of three subgenera, Kinosternon, Cryptochelys and Thyrosternum, and the abandonment of the group-based classification, at least for the K. leucostomum and K. scorpioides groups. Our results show an initial split in Kinosternon that gave rise to two main radiations, one Nearctic and one mainly Neotropical. Most speciation events in Kinosternon occurred during the Quaternary and we hypothesize that they were mediated by both climatic and geological events. Additionally, our data imply that at least three South American colonizations occurred, two in the K. leucostomum group, and one in the K. scorpioides group. Additionally, we hypothesize that discordance between mitochondrial and nuclear phylogenetic signal is due to mitochondrial capture from an extinct kinosternine lineage., (Published by Elsevier Inc.)