The First Genome of the Balearic Shearwater (Puffinus mauretanicus) Provides a Valuable Resource for Conservation Genomics and Sheds Light on Adaptation to a Pelagic lifestyle

Abstract

The Balearic shearwater (Puffinus mauretanicus) is the most threatened seabird in Europe and member of the most speciose group of pelagic seabirds, the order Procellariiformes, which exhibit extreme adaptations to a pelagic lifestyle. The fossil record suggests that human colonization of the Balearic Islands resulted in a sharp decrease of the Balearic shearwater 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. Here, we generated the first high-quality reference genome for the species, with a completeness amongst the highest across available avian species, using a combination of short and long reads. We used this reference genome to study critical aspects relevant to the conservation status of the Balearic shearwater and to gain insights into the adaptation to a pelagic lifestyle of the order Procellariiformes. We detected relatively high levels of genome-wide heterozygosity in the Balearic shearwater despite its reduced population size. However, the reconstruction of its historical demography uncovered an abrupt population decline potentially linked to a reduction of the neritic zone during the Penultimate Glacial Period (∼194-135 kya). 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. The reference genome obtained will be the keystone for future developments of genetic tools in conservation efforts for this Critically Endangered species.

The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics

“…As of November 2023, 52 genomes representing species from a variety of taxa, habitats, and ecosystems are underway under the CBP umbrella ( https://goat.genomehubs.org/projects/CBP ), five of which have already been published ( 9 , 27–30 ) (Figure 4 ). The CBP has followed a bottom-up approach, being responsive to the interests of the local research community.…”

“…in preparation). Briefly, reads were mapped to the P. mauretanicus reference genome ( 9 ) using BWA mem v0.7.17 ( 10 ) with default parameters and variant calling was performed by combining HaplotypeCaller in GATK4 v4.1.9 ( 11 ) and Freebayes v1.2 ( 12 ). We further filtered the resulting SNP dataset with VCFtools v.0.1.15 ( 13 ) using quality (–minQ 30), coverage (–minDP 5 and –maxDP 200) and missingness (–max-missing 0.75) thresholds.…”

The BioGenome Portal: a web-based platform for biodiversity genomics data management

“…As of December 2023, the CBP instance contains a total of 58 organisms ( Figure 4 ), five of them with already published assemblies (12–16).…”

“…As of December 2023, the CBP instance contains a total of 58 organisms (Figure 4), five of them with already published assemblies (12)(13)(14)(15)(16). One of the unique features tailored for this instance is the integration of region-specific taxonomic information, focusing on the biodiversity found in Catalonia.…”

Past volcanic activity predisposes an endemic threatened seabird to negative anthropogenic impacts

“…Currently, few mutation rate and generation time estimates are available for Procellariiformes, hence demographic analyses for the Mascarene petrel were performed using the mutation rate of the Northern fulmar ( Fulmarus glacialis ; 2.89 × 10 −9 substitutions per nucleotide per generation) 53 . This mutation rate is the only one currently available for Procellariiformes and has been used for similar analyses in other species from the same family, e.g., Puffinus mauretanicus 118 . Due to the recent rediscovery of the Mascarene petrel, some demographic parameters requiring long-term monitoring of marked birds (especially prebreeding survival rate and age at first breeding) are still missing, precluding the estimation of its generation time (GT).…”