Last exit before the brink: Conservation genomics of the Cambodian population of the critically endangered southern river terrapin

Abstract

The southern river terrapin, Batagur affinis is one of the world's 25 most endangered freshwater turtle species. The major portion of the global population is currently found in peninsular Malaysia, with the only remnant Indochinese population in southern Cambodia. For more than a decade, wild nests in this remnant Cambodian population have been fenced and hatchlings reared in captivity. Here we amplified 10 microsatellite markers from all 136 captive individuals, obtained 2,658 presumably unlinked and neutral single nucleotide polymorphisms from 72 samples with ddRAD‐seq, and amplified 784 bp of mtDNA from 50 samples. Our results reveal that the last Indochinese population comprised only four kinship groups as of 2012, with all offspring sired from <10 individuals in the wild. We demonstrate an obvious decrease in genetic contributions of breeders in the wild from 2006–2012 and identify high‐value breeders instrumental for ex‐situ management of the contemporary genetic stock of the species.

Low‐coverage reduced representation sequencing reveals subtle within‐island genetic structure in Aldabra giant tortoises

“…Using molecular markers developed for other species bears the risk of ascertainment bias and an underestimation of genetic variation (Delport et al, 2006; Ellegren et al, 1995). Similar problems have been encountered in other microsatellite studies of, for instance, turtles (Çilingir et al, 2019), fish (Carreras et al, 2017), and mammals (Hendricks et al, 2017; Mesnick et al, 2011).…”

Chromosomal‐level genome assembly of the scimitar‐horned oryx: Insights into diversity and demography of a species extinct in the wild

“…This has opened up the opportunity for precisely measuring genetic diversity, a critical aspect of conservation management, particularly when selecting founders for reintroduction (IUCN/SSC, 2013). However, only a handful of studies have employed genomic approaches for measuring genetic diversity in captive species (Çilingir et al., 2019; Robinson et al., 2019; Willoughby, Ivy, Lacy, Doyle, & DeWoody, 2017) and therefore most estimates are based on traditional markers such as microsatellites and fixed panels of SNPs. These can be associated with high sampling variance and ascertainment bias (Väli, Einarsson, Waits, & Ellegren, 2008), making comparisons across species and populations problematic.…”

Growth patterns of captive painted terrapins Batagur borneoensis in the Aceh Province, Indonesia

“…Various human activities continue to exploit natural resources uncontrollably, which is the habitat of various biota that live in it, including the Batagur habitat. For now, this animal is only found in several countries, including Malaysia, Thailand and Cambodia, in these three countries B. affinis is found, this animal is also in very poor condition, so a conservation process has been carried out (Moll et al 2015;Çilingir et al 2019;Jualaong et al 2020;Camara and Jamil 2021). Likewise, with B. borneoensis, this animal is now only found in Indonesia and also neighboring Malaysia.…”