Genome-wide analysis resolves the radiation of New Zealand’s freshwater Galaxias vulgaris complex and reveals a candidate species obscured by mitochondrial capture

Abstract Freshwater fish radiations are often characterized by multiple closely-related species in close proximity, which can lead to introgression and associated discordance of mitochondrial and nuclear characterizations of species diversity. As a case in point, single locus nuclear versus mitochondrial analyses of New Zealand’s stream-resident Galaxias vulgaris complex have yielded conflicting phylogenies. We generate and analyze a genome-wide data set comprising 52,352 SNPs across 187 Galaxias specimens to resolve the phylogeny of this recent fish radiation. We conduct phylogenetic, PCA, STRUCTURE, and ABBA-BABA analyses to evaluate the evolutionary relationships of lineages in the context of natural and anthropogenic river drainage alterations. In addition to the 11 previously recognized stream-resident lineages, genome-wide data reveal a twelfth candidate species (G. ‘Pomahaka’), apparently obscured by introgressive mitochondrial capture. We identify additional examples of mito-nuclear discordance and putative mitochondrial capture, likely mediated by geological and anthropogenic modification of drainage boundaries. Our study highlights the need for genome-wide approaches for delimiting freshwater biodiversity. Genetic data also reveal the influence of drainage history on freshwater biodiversity, including the rapid divergence of recently fragmented fish populations, and the conservation genetic risks of anthropogenic translocations events.