Mexico's final death blow to the vaquita

Human activities and climate change threaten marine biodiversity worldwide, though sensitivity to these stressors varies considerably by species and taxonomic group. Mapping the spatial distribution of 14 anthropogenic stressors from 2003 to 2013 onto the ranges of 1271 at-risk marine species sensitive to them, we found that, on average, species faced potential impacts across 57% of their ranges, that this footprint expanded over time, and that the impacts intensified across 37% of their ranges. Although fishing activity dominated the footprint of impacts in national waters, climate stressors drove the expansion and intensification of impacts. Mitigating impacts on at-risk biodiversity is critical to supporting resilient marine ecosystems, and identifying the co-occurrence of impacts across multiple taxonomic groups highlights opportunities to amplify the benefits of conservation management.

Abstract The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large‐mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long‐read sequencing and long‐range scaffolding methods with long‐ and short‐read RNA sequencing to generate a near error‐free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome‐length autosome scaffolds and the X‐chromosome scaffold, with a scaffold N50 of 115 Mb. Genome‐wide heterozygosity is the lowest (0.01%) of any mammalian species analysed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long‐term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long‐term population stability at less than 5,000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

Mammals diversified by colonizing drastically different environments, with each transition yielding numerous molecular changes including losses of protein function. While not initially deleterious, these losses could subsequently carry deleterious pleiotropic consequences. Here we use phylogenetic methods to identify convergent functional losses across independent marine mammal lineages. In one extreme case, Paraoxonase 1 ( PON1 ) accrued lesions in all marine lineages, while remaining intact in all terrestrial mammals. These lesions coincide with PON1 enzymatic activity loss in marine species’ blood plasma. This convergent loss is likely explained by parallel shifts in marine ancestors’ lipid metabolism and/or bloodstream oxidative environment affecting PON1’s role in fatty acid oxidation. PON1 loss also eliminates marine mammals’ main defense against neurotoxicity from specific man-made organophosphorus compounds, implying potential risks in modern environments. Organophosphate toxicity may threaten modern marine mammals due to their ancestors’ repeated loss of PON1 for oxidative or metabolic reasons.