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Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium
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  • Jesse Conklin,
  • Yvonne Verkuil,
  • Philip Battley,
  • Chris Hassell,
  • James Johnson,
  • Job ten Horn,
  • Pavel Tomkovich,
  • Allan Baker,
  • Theunis Piersma,
  • Michael Fontaine
Jesse Conklin
Rijksuniversiteit Groningen
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Yvonne Verkuil
Rijksuniversiteit Groningen
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Philip Battley
Massey University
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Chris Hassell
Global Flyway Network
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James Johnson
US Fish and Wildlife Service Alaska Region
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Job ten Horn
Royal Netherlands Institute for Sea Research (NIOZ)
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Pavel Tomkovich
Lomonosov Moscow State University
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Allan Baker
ROM
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Theunis Piersma
Royal Netherlands Institute for Sea Research (NIOZ)
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Michael Fontaine
Université de Montpellier, CNRS, IRD
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Abstract

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 persisted at the LGM in both Palearctic and Nearctic refugia, followed by at least two instances of secondary contact and admixture. In two flyways, we detected clear genetic structure between population pairs with similar migrations and substantial geographic overlap in the non-breeding season. Conversely, other populations were only weakly differentiated despite clearly divergent migratory phenotypes and little or no apparent contact throughout the annual cycle. In general, the magnitude of genetic differentiation did not match that of phenotypic differences among populations, suggesting that flyway-specific phenotypes developed quite rapidly and do not necessarily impose barriers to gene flow. Our results suggest that population structure and migratory phenotypes in red knots arose from a complex interplay among phylogeography, plasticity, and selective processes.

Peer review status:IN REVISION

18 Jun 2021Submitted to Molecular Ecology
19 Jun 2021Assigned to Editor
19 Jun 2021Submission Checks Completed
11 Jul 2021Reviewer(s) Assigned
18 Aug 2021Review(s) Completed, Editorial Evaluation Pending
20 Sep 2021Editorial Decision: Revise Minor