title: Genome sequence, population history, and pelage genetics of the endangered African wild dog (Lycaon pictus).
abstract: The 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.
  
  
  
  We 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.
  
  
  
  We 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.
authors.affiliation: Center for Conservation Genomics, Smithsonian Conservation Biology Institute, 3001 Connecticut Avenue NW, Washington, DC, 20008, USA. CampanaM@si.edu.|Department of Environmental Science and Policy, George Mason University, 4400 University Drive, Fairfax, VA, 22030, USA. CampanaM@si.edu.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Campana
authors.affiliation: Center for Conservation Genomics, Smithsonian Conservation Biology Institute, 3001 Connecticut Avenue NW, Washington, DC, 20008, USA.|Department of Environmental Science and Policy, George Mason University, 4400 University Drive, Fairfax, VA, 22030, USA.|Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, Washington, DC, 20013, USA.
authors.forename: Lillian D
authors.initials: LD
authors.lastname: Parker
authors.affiliation: Center for Conservation Genomics, Smithsonian Conservation Biology Institute, 3001 Connecticut Avenue NW, Washington, DC, 20008, USA.|Department of Environmental Science and Policy, George Mason University, 4400 University Drive, Fairfax, VA, 22030, USA.|Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, Washington, DC, 20013, USA.
authors.forename: Melissa T R
authors.initials: MT
authors.lastname: Hawkins
authors.affiliation: Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
authors.forename: Hillary S
authors.initials: HS
authors.lastname: Young
authors.affiliation: Department of Environmental Science and Policy, George Mason University, 4400 University Drive, Fairfax, VA, 22030, USA.|Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, Washington, DC, 20013, USA.
authors.forename: Kristofer M
authors.initials: KM
authors.lastname: Helgen
authors.affiliation: Department of Wildlife, Humboldt State University, 1 Harpst St, Arcata, CA, 95521, USA.
authors.forename: Micaela
authors.initials: M
authors.lastname: Szykman Gunther
authors.affiliation: Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.
authors.forename: Rosie
authors.initials: R
authors.lastname: Woodroffe
authors.affiliation: Center for Conservation Genomics, Smithsonian Conservation Biology Institute, 3001 Connecticut Avenue NW, Washington, DC, 20008, USA.|Department of Environmental Science and Policy, George Mason University, 4400 University Drive, Fairfax, VA, 22030, USA.
authors.forename: Jesús E
authors.initials: JE
authors.lastname: Maldonado
authors.affiliation: Center for Conservation Genomics, Smithsonian Conservation Biology Institute, 3001 Connecticut Avenue NW, Washington, DC, 20008, USA.
authors.forename: Robert C
authors.initials: RC
authors.lastname: Fleischer
mesh_terms: D000818:Animals; D000835:Animals, Wild / Q000235:genetics*; D046028:Canidae / Q000235:genetics*; D002875:Chromosomes; D056727:Endangered Species; D005828:Genetics, Population; D016678:Genome; D054629:Genome, Mitochondrial; D023281:Genomics; D005843:Geography; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic
keywords: Genome; Lycaon pictus; Pelage; Population history; Selection