Leveraging genomics to understand threats to migratory birds

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.