title: Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates.
abstract: Colugos are among the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculoskeletal-related genes that likely underlie their nocturnal and gliding adaptations. Phylogenomic analysis and catalogs of rare genomic changes overwhelmingly support the contested hypothesis that colugos are the sister group to primates (Primatomorpha), to the exclusion of treeshrews. We captured ~140 kb of orthologous sequence data from colugo museum specimens sampled across their range and identified large genetic differences between many geographically isolated populations that may result in a >300% increase in the number of recognized colugo species. Our results identify conservation units to mitigate future losses of this enigmatic mammalian order.
authors.affiliation: Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX 77843, USA.
authors.forename: Victor C
authors.identifier: 0000-0002-7962-4806
authors.initials: VC
authors.lastname: Mason
authors.affiliation: Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX 77843, USA.
authors.forename: Gang
authors.initials: G
authors.lastname: Li
authors.affiliation: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Patrick
authors.identifier: 0000-0003-1179-2173
authors.initials: P
authors.lastname: Minx
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany.
authors.forename: Jürgen
authors.identifier: 0000-0002-4686-861X
authors.initials: J
authors.lastname: Schmitz
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany.; Institute of Evolution and Biodiversity, University of Münster, D-48149 Münster, Germany.
authors.forename: Gennady
authors.initials: G
authors.lastname: Churakov
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany.
authors.forename: Liliya
authors.initials: L
authors.lastname: Doronina
authors.affiliation: University of Calgary, Calgary, Alberta T2N 1N4, Canada.
authors.forename: Amanda D
authors.identifier: 0000-0002-0612-2514
authors.initials: AD
authors.lastname: Melin
authors.affiliation: Departments of Anthropology and Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
authors.forename: Nathaniel J
authors.identifier: 0000-0001-5916-418X
authors.initials: NJ
authors.lastname: Dominy
authors.affiliation: Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore 637616, Singapore.; Lee Kong Chian Natural History Museum, National University of Singapore, Singapore 117377 , Singapore.
authors.forename: Norman T-L
authors.initials: NT
authors.lastname: Lim
authors.affiliation: Department of Biology, University of California, Riverside, Riverside, CA 92521, USA.
authors.forename: Mark S
authors.initials: MS
authors.lastname: Springer
authors.affiliation: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Richard K
authors.identifier: 0000-0002-1992-1358
authors.initials: RK
authors.lastname: Wilson
authors.affiliation: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Wesley C
authors.identifier: 0000-0003-2255-2730
authors.initials: WC
authors.lastname: Warren
authors.affiliation: Division of Mammals, Smithsonian Institution, National Museum of Natural History, Washington, DC 20013, USA.
authors.forename: Kristofer M
authors.initials: KM
authors.lastname: Helgen
authors.affiliation: Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX 77843, USA.
authors.forename: William J
authors.initials: WJ
authors.lastname: Murphy
mesh_terms: D000818:Animals; D044822:Biodiversity; D002685:Chiroptera / Q000145:classification / Q000235:genetics*; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D007900:Lemur / Q000145:classification / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D011323:Primates / Q000145:classification / Q000235:genetics*
keywords: Colugo; Southeast Asia; biogeography; genetics; genomic analysis; phylogenomics; population dynamics