Conservation genomics of the endangered Burmese roofed turtle

Abstract

The Burmese roofed turtle (Batagur trivittata) is one of the world's most endangered turtles. Only one wild population remains in Myanmar. There are thought to be 12 breeding turtles in the wild. Conservation efforts for the species have raised >700 captive turtles since 2002, predominantly from eggs collected in the wild. We collected tissue samples from 445 individuals (approximately 40% of the turtles' remaining global population), applied double-digest restriction-site associated DNA sequencing (ddRAD-Seq), and obtained approximately 1500 unlinked genome-wide single nucleotide polymorphisms. Individuals fell into 5 distinct genetic clusters, 4 of which represented full-sib families. We inferred a low effective population size (≤10 individuals) but did not detect signs of severe inbreeding, possibly because the population bottleneck occurred recently. Two groups of 30 individuals from the captive pool that were the most genetically diverse were reintroduced to the wild, leading to an increase in the number of fertile eggs (n = 27) in the wild. Another 25 individuals, selected based on the same criteria, were transferred to the Singapore Zoo as an assurance colony. Our study demonstrates that the research-to-application gap in conservation can be bridged through application of cutting-edge genomic methods.

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

“…As previously observed in Batagur trivittata (Çilingir et al, ), the sister species of B. affinis , global G IT is smaller than zero (global G IT = −0.025 ± 0.005; individual inbreeding coefficients −0.225 to 0.27; Table ). This could be interpreted as a lack of severe inbreeding, assuming our dataset represents only the first generation of a potentially long‐lived turtle's population (estimated age of maturity is 25 years; Moll et al, ) whose bottleneck is relatively recent.…”

“…De novo and reference‐based mapping of loci, followed by missing data and MAF filtering, yielded six different SNP datasets (Table ). We conducted downstream analyses using SNP set A2 (2,658 SNPs, mean PIC = 0.28; Table ) because it includes SNPs from the highest number of individuals with the highest mean PIC value (Çilingir et al, ).…”

Landscape limits gene flow and drives population structure in Agassiz’s desert tortoise (Gopherus agassizii)

“…Second, the approach can identify genes or neighboring genes of loci that strongly conform to a non-neutral model 26 . In a recent conservation genomics study of the Burmese roofed turtle ( Batagur trivittata ), from about 1500 SNPs, not a single locus departed significantly from neutrality 96 . In contrast, our analyses discover at least 32 loci under potential diversifying selection.…”

Genetic diversity, structure, and kinship analysis ofTrachemys venusta venustain Wildlife Management Units and wild populations in south Mexico. Implications for conservation and management

“…A captive management program has been established for this species, and it was thought that only 12 breeding turtles existed in the wildlife. Since 2002, more than 700 individuals of this species have been obtained and after selecting individuals with a high genetic diversity and reintroducing them to their natural habitat, the program reported an increase in the fertility of the eggs [90]. Furthermore, our results could be used to create predictive models of exploitation, since T. venusta venusta is a highly valued species for human consumption and as pet, as has been proposed for the turtle Trachemys scripta elegans Wied-Neuwied, 1839 (Testudines, Emydidae), that is principally exploited as a pet [91].…”