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Genomic Analysis Reveals Hidden Biodiversity Within Colugos, the Sister Group to Primates Victor C

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Genomic Analysis Reveals Hidden Biodiversity Within Colugos, the Sister Group to Primates Victor C Washington University School of Medicine Digital Commons@Becker Open Access Publications 2016 Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates Victor C. Mason Texas A & M University - College Station Gang Li Texas A & M University - College Station Patrick Minx Washington University School of Medicine in St. Louis Jürgen Schmitz University of Münster Gennady Churakov University of Münster See next page for additional authors Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Mason, Victor C.; Li, Gang; Minx, Patrick; Schmitz, Jürgen; Churakov, Gennady; Doronina, Liliya; Melin, Amanda D.; Dominy, Nathaniel J.; Lim, Norman T-L; Springer, Mark S.; Wilson, Richard K.; Warren, Wesley C.; Helgen, Kristofer M.; and Murphy, William J., ,"Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates." Science Advances.2,8. e1600633. (2016). https://digitalcommons.wustl.edu/open_access_pubs/5209 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Authors Victor C. Mason, Gang Li, Patrick Minx, Jürgen Schmitz, Gennady Churakov, Liliya Doronina, Amanda D. Melin, Nathaniel J. Dominy, Norman T-L Lim, Mark S. Springer, Richard K. Wilson, Wesley C. Warren, Kristofer M. Helgen, and William J. Murphy This open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/5209 RESEARCH ARTICLE ZOOLOGICAL POPULATION GENETICS 2016 © The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. Distributed Genomic analysis reveals hidden biodiversity under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC). within colugos, the sister group to primates 10.1126/sciadv.1600633 Victor C. Mason,1 Gang Li,1 Patrick Minx,2 Jürgen Schmitz,3 Gennady Churakov,3,4 Liliya Doronina,3 Amanda D. Melin,5 Nathaniel J. Dominy,6 Norman T-L. Lim,7,8 Mark S. Springer,9 Richard K. Wilson,2 Wesley C. Warren,2 Kristofer M. Helgen,10* William J. Murphy1* Colugos are among the most poorly studied mammals despite their centrality to resolving supraordinal primate re- lationships. 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 Downloaded from 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. INTRODUCTION http://advances.sciencemag.org/ As members of a strictly arboreal lineage of Southeast Asian gliding origins and taxonomic diversity remain unresolved, despite their impor- mammals, colugos (Order Dermoptera) have been known to science tance to the interpretation of early primate origins and evolution, and to for centuries. However, the absence of captive individuals and a cryptic, developing effective conservation strategies, respectively (8, 17, 18). nocturnal lifestyle have left basic questions surrounding their ecology and evolutionary history unanswered (1–3). At various times within the past century, colugos have been allied to mammals as divergent as in- RESULTS AND DISCUSSION sectivores and bats, and have played a central role in discussions of primate ancestry (4, 5). The phylogenetic position of colugos relative to Assembling a colugo reference genome other euarchontan orders remains highly controversial, with competing To produce the first detailed genetic insights into the poorly known studies favoring an association of colugos with either primates or treeshrews history of this enigmatic mammalian order, we produced a draft genome (6–12). Current taxonomy describes the order Dermoptera as one of assembly from a male Sunda colugo from West Java. We generated ~55× the least speciose within all of Mammalia, consisting of just two spe- depth of coverage using Illumina sequence reads and produced an as- on August 31, 2016 cies in monotypic genera: the Sunda colugo, Galeopterus variegatus, sembly (G_variegatus-3.0.2) that is 3.2 giga–base pairs (Gbp) in length and the Philippine colugo, Cynocephalus volans (13). This low species (see Materials and Methods). This assembly is longer than most eutherian richness is surprising because colugos are widely distributed throughout genomes, with a scaffold N50 of 245.2 kbp and contig N50 of 20.7 kbp. the Southeast Asian mainland and archipelago, a region of otherwise The assembly was annotated with the National Center for Biotechnology remarkable biodiversity (14). Colugos also have the most elaborate Information (NCBI) annotation pipeline and colugo RNA sequencing gliding membrane among living vertebrates, which inhibits terrestrial (RNAseq) libraries (see Materials and Methods), which identified 23,081 movement and dispersal outside of forests (1, 2). Population differenti- protein-coding genes. To test competing hypotheses concerning the re- ation has been supported by morphology (3)andhighmitochondrial lationship of colugos to other mammals, we performed comparative ge- divergence between some Sunda colugo populations (15, 16). These nomic analyses with a 2.5-Mbp one-to-one orthologous coding DNA distinctions may reflect valid species isolated in allopatry but remain un- sequence alignment between colugo and 17 other sequenced mammali- substantiated in the absence of broader geographic and genomic sampling an genomes (see Materials and Methods and table S1). These alignments and comparison. Thus, evolutionary questions surrounding dermopteran were augmented with reference assemblies from a male Philippine colugo on the basis of 14× Illumina sequencing coverage, and from a pentailed 1Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, treeshrew (Ptilocercus lowii) on the basis of ~5× coverage, to mitigate 2 Texas A&M University, College Station, TX 77843, USA. McDonnell Genome Institute, long-branch attraction effects (see Materials and Methods). Washington University School of Medicine, St. Louis, MO 63108, USA. 3Institute of Experimen- tal Pathology (ZMBE), University of Münster, D-48149 Münster, Germany. 4Institute of Evolu- tion and Biodiversity, University of Münster, D-48149 Münster, Germany. 5University of The closest living relative of primates Calgary, Calgary, Alberta T2N 1N4, Canada. 6Departments of Anthropology and Biological Sciences, Dartmouth College, Hanover, NH 03755, USA. 7Natural Sciences and Science Edu- The relationship of colugos to other mammalian orders remains a topic cation, National Institute of Education, Nanyang Technological University, Singapore 637616, of considerable debate. Craniodental characters primarily support colugos Singapore. 8Lee Kong Chian Natural History Museum, National University of Singapore, as sister to treeshrews (Sundatheria) (10), whereas retrotransposon inser- 9 Singapore 117377 , Singapore. Department of Biology, University of California, Riverside, tions and some interpretations of postcranial skeleton characters suggest Riverside, CA 92521, USA. 10Division of Mammals, Smithsonian Institution, National Museum of Natural History, Washington, DC 20013, USA. that colugos are sister to primates (Primatomorpha) (4, 6). Previous studies *Corresponding author. Email: [email protected] (W.J.M.); [email protected] (K.M.H.) have demonstrated that evolutionary relationships based solely on phenomic Mason et al. Sci. Adv. 2016; 2 :e1600633 10 August 2016 1of15 RESEARCH ARTICLE data sets generate numerous polyphyletic relationships of convergently OR gene repertoires that began in the ancestral lineage of Primato- evolved mammals positioned within different superorders of placental morpha. We also found evidence for an increased importance of vision mammals (10, 19). To address these conflicting hypotheses, we con- and hearing in the colugo lineage based on significant enrichment for structed maximum likelihood and coalescent-based phylogenies with the positively selected genes involved in these sensory modalities (Padj = genome-wide supermatrix of 21 species from 8 eutherian orders (fig. S1). 0.0097 and Padj = 0.004, respectively) including genes that, when mutated, Our results consistently supported the Primatomorpha hypothesis (4), cause sensorial hearing loss and a variety of visual pathologies, notably confirming colugos as the sister group of primates (Fig. 1 and fig. S1) macular degeneration (Fig. 2C and databases S1 and S2). The increased (7, 9, 18). Because tree-building methods applied to deep, star-like radia- number of loss-of-function OR gene mutations in colugos is consistent tions with
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