Geology topics

Vincent Bretagnolle

Publications and source records attributed to Vincent Bretagnolle.

4 recordsLinked to original sources

USGS2023

Global assessment of marine plastic exposure for oceanic birds

Plastic pollution is distributed patchily around the world’s oceans. Likewise, marine organisms that are vulnerable to plastic ingestion or entanglement have uneven distributions. Understanding where wildlife encounters plastic is crucial for targeting research and mitigation. Oceanic seabirds, particularly petrels, frequently ingest plastic, are highly threatened, and cover vast distances during foraging and migration. However, the spatial overlap between petrels and plastics is poorly understood. Here we combine marine plastic density estimates with individual movement data for 7137 birds of 77 petrel species to estimate relative exposure risk. We identify high exposure risk areas in the Mediterranean and Black seas, and the northeast Pacific, northwest Pacific, South Atlantic and southwest Indian oceans. Plastic exposure risk varies greatly among species and populations, and between breeding and non-breeding seasons. Exposure risk is disproportionately high for Threatened species. Outside the Mediterranean and Black seas, exposure risk is highest in the high seas and Exclusive Economic Zones (EEZs) of the USA, Japan, and the UK. Birds generally had higher plastic exposure risk outside the EEZ of the country where they breed. We identify conservation and research priorities, and highlight that international collaboration is key to addressing the impacts of marine plastic on wide-ranging species.

Nature Communications↗

USGS2021

Palaeoceanographic changes in the late Pliocene promoted rapid diversification in pelagic seabirds

Aim Palaeoceanographic changes can act as drivers of diversification and speciation, even in highly mobile marine organisms. Shearwaters are a group of globally distributed and highly mobile pelagic seabirds. Despite a recent well-resolved phylogeny, shearwaters have controversial species limits, and show periods of both slow and rapid diversification. Here, we explore the role of palaeoceanographic changes on shearwaters' diversification and speciation. We investigate shearwater biogeography and the evolution of a key phenotypic trait, body size, and we assess the validity of their current taxonomy. Location Worldwide. Taxa Shearwaters (Order Procellariiformes, Family Procellariidae, Genera Ardenna , Calonectris and Puffinus ). Methods We generated genomic (ddRAD) data to infer a time-calibrated species tree for the shearwaters. We estimated ancestral ranges and evaluated the roles of founder events, vicariance and surface ocean currents in driving diversification. We performed phylogenetic generalised least squares to identify potential predictors of variability in body size along the phylogeny. To assess the validity of the current taxonomy, we analysed genomic patterns of recent shared ancestry and differentiation among shearwater taxa. Results We identified a period of high dispersal and rapid speciation during the Late Pliocene–early Pleistocene. Species dispersal appears to be favoured by surface ocean currents, and founder events are supported as the main mode of speciation in these highly mobile pelagic seabirds. Body mass shows significant associations with life strategies and local conditions. The current taxonomy shows some incongruences with the patterns of genomic divergence. Main Conclusions A reduction of neritic areas during the Pliocene seems to have driven global extinctions of shearwater species, followed by a subsequent burst of speciation and dispersal probably promoted by Plio-Pleistocene climatic shifts. 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 palaeoceanographic events.

Journal of Biogeography↗

USGS2021

Integrating sequence capture and restriction-site associated DNA sequencing to resolve recent radiations of pelagic seabirds

The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic data sets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds that are among the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq data sets for phylogenetics, divergence time estimation, and inference of introgression, and we propose a strategy to optimize RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales.

Systematic Biology↗

USGS2018

Evidence for a duplicated mitochondrial region in Audubon’s shearwater based on MinION sequencing

Mitochondrial genetic markers have been extensively used to study the phylogenetics and phylogeography of many birds, including seabirds of the order Procellariiformes. Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated, but no DNA fragment covering the entire duplication has been sequenced. We sequenced the complete mitochondrial genome of a non-albatross species of Procellariiformes, Puffinus lherminieri (Audubon’s shearwater) using the long-read MinION (ONT) technology. Two mitogenomes were assembled from the same individual, differing by 52 SNPs and in length. The shorter was 19 kb long while the longer was 21 kb, due to the presence of two identical copies of nad6 , three tRNA, and two dissimilar copies of the control region (CR). Contrary to albatrosses, cob was not duplicated. We further detected a complex repeated region of undetermined length between the CR and 12S. Long-read sequencing suggests heteroplasmy and a novel arrangement within the duplicated region, indicating a complex evolution of the mitogenome in Procellariiformes.

Mitochondrial DNA Part A↗