@article{33c376da8f634a9095ef39e04240bebf,
title = "Genotyping-by-sequencing reveals genomic homogeneity among overwintering Pacific Dunlin (Calidris alpina pacifica) aggregations along the Pacific coast of North America",
abstract = "Information on how migratory populations are genetically structured during the overwintering season of the annual cycle can improve our understanding of the strength of migratory connectivity and help identify populations as units for management. Here, we use a genotype-by-sequencing approach to investigate whether population genetic structure exists among overwintering aggregations of the Pacific Dunlin subspecies (Calidris alpina pacifica) sampled at 2 spatial scales (within and among overwintering sites) in the eastern Pacific Flyway. Genome-wide analyses of 874 single nucleotide polymorphisms across 80 sampled individuals revealed no evidence for genetic differentiation among aggregations overwintering at 3 locations within the Fraser River Estuary (FRE) of British Columbia. Similarly, comparisons of aggregations in the FRE and those overwintering in southern sites in California and Mexico indicated no genetic segregation between northern and southern overwintering areas. These results suggest that Pacific Dunlin within the FRE, Sacramento Valley (California), and Guerrero Negro (Mexico) are genetically homogeneous, with no evident genetic structure between sampled sites or regions across the overwintering range. Despite no evidence for differentiation among aggregations, we identified a significant effect of geographical distance between sites on the distribution of individual genotypes in a redundancy analysis. A small proportion of the total genotypic variance (R2 =0.036, P = 0.011) was explained by the combined effect of latitude and longitude, suggesting weak genomic patterns of isolation-by-distance that are consistent with chain-like migratory connectivity between breeding and overwintering areas. Our study represents the first genome-scale investigation of population structure for a Dunlin subspecies and provides essential baseline estimates of genomic diversity and differentiation within the Pacific Dunlin.",
author = "Iva Popovic and Toews, {David P.L.} and Keever, {Carson C.} and {St. Clair}, {C. Toby} and Barbaree, {Blake A.} and Guillermo Fern{\'a}ndez and James Rourke",
note = "Funding Information: We would like to thank R. Ydenberg, M. Winterbottom, and D. Irwin for their assistance and technical advice throughout the course of the project. We thank L. M. Enr{\'i}quez Paredes for technical support on molecular sample processing. We would also like to acknowledge M. Reiter, B. Schwarz, and I. Jong for providing assistance with fieldwork coordination and the C. Riginos lab group, especially J. Thia and A. M. Matias, at the University of Queensland for useful comments on this manuscript. We would also like to acknowledge coordinators of the western hemisphere shorebird group meeting in Burnaby, BC (Simon Fraser University), and Santa Marta, Colombia (Asociaci{\'o}n Calidris), for facilitating cross-border collaborations required to coordinate advancement of understanding and management of migratory shorebirds. Funding statement: The Vancouver Fraser Port Authority provided funding to conduct this research. Funding for field studies in the Sacramento Valley was provided to Point Blue from the S. D. Bechtel Jr. Foundation through the Migratory Bird Conservation Partnership (http://www.camigratorybirds. org/). Funding for field studies conducted in Guerrero Negro, Baja California, Mexico, was provided by the Mexican National Council for Science and Technology (CB2007-82671 and CB2010-155353) and the Universidad Nacional Aut{\'o}noma de M{\'e}xico (PAPIIT-DGAPA: IN212809-3). Ethics statement: Capture, handling, and sampling methods employed in the Fraser River Estuary were approved by the Simon Fraser University animal care committee (Protocol # 1043B-03), and all field staff handling birds were trained in ethical treatment of animals involved in scientific research (SFU Animal Care Course). Work conducted in California was in accordance with animal use and care guidelines from the North American Banding Council{\textquoteright}s Shorebird Banding Guide and its Ethics statement; permissions were authorized through the US Geological Survey Bird Banding Lab and permit #09361. The work conducted in Mexico met Mexican legal requirements regarding animal welfare. Additionally, field work was annually supervised and approved by Direcci{\'o}n General de Vida Silvestre, Secretar{\'i}a de Gesti{\'o}n para la Protecci{\'o}n Ambiental (SGPA/DGVS/04672/08 and SGPA/ DGVS/07826/09). Author contributions: IP, DPLT, and CTS wrote the paper. JR, BBA, GF, and CCK substantially edited the paper. DPLT, IP, and CCK designed the methods, collected the genetic data, and analyzed the data. CTS, BBA, and GF collected the field data and supervised data collection. CCK, JR, DPLT, CTS, and IP conceived the idea and design of this study. Data depository: Analyses reported in this article can be reproduced using the genomic datasets provided by Popovic et al. (2019) Funding Information: The Vancouver Fraser Port Authority provided funding to conduct this research. Funding for field studies in the Sacramento Valley was provided to Point Blue from the S. D. Bechtel Jr. Foundation through the Migratory Bird Conservation Partnership (http://www.camigratorybirds. org/). Funding for field studies conducted in Guerrero Negro, Baja California, Mexico, was provided by the Mexican National Council for Science and Technology (CB2007-82671 and CB2010-155353) and the Universidad Nacional Aut?noma de M?xico (PAPIIT-DGAPA: IN212809-3). Publisher Copyright: Copyright {\textcopyright} 2019 American Ornithological Society. All rights reserved.",
year = "2019",
month = aug,
day = "1",
doi = "10.1093/condor/duz036",
language = "English (US)",
volume = "59",
journal = "The Gerontologist",
issn = "0016-9013",
publisher = "Oxford University Press",
number = "4",
}