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African Wild Dog Genome Provides Population, Trait Insights

NEW YORK (GenomeWeb) – Researchers from the Smithsonian Conservation Biology Institute and elsewhere have sequenced the genome of the African wild dog, Lycaon pictus, using the sequence as a resource for population studies on the animal.

As reported in BMC Genomics, the team did genome sequencing on two African wild dogs — one from Kenya and another from South Africa — defining almost 1.1 million SNPs or small insertions and deletions that were used to assess African wild dog traits relative to domestic dogs and to estimate demographic patterns in the animals over 1 million years or so.

The African wild dog is endangered due to factors such as disease, human persecution, and habitat fragmentation, the group noted. It now resides on scraps of its former range on the African continent.

"The genomes from these two populations represent some of the first published wild canid genomes and are particularly valuable given the susceptibility of wild dogs to disease and habitat fragmentation," senior author Robert Fleischer, a conservation genomics researcher at the Smithsonian Conservation Biology Institute, and his co-authors wrote.

Using Illumina HiSeq 2500 instruments, the researchers sequenced genomic DNA isolated from a female African wild dog sampled in 2003 from a re-colonized population in Kenya and a male representative from a managed population in a park in South Africa's KwaZulu-Natal province. The resulting reads covered the domestic dog genome at average depths of 5.8-fold and 5.7-fold coverage, respectively.

Compared with the domestic dog genome, the team defined more than 14.3 million SNPs and 2.6 million indels in the L. pictus genomes, including almost 1.1 million variants that were polymorphic between the two African wild dogs.

Based on variant patterns across the autosomal chromosome sequences, the researchers estimated that the African wild dog experienced sharp declines in population size at least twice before: once between 700,000 and 200,000 years ago and again from 70,000 to 10,000 years ago.

From stretches of sequence with low genetic diversity in the new genomes, they noted that present-day Lycaon populations may be subject to inbreeding and/or within-population selection that have left their marks on African wild dog genomes.

Still, the study's authors cautioned that "[f]urther research is needed to clarify whether these population reductions and low diversity regions are characteristic of the species as a whole."

Finally, by searching for signs of selection in the African wild dog genomes, the team uncovered potential genetic contributors to some of the distinct dietary and physical adaptation in the African wild dog, from its hyper-carnivory to its anatomical adaptations.

For example, the authors narrowed in on four candidate genes — ASIP, MITF, MLPH, and PMEL — suspected of influencing coat composition and the characteristic 'painted' coloring in African wild dogs. They noted that additional functional research will be needed to confirm the apparent ties between variants in such genes and African wild dog traits.