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

Aim: 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. Our goal
is to use genome-wide divergence patterns among these fishes to evaluate
the potential role of mitochondrial capture in obscuring species diversity
and to understand how ancient and anthropogenic drainage modification
explains this diversity. Location: Freshwater ecosystems of New Zealand.
Methods: 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. Results:
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. Main conclusions: 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.