DOI: 10.5068/d1dd4f
title: Leveraging genomics to understand threats to migratory birds

description: Understanding of how risk factors affect populations across their annual
 cycle is a major challenge for conserving migratory birds. For example,
 disease outbreaks may happen on the breeding grounds, the wintering
 grounds, or during migration, and are expected to accelerate under climate
 change. The ability to identify the geographic origins of individuals
 impacted, especially outside of breeding areas, might make it possible to
 predict demographic trends and inform conservation decision making.
 However, such an effort is made more challenging by the degraded state of
 carcasses and resulting low quality of DNA available. Here we describe a
 rapid and low-cost approach for identifying the origins of birds sampled
 across their annual cycle that is robust even when DNA quality is poor. We
 illustrate the approach in the common loon (Gavia immer), an iconic
 migratory aquatic bird that is under increasing threat on both its
 breeding and wintering areas. Using 300 samples collected from across the
 breeding range we develop a panel of 158 SNP loci that diverge across six
 genetic subpopulations. Using this SNP panel we identify the breeding
 grounds for 167 live nonbreeding individuals and carcasses. For example,
 genetic assignment of loons sampled during botulism outbreaks in parts of
 the Great Lakes provide evidence for the significant role the lakes play
 as migratory stopover areas for loons that breed across wide swaths of
 Canada, and highlights the vulnerability of a large segment of the
 breeding population to botulism outbreaks that are occurring in the Great
 Lakes with increasing frequency. Our results illustrate that the use of
 SNP panels to identify breeding origins of carcasses collected during the
 non-breeding season can improve our understanding of the
 population-specific impacts of mortality from disease and anthropogenic
 stressors, ultimately allowing more effective management.
description: Through a large collaborative effort,
 we collected samples from breeding, wintering and migrating common loons
 from across North America during the years 1979 and 1992-2016. Samples for
 genetic analysis included blood samples collected from birds captured in
 known breeding areas across North America during the breeding season, and
 samples collected from wintering or migratory birds, including: a)
 feathers from bird carcasses resulting from botulism outbreaks in the
 Great Lakes or collisions at solar facilities in southern California, b)
 blood or feathers collected from birds that were dead or moribund from
 mostly unknown causes from Florida and the northeastern seaboard, and c)
 blood from living, healthy birds from Morro Bay, CA, and coastal
 Louisiana. Tissue samples and previously extracted DNA were sent to UCLA
 for SNP genotyping and/or library preparation. Samples were transferred to
 UCLA under a protocol approved by the Research Safety and Animal Welfare
 Administration, University of California Los Angeles: ARC# 2017-073-03,
 approved 10/28/2017. The datasets provided include 1) a RAD-PE dataset
 (COLO-cleaned-150-100K.unrel...vcf) containing genotypes of 129 breeding
 loon samples and an accompanying file containing sample metadata, 2)
 a fluidigm genotype dataset(ped and map file) that includes the genotypes
 of 467 breeding, wintering and migrating loons at 158 loci, and an
 accompanying file containing sample metadata, 3) an input dataset for
 conducting PCA in base R based on ddRAD sequencing of 106 breeding loons
 (A1634.SNPs). Please see the paper Larison et al. Leveraging Genomics to
 Understand Threats to Migratory Birds [details TBP] for details.