Conservation genetics of Madagascar’s critically endangered ploughshare tortoise (Astrochelys yniphora)

The critically endangered ploughshare tortoise, Astrochelys yniphora, is endemic to the Baly Bay region of western Madagascar. In 2015, the wild population was estimated to be < 500 subadults/adults across a fragmented habitat, with subsequent field surveys reporting a further decline to a perilously low number of adult tortoises. The primary cause of this decline was poaching for the illegal international pet trade, which has escalated since 2006 leading to the extirpation of ploughshare tortoises from at least two localities. Seizures of smuggled tortoises increased over this same period, with most confiscated animals being incorporated into assurance populations. This study presents a genetic reference, including samples from the extirpated localities. Mitochondrial sequence data and 25 nuclear microsatellite markers were utilized to estimate genetic diversity of the wild population prior to a > 50% decline, identify Management Units (MUs), and present a dataset to assign confiscated individuals to their subpopulation of origin. Despite a long history of exploitation, heterozygosity appeared healthy, ranging from 0.612 to 0.758 across four localities, and no recent genetic bottlenecks were observed. In contrast, the Western Complex, consisting of the Ambatomainty, Andrafiafaly, and Andranolava regions, exhibited a possible decline in allelic diversity. Four genetic clusters were recovered and used to define three MUs corresponding to the following localities: Cap Sada, Beheta, and a combined Western Complex plus Betainalika. Results are discussed in the context of conservation genetic management advising that MUs be treated as conservation units for wild and captive management to maintain the breadth of genetic diversity present in the wild.