title: Purifying selection and genetic drift shaped Pleistocene evolution of the mitochondrial genome in an endangered Australian freshwater fish.
abstract: Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We used complete mitochondrial genome sequences to build a phylogeny, estimate lineage divergence times and identify signatures of purifying and positive selection acting on mitochondrial genes for 25 Macquarie perch from three basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin (SB). Phylogenetic analysis resolved basin-level clades, supporting incipient speciation previously inferred from differentiation in allozymes, microsatellites and mitochondrial control region. The estimated time of lineage divergence suggested an early- to mid-Pleistocene split between SB and the common ancestor of HNB+MDB, followed by mid-to-late Pleistocene splitting between HNB and MDB. These divergence estimates are more recent than previous ones. Our analyses suggested that evolutionary drivers differed between inland MDB and coastal HNB. In the cooler and more climatically variable MDB, mitogenomes evolved under strong purifying selection, whereas in the warmer and more climatically stable HNB, purifying selection was relaxed. Evidence for relaxed selection in the HNB includes elevated transfer RNA and 16S ribosomal RNA polymorphism, presence of potentially mildly deleterious mutations and a codon (ATP6113) displaying signatures of positive selection (ratio of nonsynonymous to synonymous substitution rates (dN/dS) >1, radical change of an amino-acid property and phylogenetic conservation across the Percichthyidae). In addition, the difference could be because of stronger genetic drift in the smaller and historically more subdivided HNB with low per-population effective population sizes.
authors.affiliation: School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia.
authors.forename: A
authors.initials: A
authors.lastname: Pavlova
authors.affiliation: School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.|Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.
authors.forename: H M
authors.initials: HM
authors.lastname: Gan
authors.affiliation: School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.|Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.
authors.forename: Y P
authors.initials: YP
authors.lastname: Lee
authors.affiliation: School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.|Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.
authors.forename: C M
authors.initials: CM
authors.lastname: Austin
authors.affiliation: NSW Department of Primary Industries, Batemans Bay, New South Wales, Australia.
authors.forename: D M
authors.initials: DM
authors.lastname: Gilligan
authors.affiliation: Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia.
authors.forename: M
authors.initials: M
authors.lastname: Lintermans
authors.affiliation: School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia.
authors.forename: P
authors.initials: P
authors.lastname: Sunnucks
mesh_terms: D000818:Animals; D001315:Australia; D001499:Bayes Theorem; D002980:Climate; D003062:Codon; D056727:Endangered Species; D019143:Evolution, Molecular; D005618:Fresh Water; D040961:Genetic Drift; D054629:Genome, Mitochondrial; D018895:Microsatellite Repeats; D010471:Perches / Q000235:genetics*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D012641:Selection, Genetic
chemical_list: D003062:Codon; D012336:RNA, Ribosomal, 16S; D012343:RNA, Transfer