Microsatellite and mitochondrial DNA D-loop based analysis of genetic diversity in captive populations of Crocodylus siamensis in China

Reintroduction of threatened species is a common strategy used to mitigate population decline and reduce the risk of extinction. In order to assess the success of such reintroduction programs, it is critical to monitor the demographic and genetic features of reintroduced populations. In this work, we conducted a genetic assessment of the Critically Endangered crocodile species Crocodylus siamensis to determine the genetic diversity, utilising both microsatellite markers and mitochondrial DNA D-loop region. The genetic analysis revealed a moderate level of genetic diversity within the sampled populations, as indicated by the microsatellite markers (Ho = 0.505 ± 0.080; He = 0.297 ± 0.091) and mtDNA D-loop (hd = 0.622 ± 0.061; Pi = 0.01294 ± 0.00041). Notably, 22 distinct haplotypes were observed. Additionally, we identified evidence of hybridisation that might have occurred between C. siamensis and Crocodylus niloticus raising concerns about the potential compromise of the species' genetic integrity. This study represents the first genetic assessment of captive bred C. siamensis populations in China, encompassing both microsatellite and mtDNA D-loop analyses. To ensure preservation of C. siamensis, we recommend identifying and excluding hybrid individuals from conservation programmes. Our findings support the feasibility of implementing breeding and captive management plans for C. siamensis, providing a solid theoretical basis for their reintroduction and captive breeding to safeguard and augment the population of this Critically Endangered freshwater crocodile. This research marks the initial step towards establishing a scientifically sound source population for the conservation of C. siamensis in China. Keywords: protection, reintroduction genotype, haplotypic diversity, nucleotide diversity