title: Convergent evolution of the genomes of marine mammals.
abstract: Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.
authors.affiliation: 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. [2] Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Foote
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Yue
authors.initials: Y
authors.lastname: Liu
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA.
authors.forename: Gregg W C
authors.initials: GW
authors.lastname: Thomas
authors.affiliation: Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia.
authors.forename: Tomáš
authors.initials: T
authors.lastname: Vinař
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
authors.forename: Jessica
authors.identifier: 0000000197136200
authors.initials: J
authors.lastname: Alföldi
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Jixin
authors.initials: J
authors.lastname: Deng
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Shannon
authors.initials: S
authors.lastname: Dugan
authors.affiliation: Dolfinarium Harderwijk, Harderwijk, the Netherlands.
authors.forename: Cornelis E
authors.initials: CE
authors.lastname: van Elk
authors.affiliation: Sirenia Project, Southeast Ecological Science Center, US Geological Survey, Gainesville, Florida, USA.
authors.forename: Margaret E
authors.initials: ME
authors.lastname: Hunter
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Vandita
authors.initials: V
authors.lastname: Joshi
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Ziad
authors.initials: Z
authors.lastname: Khan
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Christie
authors.initials: C
authors.lastname: Kovar
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Sandra L
authors.initials: SL
authors.lastname: Lee
authors.affiliation: 1] Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Lindblad-Toh
authors.affiliation: 1] Marine Biomedicine and Environmental Science Center, Medical University of South Carolina, Charleston, South Carolina, USA. [2] Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
authors.forename: Annalaura
authors.initials: A
authors.lastname: Mancia
authors.affiliation: Center for Theoretical Evolutionary Genomics, University of California, Berkeley, Berkeley, California, USA.
authors.forename: Rasmus
authors.initials: R
authors.lastname: Nielsen
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Xiang
authors.initials: X
authors.lastname: Qin
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Jiaxin
authors.initials: J
authors.lastname: Qu
authors.affiliation: Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California, USA.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Raney
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
authors.forename: Nagarjun
authors.initials: N
authors.lastname: Vijay
authors.affiliation: 1] Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. [2] Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Jochen B W
authors.initials: JB
authors.lastname: Wolf
authors.affiliation: 1] School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA. [2] Department of Biology, Indiana University, Bloomington, Indiana, USA.
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Hahn
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Donna M
authors.initials: DM
authors.lastname: Muzny
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Kim C
authors.initials: KC
authors.lastname: Worley
authors.affiliation: 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. [2] Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia.
authors.forename: M Thomas P
authors.identifier: 0000000258057195
authors.initials: MT
authors.lastname: Gilbert
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Gibbs
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D019943:Amino Acid Substitution; D000818:Animals; D019143:Evolution, Molecular; D016678:Genome; D006801:Humans; D008322:Mammals / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny; D012641:Selection, Genetic