A phylogenomic analysis of turtles

Nicholas G Crawford; James F Parham; Anna B Sellas; Brant C Faircloth; Travis C Glenn; Theodore J Papenfuss; James B Henderson; Madison H Hansen; W Brian Simison

doi:10.1016/j.ympev.2014.10.021

A phylogenomic analysis of turtles

Mol Phylogenet Evol. 2015 Feb:83:250-7. doi: 10.1016/j.ympev.2014.10.021. Epub 2014 Nov 4.

Authors

Nicholas G Crawford¹, James F Parham², Anna B Sellas³, Brant C Faircloth⁴, Travis C Glenn⁵, Theodore J Papenfuss⁶, James B Henderson³, Madison H Hansen⁷, W Brian Simison³

Affiliations

¹ 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.
² John D. Cooper Archaeological and Paleontological Center, Department of Geological Sciences, California State University, Fullerton, CA 92834, USA. Electronic address: [email protected].
³ Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA.
⁴ Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
⁵ Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA.
⁶ Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA.
⁷ 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.

PMID: 25450099
DOI: 10.1016/j.ympev.2014.10.021

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.

Keywords: Biogeography; Phylogeography; Systematics; Turtles; Ultraconserved elements.

Publication types

Research Support, N.I.H., Intramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Bayes Theorem
Conserved Sequence
Likelihood Functions
Phylogeny*
Sequence Alignment
Sequence Analysis, DNA
Turtles / classification*
Turtles / genetics

Abstract

Publication types

MeSH terms

Grants and funding