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Genetic structure in the nonbreeding range of rufa Red Knots suggests distinct Arctic breeding populations

Citation

Verkuil, Yvonne et al. (2022), Genetic structure in the nonbreeding range of rufa Red Knots suggests distinct Arctic breeding populations, Dryad, Dataset, https://doi.org/10.5061/dryad.7d7wm37rt

Abstract

An understanding of the migratory connectivity between breeding and nonbreeding areas is fundamental to the management of long-distance migrants under pressure from habitat change along their flyways. Here we describe evidence for genetic structure within the nonbreeding range of the endangered Arctic-Canadian rufa subspecies of Red Knots (Calidris canutus). Using blood and tissue samples from the major nonbreeding regions in Argentina (Tierra del Fuego and Río Negro), northern Brazil (Maranhão), and southeastern USA (Florida), we estimated genetic structure in 514 amplified fragment length polymorphism (AFLP) loci, applying cluster assignment analyses in DAPC, assignPOP, and STRUCTURE. Using a priori location information, individuals could be correctly re-assigned to their nonbreeding regions, which validated that the assignment accuracy of the data was sufficient. Without using a priori location information, we detected 3–5 genotype clusters, and posterior assignment probabilities of samples to these genotype clusters varied among the three regions. Lastly a chi-square test confirmed that allele frequencies varied significantly among nonbreeding regions, rejecting the hypothesis that samples were drawn from a single gene pool. Our findings hint at undescribed structure within the Red Knot rufa breeding range in the Canadian Arctic and indicate that each rufa nonbreeding area in this study hosts a different subsample of these breeding populations. The observation that nonbreeding sites of rufa Red Knots contain different genetic pools argues for separate conservation management of these sites.

Methods

Samples in Argentina, N Brazil and SE USA were collected over various years and sites which allows to control for batch effects. Samples were collected during the boreal winter, except for Río Negro, Argentina, which only hosts birds during the migratory season.To understand the relative scale of potential differences and to ensure our sample collection contained rufa only, the subspecies C. c. roselaari was included. For this subspecies, samples were included from a stopover area in NW USA (Alaska) and from a non-breeding area in Mexico.

For this study we apply a few hundred AFLP markers aquired by standard lab procedures as described in the paper.

The data was analysed with population genetics software packages, as described in the paper.

Usage Notes

See VERKUIL 2021_DATA README.txt

 

Full dataset: AFLPforStructureRufaRoselaari4Pops

 

In summary:

For DAPC and assignPOP analyses use:

AFLP35missing.txt

For STRUCTURE analyses use:

AFLPforStructureRufaRoselaari4PopsLessthen35missing.txt

Chi_square test use:

All_testCHI2.txt

TdF-Mar_testCHI.txt

Florida-Mar_testCHI.txt

TdF-Florida_testCHI.txt

Funding

ROM Governor's Fund

Natural Sciences and Engineering Research Council of Canada, Award: 403501

BirdLife Netherlands

BirdLife Netherlands