Red-list status and extinction risk of the world's whales, dolphins, and porpoises.

To understand the scope and scale of the loss of biodiversity, tools are required that can be applied in a standardized manner to all species globally, spanning realms from land to the open ocean. We used data from the International Union for the Conservation of Nature Red List to provide a synthesis of the conservation status and extinction risk of cetaceans. One in 4 cetacean species (26% of 92 species) was threatened with extinction (i.e., critically endangered, endangered, or vulnerable) and 11% were near threatened. Ten percent of cetacean species were data deficient, and we predicted that 2-3 of these species may also be threatened. The proportion of threatened cetaceans has increased: 15% in 1991, 19% in 2008, and 26% in 2021. The assessed conservation status of 20% of species has worsened from 2008 to 2021, and only 3 moved into categories of lesser threat. Cetacean species with small geographic ranges were more likely to be listed as threatened than those with large ranges, and those that occur in freshwater (100% of species) and coastal (60% of species) habitats were under the greatest threat. Analysis of odontocete species distributions revealed a global hotspot of threatened small cetaceans in Southeast Asia, in an area encompassing the Coral Triangle and extending through nearshore waters of the Bay of Bengal, northern Australia, and Papua New Guinea and into the coastal waters of China. Improved management of fisheries to limit overfishing and reduce bycatch is urgently needed to avoid extinctions or further declines, especially in coastal areas of Asia, Africa, and South America.

Estado en la lista roja y riesgo de extinción de las ballenas, delfines y marsopas del mundo Resumen Para comprender el alcance y la escala de la pérdida de biodiversidad, se necesitan herramientas que puedan aplicarse de forma estandarizada a todas las especies a nivel mundial y que abarquen todos los ámbitos desde la tierra hasta el océano. Utilizamos datos de la Lista Roja de la Unión Internacional para la Conservación de la Naturaleza para proporcionar una síntesis del estado de conservación y el riesgo de extinción de los cetáceos. Una de cada 4 especies de cetáceos (26% de 92 especies) se encuentra amenazada (es decir, en peligro crítico, en peligro o vulnerable) y el 11% de las especies está clasificado como casi amenazada. El 10% de las especies de cetáceos carecía de datos, por lo que predijimos que 2-3 de estas especies también podrían estar amenazadas. La proporción de cetáceos amenazados ha aumentado: 15% en 1991, 19% en 2008 y 26% en 2021. El estado de conservación evaluado del 20% de las especies ha empeorado de 2008 a 2021, pues sólo 3 pasaron a categorías de menor amenaza. Las especies de cetáceos con áreas de distribución geográficas pequeñas tenían más probabilidades de ser catalogadas como amenazadas que aquellas con áreas de distribución extensas, y aquellas que ocurren en hábitats de agua dulce (100% de las especies) y costeros (60% de las especies) eran las que se encontraban bajo mayor amenaza. La superposición de los mapas de distribución de las especies reveló la existencia de puntos calientes de pequeños cetáceos amenazados en el sudeste asiático y en una zona que abarca el Triángulo de Coral y se extiende por las aguas cercanas a la costa de la Bahía de Bengala, el norte de Australia, Papúa Nueva Guinea y las aguas costeras de China. Urge mejorar la gestión de las pesquerías para limitar la sobrepesca y reducir la captura accesoria con el fin de evitar extinciones o mayores descensos, especialmente en las zonas costeras de Asia, África y Sudamérica.

Passive acoustic monitoring of the decline of Mexico's critically endangered vaquita.

The vaquita (Phocoena sinus) is the world's most endangered marine mammal with approximately 245 individuals remaining in 2008. This species of porpoise is endemic to the northern Gulf of California, Mexico, and historically the population has declined because of unsustainable bycatch in gillnets. An illegal gillnet fishery for an endangered fish, the totoaba (Totoaba macdonaldi), has recently resurged throughout the vaquita's range. The secretive but lucrative wildlife trade with China for totoaba swim bladders has probably increased vaquita bycatch mortality by an unknown amount. Precise population monitoring by visual surveys is difficult because vaquitas are inherently hard to see and have now become so rare that sighting rates are very low. However, their echolocation clicks can be identified readily on specialized acoustic detectors. Acoustic detections on an array of 46 moored detectors indicated vaquita acoustic activity declined by 80% between 2011 and 2015 in the central part of the species' range. Statistical models estimated an annual rate of decline of 34% (95% Bayesian credible interval -48% to -21%). Based on results from 2011 to 2014, the government of Mexico enacted and is enforcing an emergency 2-year ban on gillnets throughout the species' range to prevent extinction, at a cost of US$74 million to compensate fishers. Developing precise acoustic monitoring methods proved critical to exposing the severity of vaquitas' decline and emphasizes the need for continual monitoring to effectively manage critically endangered species.

Last call: Passive acoustic monitoring shows continued rapid decline of critically endangered vaquita.

The vaquita is a critically endangered species of porpoise. It produces echolocation clicks, making it a good candidate for passive acoustic monitoring. A systematic grid of sensors has been deployed for 3 months annually since 2011; results from 2016 are reported here. Statistical models (to compensate for non-uniform data loss) show an overall decline in the acoustic detection rate between 2015 and 2016 of 49% (95% credible interval 82% decline to 8% increase), and total decline between 2011 and 2016 of over 90%. Assuming the acoustic detection rate is proportional to population size, approximately 30 vaquita (95% credible interval 8-96) remained in November 2016.

Ultrasonic antifouling devices negatively impact Cuvier's beaked whales near Guadalupe Island, México.

Widespread use of unregulated acoustic technologies in maritime industries raises concerns about effects on acoustically sensitive marine fauna worldwide. Anthropogenic noise can disrupt behavior and may cause short- to long-term disturbance with possible population-level consequences, particularly for animals with a limited geographic range. Ultrasonic antifouling devices are commercially available, installed globally on a variety of vessel types, and are marketed as an environmentally-friendly method for biofouling control. Here we show that they can be an acoustic disturbance to marine wildlife, as seasonal operation of these hull-mounted systems by tourist vessels in the marine protected area of Guadalupe Island, México resulted in the reduced presence of a potentially resident population of Cuvier's beaked whales (Ziphius cavirostris). Human activities are rapidly altering soundscapes on local and global scales, and these findings highlight the need to identify key noise sources and assess their impacts on marine life to effectively manage oceanic ecosystems.

The critically endangered vaquita is not doomed to extinction by inbreeding depression.

In cases of severe wildlife population decline, a key question is whether recovery efforts will be impeded by genetic factors, such as inbreeding depression. Decades of excess mortality from gillnet fishing have driven Mexico's vaquita porpoise (Phocoena sinus) to ~10 remaining individuals. We analyzed whole-genome sequences from 20 vaquitas and integrated genomic and demographic information into stochastic, individual-based simulations to quantify the species' recovery potential. Our analysis suggests that the vaquita's historical rarity has resulted in a low burden of segregating deleterious variation, reducing the risk of inbreeding depression. Similarly, genome-informed simulations suggest that the vaquita can recover if bycatch mortality is immediately halted. This study provides hope for vaquitas and other naturally rare endangered species and highlights the utility of genomics in predicting extinction risk.

Reference genome and demographic history of the most endangered marine mammal, the vaquita.

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.

Vaquitas (Phocoena sinus) continue to die from bycatch not pollutants.

BACKGROUND: The vaquita of Mexico is critically endangered, with a population less than 19 individuals in 2018. The population continues to decline and gillnet use continues in vaquita habitat. METHODS: Nine vaquita carcases were examined from 2016 to 2018 to establish cause of death. Concentrations of polychlorinated biphenyls (PCBs), DDTs and polybrominated diphenyl ethers (PBDEs) in blubber (n=3) were determined using gas chromatography/mass spectrometry and faeces tested for domoic acid and saxitoxin. RESULTS: Carcases were in good nutritional status and had lesions and full stomachs consistent with fisheries bycatch. PCB, DDT and PBDE concentrations ranged between 94 and 180 ng/g, 500 and 1200 ng/g and 97 and 210 ng/g lipid weight, respectively, which are low compared with other marine mammals. No saxitoxin or domoic acid was detected. CONCLUSION: These findings support the conclusion that bycatch is the primary source of vaquita population decline and emphasise the need for stronger measures to eliminate gillnets from the Upper Gulf of California, Mexico.

Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum.

Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall's) and southern species (spectacled and Burmeister's). In contrast to previous studies, spectacled and Burmeister's porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall's, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation.

Decline towards extinction of Mexico's vaquita porpoise (Phocoena sinus).

The vaquita (Phocoena sinus) is a small porpoise endemic to Mexico. It is listed by IUCN as Critically Endangered because of unsustainable levels of bycatch in gillnets. The population has been monitored with passive acoustic detectors every summer from 2011 to 2018; here we report results for 2017 and 2018. We combine the acoustic trends with an independent estimate of population size from 2015, and visual observations of at least seven animals in 2017 and six in 2018. Despite adoption of an emergency gillnet ban in May 2015, the estimated rate of decline remains extremely high: 48% decline in 2017 (95% Bayesian credible interval (CRI) 78% decline to 9% increase) and 47% in 2018 (95% CRI 80% decline to 13% increase). Estimated total population decline since 2011 is 98.6%, with greater than 99% probability the decline is greater than 33% yr-1. We estimate fewer than 19 vaquitas remained as of summer 2018 (posterior mean 9, median 8, 95% CRI 6-19). From March 2016 to March 2019, 10 dead vaquitas killed in gillnets were found. The ongoing presence of illegal gillnets despite the emergency ban continues to drive the vaquita towards extinction. Immediate management action is required if the species is to be saved.

A multi-trial diagnostic tool in fin whale (Balaenoptera physalus) skin biopsies of the Pelagos Sanctuary (Mediterranean Sea) and the Gulf of California (Mexico).

The main objective of this study was to apply a set of sensitive non-lethal biomarkers in skin biopsies of fin whales (Balaenoptera physalus) to evaluate the toxicological status of this mysticete in the Pelagos Sanctuary (Mediterranean Sea) and in the Gulf of California (Sea of Cortez-Mexico). We developed a "multi-trial diagnostic tool" (based on field and in vitro studies), combining molecular biomarkers (western blot of CYP1A1, CYP2B) and gene expression (qRT-PCR of HSP70, ERα, AHR, E2F-1) with the analysis of OCs, PAHs and PBDEs. The study revealed a higher level of toxicological stress in the Mediterranean fin whales.

Genetic drift vs. natural selection in a long-term small isolated population: major histocompatibility complex class II variation in the Gulf of California endemic porpoise (Phocoena sinus).

Although many studies confirm long-term small isolated populations (e.g. island endemics) commonly sustain low neutral genetic variation as a result of genetic drift, it is less clear how selection on adaptive or detrimental genes interplay with random forces. We investigated sequence variation at two major histocompatibility complex (Mhc) class II loci on a porpoise endemic to the upper Gulf of California, México (Phocoena sinus, or vaquita). Its unique declining population is estimated around 500 individuals. Single-strand conformation polymorphism analysis revealed one putative functional allele fixed at the locus DQB (n = 25). At the DRB locus, we found two presumed functional alleles (n = 29), differing by a single nonsynonymous nucleotide substitution that could increase the stability at the dimer interface of alphabeta-heterodimers on heterozygous individuals. Identical trans-specific DQB1 and DRB1 alleles were identified between P. sinus and its closest relative, the Burmeister's porpoise (Phocoena spinipinnis). Comparison with studies on four island endemic mammals suggests fixation of one allele, due to genetic drift, commonly occurs at the DQA or DQB loci (effectively neutral). Similarly, deleterious alleles of small effect are also effectively neutral and can become fixed; a high frequency of anatomical malformations on vaquita gave empirical support to this prediction. In contrast, retention of low but functional polymorphism at the DRB locus was consistent with higher selection intensity. These observations indicated natural selection could maintain (and likely also purge) some crucial alleles even in the face of strong and prolonged genetic drift and inbreeding, suggesting long-term small populations should display low inbreeding depression. Low levels of Mhc variation warn about a high susceptibility to novel pathogens and diseases in vaquita.