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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.

AbstractThe 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 resulting from inadvertent deaths due to the increasing use of large-mesh gillnets for more than 20 years. 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 analyzed 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 5000 (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.

The Irrawaddy dolphin (Orcaella brevirostris) is an endangered cetacean that ranges throughout much of Southeast Asia and lives in coastal, estuarine, and riverine habitats including three river systems: Ayeyarwady, Mekong, and Mahakam. Many populations face risks from human interference, but overall rangewide diversity and connectivity is not well‐understood. Here we sequenced 77 complete mitogenomes from across the range of the Irrawaddy dolphin including all obligate riverine populations; eighteen of these were sequenced from historical museum specimens. Phylogenetic analysis showed haplotypes from each riverine population formed separate clades nested within the wider species implying each river system was separately invaded only once. All Irrawaddy dolphin mitogenomes were dated to a last common ancestor ~764 kya. Most lineages appeared after inundation cycles of the Sunda Shelf were initiated ~400 kya. Despite the lack of monophyly among many haplotypes from the same population, no population shared any haplotypes. Rangewide nucleotide diversity was average compared to other odontocetes, but riverine populations were especially low. Differentiation was significant among all populations analyzed with the most divergence occurring between isolated riverine populations. These analyses add more evidence for the necessity of conservation efforts directed towards riverine and other isolated populations of the Irrawaddy dolphin. [ABSTRACT FROM AUTHOR]

Neritic, long‐beaked common dolphins have been described as species distinct from the more oceanic and globally distributed short‐beaked species, Delphinus delphis, although recent molecular studies have challenged this view. In the eastern North Pacific (ENP), the taxonomic status of the long‐beaked (bairdii) form has been controversial since its original description in 1873, and has vacillated between species, subspecies, and geographic forms several times. It is currently provisionally viewed as a subspecies of Delphinus delphis, D. d. bairdii. To clarify this situation, we reviewed the literature and conducted additional analyses using both newly obtained genetic and cranial morphometric data sets. The results indicate that there are diagnostic differences in skull morphology and coloration between the eastern Pacific long‐and short‐beaked forms, and near‐perfect diagnosability in mitochondrial DNA. These differences, along with indications of ecological distinctions, including important differences in life history parameters and reproductive timing, indicate that these forms are well on their way down separate evolutionary pathways. As such, we consider them to be distinct species in the eastern Pacific. The long‐beaked species is referable to Delphinus bairdii Dall, 1873, and is redescribed as such herein. [ABSTRACT FROM AUTHOR]

Small, island-associated populations of cetaceans have evolved around numerous oceanic islands, likely due to habitat discontinuities between nearshore and offshore waters. However, little is known about the ecology and structure of cetacean populations around the Mariana Islands, a remote archipelago in the western Pacific Ocean. We present sighting, photo-identification, and genetic data collected during twelve years of surveys around these islands that reveal the existence of a small, island-associated population of bottlenose dolphins. Nearly half of the photo-identified individuals were encountered in more than one year. Both haplotypic and nuclear genetic diversity among sampled individuals was low (haplotypic diversity = 0.701, nuclear heterozygosity = 0.658), suggesting low abundance. We used mark-recapture analysis of photo-identification data to estimate yearly abundance in the southern portion of the population's range from 2011 to 2018. Each abundance estimate was less than 54 individuals, with each upper 95% confidence interval below 100. Additional survey effort is necessary to generate a full population abundance estimate. We found extensive introgression of Fraser's dolphin DNA into both the mitochondrial and nuclear genomes of the population, suggesting at least two hybridization events more than two generations in the past. The Mariana Islands are used extensively by the U.S. military for land and sea training operations. Thus, this unique bottlenose dolphin population likely faces high exposure to multiple threats. [ABSTRACT FROM AUTHOR]

The 20th century commercial whaling industry severely reduced populations of great whales throughout the Southern Hemisphere. The effect of this exploitation on genetic diversity and population structure remains largely undescribed. Here, we compare pre- and post-whaling diversity of mitochondrial DNA (mtDNA) control region sequences for 3 great whales in the South Atlantic, such as the blue, humpback, and fin whale. Pre-whaling diversity is described from mtDNA extracted from bones collected near abandoned whaling stations, primarily from the South Atlantic island of South Georgia. These bones are known to represent the first stage of 20th century whaling and thus pre-whaling diversity of these populations. Post-whaling diversity is described from previously published studies reporting large-scale sampling of living whales in the Southern Hemisphere. Despite relatively high levels of surviving genetic diversity in the post-whaling populations, we found evidence of a probable loss of mtDNA lineages in all 3 species. This is evidenced by the detection of a large number of haplotypes found in the pre-whaling samples that are not present in the post-whaling samples. A rarefaction analysis further supports a loss of haplotypes in the South Atlantic humpback and Antarctic blue whale populations. The bones from former whaling stations in the South Atlantic represent a remarkable molecular archive for further investigation of the decline and ongoing recovery in the great whales of the Southern Hemisphere. [ABSTRACT FROM AUTHOR]

The title of Perrin's presentation was, "The problem of porpoise [= dolphin] mortality in the U. S. tropical tuna fishery" (Perrin, [5]). Bill invited Louella the following year to attend the IWC gill net meeting in La Jolla in 1991 (Perrin et al., [15]) where she presented the bycatch data she gathered from gill net fisheries in the Philippines. Besides being the first person to alert the world to the massive kills of dolphins that were happening in the eastern tropical Pacific tuna fishery in the 1960s, decades later Bill created a compilation of the thousands of documents related to the controversy, along with a searchable bibliography (Perrin, [9]). Bill's critical early research on oceanic dolphins brought world attention to the longstanding and growing problem of incidental mortality of cetaceans in fisheries, but it was also transformative given the huge and enduring impact it had on cetacean science. [Extracted from the article]

Integrative taxonomy can help us to gain a better understanding of the degree of evolutionary divergence between taxa. In the western North Atlantic (wNA), two ecotypes (coastal and offshore) of common bottlenose dolphin, Tursiops truncatus , exhibit some external morphological differences, and previous genetic findings suggested that they could be different species. However, their taxonomy remains unsettled. Using an integrative approach comparing traditional and geometric morphometrics, mitochondrial and nuclear DNA, we evaluated evolutionary relationships between these ecotypes. We observed congruence among these lines of evidence, strongly indicating that the wNA ecotypes are following distinct evolutionary trajectories. Based on mitochondrial DNA analyses, we detected significant divergence (Nei's d A = 0.027), unshared haplotypes and one fixed difference leading to complete diagnosability (percentage diagnosable = 100%) of the wNA coastal ecotype. We found morphological diagnosability and negligible nuclear gene flow between the wNA ecotypes. Integration of these multiple lines of evidence revealed that the wNA coastal ecotype is an independent evolutionary unit, appearing to be more closely related to coastal dolphins in the Gulf of Mexico and Caribbean Sea than to their parapatric offshore neighbours, while the offshore dolphins form a relatively cohesive worldwide unit, T. truncatus. We propose that this coastal ecotype is recognized as a distinct species, resurrecting the name Tursiops erebennus. [ABSTRACT FROM AUTHOR]

In order to help develop hypotheses of connectivity among North Pacific fin whales, we examine recordings from 10 regions collected in the spring and fall. We develop a Random Forest model to classify fin whale note types that avoids manual note classification errors. We also present a method that objectively quantifies the note and pattern composition of recordings. We find that fin whale recordings near Hawaii have distinctive patterns, similar to those found in other regions in the central North Pacific, suggesting potential migration pathways. Our results are consistent with previous studies that suggest there may be two different populations utilizing the Chukchi Sea and central Aleutians in the fall and mix to some degree in the southern Bering Sea. Conversely, we found little difference between spring and fall recordings in the eastern Gulf of Alaska, suggesting some residency of whales in this region. This is likely due to fine scale similarities of calls among the inshore regions of British Columbia, while offshore areas are being utilized by whales traveling from various distant areas. This study shows how our novel approach to characterize recordings is an objective and informative way to standardize spatial and temporal comparisons of fin whale recordings. [ABSTRACT FROM AUTHOR]