title: Recurrent evolution of melanism in South American felids.
abstract: Morphological variation in natural populations is a genomic test bed for studying the interface between molecular evolution and population genetics, but some of the most interesting questions involve non-model organisms that lack well annotated reference genomes. Many felid species exhibit polymorphism for melanism but the relative roles played by genetic drift, natural selection, and interspecies hybridization remain uncertain. We identify mutations of Agouti signaling protein (ASIP) or the Melanocortin 1 receptor (MC1R) as independent causes of melanism in three closely related South American species: the pampas cat (Leopardus colocolo), the kodkod (Leopardus guigna), and Geoffroy's cat (Leopardus geoffroyi). To assess population level variation in the regions surrounding the causative mutations we apply genomic resources from the domestic cat to carry out clone-based capture and targeted resequencing of 299 kb and 251 kb segments that contain ASIP and MC1R, respectively, from 54 individuals (13-21 per species), achieving enrichment of ~500-2500-fold and ~150x coverage. Our analysis points to unique evolutionary histories for each of the three species, with a strong selective sweep in the pampas cat, a distinctive but short melanism-specific haplotype in the Geoffroy's cat, and reduced nucleotide diversity for both ancestral and melanism-bearing chromosomes in the kodkod. These results reveal an important role for natural selection in a trait of longstanding interest to ecologists, geneticists, and the lay community, and provide a platform for comparative studies of morphological variation in other natural populations.
authors.affiliation: Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.
authors.forename: Alexsandra
authors.initials: A
authors.lastname: Schneider
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America.
authors.forename: Corneliu
authors.initials: C
authors.lastname: Henegar
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Day
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America.
authors.forename: Devin
authors.initials: D
authors.lastname: Absher
authors.affiliation: Laboratorio de Ecología Molecular & Instituto de Ecologia y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
authors.forename: Constanza
authors.initials: C
authors.lastname: Napolitano
authors.affiliation: Jaguar Conservation Fund, Instituto Onça-Pintada, Mineiros, Goiás, Brazil.
authors.forename: Leandro
authors.initials: L
authors.lastname: Silveira
authors.affiliation: Basic Research Laboratory, Frederick National Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America.
authors.forename: Victor A
authors.initials: VA
authors.lastname: David
authors.affiliation: Theodosius Dobzhansky Center for Genome Informatics, St. Petersburg State University, St. Petersburg, Russia.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: O'Brien
authors.affiliation: Basic Research Laboratory, Frederick National Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America.
authors.forename: Marilyn
authors.initials: M
authors.lastname: Menotti-Raymond
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America.
authors.forename: Gregory S
authors.initials: GS
authors.lastname: Barsh
authors.affiliation: Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Eizirik
mesh_terms: D054366:Agouti Signaling Protein / Q000235:genetics*; D000818:Animals; D002415:Cats; D019143:Evolution, Molecular; D014644:Genetic Variation; D005828:Genetics, Population; D006239:Haplotypes; D008548:Melanosis / Q000235:genetics*; D009154:Mutation; D010802:Phylogeny; D044102:Receptor, Melanocortin, Type 1 / Q000235:genetics*; D012641:Selection, Genetic / Q000235:genetics*; D013020:South America; D013045:Species Specificity
chemical_list: D054366:Agouti Signaling Protein; D044102:Receptor, Melanocortin, Type 1