Vol.:(0123456789) 1 3 Conservation Genetics https://doi.org/10.1007/s10592-019-01236-7 RESEARCH ARTICLE Conservation genetics of Madagascar’s critically endangered ploughshare tortoise (Astrochelys yniphora) Angelo R. Mandimbihasina 1,2  · Cynthia L. Frasier 3  · Ryan A. Hagenson 3  · Brittani A. D. Robertson 3  · Shannon E. Engberg 3  · Richard E. Lewis 1  · Lance G. Woolaver 1  · Emilienne Razafmahatratra 2  · Lydia L. Rabetafka 2  · Edward E. Louis Jr. 3,4 Received: 7 January 2019 / Accepted: 5 November 2019 © Springer Nature B.V. 2019 Abstract The critically endangered ploughshare tortoise, Astrochelys yniphora, is endemic to the Baly Bay region of western Mada- gascar. In 2015, the wild population was estimated to be < 500 subadults/adults across a fragmented habitat, with subsequent feld 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 confscated 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 confscated 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, Andrafafaly, and Andranolava regions, exhibited a possible decline in allelic diversity. Four genetic clusters were recovered and used to defne 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. Keywords Baly Bay National Park · Chelonian · Microsatellites · Mitochondrial DNA · Population structure Introduction Between 2006 and 2015, the wild ploughshare tortoise (Astrochelys yniphora) population was estimated to have declined by 50%, driven by their value on the pet trade black market which can exceed 45,000 USD per tortoise (Mandim- bihasina et al. 2018; Morgan and Chng 2018). The illegal pet trade was predated by extensive commercial exploita- tion documented back to the 1600s when ploughshare tor- toises were exported to the Comoros for food and used by passing sailing vessels as a source of protein (Vaillant and Grandidier 1910; Mandimbihasina and Woolaver 2014). Intense harvesting of wild populations, such as recorded for ploughshare tortoises, can result in signifcant genetic change, yet these changes will not be recognized unless a genetic reference exists for a species (Allendorf et al. 2008). Unfortunately, there is no genetic baseline available for the Angelo Mandimbihasina and Cynthia Frasier are co-frst authors. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10592-019-01236-7) contains supplementary material, which is available to authorized users. * Edward E. Louis Jr. genetics@omahazoo.com 1 Durrell Wildlife Conservation Trust, BP 8511, Lot II Y 49 J Ampasanimalo, Antananarivo, Madagascar 2 Department of Animal Biology, Ecology and Conservation, Faculty of Science, University of Antananarivo, BP 906, Antananarivo, Madagascar 3 Center for Conservation and Research, Omaha’s Henry Doorly Zoo and Aquarium, 3701 South 10th Street, Omaha, NE 68107, USA 4 Madagascar Biodiversity Partnership, LOT VO 12 Bis A, Manakambahiny, 101 Antananarivo, Madagascar