The Balearic shearwater (Puffinus mauretanicus) is the most threatened seabird in Europe. The fossil record suggests that human colonisation of the Balearic Islands resulted in a sharp decrease of the population size. Currently, populations continue to be decimated mainly due to predation by introduced mammals and bycatch in longline fisheries, and some studies predict their extinction by 2070. We present the first high-quality reference genome for the species which was obtained by a combination of short and long-read sequencing. Our hybrid assembly includes 4,169 scaffolds, with a scaffold N50 of 2.1 Mbp, a genome length of 1.2 Gbp, and BUSCO completeness of 96%, which is amongst the highest across sequenced avian species. This reference genome allowed us to study critical aspects relevant to the conservation status of the species, such as an evaluation of overall heterozygosity levels and the reconstruction of its historical demography. Our phylogenetic analysis using whole-genome information resolves current uncertainties in the order Procellariiformes systematics. Comparative genomics analyses uncover a set of candidate genes that may have played an important role into the adaptation to a pelagic lifestyle of Procellariiformes, including those for the enhancement of fishing capabilities, night vision and the development of natriuresis. This reference genome will be the keystone for future developments of genetic tools in conservation efforts for this Critically Endangered species.

In marine environments, paleoceanographic changes can act as drivers of diversification and speciation, even in highly mobile marine organisms. Shearwaters are a group of pelagic seabirds with a well-resolved phylogeny that are globally distributed and show periods of both slow and rapid diversification. Using reduced representation sequencing data, we explored the role of paleoceanographic changes on diversification and speciation in these highly mobile pelagic seabirds. We performed molecular dating, applying a multispecies coalescent approach (MSC) to account for the high levels of incomplete lineage sorting (ILS). We identified a major effect of the Pliocene marine megafauna extinction, followed by a period of high dispersal and rapid speciation. Biogeographic analyses showed that dispersal appears to be favoured by surface ocean currents, and we found that founder and vicariant events are the main processes of diversification. Body mass appears to be a key phenotypic trait potentially under selection during shearwater diversification, and it shows significant associations with life strategies and local conditions. We also found incongruences between the current taxonomy and patterns of genomic divergence, suggesting revisions to alpha taxonomy. Globally, our findings extend our understanding on the drivers of speciation and dispersal of highly mobile pelagic seabirds and shed new light on the important role of paleoceanographic events.