Population structure of pygmy (Kogia breviceps) and dwarf (Kogia sima) sperm whales in the Southern Hemisphere may reflect foraging ecology and dispersal patterns.

Little is known about the biology of pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales as these animals are difficult to observe in the wild. However, both species strand frequently along the South African, Australian and New Zealand coastlines, providing samples for these otherwise inaccessible species. The use of DNA samples from tissue and DNA extracted from historical material, such as teeth and bone, allowed a first analysis of the population structure of both species in the Southern Hemisphere. A 279 base pair consensus region of the mitochondrial cytochrome b gene was sequenced for 96 K. breviceps (53 tissue and 43 teeth or bone samples) and 29 K. sima (3 tissue and 26 teeth or bone samples), and 26 and 12 unique haplotypes were identified, respectively. K. breviceps showed a higher nucleotide diversity of 0.82% compared to 0.40% in K. sima. Significant genetic differentiation was detected in the Southern Hemisphere between K. breviceps from South Africa and New Zealand (ФST = 0.042, p < 0.05). Mitochondrial control region sequences (505 bp) were available for 44 individuals (41 K. breviceps and 3 K. sima) for comparative purposes. A comprehensive global phylogenetic analysis (maternal lineage) of our sequences together with all available Kogia mtDNA sequences largely supported previously published phylogenetic findings, but highlighted some changed inferences about oceanic divergences within both species. The higher nucleotide diversity and low population differentiation observed in K. breviceps may result from its broad foraging ecology and wide distribution, which may indicate a more opportunistic feeding behaviour and tolerance towards a larger range of water temperatures than K. sima.

Tattoo Skin Disease in Cetacea: A Review, with New Cases for the Northeast Pacific.

Tattoo skin disease (TSD) is a poxviral dermatopathy diagnosed in cetaceans. We review the literature on TSD aetiology, clinical characteristics, pathology and epidemiology and evaluate immune responses against the virus. In addition, necropsy reports for fifty-five harbour porpoises (Phocoena phocoena), twenty-two Delphinidae and four Kogiidae stranded in northern California in 2018-2021 were checked for diagnostic tattoo lesions. TSD occurs in the Mediterranean, North and Barents Seas, as well as in the Atlantic, eastern Pacific and Indian Oceans in at least 21 cetacean species, with varying prevalence. Two cetacean poxvirus (CePV) clades are recognised: CePV-1 in odontocetes and CePV-2 in mysticetes. CePV-1 isolates were recovered from six Delphinidae and one Phocoenidae in the Americas, Europe and Hong Kong. Strains from Delphinidae are closely related. Among Phocoenidae, poxviruses were sampled only in harbour porpoises around the British Isles. CePV-2 isolates were obtained from southern right whales (Eubalaena australis) and a bowhead whale (Balaena mysticetus). In healthy animals, an immune response develops over time, with young calves protected by maternal immunity. Salinity and sea surface temperature do not seem to influence TSD prevalence in free-ranging cetaceans. High concentrations of immunotoxic halogenated organochlorines may cause a more severe clinical disease. Substitution and loss of genes involved in anti-viral immunity may favour CePV entry, replication and persistence in the epidermis. Off California, Delphinidae were less often (26.3%) affected by TSD than harbour porpoises (43.6%). Male porpoises were significantly more prone (58.1%) to show clinical disease than females (25%). Among males, TSD affected a high proportion of juveniles and subadults. TSD was not detected in the Kogiidae.

Detection of Cetacean Poxvirus in Peruvian Common Bottlenose Dolphins (Tursiops truncatus) Using a Pan-Poxvirus PCR.

Cetacean poxviruses (CePVs) cause 'tattoo' skin lesions in small and large cetaceans worldwide. Although the disease has been known for decades, genomic data for these poxviruses are very limited, with the exception of CePV-Tursiops aduncus, which was completely sequenced in 2020. Using a newly developed pan-pox real-time PCR system targeting a conserved nucleotide sequence located within the Monkeypox virus D6R gene, we rapidly detected the CePV genome in typical skin lesions collected from two Peruvian common bottlenose dolphins (Tursiops truncatus) by-caught off Peru in 1993. Phylogenetic analyses based on the sequencing of the DNA polymerase and DNA topoisomerase genes showed that the two viruses are very closely related to each other, although the dolphins they infected pertained to different ecotypes. The poxviruses described in this study belong to CePV-1, a heterogeneous clade that infects many species of dolphins (Delphinidae) and porpoises (Phocoenidae). Among this clade, the T. truncatus CePVs from Peru were more related to the viruses infecting Delphinidae than to those detected in Phocoenidae. This is the first time that CePVs were identified in free-ranging odontocetes from the Eastern Pacific, surprisingly in 30-year-old samples. These data further suggest a close and long-standing pathogen-host co-evolution, resulting in different lineages of CePVs.

Cranial crassicaudiasis in two coastal dolphin species from South Africa is predominantly a disease of immature individuals.

Crassicauda spp. (Nematoda) infest the cranial sinuses of several odontocetes, causing diagnostic trabecular osteolytic lesions. We examined skulls of 77 Indian Ocean humpback dolphins Sousa plumbea and 69 Indo-Pacific bottlenose dolphins Tursiops aduncus, caught in bather-protecting nets off KwaZulu-Natal (KZN) from 1970-2017, and skulls of 6 S. plumbea stranded along the southern Cape coast in South Africa from 1963-2002. Prevalence of cranial crassicaudiasis was evaluated according to sex and cranial maturity. Overall, prevalence in S. plumbea and T. aduncus taken off KZN was 13 and 31.9%, respectively. Parasitosis variably affected 1 or more cranial bones (frontal, pterygoid, maxillary and sphenoid). No significant difference was found by gender for either species, allowing sexes to be pooled. However, there was a significant difference in lesion prevalence by age, with immature T. aduncus 4.6 times more likely affected than adults, while for S. plumbea, the difference was 6.5-fold. As severe osteolytic lesions are unlikely to heal without trace, we propose that infection is more likely to have a fatal outcome for immature dolphins, possibly because of incomplete bone development, lower immune competence in clearing parasites or an over-exuberant inflammatory response in concert with parasitic enzymatic erosion. Cranial osteolysis was not observed in mature males (18 S. plumbea, 21 T. aduncus), suggesting potential cohort-linked immune-mediated resistance to infestation. Crassicauda spp. may play a role in the natural mortality of S. plumbea and T. aduncus, but the pathogenesis and population level impact remain unknown.

Role of social behaviour in the epidemiology of lobomycosis-like disease (LLD) in estuarine common bottlenose dolphins from Ecuador.

Lobomycosis-like disease (LLD) is a chronic granulomatous skin disorder that affects Delphinidae worldwide. LLD has been observed in common bottlenose dolphins Tursiops truncatus from the Gulf of Guayaquil, Ecuador, since 1990. Although exogenous factors such as salinity and pollution may play a role in the pathogenesis of this disease in estuarine and coastal dolphin communities, we hypothesized that demography and social behaviour may also influence its epidemiology. To address this issue, the role of social behaviour in the distribution and prevalence of LLD was assessed through hierarchical cluster analysis and spatial distribution analysis in 7 dolphin communities inhabiting the inner estuary. Individuals with LLD lesions were observed in 5 of the 7 dolphin communities, with 13 of the 163 (8%) animals being positive, all adults. Among 8 dolphins of known sex, LLD affected mostly males (86%), who usually were found in pairs. Prevalence was low to moderate (5.1-13%) in dolphin communities where low-rank males had LLD. Conversely, it was high (44.4%, n = 9) in a small community where a high-rank male was infected. LLD affected both dolphins in 2 of the 4 male pairs for which large time series data were available, suggesting horizontal transmission due to contact. Thus, association with LLD-positive males seems to be an important risk factor for infections. Additionally, low-rank males had larger home ranges than high-rank males, indicating that low-status LLD-affected dolphins are likely responsible for the geographic dissemination of the disease in this population.

Clinical signs in free-ranging Guiana dolphins Sotalia guianensis during a morbillivirus epidemic: case study in Sepetiba Bay, Brazil.

From November 2017 to March 2018, a cetacean morbillivirus (CeMV) outbreak caused an unprecedented mass mortality among Guiana dolphins Sotalia guianensis in Ilha Grande Bay and Sepetiba Bay, Rio de Janeiro, Brazil. Small boat surveys were conducted to document the behavior and clinical signs presented by diseased dolphins. We observed 5 abnormally behaving, disoriented Guiana dolphins on separate days, of which 1 died stranded and 2 sank. Signs of ataxia included difficulties with swimming and maintaining a course, balance and buoyancy. At least 40 other individuals were emaciated, and 10 photo-identified dolphins had miscellaneous skin lesions, some ulcerated. Labored breathing suggestive of airway obstruction was heard in several groups. These neurological, respiratory and cutaneous signs may comprise part of the clinical constellation of CeMV infection in dolphins. The combined threat of anthropogenic pressures and CeMV lethal disease is of concern for the survival of the Guiana dolphin population in Sepetiba Bay.

Lobomycosis-like disease in common bottlenose dolphins Tursiops truncatus from Belize and Mexico: bridging the gap between the Americas.

Lobomycosis and lobomycosis-like diseases (LLD) (also: paracoccidioidomycosis) are chronic cutaneous infections that affect Delphinidae in tropical and subtropical regions worldwide. In the Americas, these diseases have been relatively well-described, but gaps still exist in our understanding of their distribution across the continent. Here we report on LLD affecting inshore bottlenose dolphins Tursiops truncatus from the Caribbean waters of Belize and from the eastern tropical Pacific Ocean off the southwestern coast of Mexico. Photo-identification and catalog data gathered between 1992 and 2017 for 371 and 41 individuals, respectively from Belize and Mexico, were examined for the presence of LLD. In Belize, 5 free-ranging and 1 stranded dolphin were found positive in at least 3 communities with the highest prevalence in the south. In Guerrero, Mexico, 4 inshore bottlenose dolphins sighted in 2014-2017 were affected by LLD. These data highlight the need for histological and molecular studies to confirm the etiological agent. Additionally, we document a single case of LLD in an adult Atlantic spotted dolphin Stenella frontalis in southern Belize, the first report in this species. The role of environmental and anthropogenic factors in the occurrence, severity, and epidemiology of LLD in South and Central America requires further investigation.

Epidemiology of tattoo skin disease in captive common bottlenose dolphins (Tursiops truncatus): Are males more vulnerable than females?

Clinical and epidemiological features of tattoo skin disease (TSD) are reported for 257 common bottlenose dolphins held in 31 facilities in the Northern Hemisphere. Photographs and biological data of 146 females and 111 males were analyzed. Dolphins were classified into three age classes: 0-3 years, 4-8 years, and older than 9 years. From 2012 to 2014, 20.6% of the 257 dolphins showed clinical TSD. The youngest dolphins with tattoo lesions were 14 and 15 months old. TSD persisted from 4 to 65 months in 30 dolphins. Prevalence varied between facilities from 5.6% to 60%, possibly reflecting variation in environmental factors. Unlike in free-ranging Delphinidae, TSD prevalence was significantly higher in males (31.5%) than in females (12.3%). Infection was age-dependent only in females. Prevalence of very large tattoos was also higher in males (28.6%) than in females (11.1%). These data suggest that male T. truncatus are more vulnerable to TSD than females, possibly because of differences in immune response and susceptibility to captivity-related stress.

A Review of the Status of the Indian Ocean Humpback Dolphin (Sousa plumbea) in Pakistan.

Limited historical and new information on Indian Ocean humpback dolphins, Sousa plumbea, in Pakistan are reviewed. Although present along most of the coast, S. plumbea concentrates in the mangrove-lined creek system of the Indus Delta (Sindh), Miani Hor (Sonmiani Bay), Kalmat Lagoon, Gwadar and the Dasht River estuary (Gwater Bay, Jiwani). Other areas of distribution comprise the Karachi coast, Kund Malir, Ormara and Pasni. In the Indus Delta, 46 small-boat surveys conducted monthly (minus July and October) in 2005-2009, documented 112 sightings (439 individuals) in major creeks, smaller channels and nearshore waters. Group sizes ranged from 1-35 animals (mean=3.92±4.60). Groups of 1-10 animals composed 91% of total (27.9% single animals). An encounter rate of 0.07-0.17 dolphins km(-1) lacked a significant trend across survey years. A discovery curve remained steep after 87 dolphins were photo-identified, suggesting the population is vastly larger. In Sonmiani Bay, Balochistan, during 9 survey days in 2011-2012, group sizes ranged from 1-68 animals (mean=11.9±13.59; n=36), totalling 428 dolphins. Incidental entanglements, primarily in gillnets, pollution (especially around Karachi), overfishing and the ship breaking industry in Gaddani, pose major threats. Incidental catches occur along the entire Pakistani coast. Of 106 stranded cetaceans, 24.5% were S. plumbea. Directed takes in Balochistan, driven by demand for bait in shark fisheries, have reportedly declined following dwindling shark stocks. Habitat degradation threats include depletion of prey and increased maritime traffic. Domestic sewage and solid waste pollution are predominant on the Balochistan coast, especially at Miani Hor, Kund Malir, Ormara, Kalmat Lagoon, Pasni, Gwadar and Jiwani. An exhaustive habitat assessment combined with appropriate fishery management is the only way to safeguard the future of S. plumbea in Pakistan.

Epidemiology of lobomycosis-like disease in bottlenose dolphins Tursiops spp. from South America and southern Africa.

We report on the epidemiology of lobomycosis-like disease (LLD), a cutaneous disorder evoking lobomycosis, in 658 common bottlenose dolphins Tursiops truncatus from South America and 94 Indo-Pacific bottlenose dolphins T. aduncus from southern Africa. Photographs and stranding records of 387 inshore residents, 60 inshore non-residents and 305 specimens of undetermined origin (inshore and offshore) were examined for the presence of LLD lesions from 2004 to 2015. Seventeen residents, 3 non-residents and 1 inshore dolphin of unknown residence status were positive. LLD lesions appeared as single or multiple, light grey to whitish nodules and plaques that may ulcerate and increase in size over time. Among resident dolphins, prevalence varied significantly among 4 communities, being low in Posorja (2.35%, n = 85), Ecuador, and high in Salinas, Ecuador (16.7%, n = 18), and Laguna, Brazil (14.3%, n = 42). LLD prevalence increased in 36 T. truncatus from Laguna from 5.6% in 2007-2009 to 13.9% in 2013-2014, albeit not significantly. The disease has persisted for years in dolphins from Mayotte, Laguna, Salinas, the Sanquianga National Park and Bahía Málaga (Colombia) but vanished from the Tramandaí Estuary and the Mampituba River (Brazil). The geographical range of LLD has expanded in Brazil, South Africa and Ecuador, in areas that have been regularly surveyed for 10 to 35 yr. Two of the 21 LLD-affected dolphins were found dead with extensive lesions in southern Brazil, and 2 others disappeared, and presumably died, in Ecuador. These observations stress the need for targeted epidemiological, histological and molecular studies of LLD in dolphins, especially in the Southern Hemisphere.

Annotated checklist and fisheries interactions of cetaceans in Togo, with evidence of Antarctic minke whale in the Gulf of Guinea.

Based on strandings and captures, 9 cetacean species, including 6 odontocetes and 3 mysticetes, are documented (photos and specimens) in Togo's coastal waters (newly-recorded species marked with an asterisk): Antarctic minke whale (Balaenoptera bonaerensis*), Bryde's whale (Balaenoptera brydei or B. edeni), humpback whale (Megaptera novaeangliae), sperm whale (Physeter macrocephalus), pygmy sperm whale (Kogia breviceps*), short-finned pilot whale (Globicephala macrorhynchus*), pantropical spotted dolphin (Stenella attenuata*), common bottlenose dolphin (Tursiops truncatus) and common dolphin Delphinus sp. An anecdotal sighting record for killer whale (Orcinus orca) is considered reliable. The lack of Sousa teuszii records in Togo is consistent with its apparent contemporaneous absence in Ghana. The B. bonaerensis specimen, entangled in a purse seine set on small pelagics, is a first record for the Gulf of Guinea. The occurrence of this Southern Ocean species north of the equator underscores the severe gaps in our understanding of cetacean distribution off western Africa. The majority of artisanal fishermen operating in Togolese coastal waters are of Ghanaian origin and are thought to promote trade and consumption of cetacean bushmeat. Because captures are illegal, enforced with some success in the main fishing centers, covert landings of cetaceans are exceedingly difficult to monitor, quantify or sample. Concern is expressed about pollution of Togo's coastal waters with heavy metals due to phosphorite mining and export from the coastal basin near Hahotoé and Kpogamé.

Emerging infectious diseases in cetaceans worldwide and the possible role of environmental stressors.

We reviewed prominent emerging infectious diseases of cetaceans, examined their potential to impact populations, re-assessed zoonotic risk and evaluated the role of environmental stressors. Cetacean morbilliviruses and papillomaviruses as well as Brucella spp. and Toxoplasma gondii are thought to interfere with population abundance by inducing high mortalities, lowering reproductive success or by synergistically increasing the virulence of other diseases. Severe cases of lobomycosis and lobomycosis-like disease (LLD) may contribute to the death of some dolphins. The zoonotic hazard of marine mammal brucellosis and toxoplasmosis may have been underestimated, attributable to frequent misdiagnoses and underreporting, particularly in developing countries and remote areas where carcass handling without protective gear and human consumption of fresh cetacean products are commonplace. Environmental factors seem to play a role in the emergence and pathogenicity of morbillivirus epidemics, lobomycosis/LLD, toxoplasmosis, poxvirus-associated tattoo skin disease and, in harbour porpoises, infectious diseases of multifactorial aetiology. Inshore and estuarine cetaceans incur higher risks than pelagic cetaceans due to habitats often severely altered by anthropogenic factors such as chemical and biological contamination, direct and indirect fisheries interactions, traumatic injuries from vessel collisions and climate change.

Epidemiological pattern of tattoo skin disease: a potential general health indicator for cetaceans.

The presence of tattoo skin disease (TSD) was examined in 1392 free-ranging and dead odontocetes comprising 17 species from the Americas, Europe, South Africa, New Zealand and Greenland. We investigated whether TSD prevalence varied with sex, age and health status. TSD was encountered in cetaceans from the Pacific and Atlantic Oceans as well as in those from the North, Mediterranean and Tasman Seas. No clear patterns related to geography and host phylogeny were detected, except that prevalence of TSD in juveniles and, in 2 species (dusky dolphin Lagenorhynchus obscurus and Burmeister's porpoise Phocoena spinipinnis), in adults was remarkably high in samples from Peru. Environmental factors and virus properties may be responsible for this finding. Sex did not significantly influence TSD prevalence except in the case of Peruvian P. spinipinnis. Generally, there was a pattern of TSD increase in juveniles compared to calves, attributed to the loss of maternal immunity. Also, in most samples, juveniles seemed to have a higher probability of suffering TSD than adults, presumably because more adults had acquired active immunity following infection. This holo-endemic pattern was inverted in poor health short-beaked common dolphins Delphinus delphis and harbour porpoises Phocoena phocoena from the British Isles, and in Chilean dolphins Cephalorhynchus eutropia from Patagonia, where adults showed a higher TSD prevalence than juveniles. Very large tattoos were seen in some adult odontocetes from the SE Pacific, NE Atlantic and Portugal's Sado Estuary, which suggest impaired immune response. The epidemiological pattern of TSD may be an indicator of cetacean population health.

Bushmeat and bycatch: the sum of the parts.

In many developing countries, the killing of wild animals for commercial purposes (the bushmeat trade) is a significant factor in the reduction of biodiversity, and probably represents a major threat to the survival of many more populations than we know. This includes marine species such as cetaceans, sea turtles and sirenians ("marine bushmeat"), which are often neglected in the discussion of this issue. Estimating the impact of the bushmeat trade anywhere is problematic because even the most thorough visual surveys of meat markets cannot easily translate an observed quantity of butchered products into the number of animals killed. In this issue of Molecular Ecology, Baker et al. provide a powerful new tool for such assessments: molecular identification of commercially available products from a depleted population of minke whales in South Korea is combined with genotyping and novel capture-recapture methods to estimate not only the number of individuals taken, but also the persistence of the resulting products in the marketplace.

Genital warts in Burmeister's porpoises: characterization of Phocoena spinipinnis papillomavirus type 1 (PsPV-1) and evidence for a second, distantly related PsPV.

We identified sequences from two distantly related papillomaviruses in genital warts from two Burmeister's porpoises, including a PV antigen-positive specimen, and characterized Phocoena spinipinnis papillomavirus type 1 (PsPV-1). The PsPV-1 genome comprises 7879 nt and presents unusual features. It lacks an E7, an E8 and a bona fide E5 open reading frame (ORF) and has a large E6 ORF. PsPV-1 L1 ORF showed the highest percentage of nucleotide identity (54-55 %) with human papillomavirus type 5, bovine papillomavirus type 3 (BPV-3) and Tursiops truncatus papillomavirus type 2 (TtPV-2). This warrants the classification of PsPV-1 as the prototype of the genus Omikronpapillomavirus. PsPV-1 clustered with TtPV-2 in the E6 and E1E2 phylogenetic trees and with TtPV-2 and BPV-3 in the L2L1 tree. This supports the hypothesis that PV evolution may not be monophyletic across all genes.

Diseases, lesions and malformations in the long-beaked common dolphin Delphinus capensis from the Southeast Pacific.

Miscellaneous lesions of the head, skull, teeth, trunk, appendages, skin and genital tract were observed in 120 of 930 long-beaked common dolphins Delphinus capensis taken in fisheries off Peru between 1985 and 2000. Seven subsamples were defined according to the varying field sampling protocols. Forty-two dolphins showed at least 2 types of injuries or diseases affecting 1 or more organs. The majority (5 of 7) of traumas encountered were diagnosed as caused by violent, fisheries-related interactions, and the skin in 20.4 % of specimens (n = 54) showed healed scars from such interactions. Prevalences of malformations and traumas of crania (n = 103) were 2.9 and 1.9%, respectively. Lytic cranial lesions were present in 31.1% of dolphins (n = 103) and accounted for 84.2% of all bone injuries. Skull damage diagnostic for Crassicauda sp. infestation was encountered in 26.5% of dolphins (n = 98) and did not differ among sex and age classes. Crassicauda sp. and tooth infections were responsible for, respectively, 78.8 and 6.1% of the lytic lesions. Adult dolphins showed a high prevalence of worn and broken teeth (35%, n = 20) as well as damaged alveoli (20%, n = 70). Prevalence of 'paired teeth', a congenital condition, was 9.4% (n = 32). Lesions of the head, body and appendages were present in 10 dolphins and included traumas, deformations (e.g. scoliokyphosis and brachygnathia) and chronic mastitis. Ovarian cysts suggestive of follicular cysts were observed in 1 of 24 females. Chronic orchitis affected 1 of 78 males. Of 12 dolphins 2 had vesicular lesions of the penis. Prevalence of cutaneous lesions, abnormalities and scars ranged between 1.8% (n = 56) and 48.2% (n = 27).

Evidence for male dispersal along the coasts but no migration in pelagic waters in dusky dolphins (Lagenorhynchus obscurus).

Using nine nuclear species-specific microsatellite loci and two mitochondrial gene fragments (cytochrome b and control region), we investigated the processes that have shaped the geographical distribution of genetic diversity exhibited by contemporary dusky dolphin (Lagenorhynchus obscurus) populations. A total of 221 individuals from four locations (Peru, Argentina, southern Africa, and New Zealand) were assayed, covering most of the species' distribution range. Although our analyses identify a general demographic decline in the Peruvian dusky dolphin stock (recently affected by high natural and human-induced mortality levels), comparison between the different molecular markers hint at an ancient bottleneck that predates recent El Niño oscillations and human exploitation. Moreover, we find evidence of a difference in dispersal behaviour of dusky dolphins along the South American coast and across the Atlantic. While data in Peruvian and Argentine waters are best explained by male-specific gene flow between these two populations, our analyses suggest that dusky dolphins from Argentina and southern Africa recently separated from an ancestral Atlantic population and, since then, diverged without considerable gene flow. The inclusion of a few New Zealand samples further confirms the low levels of genetic differentiation among most dusky dolphin populations. Only the Peruvian dusky dolphin stock is highly differentiated, especially at mitochondrial loci, suggesting that major fluctuations in its population size have led to an increased rate of genetic drift.