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

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

Biodiversity genomics projects are underway with the aim of sequencing the genomes of all eukaryotic species on Earth. Here we describe the BioGenome Portal, a web-based application to facilitate organization and access to the data produced by biodiversity genomics projects. The portal integrates user-generated data with data deposited in public repositories. The portal generates sequence status reports that can be eventually ingested by designated metadata tracking systems, facilitating the coordination task of these systems. The portal is open-source and fully customizable. It can be deployed at any site with minimum effort, contributing to the democratization of biodiversity genomics projects. We illustrate the features of the BioGenome Portal through a number of specific instances. One such instance is being used as the reference portal for the Catalan Initiative for the Earth Biogenome Project, a regional project aiming to sequencing the genomes of the species of the Catalan linguistic area.

Comparing Genetic Ne Reconstructions Over Time With Long-Time Wolf Monitoring Data in Two Populations

Many methods are now available to calculate N e , but their performance varies depending on assumptions. Although simulated data are useful to discover certain types of bias, real empirical data supported by detailed known population histories allow us to discern how well methods perform with actual messy and complex data. Here, we focus on two genomic data sets of grey wolf populations for which population size changes of the past 40-120 years are well documented. We use this background to explore in what detail we can retrieve the known population history from these populations, in the light of pitfalls relating to population history, sampling design and the change in the spatial scale at which N e is estimated as we go further back in time. The Scandinavian wolf population was founded in the early 1980s from a few individuals and has gradually expanded up to 510 wolves. Although the founder event of the Scandinavian population was detected by GONE, the founding effective population size was strongly overestimated when the most recent samples were used, but less so when older samples were considered. Nevertheless, the present-day N e corresponds to theoretical expectations. The western Great Lakes wolf population of Minnesota is the only population in the contiguous United States that persisted throughout the 20th century, surviving intense persecution. We found a good concordance between the estimated N e and trends in census size data, but the reconstruction of N e clearly highlights the difficulty of interpreting results in spatially structured populations that underwent demographic fluctuations.

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

The Catalan Initiative for the Earth BioGenome Project (CBP) is an EBP-affiliated project network aimed at sequencing the genome of the >40 000 eukaryotic species estimated to live in the Catalan-speaking territories (Catalan Linguistic Area, CLA). These territories represent a biodiversity hotspot. While covering less than 1% of Europe, they are home to about one fourth of all known European eukaryotic species. These include a high proportion of endemisms, many of which are threatened. This trend is likely to get worse as the effects of global change are expected to be particularly severe across the Mediterranean Basin, particularly in freshwater ecosystems and mountain areas. Following the EBP model, the CBP is a networked organization that has been able to engage many scientific and non-scientific partners. In the pilot phase, the genomes of 52 species are being sequenced. As a case study in biodiversity conservation, we highlight the genome of the Balearic shearwater Puffinus mauretanicus, sequenced under the CBP umbrella.

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

Humans are regularly cited as the main driver of current biodiversity extinction, but the impact of historic volcanic activity is often overlooked. Pre-human evidence of wildlife abundance and diversity are essential for disentangling anthropogenic impacts from natural events. Réunion Island, with its intense and well-documented volcanic activity, endemic biodiversity, long history of isolation and recent human colonization, provides an opportunity to disentangle these processes. We track past demographic changes of a critically endangered seabird, the Mascarene petrel Pseudobulweria aterrima, using genome-wide SNPs. Coalescent modeling suggested that a large ancestral population underwent a substantial population decline in two distinct phases, ca. 125,000 and 37,000 years ago, coinciding with periods of major eruptions of Piton des Neiges. Subsequently, the ancestral population was fragmented into the two known colonies, ca. 1500 years ago, following eruptions of Piton de la Fournaise. In the last century, both colonies declined significantly due to anthropogenic activities, and although the species was initially considered extinct, it was rediscovered in the 1970s. Our findings suggest that the current conservation status of wildlife on volcanic islands should be firstly assessed as a legacy of historic volcanic activity, and thereafter by the increasing anthropogenic impacts, which may ultimately drive species towards extinction.

Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds

Speciation is a continuous and complex process shaped by the interaction of numerous evolutionary forces. Despite the continuous nature of the speciation process, the implementation of conservation policies relies on the delimitation of species and evolutionary significant units (ESUs). Puffinus shearwaters are globally distributed and threatened pelagic seabirds. Due to remarkable morphological status the group has been under intense taxonomic debate for the past three decades. Here, we use double digest Restriction-Site Associated DNA sequencing (ddRAD-Seq) to genotype species and subspecies of North Atlantic and Mediterranean Puffinus shearwaters across their entire geographical range. We assess the phylogenetic relationships and population structure among and within the group, evaluate species boundaries, and characterise the genomic landscape of divergence. We find that current taxonomies are not supported by genomic data and propose a more accurate taxonomy by integrating genomic information with other sources of evidence. Our results show that several taxon pairs are at different stages of a speciation continuum. Our study emphasises the potential of genomic data to resolve taxonomic uncertainties, which can help to focus management actions on relevant taxa, even if they do not necessarily coincide with the taxonomic rank of species.