title: Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia.
abstract: The recently extinct (ca. 1768) Steller's sea cow (Hydrodamalis gigas) was a large, edentulous North Pacific sirenian. The phylogenetic affinities of this taxon to other members of this clade, living and extinct, are uncertain based on previous morphological and molecular studies. We employed hybridization capture methods and second generation sequencing technology to obtain >30kb of exon sequences from 26 nuclear genes for both H. gigas and Dugong dugon. We also obtained complete coding sequences for the tooth-related enamelin (ENAM) gene. Hybridization probes designed using dugong and manatee sequences were both highly effective in retrieving sequences from H. gigas (mean=98.8% coverage), as were more divergent probes for regions of ENAM (99.0% coverage) that were designed exclusively from a proboscidean (African elephant) and a hyracoid (Cape hyrax). New sequences were combined with available sequences for representatives of all other afrotherian orders. We also expanded a previously published morphological matrix for living and fossil Sirenia by adding both new taxa and nine new postcranial characters. Maximum likelihood and parsimony analyses of the molecular data provide robust support for an association of H. gigas and D. dugon to the exclusion of living trichechids (manatees). Parsimony analyses of the morphological data also support the inclusion of H. gigas in Dugongidae with D. dugon and fossil dugongids. Timetree analyses based on calibration density approaches with hard- and soft-bounded constraints suggest that H. gigas and D. dugon diverged in the Oligocene and that crown sirenians last shared a common ancestor in the Eocene. The coding sequence for the ENAM gene in H. gigas does not contain frameshift mutations or stop codons, but there is a transversion mutation (AG to CG) in the acceptor splice site of intron 2. This disruption in the edentulous Steller's sea cow is consistent with previous studies that have documented inactivating mutations in tooth-specific loci of a variety of edentulous and enamelless vertebrates including birds, turtles, aardvarks, pangolins, xenarthrans, and baleen whales. Further, branch-site dN/dS analyses provide evidence for positive selection in ENAM on the stem dugongid branch where extensive tooth reduction occurred, followed by neutral evolution on the Hydrodamalis branch. Finally, we present a synthetic evolutionary tree for living and fossil sirenians showing several key innovations in the history of this clade including character state changes that parallel those that occurred in the evolutionary history of cetaceans.
authors.affiliation: Department of Biology, University of California, Riverside, CA 92521, USA. Electronic address: mark.springer@ucr.edu.
authors.forename: Mark S
authors.initials: MS
authors.lastname: Springer
authors.affiliation: Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
authors.forename: Anthony V
authors.initials: AV
authors.lastname: Signore
authors.affiliation: Department of Biology, The University of York, Wentworth Way, Heslington, York YO10 5DD, UK.
authors.forename: Johanna L A
authors.initials: JL
authors.lastname: Paijmans
authors.affiliation: Department of Mammalogy, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA.
authors.forename: Jorge
authors.initials: J
authors.lastname: Vélez-Juarbe
authors.affiliation: Laboratory of Evolutionary Biology, Department of Anatomy, Howard University, Washington, DC 20059, USA; Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA.
authors.forename: Daryl P
authors.initials: DP
authors.lastname: Domning
authors.affiliation: Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
authors.forename: Cameron E
authors.initials: CE
authors.lastname: Bauer
authors.affiliation: Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
authors.forename: Kai
authors.initials: K
authors.lastname: He
authors.affiliation: Department of Biology, George Mason University, Fairfax, VA 22030, USA.
authors.forename: Lorelei
authors.initials: L
authors.lastname: Crerar
authors.affiliation: Center for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
authors.forename: Paula F
authors.initials: PF
authors.lastname: Campos
authors.affiliation: Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA.
authors.forename: William J
authors.initials: WJ
authors.lastname: Murphy
authors.affiliation: Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, USA.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Meredith
authors.affiliation: Department of Biology, University of California, Riverside, CA 92521, USA.
authors.forename: John
authors.initials: J
authors.lastname: Gatesy
authors.affiliation: Center for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark.
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.affiliation: Department of Mammalogy, American Museum of Natural History, New York, NY 10024, USA.
authors.forename: Ross D E
authors.initials: RD
authors.lastname: MacPhee
authors.affiliation: Department of Biology, The University of York, Wentworth Way, Heslington, York YO10 5DD, UK; Adaptive and Evolutionary Genomics, Institute for Biochemistry and Biology, Faculty of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Strasse 24-24, 14476 Potsdam, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Hofreiter
authors.affiliation: Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada. Electronic address: Kevin.Campbell@umanitoba.ca.
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Campbell
mesh_terms: D000818:Animals; D005075:Biological Evolution; D003746:Dental Enamel Proteins / Q000235:genetics; D005580:Fossils; D005796:Genes; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D020453:Sirenia / Q000033:anatomy & histology / Q000145:classification* / Q000235:genetics
chemical_list: D003746:Dental Enamel Proteins; C038456:tuftelin
keywords: Ancient DNA; Macroevolution; Sirenia; Steller’s sea cow; Teeth