title: Characterization of MHC class IIB for four endangered Australian freshwater fishes obtained from ecologically divergent populations.
abstract: Genetic diversity is an essential aspect of species viability, and assessments of neutral genetic diversity are regularly implemented in captive breeding and conservation programs. Despite their importance, information from adaptive markers is rarely included in such programs. A promising marker of significance in fitness and adaptive potential is the major histocompatibility complex (MHC), a key component of the adaptive immune system. Populations of Australian freshwater fishes are generally declining in numbers due to human impacts and the introduction of exotic species, a scenario of particular concern for members of the family Percichthyidae, several of which are listed as nationally vulnerable or endangered, and hence subject to management plans, captive breeding, and restoration plans. We used a next-generation sequencing approach to characterize the MHC IIB locus and provide a conservative description of its levels of diversity in four endangered percichthyids: Gadopsis marmoratus, Macquaria australasica, Nannoperca australis, and Nannoperca obscura. Evidence is presented for a duplicated MHC IIB locus, positively selected sites and recombination of MHC alleles. Relatively moderate levels of diversity were detected in the four species, as well as in different ecotypes within each species. Phylogenetic analyses revealed genus specific clustering of alleles and no allele sharing among species. There were also no shared alleles observed between two ecotypes within G. marmoratus and within M. australasica, which might be indicative of ecologically-driven divergence and/or long divergence times. This represents the first characterization and assessment of MHC diversity for Percichthyidae, and also for Australian freshwater fishes in general, providing key genetic resources for a vertebrate group of increasing conservation concern.
authors.affiliation: Molecular Ecology Lab, Flinders University, Adelaide 5001, South Australia, Australia; Department of Integrative Biology and Evolution, University of Veterinary Medicine, 1160 Vienna, Austria.
authors.forename: Seraina E
authors.initials: SE
authors.lastname: Bracamonte
authors.affiliation: Molecular Ecology Lab, Flinders University, Adelaide 5001, South Australia, Australia; Department of Integrative Biology and Evolution, University of Veterinary Medicine, 1160 Vienna, Austria.
authors.forename: Steve
authors.initials: S
authors.lastname: Smith
authors.affiliation: Evolutionary Biology Unit, South Australian Museum, North Terrace Adelaide, South Australia 5000 and Curator of Fishes, Museum and Art Gallery of the Northern Territory, PO Box 4646, Darwin, Northern Territory 0801, Australia.
authors.forename: Michael
authors.initials: M
authors.lastname: Hammer
authors.affiliation: Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec QC G1V 0A6, Canada.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Pavey
authors.affiliation: School of Biological Sciences, Monash University, Melbourne 3800, Victoria, Australia.
authors.forename: Paul
authors.initials: P
authors.lastname: Sunnucks
authors.affiliation: Molecular Ecology Lab, Flinders University, Adelaide 5001, South Australia, Australia. Electronic address: Luciano.Beheregaray@flinders.edu.au.
authors.forename: Luciano B
authors.initials: LB
authors.lastname: Beheregaray
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001315:Australia; D056727:Endangered Species; D005618:Fresh Water; D014644:Genetic Variation; D005838:Genotype; D000949:Histocompatibility Antigens Class II / Q000235:genetics*; D008969:Molecular Sequence Data; D010471:Perches / Q000235:genetics* / Q000276:immunology; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D000949:Histocompatibility Antigens Class II
keywords: Ecological genomics; Macquarie perch; Major histocompatibility complex; Next generation sequencing; River blackfish; Southern pygmy perch; Yarra pygmy perch