Hundreds of SNPs for the Endangered pygmy hippopotamus ( Choeropsis liberiensis )
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TECHNICAL NOTE
Hundreds of SNPs for the Endangered pygmy hippopotamus (Choeropsis liberiensis) Helen Senn • Paul O’Donoghue Ross McEwing • Rob Ogden
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Received: 4 February 2014 / Accepted: 24 March 2014 Ó Springer Science+Business Media Dordrecht 2014
Abstract The pygmy hippo is an Endangered mammal endemic to West Africa, of which only 2,000–3,000 are left in the wild. Until now genetic resources to conduct monitoring of wild populations and to facilitate captive breeding have been lacking. In this study we used restriction-site associated DNA sequencing of five pygmy hippo samples to generate 1,619 high confidence candidate single nucleotide polymorphisms (SNPs) suitable for population genetic analysis. A subset of 10 of SNPs generated were validated via resequencing with 100 % success rate and through the use of KASPar DNA probes (Kbiosciences) with 90 % success rate. To facilitate future research we present the list of 1,619 SNPs ranked according to mean genotype confidence and mean coverage. Keywords RAD sequencing SNP discovery Conservation genetics Pygmy hippopotamus Sequence data The pygmy hippopotamus (Choeropsis liberiensis, Morton 1849) is an Endangered mammal endemic to West Africa. Around 2,000–3,000 individuals exist in the wild today (Lewison and Oliver 2008). The existence of the species is
Electronic supplementary material The online version of this article (doi:10.1007/s12686-014-0178-8) contains supplementary material, which is available to authorized users. H. Senn (&) R. McEwing R. Ogden WildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, UK e-mail: [email protected] P. O’Donoghue Department of Biological Sciences, University of Chester, Parkgate Road, Chester CH1 4BJ, UK
currently confirmed within four countries: Sierra Leone, Republic of Guinea, Coˆte d’Ivoire, and Liberia (Lewison and Oliver 2008) where it is recognised as the nominate subspecies C. l. liberiensis. There are possibly populations in Nigeria on the other side of the Dahomey Gap of the subspecies C. l. heslopi, although there have been no records of its occurrence since 1945 (Mallon et al. 2011). Subspecies designation is based on craniology Corbet (1969). The main threat to the pygmy hippo comes from deforestation. Remaining forest blocks are fragmented so that populations are isolated and more accessible to hunters (Mallon et al. 2011; Lewison and Oliver 2008). Around 350 individuals are held within captive collections across the world based on 61 founder individuals that currently are living or have living descendants collected from Liberia, Ivory Coast and unknown locations between the dates 1910–2000 (Steck 2012). The pygmy hippo conservation strategy workshop held in Monrovia, Liberia, in 2010 identified a number of research objectives to further pygmy hippo conservation. These included the development of genetic markers to aid with in situ monitoring of the species via fecal sampling, management of the captive population and genetic resolution of the subspecies split. Individual ident
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