Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium

Present-day ecology and population structure are the legacies of past
climate and habitat perturbations, and this is particularly true for
species that are widely distributed at high latitudes. The red knot,
Calidris canutus, is an arctic-breeding, long-distance migratory shorebird
with six recognized subspecies defined by differences in morphology,
migration behavior, and annual-cycle phenology, in a global distribution
thought to have arisen just since the Last Glacial Maximum (LGM). We used
nextRAD sequencing of 10,881 single-nucleotide polymorphisms (SNPs) to
assess the neutral genetic structure and phylogeographic history of 172
red knots representing all known global breeding populations. Using
population genetics approaches, including model-based scenario-testing in
an approximate Bayesian computation (ABC) framework, we infer that red
knots derive from two main lineages that diverged ca. 34,000 years ago,
and thus most likely persisted at the LGM in both Palearctic and Nearctic
refugia, followed by at least two instances of secondary contact and
admixture. Within two Beringian subspecies (C. c. roselaari and rogersi),
we detected previously unknown genetic structure among sub-populations
sharing a migratory flyway, reflecting additional complexity in the
phylogeographic history of the region. Conversely, we found very weak
genetic differentiation between two Nearctic populations (rufa and
islandica) with clearly divergent migratory phenotypes and little or no
apparent contact throughout the annual cycle. Together, these results
suggest that relative gene flow among migratory populations reflects a
complex interplay of historical, geographical, and ecological factors.