Single-nucleotide polymorphism discovery and panel characterization in the African forest elephant

Ecology and Evolution
Stéphanie BourgeoisRoss McEwing

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 nonmodel 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 1,365 high-quality candidate SNP markers. A subset of 115 cand...Continue Reading

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Datasets Mentioned

BETA
SRP126637

Methods Mentioned

BETA
genotyping
electrophoresis
Assay
PCR

Software Mentioned

Stacks scripts
FastQC
Basic Local Alignment Search Tool ( BLAST )
BLAST
R R Core Team
SNPviewer
R package LDheatmap
PLINK
ddRAD
LGC Genomics

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