title: Interspecific hybridization causes long-term phylogenetic discordance between nuclear and mitochondrial genomes in freshwater fishes.
abstract: Classification, phylogeography and the testing of evolutionary hypotheses rely on correct estimation of species phylogeny. Early molecular phylogenies often relied on mtDNA alone, which acts as a single linkage group with one history. Over the last decade, the use of multiple nuclear sequences has often revealed conflict among gene trees. This observation can be attributed to hybridization, lineage sorting, paralogy or selection. Here, we use 54 groups of fishes from 48 studies to estimate the degree of concordance between mitochondrial and nuclear gene trees in two ecological grades of fishes: marine and freshwater. We test the hypothesis that freshwater fish phylogenies should, on average, show more discordance because of their higher propensity for hybridization in the past. In keeping with this idea, concordance between mitochondrial and nuclear gene trees (as measured by proportion of components shared) is on average 50% higher in marine fishes. We discuss why this difference almost certainly results from introgression caused by greater historical hybridization among lineages in freshwater groups, and further emphasize the need to use multiple nuclear genes, and identify conflict among them, in estimation of species phylogeny.
authors.affiliation: Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
authors.forename: Graham P
authors.identifier: http://orcid.org/0000-0002-6408-7868
authors.initials: GP
authors.lastname: Wallis
authors.affiliation: Women's and Children's Health, Paediatrics & Child Health, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
authors.forename: Sophia R
authors.initials: SR
authors.lastname: Cameron-Christie
authors.affiliation: Molecular Pathology Laboratory, Canterbury Health Laboratories, PO Box 151, Christchurch, 8140, New Zealand.|Department of Pathology, University of Otago, Riccarton Avenue, PO Box 4345, Christchurch, 8140, New Zealand.
authors.forename: Hannah L
authors.initials: HL
authors.lastname: Kennedy
authors.affiliation: Melbourne IVF, Suite 10, 320 Victoria Parade, East Melbourne, Vic., 3002, Australia.
authors.forename: Gemma
authors.initials: G
authors.lastname: Palmer
authors.affiliation: National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.
authors.forename: Tessa R
authors.initials: TR
authors.lastname: Sanders
authors.affiliation: Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand.
authors.forename: David J
authors.initials: DJ
authors.lastname: Winter
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D005399:Fishes / Q000145:classification*; D005618:Fresh Water; D054629:Genome, Mitochondrial; D006824:Hybridization, Genetic; D010802:Phylogeny
chemical_list: D004272:DNA, Mitochondrial
keywords: concordance; discordance; freshwater fish; hybrid; introgression; marine; meta-analysis; phylogeny