Genetic diversity and population structure of the Asian yellow pond turtle (Mauremys mutica)

Abstract

To investigate the genetic diversity and structure of farmed Asian yellow pond turtle ( Mauremys mutica ), we performed whole-genome resequencing on 180 individuals collected from eight farms spanning six regions in China. A total of 2072,663,419 single nucleotide polymorphisms (SNPs) were identified. Analysis of genetic diversity paremeters revealed relatively low overall diversity: nucleotide diversity (π) ranged from 0.00289 to 0.00363, observed heterozygosity ( Ho ) from 0.107 to 0.159, and polymorphism information content (PIC) from 0.102 to 0.128. Inbreeding coefficient ( F HOM ) varied between 0.148 and 0.367. Population genetic analyses indicated moderate genetic differentiation (genetic differentiation index F st ranging from 0.0007 to 0.1265) alongside evidence of historical or ongoing gene flow ( N m from 1.7263 to 356.8929) among the farmed populations. Phylogenetic and principal component analyses revealed shallow population structure with extensive admixture, reflecting decades of human-mediated stock exchange. This first whole-genome characterization of captive M. mutica provides critical baseline data for germplasm conservation and management, and offers genomic insights to guide sustainable breeding strategies for this economically important but genetically depleted species.