Abstract
Landlocking of diadromous fish in freshwater systems can have
significant genomic consequences. For instance, the loss of the
migratory life stage can dramatically reduce gene flow across
populations, leading to increased genetic structuring, and stronger
effects of local adaptation. These genomic consequences have been
well-studied in some mainland systems, but the evolutionary impacts of
landlocking in island ecosystems are largely unknown. In this study, we
used a genotyping-by-sequencing (GBS) approach to examine the
evolutionary history of landlocking in common smelt (Retropinna
retropinna) on Chatham Island, a small isolated oceanic island 650 km
southeast of mainland New Zealand. We examined the relationship among
the Chatham Island and mainland smelt, and used coalescent analyses to
test the number and timing of landlocking events on Chatham Island. Our
genomic analysis, based on 21,135 SNPs across 169 individuals, revealed
that the Chatham Island smelt were genomically distinct from the
mainland New Zealand fish, consistent with a single ancestral
colonisation event of Chatham Island in the Pleistocene. Significant
genetic structure was also evident within the Chatham Island smelt, with
a diadromous Chatham Island smelt group, along with three geographically
structured landlocked groups. Coalescent demographic analysis supported
three independent landlocking events, with this loss of diadromy
significantly pre-dating human colonisation. Our results illustrate how
landlocking of diadromous fish can occur repeatedly across a narrow
spatial scale, and highlight a unique system to study the genomic basis
of repeated adaptation.