Fine‐scale habitat preferences influence within‐river population connectivity: a case‐study using two sympatric N ew Z ealand G alaxias fish species

SummaryUnderstanding the ecological factors governing population connectivity in freshwater systems represents an ongoing challenge for aquatic biologists. We used genetic analysis to test the hypothesis that fine‐scale habitat preferences can influence within‐river connectivity patterns in freshwater‐limited fishes. Genetic variation among sampling sites within systems was compared for co‐distributed fish taxa Galaxias gollumoides (low‐velocity pool/swamp habitat) versus an undescribed species, Galaxias ‘southern’ (high‐velocity riffle habitat), using ϕ statistics. These analyses incorporated 1624 bp of mtDNA from 429 galaxiid specimens, encompassing 95 localities across four river systems in Southland, New Zealand. Although similar numbers of haplotypes per river were detected in both taxa, spatial partitioning of this genetic variation within rivers was significantly stronger for G. gollumoides (mean ϕ ST  = 0.539) than for G. ‘ southern’ (mean ϕ ST  = 0.142). Within‐catchment genetic divergence values were also higher for the former species. These finding suggest that a combination of main‐channel habitat continuity and high water velocity facilitates relatively high connectivity in G. ‘ southern’, whereas G. gollumoides populations are genetically isolated in fragmented low‐velocity habitats. We conclude that population connectivity can be strongly influenced by habitat preference, leading to profound differences in the phylogeography, diversity and conservation status of freshwater fish lineages.