Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/26545
Appears in Collections:Biological and Environmental Sciences Journal Articles
Peer Review Status: Refereed
Title: Single-nucleotide polymorphism discovery and panel characterization in the African forest elephant
Author(s): Bourgeois, Stephanie
Senn, Helen
Kaden, Jenny
Taggart, John
Ogden, Robert
Jeffery, Kathryn Jane
Bunnefeld, Nils
Abernethy, Katharine
McEwing, Ross
Contact Email: kathryn.jeffery1@stir.ac.uk
Keywords: forest elephant
Gabon
SNP
ddRAD
Issue Date: Feb-2018
Citation: Bourgeois S, Senn H, Kaden J, Taggart J, Ogden R, Jeffery KJ, Bunnefeld N, Abernethy K & McEwing R (2018) Single-nucleotide polymorphism discovery and panel characterization in the African forest elephant, Ecology and Evolution, 8 (4), pp. 2207-2217.
Abstract: The continuing decline in forest elephant (Loxodonta cyclotis) numbers due to poaching and habitat reduction is driving the search for new tools to inform management and conservation. For dense rainforest species, basic ecological data on populations and threats can be challenging and expensive to collect, impeding conservation action in the field. As such, genetic monitoring is being increasingly implemented to complement or replace more burdensome field techniques. Single nucleotide polymorphisms (SNPs) are particularly cost-effective and informative markers that can be used for a range of practical applications, including population census, assessment of human impact on social and genetic structure, and investigation of the illegal wildlife trade. SNP resources for elephants are scarce, but next generation sequencing provides the opportunity for rapid, inexpensive generation of SNP markers in non-model species. Here we sourced forest elephant DNA from 23 samples collected from 10 locations within Gabon, Central Africa, and applied double-digest restriction-site-associated DNA (ddRAD) sequencing to discover 31,851 tags containing SNPs that were reduced to a set of 1365 high-quality candidate SNP markers. A subset of 115 candidate SNPs was then selected for assay design and validation using 56 additional samples. Genotyping resulted in a high conversion rate (93%) and a low per allele error rate (0.07%). This study provides the first panel of 107 validated SNP markers for forest elephants. This resource presents great potential for new genetic tools to produce reliable data and underpin a step-change in conservation policies for this elusive species.
DOI Link: http://dx.doi.org/10.1002/ece3.3854
Rights: © 2018 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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