Abstract
Hynobius amjiensis was considered as one of the 29 most threatened amphibian in China. To effectively conserve, manage and recover the population of this critically endangered species, 33 single nucleotide polymorphism (SNP) markers were developed using double digest restriction-site associated DNA (ddRAD) sequencing. The minor allele frequency per locus ranged from 0.0161 to 0.5000. The observed heterozygosity and expected heterozygosity varied from 0.0323 to 0.6667 (average 0.3303) and from 0.0317 to 0.5000 (average 0.2772), respectively. The inbreeding coefficient value ranged between − 0.3315 and 0.0000. No significant deviation from Hardy–Weinberg equilibrium (P > 0.05) were found in all loci. These novel SNPs will be helpful for the population genetic assessment and conservation of H. amjiensis.
Highlights
Anji salamander (Hynobius amjiensis) was an endemic species in China
The inbreeding coefficient value ranged between − 0.3315 and 0.0000
No significant deviation from Hardy-Weinberg equlibrium (P > 0.05) were found in all loci. These novel single nucleotide polymorphism (SNP) will be helpful for the population genetic assessment and conservation of H. amjiensis
Summary
Anji salamander (Hynobius amjiensis) was an endemic species in China. Due to limited distribution and small population size, it was listed as a critically endangered species in the International Union for Conservation of Nature (IUCN) Red List of Threatened Species (Gu and Lau 2004). A specific National Natural Reserve was constructed to conserve the species in situ. As a key species in national biodiversity survey, it was investigated annually to understand the distribution and population size extensively and deeply by the State Forestry Administration of China from 2012 (Yang et al 2016). 33 novel SNP loci were developed using double digest restriction-site associated DNA sequencing (ddRADseq) in H. amjiensis. The minor allele frequency (MAF) and P value representing the deviations from Hardy-Weinberg equilibrium (HWE) for each locus were tested using VCFtools (Danecek et al 2011). No loci showed significant deviation from Hardy-Weinberg equilibrium (P > 0.05) These novel SNP markers will contribute to the understanding of population genetic structure and be useful for the population conservation of H. amjiensis
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