Conservation Genomics of Freshwater Turtle Assemblages
Keywords:
conservation genomics, freshwater turtles, ddRAD-seq, population structure, genetic diversity, inbreeding, local adaptation, invasive species, hybridisation, Emys orbicularis, management units, genetic rescueAbstract
Freshwater turtles are among the most imperilled vertebrate groups globally, with over 60% of species threatened withextinction due to overexploitation, habitat loss, and invasive species introductions. Conservation genomics — the application of whole-genome or reduced-representation genomic methods to inform conservation management — offers unprecedented resolution for delineating management units, detecting inbreeding depression, and identifying locally adaptive genetic variation in threatened freshwater turtle assemblages. This study applied double-digest restriction-site associated DNA sequencing (ddRAD-seq) to characterise genomic diversity, population structure, and signatures of local
adaptation in five freshwater turtle species — Emys orbicularis, Mauremys rivulata, Mauremys leprosa, Pelodiscus sinensis (invasive), and Trachemys scripta (invasive) — sampled from 42 wetland sites across Italy, Spain, and Switzerland (n = 824 individuals). A total of 18,642 high-quality SNPs were retained after quality filtering. STRUCTURE and ADMIXTURE analyses resolved 3–7 genetic clusters per species, revealing substantial cryptic population subdivision not apparent from morphological or distribution data. Mean observed heterozygosity was significantly lower in isolated populations (Ho = 0.184 ± 0.028) than in connected wetland networks (Ho = 0.241 ± 0.034; Wilcoxon p < 0.001). Genomic inbreeding coefficients (FROH) exceeded 0.20 in 8 of 42 populations, identifying priority targets for genetic rescue interventions. Genotype-environment association (GEA) analysis identified 142 putatively adaptive SNPs associated with water temperature, pH, and turbidity gradients. Invasive T. scripta showed evidence of hybridisation with native E. orbicularis at 4 of 42 sites, with admixture proportions of 4.2–18.6%. These findings provide a genomic framework for management unit delineation, genetic rescue prioritisation, and adaptive potential assessment in
European freshwater turtle conservation.
