Nuclear and mitochondrial patterns of population structure in North Pacific false killer whales (Pseudorca crassidens)

Kin relationships in cultural species of the marine realm: case study of a matrilineal social group of sperm whales off Mauritius island, Indian Ocean

Understanding the organization and dynamics of social groups of marine mammals through the study of kin relationships is particularly challenging. Here, we studied a stable social group of sperm whales off Mauritius, using underwater observations, individual-specific identification, non-invasive sampling and genetic analyses based on mitochondrial sequencing and microsatellite profiling. Twenty-four sperm whales were sampled between 2017 and 2019. All individuals except one adult female shared the same mitochondrial DNA (mtDNA) haplotype-one that is rare in the western Indian Ocean-thus confirming with near certainty the matrilineality of the group. All probable first- and second-degree kin relationships were depicted in the sperm whale social group: 13 first-degree and 27 second-degree relationships were identified. Notably, we highlight the likely case of an unrelated female having been integrated into a social unit, in that she presented a distinct mtDNA haplotype and no close relationships with any members of the group. Investigating the possible matrilineality of sperm whale cultural units (i.e. vocal clans) is the next step in our research programme to elucidate and better apprehend the complex organization of sperm whale social groups.

Life history and social structure as drivers of persistent organic pollutant levels and stable isotopes in Hawaiian false killer whales (Pseudorca crassidens)

False killer whales are long-lived, slow to mature, apex predators, and therefore susceptible to bioaccumulation of persistent organic pollutants (POPs). Hawaiian waters are home to three distinct populations: pelagic; Northwestern Hawaiian Islands (NWHI) insular; and main Hawaiian Islands (MHI) insular. Following a precipitous decline over recent decades, the MHI population was listed as "endangered" under the Endangered Species Act in 2012. This study assesses the risk of POP exposure to these populations by examining pollutant concentrations and ratios from blubber samples (n = 56) related to life history characteristics and MHI social clusters. Samples were analyzed for PCBs, DDTs, PBDEs, and some organochlorine pesticides. Skin samples (n = 52) were analyzed for stable isotopes δ¹³C and δ¹⁵N to gain insight into MHI false killer whale foraging ecology. Pollutant levels were similar among populations, although MHI whales had a significantly higher mean ratio of DDTs/PCBs than NWHI whales. The ∑PCB concentrations of 28 MHI individuals (68%) sampled were equal to or greater than suggested thresholds for deleterious health effects in marine mammals. The highest POP values among our samples were found in four stranded MHI animals. Eight of 24 MHI adult females have not been documented to have given birth; whether they have yet to reproduce, are reproductive senescent, or are experiencing reproductive dysfunction related to high POP exposure is unknown. Juvenile/sub-adults had significantly higher concentrations of certain contaminants than those measured in adults, and may be at greater risk of negative health effects during development. Multivariate analyses, POP ratios, and stable isotope ratios indicate varying risk of POP exposure, foraging locations and potentially prey items among MHI social clusters. Our findings provide invaluable insight into the ongoing risk POPs pose to the MHI population's viability, as well as consideration of risk for the NWHI and pelagic stocks.

Global phylogeography and genetic diversity of the long-finned pilot whale Globicephala melas, with new data from the southeastern Pacific

The matrilineal long-finned pilot whale presents an antitropical distribution and is divided into two subspecies, one in the temperate seas of the Southern Hemisphere and the other restricted to the North Atlantic and Mediterranean. Until now, population genetic and phylogeographic studies have included localities of most of its Northern Hemisphere distribution, while only the southwestern Pacific has been sampled in the Southern Hemisphere. We add new genetic data from the southeastern Pacific to the published sequences. Low mitochondrial and nuclear diversity was encountered in this new area, as previously reported for other localities. Four haplotypes were found with only one new for the species. Fifteen haplotypes were detected in the global dataset, underlining the species’ low diversity. As previously reported, the subspecies shared two haplotypes and presented a strong phylogeographic structure. The extant distribution of this species has been related to dispersal events during the Last Glacial Maximum. Using the genetic data and Approximate Bayesian Calculations, this study supports this historical biogeographic scenario. From a taxonomic perspective, even if genetic analyses do not support the subspecies category, this study endorses the incipient divergence process between hemispheres, thus maintaining their status and addressing them as Demographically Independent Populations is recommended.

Evolutionary impacts differ between two exploited populations of northern bottlenose whale (Hyperoodon ampullatus)

Interpretation of conservation status should be informed by an appreciation of genetic diversity, past demography, and overall trends in population size, which contribute to a species' evolutionary potential and resilience to genetic risks. Low genetic diversity can be symptomatic of rapid demographic declines and impose genetic risks to populations, but can also be maintained by natural processes. The northern bottlenose whale Hyperoodon ampullatus has the lowest known mitochondrial diversity of any cetacean and was intensely whaled in the Northwest Atlantic over the last century, but whether exploitation imposed genetic risks that could limit recovery is unknown. We sequenced full mitogenomes and genotyped 37 novel microsatellites for 128 individuals from known areas of abundance in the Scotian Shelf, Northern and Southern Labrador, Davis Strait, and Iceland, and a newly discovered group off Newfoundland. Despite low diversity and shared haplotypes across all regions, both markers supported the Endangered Scotian Shelf population as distinct from the combined northern regions. The genetic affinity of Newfoundland was uncertain, suggesting an area of mixing with no clear population distinction for the region. Demographic reconstruction using mitogenomes suggests that the northern region underwent population expansion following the last glacial maximum, but for the peripheral Scotian Shelf population, a stable demographic trend was followed by a drastic decline over a temporal scale consistent with increasing human activity in the Northwest Atlantic. Low connectivity between the Scotian Shelf and the rest of the Atlantic likely compounded the impact of intensive whaling for this species, potentially imposing genetic risks affecting recovery of this population. We highlight how the combination of historical environmental conditions and modern exploitation of this species has had very different evolutionary impacts on structured populations of northern bottlenose whales across the western North Atlantic.

Oceanographic barriers, divergence, and admixture: Phylogeography and taxonomy of two putative subspecies of short-finned pilot whale

Genomic phylogeography plays an important role in describing evolutionary processes and their geographic, ecological, or cultural drivers. These drivers are often poorly understood in marine environments, which have fewer obvious barriers to mixing than terrestrial environments. Taxonomic uncertainty of some taxa (e.g., cetaceans), due to the difficulty in obtaining morphological data, can hamper our understanding of these processes. One such taxon, the short-finned pilot whale, is recognized as a single global species but includes at least two distinct morphological forms described from stranding and drive hunting in Japan, the "Naisa" and "Shiho" forms. Using samples (n = 735) collected throughout their global range, we examine phylogeographic patterns of divergence by comparing mitogenomes and nuclear SNP loci. Our results suggest three types within the species: an Atlantic Ocean type, a western/central Pacific and Indian Ocean (Naisa) type, and an eastern Pacific Ocean and northern Japan (Shiho) type. mtDNA control region differentiation indicates these three types form two subspecies, separated by the East Pacific Barrier: Shiho short-finned pilot whale, in the eastern Pacific Ocean and northern Japan, and Naisa short-finned pilot whale, throughout the remainder of the species' distribution. Our data further indicate two diverging populations within the Naisa subspecies, in the Atlantic Ocean and western/central Pacific and Indian Oceans, separated by the Benguela Barrier off South Africa. This study reveals a process of divergence and speciation within a globally-distributed, mobile marine predator, and indicates the importance of the East Pacific Barrier to this evolutionary process.

The incidence of bent dorsal fins in free-ranging cetaceans

Laterally bent dorsal fins are rarely observed in free-ranging populations of cetaceans, contrary to captivity, where most killer whale Orcinus orca adult males have laterally collapsed fins. This topic has been poorly explored, and data/information on its occurrence and possible causes are limited. The present study: (i) undertakes a review of the available information on bent dorsal fins in free-ranging cetaceans, and updates it with new records, (ii) reports on the proportion of bent fins in different study populations, and (iii) discusses possible causes. An empirical approach based on bibliographic research and compilation of 52 new records collected worldwide resulted in a total of 17 species of cetaceans displaying bent dorsal fins. The species with the highest number of records (64%) and from most locations was O. orca. On average, individuals with bent dorsal fins represent < 1% of their populations, with the exception of false killer whales Pseudorca crassidens and O. orca. While line injuries associated with fisheries interactions may be the main cause for P. crassidens, and the vulnerability to health issues caused by the evolutionary enlargement of the fin may be the cause for O. orca adult males, factors contributing to this abnormality for other species are still unclear. The occurrence of bent dorsals could be influenced by a set of variables rather than by a single factor but, irrespective of the cause, it is suggested that it does not directly affect the animals' survivorship. While still rare in nature, this incident is more common (at least 101 known cases) and widespread (geographically and in species diversity) than hypothesized, and is not confined only to animals in captive environments. Investigation into the occurrence of bent fins may be an interesting avenue of research.

Genetic diversity and connectivity in the East African giant mud crab Scylla serrata: Implications for fisheries management

The giant mud crab Scylla serrata provides an important source of income and food to coastal communities in East Africa. However, increasing demand and exploitation due to the growing coastal population, export trade, and tourism industry are threatening the sustainability of the wild stock of this species. Because effective management requires a clear understanding of the connectivity among populations, this study was conducted to assess the genetic diversity and connectivity in the East African mangrove crab S. serrata. A section of 535 base pairs of the cytochrome oxidase subunit I (COI) gene and eight microsatellite loci were analysed from 230 tissue samples of giant mud crabs collected from Kenya, Tanzania, Mozambique, Madagascar, and South Africa. Microsatellite genetic diversity (H_e) ranged between 0.56 and 0.6. The COI sequences showed 57 different haplotypes associated with low nucleotide diversity (current nucleotide diversity = 0.29%). In addition, the current nucleotide diversity was lower than the historical nucleotide diversity, indicating overexploitation or historical bottlenecks in the recent history of the studied population. Considering that the coastal population is growing rapidly, East African countries should promote sustainable fishing practices and sustainable use of mangrove resources to protect mud crabs and other marine fauna from the increasing pressure of exploitation. While microsatellite loci did not show significant genetic differentiation (p > 0.05), COI sequences revealed significant genetic divergence between sites on the East coast of Madagascar (ECM) and sites on the West coast of Madagascar, mainland East Africa, as well as the Seychelles. Since East African countries agreed to achieve the Convention on Biological Diversity (CBD) target to protect over 10% of their marine areas by 2020, the observed pattern of connectivity and the measured genetic diversity can serve to provide useful information for designing networks of marine protected areas.

Genetic population structure and relatedness in the narrow-striped mongoose (Mungotictis decemlineata), a social Malagasy carnivore with sexual segregation

Information on the genetic structure of animal populations can allow inferences about mechanisms shaping their social organization, dispersal, and mating system. The mongooses (Herpestidae) include some of the best-studied mammalian systems in this respect, but much less is known about their closest relatives, the Malagasy carnivores (Eupleridae), even though some of them exhibit unusual association patterns. We investigated the genetic structure of the Malagasy narrow-striped mongoose (Mungotictis decemlineata), a small forest-dwelling gregarious carnivore exhibiting sexual segregation. Based on mtDNA and microsatellite analyses, we determined population-wide haplotype structure and sex-specific and within-group relatedness. Furthermore, we analyzed parentage and sibship relationships and the level of reproductive skew. We found a matrilinear population structure, with several neighboring female units sharing identical haplotypes. Within-group female relatedness was significantly higher than expected by chance in the majority of units. Haplotype diversity of males was significantly higher than in females, indicating male-biased dispersal. Relatedness within the majority of male associations did not differ from random, not proving any kin-directed benefits of male sociality in this case. We found indications for a mildly promiscuous mating system without monopolization of females by males, and low levels of reproductive skew in both sexes based on parentages of emergent young. Low relatedness within breeding pairs confirmed immigration by males and suggested similarities with patterns in social mongooses, providing a starting point for further investigations of mate choice and female control of reproduction and the connected behavioral mechanisms. Our study contributes to the understanding of the determinants of male sociality in carnivores as well as the mechanisms of female competition in species with small social units.