Genome sequence, population history, and pelage genetics of the endangered African wild dog (Lycaon pictus)

Abstract

BackgroundThe African wild dog (Lycaon pictus) is an endangered African canid threatened by severe habitat fragmentation, human-wildlife conflict, and infectious disease. A highly specialized carnivore, it is distinguished by its social structure, dental morphology, absence of dewclaws, and colorful pelage.ResultsWe sequenced the genomes of two individuals from populations representing two distinct ecological histories (Laikipia County, Kenya and KwaZulu-Natal Province, South Africa). We reconstructed population demographic histories for the two individuals and scanned the genomes for evidence of selection.ConclusionsWe show that the African wild dog has undergone at least two effective population size reductions in the last 1,000,000 years. We found evidence of Lycaon individual-specific regions of low diversity, suggestive of inbreeding or population-specific selection. Further research is needed to clarify whether these population reductions and low diversity regions are characteristic of the species as a whole. We documented positive selection on the Lycaon mitochondrial genome. Finally, we identified several candidate genes (ASIP, MITF, MLPH, PMEL) that may play a role in the characteristic Lycaon pelage.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3368-9) contains supplementary material, which is available to authorized users.

Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation

“…Such approaches have been used to predict the mechanistic effects of amino acid substitutions observed in OXPHOS subunits across diverse species (Scott et al, 2011; Finch et al, 2014; Caballero et al, 2015; Zhang and Broughton, 2015; Campana et al, 2016; Morales et al, 2016a). This approach was first highlighted by Garvin et al (2011) who detected an amino acid under positive selection in the Pacific salmon in an unusual region of OXPHOS complex I: the piston-like horizontal helix (helix HL) of ND5.…”

BaitsTools: Software for hybridization capture bait design

“…To benchmark typical baitstools performance, baits were generated and filtered using sequence data from previously sequenced African wild dog ( Lycaon pictus ) genomes (Campana, Hawkins et al., , Campana, Parker et al., ), reference sequences from GenBank (accessions: , , , ) (Bjornerfeldt, Webster, & Vilà, ; Kim, Lee, Jeong, & Ha, ; Koepfli et al., ; Lindblad‐Toh et al., ), and simulated Stacks data and ipyrad loci (available: ipyrad.readthedocs.io/output_formats.html). Benchmarked data sets are included in the example data within the baitstools repository, except for the Canis familiaris X chromosome sequence (GenBank accession: ) due to file size limitations.…”

“…Furthermore, to compare performance between baitstools tilebaits and BaitDesigner ( picard version 2.9.4), baits were generated from a 16,725 bp Lycaon pictus mitogenome (GenBank accession: ; Campana, Hawkins et al., , Campana, Parker et al., ) under analogous settings. Each program generated 120 bp baits with a 60 bp offset between baits.…”

“…CM007595.1; Campana, Hawkins et al, 2016, Campana, Parker et al, 2016 under analogous settings. Each program generated 120 bp baits with a 60 bp offset between baits.…”

“…Targeted high‐throughput sequencing using hybridization capture (e.g., Gnirke et al., ) is a critical tool in molecular ecology and genomics. Applications include genomic investigations of nonmodel organisms using ultra‐conserved elements (Faircloth et al., ; Lim & Braun, ), exome capture (e.g., Ng et al., ), single nucleotide polymorphism (SNP) analysis (e.g., Burbano et al., ), targeted metagenomics (e.g., Campana, Hawkins et al., , Campana, Parker et al., ), and ancient DNA enrichment and museomics (e.g., Burbano et al., ; Hawkins et al., ; Lim & Braun, ), among others. Hybridization capture utilizes oligonucleotide baits to enrich target molecules from nucleic acid libraries through hybridization of the baits to complementary nucleotide sequences in the libraries, isolation of the hybridized molecules and removal of the nontarget library molecules.…”