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.

Conservation of breeding seabirds typically requires detailed data on where they feed at sea. Ecological niche models (ENMs) can fill data gaps, but rarely perform well when transferred to new regions. Alternatively, the foraging radius approach simply encircles the sea surrounding a breeding seabird colony (a foraging circle), but overestimates foraging habitat. Here, we investigate whether ENMs can transfer (predict) foraging niches of breeding tropical seabirds between global colonies, and whether ENMs can refine foraging circles. We collate a large global dataset of tropical seabird tracks (12000 trips, 16 species, 60 colonies) to build a comprehensive summary of tropical seabird foraging ranges and to train ENMs. We interrogate ENM transferability and assess the confidence with which unsuitable habitat predicted by ENMs can be excluded from within foraging circles. We apply this refinement framework to the Great Barrier Reef (GBR), Australia to identify a network of candidate marine protected areas (MPAs) for seabirds. We found little ability to generalise and transfer breeding tropical seabird foraging niches across all colonies for any species (mean AUC: 0.56, range 0.4-0.82). Low global transferability was partially explained by colony clusters that predicted well internally but other colony clusters poorly. After refinement with ENMs, foraging circles still contained 89% of known foraging areas from tracking data, providing confidence that important foraging habitat was not erroneously excluded by greater refinement from high transferability ENMs nor minor refinement from low transferability ENMs. Foraging radii estimated the total foraging area of the GBR breeding seabird community as 2,941,000 km2, which was refined by excluding between 197,000 km2 and 1,826,000 km2 of unsuitable foraging habitat. ENMs trained on local GBR tracking achieved superior refinement over globally trained models, demonstrating the value of local tracking. Our framework demonstrates an effective method to delineate candidate MPAs for breeding seabirds in data-poor regions.

Predator-prey interactions provide key information on the role of each species in the community and an overall assessment of the stability of food webs. DNA metabarcoding has the potential to provide highly informative data which substantially enhance trophic interactions analysis, by providing higher taxonomic detail compared to earlier methods. Here we show, using the Cabo Verde seabird community, that the integrated analysis of trophic networks based on DNA metabarcoding of faecal samples can increase considerably our understanding of the trophic interactions in whole communities. Results revealed that these seabird species prey mostly on fish, with most seabirds relying heavily on very few prey species, which are also targeted by fisheries. This community shows high specialization and modularity levels, i.e., is dominated by seabird species with specialized diets. Such network structure has implications for its management and conservation because specialist predators are especially vulnerable to prey depletion. The Cape Verde shearwater (Calonectris edwardsii), identified as the main network connector species, was confirmed to be a suitable sentinel species of changes in this marine food web. Our results clearly show that network analysis can be used effectively to maximize the potential of DNA metabarcoding in studying trophic interactions of complex communities.

Seabirds, particularly Procellariiformes, are highly mobile organisms with a great capacity for long dispersal, though simultaneously showing high philopatry, two conflicting characteristics that may lead to contrasted patterns of genetic population structure. Landmasses were suggested to explain differentiation patterns observed in seabirds, but philopatry, isolation-by-distance, segregation between breeding and non-breeding zones, and oceanographic conditions (sea surface temperatures) may also contribute to differentiation patterns. No study has simultaneously contrasted the multiple factors contributing to the diversification of seabird species, especially in the grey zone of speciation. We conducted a multi-locus phylogeographic study on a widespread shearwater species complex (Puffinus lherminieri/bailloni), showing highly homogeneous morphology. We sequenced three mitochondrial and six nuclear markers on all extant populations (five nominal lineages, 13 populations). We found sharp differentiation among populations separated by the African continent with both mitochondrial and nuclear markers, while only mitochondrial markers allowed characterizing the five nominal lineages. No differentiation could be detected within these five lineages, questioning the strong level of philopatry showed by these shearwaters. Finally, we propose that Atlantic populations likely originated from the Indian Ocean. Within the Atlantic, a stepping-stone process accounts for the current distribution. Based on our divergence times estimates, we suggest that the observed pattern of differentiation mostly resulted from variation in sea surface temperatures.

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.