Data from: Managing cryptic biodiversity: Fine-scale intralacustrine speciation along a benthic gradient in Alpine whitefish (Coregonus spp.)

Whitefish (Coregonus spp.) are an important catch for many freshwater
fisheries, particularly in Switzerland. In support of this, supplemental
stocking of whitefish species is carried out, despite lacking complete
knowledge of the extent, distribution and origin of whitefish diversity in
these lakes, potentially threatening local endemics via artificial gene
flow. Here, we investigate phenotypic and genetic differentiation among
coexisting whitefish species spawning along a depth gradient in a
subalpine Swiss lake to better delineate intralacustrine whitefish
biodiversity. We find depth-related clines in adaptive morphology and in
neutral genetic markers. This individual variation is structured in three
distinct clusters with spatial overlap. Individual genetic distances
correlate strongly with differences in growth rate and gill-raker number,
consistent with predictions of isolation-by-adaptation and ecological
speciation. Genetic differentiation between species suggests reproductive
isolation, despite demographic admixture on spawning grounds. Our results
are consistent with clinal speciation resulting in three species
coexisting in close ecological parapatry, one (C. sp. “benthic
intermediate”) being previously unknown. A second unknown species spawning
in close proximity was found to be of potential allochthonous origin. This
study highlights the importance of taxonomically unbiased sampling
strategies to both understand evolutionary mechanisms structuring
biodiversity and to better inform conservation and fisheries management.