title: Initial Evidence for Adaptive Selection on the NADH Subunit Two of Freshwater Dolphins by Analyses of Mitochondrial Genomes.
abstract: A small number of cetaceans have adapted to an entirely freshwater environment, having colonized rivers in Asia and South America from an ancestral origin in the marine environment. This includes the 'river dolphins', early divergence from the odontocete lineage, and two species of true dolphins (Family Delphinidae). Successful adaptation to the freshwater environment may have required increased demands in energy involved in processes such as the mitochondrial osmotic balance. For this reason, riverine odontocetes provide a compelling natural experiment in adaptation of mammals from marine to freshwater habitats. Here we present initial evidence of positive selection in the NADH dehydrogenase subunit 2 of riverine odontocetes by analyses of full mitochondrial genomes, using tests of selection and protein structure modeling. The codon model with highest statistical support corresponds to three discrete categories for amino acid sites, those under positive, neutral, and purifying selection. With this model we found positive selection at site 297 of the NADH dehydrogenase subunit 2 (dN/dS>1.0,) leading to a substitution of an Ala or Val from the ancestral state of Thr. A phylogenetic reconstruction of 27 cetacean mitogenomes showed that an Ala substitution has evolved at least four times in cetaceans, once or more in the three 'river dolphins' (Families Pontoporidae, Lipotidae and Inidae), once in the riverine Sotalia fluviatilis (but not in its marine sister taxa), once in the riverine Orcaella brevirostris from the Mekong River (but not in its marine sister taxa) and once in two other related marine dolphins. We located the position of this amino acid substitution in an alpha-helix channel in the trans-membrane domain in both the E. coli structure and Sotalia fluviatilis model. In E. coli this position is located in a helix implicated in a proton translocation channel of respiratory complex 1 and may have a similar role in the NADH dehydrogenases of cetaceans.
authors.affiliation: Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Biological Sciences Department, Universidad de los Andes, Bogota, Colombia.
authors.forename: Susana
authors.initials: S
authors.lastname: Caballero
authors.affiliation: Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Biological Sciences Department, Universidad de los Andes, Bogota, Colombia; School of Biological Sciences, The University of Sydney, NSW, Australia.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Duchêne
authors.affiliation: Grupo de Investigaciones en Bioquímica y Biología Molecular de Parásitos, Biological Sciences Department, Universidad de los Andes, Bogota, Colombia.
authors.forename: Manuel F
authors.initials: MF
authors.lastname: Garavito
authors.affiliation: Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, Oregon, United States of America.
authors.forename: Beth
authors.initials: B
authors.lastname: Slikas
authors.affiliation: Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, Oregon, United States of America.
authors.forename: C Scott
authors.initials: CS
authors.lastname: Baker
mesh_terms: D000222:Adaptation, Physiological; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000818:Animals; D004289:Dolphins / Q000145:classification / Q000235:genetics*; D054629:Genome, Mitochondrial; D008969:Molecular Sequence Data; D009243:NAD / Q000737:chemistry / Q000235:genetics*; D010802:Phylogeny; D021122:Protein Subunits / Q000737:chemistry / Q000235:genetics; D012641:Selection, Genetic
chemical_list: D021122:Protein Subunits; D009243:NAD