Complex population structure of the Atlantic puffin revealed by whole genome analyses

Abstract

The factors underlying gene flow and genomic population structure in vagile seabirds are notoriously difficult to understand due to their complex ecology with diverse dispersal barriers and extensive periods at sea. Yet, such understanding is vital for conservation management of seabirds that are globally declining at alarming rates. Here, we elucidate the population structure of the Atlantic puffin (Fratercula arctica) by assembling its reference genome and analyzing genome-wide resequencing data of 72 individuals from 12 colonies. We identify four large, genetically distinct clusters, observe isolation-by-distance between colonies within these clusters, and obtain evidence for a secondary contact zone. These observations disagree with the current taxonomy, and show that a complex set of contemporary biotic factors impede gene flow over different spatial scales. Our results highlight the power of whole genome data to reveal unexpected population structure in vagile marine seabirds and its value for seabird taxonomy, evolution and conservation.

Low‐coverage reduced representation sequencing reveals subtle within‐island genetic structure in Aldabra giant tortoises

“…Our study underlines the importance of genetically informed management decisions by showing unexpected population structure as previously discovered in Iberian wolves, Peruvian diving petrels, and Atlantic puffins, among others (Cristofari et al, 2019; Kersten et al, 2021; Silva et al, 2018). Considering that both reduced representation sequencing and low‐coverage approaches aim to decrease costs, our approach could be used in the population genomics of other vertebrates to address similar research questions.…”

Sympatry of genetically distinct Atlantic Puffins (Fratercula arctica) in the High Arctic

“…Sequencing reads were mapped to the Atlantic Puffin assembly (European Nucleotide Archive Accession: CAJHIB020000000.2) using PALEOMIX v1.2.14 (Schubert et al 2014), and analysed together with previously published genome data from 71 individuals representing 12 breeding colonies that acted as an integral reference for this study (Fig. 1a; Kersten et al 2021, Kersten 2022. Further details on the methods and analyses can be found in Appendix S1.…”

“…Puffin colonies were divided into seven groups that included the four previously identified (Kersten et al 2021) genetic clusters (Spitsbergen (n = 6), Iceland/Norway/Faroes (n = 42), Isle of May (n = 5), Canada (n = 12)) and the hybrid population on Bjørnøya (n = 6), as well as the two Thule size classes. These previous analyses by Kersten et al (2021) detected varying levels of genetic diversity in the different clusters.…”

“…The largest Puffins (F. a. naumanni) form the most distinct genetic cluster and inhabit the High Arctic (e.g. Spitsbergen; Salomonsen 1944, Burnham et al 2020a, Kersten et al 2021. Finally, there is an F. a. arctica/F.…”

“…a. naumanni hybrid population on the island of Bjørnøya (Fig. 1; Harris & Wanless 2011, Kersten et al 2021.…”