title: A phylogenomic analysis of turtles.
abstract: Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2381 ultraconserved element (UCE) loci representing a total of 1,718,154bp of aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. This robust phylogeny shows that proposed phylogenetic names correspond to well-supported clades, and this topology is more consistent with the temporal appearance of clades and paleobiogeography. Future studies of turtle phylogeny using fossil turtles should use this topology as a scaffold for their morphological phylogenetic analyses.
authors.affiliation: Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Nicholas G
authors.initials: NG
authors.lastname: Crawford
authors.affiliation: John D. Cooper Archaeological and Paleontological Center, Department of Geological Sciences, California State University, Fullerton, CA 92834, USA. Electronic address: jparham@fullerton.edu.
authors.forename: James F
authors.initials: JF
authors.lastname: Parham
authors.affiliation: Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA.
authors.forename: Anna B
authors.initials: AB
authors.lastname: Sellas
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
authors.forename: Brant C
authors.initials: BC
authors.lastname: Faircloth
authors.affiliation: Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA.
authors.forename: Travis C
authors.initials: TC
authors.lastname: Glenn
authors.affiliation: Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA.
authors.forename: Theodore J
authors.initials: TJ
authors.lastname: Papenfuss
authors.affiliation: Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA.
authors.forename: James B
authors.initials: JB
authors.lastname: Henderson
authors.affiliation: Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA; Mathematical and Computational Biology Department, Harvey Mudd College, 301 Platt Boulevard, Claremont, CA 9171, USA.
authors.forename: Madison H
authors.initials: MH
authors.lastname: Hansen
authors.affiliation: Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA.
authors.forename: W Brian
authors.initials: WB
authors.lastname: Simison
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D017124:Conserved Sequence; D016013:Likelihood Functions; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014426:Turtles / Q000145:classification* / Q000235:genetics
keywords: Biogeography; Phylogeography; Systematics; Turtles; Ultraconserved elements