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.

Phylogenomics of the genus Tursiops and closely related Delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers.

Phylogeographic inference has provided extensive insight into the relative roles of geographical isolation and ecological processes during evolutionary radiations. However, the importance of cross-lineage admixture in facilitating adaptive radiations is increasingly being recognised, and suggested as a main cause of phylogenetic uncertainty. In this study, we used a double digest RADseq protocol to provide a high resolution (~4 Million bp) nuclear phylogeny of the Delphininae. Phylogenetic resolution of this group has been especially intractable, likely because it has experienced a recent species radiation. We carried out cross-lineage reticulation analyses, and tested for several sources of potential bias in determining phylogenies from genome sampling data. We assessed the divergence time and historical demography of T. truncatus and T. aduncus by sequencing the T. aduncus genome and comparing it with the T. truncatus reference genome. Our results suggest monophyly for the genus Tursiops, with the recently proposed T. australis species falling within the T. aduncus lineage. We also show the presence of extensive cross-lineage gene flow between pelagic and European coastal ecotypes of T. truncatus, as well as in the early stages of diversification between spotted (Stenella frontalis; Stenella attenuata), spinner (Stenella longirostris), striped (Stenella coeruleoalba), common (Delphinus delphis), and Fraser's (Lagenodelphis hosei) dolphins. Our study suggests that cross-lineage gene flow in this group has been more extensive and complex than previously thought. In the context of biogeography and local habitat dependence, these results improve our understanding of the evolutionary processes determining the history of this lineage.

Genomics of Population Differentiation in Humpback Dolphins, Sousa spp. in the Indo-Pacific Ocean.

Speciation is a fundamental process in evolution and crucial to the formation of biodiversity. It is a continuous and complex process, which can involve multiple interacting barriers leading to heterogeneous genomic landscapes with various peaks of divergence among populations. In this study, we used a population genomics approach to gain insights on the speciation process and to understand the population structure within the genus Sousa across its distribution in the Indo-Pacific region. We found 5 distinct clusters, corresponding to S. plumbea along the eastern African coast and the Arabian Sea, the Bangladesh population, S. chinensis off Thailand and S. sahulensis off Australian waters. We suggest that the high level of differentiation found, even across geographically close areas, is likely determined by different oceanographic features such as sea surface temperature and primary productivity.

Multiple processes drive genetic structure of humpback whale (Megaptera novaeangliae) populations across spatial scales.

Elucidating patterns of population structure for species with complex life histories, and disentangling the processes driving such patterns, remains a significant analytical challenge. Humpback whale (Megaptera novaeangliae) populations display complex genetic structures that have not been fully resolved at all spatial scales. We generated a data set of nuclear markers for 3575 samples spanning the seven breeding stocks and substocks found in the South Atlantic and western and northern Indian Oceans. For the total sample, and males and females separately, we assessed genetic diversity, tested for genetic differentiation between putative populations and isolation by distance, estimated the number of genetic clusters without a priori population information and estimated rates of gene flow using maximum-likelihood and Bayesian approaches. At the ocean basin scale, structure is governed by geographical distance (IBD P < 0.05) and female fidelity to breeding areas, in line with current understanding of the drivers of broadscale population structure. Consistent with previous studies, the Arabian Sea breeding stock was highly genetically differentiated (FST 0.034-0.161; P < 0.01 for all comparisons). However, the breeding stock boundary between west South Africa and east Africa was more porous than expected based on genetic differentiation, cluster and geneflow analyses. Instances of male fidelity to breeding areas and relatively high rates of dispersal for females were also observed between the three substocks in the western Indian Ocean. The relationships between demographic units and current management boundaries may have ramifications for assessments of the status and continued protections of populations still in recovery from commercial whaling.

Indo-Pacific Humpback Dolphins in Borneo: A Review of Current Knowledge with Emphasis on Sarawak.

Indo-Pacific humpback dolphins (Sousa chinensis) are documented from various locations along Borneo's coast, including three sites in Sarawak, Malaysia, three sites in Sabah, Malaysia, three locations in Kalimantan, Indonesia and the limited coastal waters of the Sultanate of Brunei. Observations in all these areas indicate a similar external morphology, which seems to fall somewhere between that documented for Chinese populations known as S. chinensis, and that of Sousa sahulensis in Australia and Papua New Guinea. Sightings occur in shallow nearshore waters, often near estuaries and river mouths, and associations with Irrawaddy dolphins (Orcaella brevirostris) are frequently documented. Population estimates exist for only two locations and sightings information throughout Borneo indicates that frequency of occurrence is rare and group size is usually small. Threats from fisheries by-catch and coastal development are present in many locations and there are concerns over the ability of these small and fragmented populations to survive. The conservation and taxonomic status of humpback dolphins in Borneo remain unclear, and there are intriguing questions as to where these populations fit in our evolving understanding of the taxonomy of the genus.

The world's most isolated and distinct whale population? Humpback whales of the Arabian Sea.

A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as "Endangered" on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to "Critically Endangered" on the IUCN Red List.

Cutaneous nodules in Irrawaddy dolphins: an emerging disease in vulnerable populations.

The presence of cutaneous nodules is reported in vulnerable populations of Irrawaddy dolphins Orcaella brevirostris from Malaysia (Kuching, Bintulu-Similajau, Kinabatangan-Segama and Penang Island), India (Chilika Lagoon) and Bangladesh (Sundarbans). Approximately 5700 images taken for photo-identification studies in 2004 to 2013 were examined for skin disorders. Nodules were detected in 6 populations. They appeared as circumscribed elevations of the skin and varied in size from 2 to >30 mm, were sparse or numerous and occurred on all visible body areas. In 8 photo-identified (PI) dolphins from India and Malaysia, the lesions remained stable (N = 2) or progressed (N = 6) over months but did not regress. The 2 most severely affected individuals were seen in Kuching and the Chilika Lagoon. Their fate is unknown. Cutaneous nodules were sampled in a female that died in a gillnet in Kuching in 2012. Histologically, the lesions consisted of thick collagen bundles covered by a moderately hyperplasic epithelium and were diagnosed as fibropapillomas. Whether the nodules observed in the other O. brevirostris were also fibropapillomas remains to be investigated. Disease prevalence ranged from 2.2% (N = 46; Bintulu-Similajau) to 13.9% (N = 72; Chilika) in 4 populations from Malaysia and India. It was not significantly different in 3 study areas in eastern Malaysia. In Chilika, prevalence was significantly higher (p = 0.00078) in 2009 to 2011 (13.9%) than in 2004 to 2006 (2.8%) in 72 PI dolphins. The emergence of a novel disease in vulnerable O. brevirostris populations is of concern.

Population differentiation of 2 forms of Bryde's whales in the Indian and Pacific Oceans.

Accurate identification of units for conservation is particularly challenging for marine species as obvious barriers to gene flow are generally lacking. Bryde's whales (Balaenoptera spp.) are subject to multiple human-mediated stressors, including fisheries bycatch, ship strikes, and scientific whaling by Japan. For effective management, a clear understanding of how populations of each Bryde's whale species/subspecies are genetically structured across their range is required. We conducted a population-level analysis of mtDNA control region sequences with 56 new samples from Oman, Maldives, and Bangladesh, plus published sequences from off Java and the Northwest Pacific. Nine diagnostic characters in the mitochondrial control region and a maximum parsimony phylogenetic analysis identified 2 genetically recognized subspecies of Bryde's whale: the larger, offshore form, Balaenoptera edeni brydei, and the smaller, coastal form, Balaenoptera edeni edeni. Genetic diversity and differentiation indices, combined with a reconstructed maximum parsimony haplotype network, indicate strong differences in the genetic diversity and population structure within each subspecies. Discrete population units are identified for B. e. brydei in the Maldives, Java, and the Northwest Pacific and for B. e. edeni between the Northern Indian Ocean (Oman and Bangladesh) and the coastal waters of Japan.

Population structure of humpback whales from their breeding grounds in the South Atlantic and Indian Oceans.

Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527 samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence, the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed fidelity of migratory destinations, along with other ecological and oceanographic features in the region.