Genetic structure of Atlantic Puffins (Fratercula arctica) breeding in Atlantic Canada

The Atlantic Puffin (Fratercula arctica; hereafter ‘puffin’) breeds at the southern limit of its range in the Gulf of Maine, where waters are warming faster than most of the world’s oceans. Puffin productivity and survival have decreased in the Gulf of Maine with warming, but population-level declines have not been detected. Understanding the connectivity between Gulf of Maine breeding colonies and colonies to the north has become a priority to determine the demographic importance of immigration, but mark-recapture and tracking studies have yet to resolve this question. In this study, we used double digest restriction-site associated DNA sequencing (ddRADseq) to quantify neutral genetic differentiation among five breeding colonies in Atlantic Canada, identify outlier single nucleotide polymorphisms (SNPs), and determine if puffins can be reliably assigned to their breeding colony. We identified a new genetic cluster of puffins, represented by Machias Seal Island, and recommend that this colony be considered separately from Newfoundland and Québec for management. We found three outlier SNPs, with the rare alleles predominantly present in Machias Seal Island puffins, and recommend further research to determine the extent that selection may be contributing to the differentiation of Machias Seal Island. Puffins could be reliably assigned to the Machias Seal Island or the northern-colony genetic cluster, including with a subset of the 200 highest-\(F_{ST}\) SNPs. Finally, we did not identify evidence of inbreeding at any colony, suggesting that effective population sizes are large enough to buffer against these negative effects.