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\begin{document}

\title{Global flyway evolution in red knots \emph{Calidris canutus} and genetic
evidence for a Nearctic refugium}



\author[1]{Jesse Conklin}%
\author[1]{Yvonne Verkuil}%
\author[2]{Philip Battley}%
\author[3]{Chris Hassell}%
\author[4]{James Johnson}%
\author[5]{Job ten Horn}%
\author[6]{Pavel Tomkovich}%
\author[7]{Allan Baker}%
\author[5]{Theunis Piersma}%
\author[8]{Michael Fontaine}%
\affil[1]{Rijksuniversiteit Groningen}%
\affil[2]{Massey University}%
\affil[3]{Global Flyway Network}%
\affil[4]{US Fish and Wildlife Service Alaska Region}%
\affil[5]{Royal Netherlands Institute for Sea Research (NIOZ)}%
\affil[6]{Lomonosov Moscow State University}%
\affil[7]{ROM}%
\affil[8]{Université de Montpellier, CNRS, IRD}%


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  \date{June 10, 2024}


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\begin{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,
\emph{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.%
\end{abstract}%



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