Molecular ecology meets remote sensing: environmental drivers to population structure of humpback dolphins in the Western Indian Ocean

Genetic stock structure of the silky shark Carcharhinus falciformis in the Indo-Pacific Ocean

The silky shark, Carcharhinus falciformis, is a cosmopolitan species commonly caught as a bycatch for longline fisheries. However, the genetic stock structure for the Indo-Pacific Ocean is not well-defined yet. Here, we used eight microsatellite loci to examine the genetic stock structure and effective population size of 307 silky sharks across 5 Indo-Pacific sampling locations. A major genetic break was found between Aceh and the remaining locations (FST = 0.0505-0.0828, p = 0.001). The Indian Ocean displayed a slightly lower effective population estimate (Ne) compared to the Pacific Ocean, potentially due to the higher fishing pressure in the Indian Ocean region. The lowest Ne was found in the Aceh population (Ne = 2.3), suggesting it might be a small and endemic population. These findings offer valuable information for the conservation and management of the silky shark. We suggest that the population around Aceh waters constitutes a distinct stock and should be managed independently. Further investigations into migratory and movement patterns are needed to define the boundaries of different stocks, ensuring effective management the silky shark across the Indo-Pacific region.

Reconstructing the colonization history of Indo-Pacific bottlenose dolphins (Tursiops aduncus) in Northwestern Australia

Bottlenose dolphins (Tursiops spp.) are found in waters around Australia, with T. truncatus typically occupying deeper, more oceanic habitat, while T. aduncus occur in shallower, coastal waters. Little is known about the colonization history of T. aduncus along the Western Australian coastline; however, it has been hypothesized that extant populations are the result of an expansion along the coastline originating from a source in the north of Australia. To investigate the history of coastal T. aduncus populations in the area, we generated a genomic SNP dataset using a double-digest restriction-site-associated DNA (ddRAD) sequencing approach. The resulting dataset consisted of 103,201 biallelic SNPs for 112 individuals which were sampled from eleven coastal and two offshore sites between Shark Bay and Cygnet Bay, Western Australia. Our population genomic analyses showed a pattern consistent with the proposed source in the north with significant isolation by distance along the coastline, as well as a reduction in genomic diversity measures along the coastline with Shark Bay showing the most pronounced reduction. Our demographic analysis indicated that the expansion of T. aduncus along the coastline began around the last glacial maximum and progressed southwards with the Shark Bay population being founded only 13 kya. Our results are in line with coastal colonization histories inferred for Tursiops globally, highlighting the ability of delphinids to rapidly colonize novel coastal niches as habitat is released during glacial cycle-related global sea level and temperature changes.

Commerson's dolphin population structure: evidence for female phylopatry and male dispersal

A key in species conservation is understanding the amount and distribution of genetic diversity and how environmental changes that occurred in the recent past may have influenced current patterns of population structure. Commerson's dolphin, Cephalorhynchus commersonii, has two subspecies, one of which is endemic to South America (C. commersonii commersonii) and little is known about its population genetics. Our objective was to investigate the population genetics of this subspecies throughout its distribution. Using 70 skin samples and information available in GenBank, 308 mitochondrial DNA sequences and 28 species-specific microsatellites were analyzed. The species presented low genetic diversity when compared to other dolphin species, but was consistent with other species within the genus. Strong population structure based on mitochondrial DNA was exhibited throughout its entire distribution, a pattern consistent with female philopatry. However, this pattern was not detected when using microsatellites, suggesting male-mediated gene flow. Demographic tests suggested a population expansion beginning approximately 15,000 years ago, after the Last Glacial Maximum. In a climate change scenario, we recommended considering each sampling location as an independent population management unit in order to evaluate the impact of possible environmental changes on the distribution of genetic information within the species.

Seascape Genetics of the Atlantic Spotted Dolphin (Stenella frontalis) Based on Mitochondrial DNA

The Atlantic spotted dolphin (Stenella frontalis) is endemic to tropical, subtropical, and warm temperate waters of the Atlantic Ocean. Throughout its distribution, both geographic distance and environmental variation may contribute to population structure of the species. In this study, we follow a seascape genetics approach to investigate population differentiation of Atlantic spotted dolphins based on a large worldwide dataset and the relationship with marine environmental variables. The results revealed that the Atlantic spotted dolphin exhibits population genetic structure across its distribution based on mitochondrial DNA control region (mtDNA-CR) data. Analyses based on the contemporary landscape suggested, at both the individual and population level, that the population genetic structure is consistent with the isolation-by-distance model. However, because geography and environmental matrices were correlated, and because in some, but not all analyses, we found a significant effect for the environment, we cannot rule out the addition contribution of environmental factors in structuring genetic variation. Future analyses based on nuclear data are needed to evaluate whether local processes, such as social structure and some level of philopatry within populations, may be contributing to the associations among genetic structure, geographic, and environmental distance.

Low mitochondrial genetic diversity in the Indian Ocean humpback dolphin Sousa plumbea in South African waters

The Indian Ocean humpback dolphin Sousa plumbea has been described as South Africa’s most endangered marine mammal due to its low abundance, reliance on coastal habitats with increasing anthropogenic threats and high rates of mortality from bycatch in bather protection nets (BPNs). Although the species has been well studied in South Africa, only a single study has examined its molecular ecology to date, and its population structure remains poorly understood. However, understanding population structure is vital for the conservation and management of a species. To address these research gaps for S. plumbea in South African waters, we analysed the mitochondrial D-loop of 157 museum skin and tooth samples collected between 1963 and 2017 from across the species’ geographic range in South Africa. Our data show that the humpback dolphin has extremely low mitochondrial diversity (haplotype diversity, HD = 0.47; nucleotide diversity, π = 0.2%) with only 3 haplotypes identified, which is comparable to the Critically Endangered Māui dolphin Cephalorhynchus hectori maui and the Critically Endangered Mekong population of Irrawaddy dolphin Orcaella brevirostris. Mitochondrial genetic diversity has not changed significantly in the last 50 yr, despite the high levels of bycatch in BPNs over this time period. Furthermore, we found no evidence of differentiation between dolphins from the KwaZulu-Natal Coast and the Cape South Coast (Western Cape and Eastern Cape). The extremely low mitochondrial diversity we found adds to the growing body of evidence that the humpback dolphin is becoming increasingly vulnerable and that urgent conservation efforts are required for the survival of the species.

Movement ecology of black marlin Istiompax indica in the Western Indian Ocean

The black marlin Istiompax indica is an apex marine predator and is susceptible to overfishing. The movement ecology of the species remains poorly known, particularly within the Indian Ocean, which has hampered assessment of their conservation status and fisheries management requirements. Here, we used pop-up archival satellite tags to track I. indica movement and examine their dispersal. Forty-nine tags were deployed off Kenya during both the north-east (November-April) and south-west (August-September) monsoon seasons, providing locations from every month of the year. Individual I. indica were highly mobile and track distance correlated with the duration of tag attachment. Mean track duration was 38 days and mean track distance was >1800 km. Individuals dispersed in several directions: north-east into Somalian waters and up to northern Oman, east towards the Seychelles, and south into the Mozambique Channel. Their core habitat shifted seasonally and overlapped with areas of high productivity off Kenya, Somalia and Oman during the first half of the year. A second annual aggregation off the Kenyan coast, during August and September, did not coincide with high chlorophyll-a (chl-a) concentrations or thermal fronts, and the drivers of the species' presence and movement from this second aggregation was unclear. We tested their habitat preferences by comparing environmental conditions at track locations to the conditions at locations along simulated tracks based on the empirical data. Observed I. indica preferred cooler water with higher chl-a concentrations and stayed closer to the coast than simulated tracks. The rapid and extensive dispersal of I. indica from Kenya suggests that there is likely a single stock in the Western Indian Ocean, with individuals swimming between areas of high commercial catches off northern Somalia and Oman, and artisanal and recreational fisheries catches throughout East Africa and Mozambique.

Genetic structure of the endangered Irrawaddy dolphin (Orcaella brevirostris) in the Gulf of Thailand

The Irrawaddy dolphin (Orcaella brevirostris) is an endangered, small cetacean species which is widely distributed in rivers, estuaries, and coastal waters throughout the tropical and subtropical Indo-Pacific. Despite the extensive distribution of this species, little is known of individual movements or genetic exchange among regions in Thailand. Here, we evaluate the genetic diversity and genetic structure of O. brevirostris in the eastern, northern and western Gulf of Thailand, and Andaman Sea. Although phylogenetic relationships and network analysis based on 15 haplotypes obtained from 32 individuals reveal no obvious divergence, significant genetic differentiation in mitochondrial DNA (overall FST = 0.226, P < 0.001; ΦST = 0.252, P < 0.001) is apparent among regions. Of 18 tested microsatellite loci, 10 are polymorphic and successfully characterized in 28 individuals, revealing significant genetic differentiation (overall FST = 0.077, P < 0.05) among the four sampling sites. Structure analysis reveals two inferred genetic clusters. Additionally, Mantel analysis demonstrates individual-by-individual genetic distances and geographic distances follow an isolation-by-distance model. We speculate that the significant genetic structure of O. brevirostris in Thailand is associated with a combination of geographical distribution patterns, environmental and anthropogenic factors, and local adaptations.

Early divergence and differential population histories of the Indo-Pacific humpback dolphin in the Pacific and Indian Oceans

The currently recognized Indo-Pacific humpback dolphin occurs in estuaries and surrounding shallow waters from the South China Sea to the Asian coast of the Indian Ocean. However, a recent study suggested that the humpback dolphin from the Bay of Bengal may represent a distinct phylogenetic species. In this study, we sequenced 915-bp mtDNA segments from five geographic populations in both Chinese and Thai waters; together with previously published sequences, these data revealed that the ancestral Indo-Pacific humpback dolphin might have split during the transition from the Oligocene to Miocene (23.45 Mya, 95% HPD: 16.65-26.55 Mya), and then dispersed along the Pacific and Indian Ocean coasts of Asia. Genetic differentiation was detected between most of the examined populations, except for only a few pairwise populations in the northern South China Sea. Genetic differentiation/distance between the humpback dolphins from the northern and southern South China Sea met the sub-species threshold value proposed for marine mammals, whereas that between the humpback dolphins in the Pacific and the Indian Ocean was above the species threshold. Bayesian inference of historic gene flow indicated low but constant northward gene flow along the Indian Ocean coast; however, there was a recent abrupt increase in gene flow in the Pacific region, likely due to the shortening coastline at the low stand of sea level. Our results revealed that the current taxonomic classification of Indo-Pacific humpback dolphins may not reflect their phylogeography.

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.

Cultural Transmission of Fine-Scale Fidelity to Feeding Sites May Shape Humpback Whale Genetic Diversity in Russian Pacific Waters

Mitochondrial DNA (mtDNA) differences between humpback whales on different feeding grounds can reflect the cultural transmission of migration destinations over generations, and therefore represent one of the very few cases of gene-culture coevolution identified in the animal kingdom. In Russian Pacific waters, photo-identification (photo-ID) studies have shown minimal interchange between whales feeding off the Commander Islands and those feeding in the Karaginsky Gulf, regions that are separated by only 500 km and have previously been lumped together as a single Russian feeding ground. Here, we assessed whether genetic differentiation exists between these 2 groups of humpback whales. We discovered a strong mtDNA differentiation between the 2 feeding sites (FST = 0.18, ΦST = 0.14, P < 0.001). In contrast, nuclear DNA (nuDNA) polymorphisms, determined at 8 microsatellite loci, did not reveal any differentiation. Comparing our mtDNA results with those from a previous ocean-basin study reinforced the differences between the 2 feeding sites. Humpback whales from the Commanders appeared most similar to those of the western Gulf of Alaska and the Aleutian feeding grounds, whereas Karaginsky differed from all other North Pacific feeding grounds. Comparison to breeding grounds suggests mixed origins for the 2 feeding sites; there are likely connections between Karaginsky and the Philippines and to a lesser extent to Okinawa, Japan, whereas the Commanders are linked to the Mexican breeding grounds. The mtDNA differentiation between the Commander Islands and Karaginsky Gulf suggests a case of gene-culture coevolution, correlated to fidelity to a specific feeding site within a particular feeding ground. From a conservation perspective, our findings emphasize the importance of considering these 2 feeding sites as separate management units.

Conservation genetics and genomics of threatened vertebrates in China

Conservation genetics and genomics are two independent disciplines that focus on using new techniques in genetics and genomics to solve problems in conservation biology. During the past two decades, conservation genetics and genomics have experienced rapid progress. Here, we summarize the research advances in the conservation genetics and genomics of threatened vertebrates (e.g., carnivorans, primates, ungulates, cetaceans, avians, amphibians and reptiles) in China. First, we introduce the concepts of conservation genetics and genomics and their development. Second, we review the recent advances in conservation genetics research, including noninvasive genetics and landscape genetics. Third, we summarize the progress in conservation genomics research, which mainly focuses on resolving genetic problems relevant to conservation such as genetic diversity, genetic structure, demographic history, and genomic evolution and adaptation. Finally, we discuss the future directions of conservation genetics and genomics.

Re-assessment of the Conservation Status of the Atlantic Humpback Dolphin, Sousa teuszii (), Using the IUCN Red List Criteria

The Atlantic humpback dolphin (Sousa teuszii) is an obligate shallow water dolphin that is endemic to the western coasts of Africa, ranging from Western Sahara to Angola. The species occurs exclusively in a limited number of near-shore habitats, a tendency that routinely exposes it to a suite of lethal and deleterious anthropogenic threats. These include habitat degradation, accidental capture in artisanal fishing nets, and hunting for use as food and bait. The species also competes with rapidly expanding human populations for coastal resources in some of the poorest countries on Earth. Data for most aspects of the species' ecology are sparse, but S. teuszii is considered by most qualified observers to be rare and greatly threatened. A lack of appropriate survey data precludes a quantitative assessment of population trends and status. Most populations for which any data are available are considered to be extremely small, numbering in the tens or low hundreds of individuals. The available published estimates suggest that the total population likely falls below 3000 individuals. Declines in abundance have been observed or are suspected for each population and will continue, given projected expansions of identified threats that affect most of the species' known range, and a corresponding lack of appropriate management actions. The apparent scale of threats, the presumed isolation of most populations, and a lack of directed conservation efforts in most areas suggest that the species qualifies for a listing of Critically Endangered (under criteria A3cd) on the IUCN Red List.

Ecology and Conservation Status of Indian Ocean Humpback Dolphins (Sousa plumbea) in Madagascar

The Indian Ocean humpback dolphin (Sousa plumbea) has been studied in several range states in the Southwest Indian Ocean, however little information exists on populations in Madagascar. Here, we review available literature and describe a study on S. plumbea conducted between 2004 and 2013 on the west coast of Madagascar, involving boat-based field surveys in the southwest and northwest regions, and interview surveys with local fishers from villages along most of the west coast. Field surveys in the southwest region of Anakao/St. Augustine Bay revealed low encounter rates and mean group size, and markedly declining trends in both from 1999 to 2013. Conversely, in the northwest region around Nosy Be and Nosy Iranja, encounter rates were higher, as were mean group sizes, suggesting an apparently more abundant and less impacted population. Interview surveys revealed by-catch of coastal dolphins along the entire west coast, including S. plumbea, as well as other species. Directed hunting, including drive hunts of groups of dolphins, was reported primarily in the southern regions, in the range of the Vezo Malagasy ethnicity; however, there was evidence of hunting starting in one area in the northwest, where hunting dolphins is normally considered taboo for the predominant Sakalava ethnicity. Thus, the conservation status of S. plumbea in Madagascar appears to be spatially heterogeneous, with some areas where the local population is apparently more impacted than others. Conservation measures are recommended to mitigate further decline in the southwest of Madagascar, while protecting habitat and ensuring resilience in the northwest.

Humpback Dolphin (Genus Sousa) Behavioural Responses to Human Activities

Humpback dolphins (genus Sousa) use shallow, near-shore waters throughout their range. This coastal distribution makes them vulnerable to recreational and commercial disturbances, especially near heavily populated and industrialized areas. Most research focusing on Sousa and human activities has emphasized direct impacts and threats, involving injury and death, with relatively little focus on indirect effects on dolphins, such as changes in behaviour that may lead to deleterious effects. Understanding behaviour is important in resolving human-wildlife conflict and is an important component of conservation. This chapter gives an overview of animal behavioural responses to human activity with examples from diverse taxa; reviews the scientific literature on behavioural responses of humpback dolphins to human activity throughout their range, including marine vessel traffic, dolphin tourism, cetacean-fishery interactions, noise pollution, and habitat alteration; and highlights information and data gaps for future humpback dolphin research to better inform behaviour-based management decisions that contribute to conservation efforts.

Assessment of the Conservation Status of the Indian Ocean Humpback Dolphin (Sousa plumbea) Using the IUCN Red List Criteria

Indian Ocean humpback dolphins (Sousa plumbea) are obligate shallow-water dolphins that occur exclusively in the near-shore waters of the Indian Ocean, from South Africa to the Bay of Bengal. They have a narrow habitat preference, restricted distribution and do not appear very abundant across any part of their range. There is no estimate of total species abundance; all populations that have been quantitatively evaluated have been small in size, usually fewer than 200 individuals. Fishing, dredging, land reclamation, construction blasting, port and harbour construction, pollution, boat traffic and other coastal development activities all occur, or are concentrated within, humpback dolphin habitat and threaten their survival. Although data are far from sufficient to make a rigorous quantitative assessment of population trends for this species, the scale of threats is large enough over a significant enough portion of the range to suspect or infer a decline of at least 50% over three generations, which qualifies it for listing on the IUCN Red List as Endangered. The issue primarily responsible is incidental mortality in fisheries, but the loss and degradation of habitat is likely a contributing factor. None of the threats have been adequately addressed in any part of the species' range, even though threat levels are increasing virtually everywhere.

Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift

The evolution of diversity in the marine ecosystem is poorly understood, given the relatively high potential for connectivity, especially for highly mobile species such as whales and dolphins. The killer whale (Orcinus orca) has a worldwide distribution, and individual social groups travel over a wide geographic range. Even so, regional populations have been shown to be genetically differentiated, including among different foraging specialists (ecotypes) in sympatry. Given the strong matrifocal social structure of this species together with strong resource specializations, understanding the process of differentiation will require an understanding of the relative importance of both genetic drift and local adaptation. Here we provide a high-resolution analysis based on nuclear single-nucleotide polymorphic markers and inference about differentiation at both neutral loci and those potentially under selection. We find that all population comparisons, within or among foraging ecotypes, show significant differentiation, including populations in parapatry and sympatry. Loci putatively under selection show a different pattern of structure compared to neutral loci and are associated with gene ontology terms reflecting physiologically relevant functions (e.g. related to digestion). The pattern of differentiation for one ecotype in the North Pacific suggests local adaptation and shows some fixed differences among sympatric ecotypes. We suggest that differential habitat use and resource specializations have promoted sufficient isolation to allow differential evolution at neutral and functional loci, but that the process is recent and dependent on both selection and drift.

Integrating multiple lines of evidence to better understand the evolutionary divergence of humpback dolphins along their entire distribution range: a new dolphin species in Australian waters?

The conservation of humpback dolphins, distributed in coastal waters of the Indo-West Pacific and eastern Atlantic Oceans, has been hindered by a lack of understanding about the number of species in the genus (Sousa) and their population structure. To address this issue, we present a combined analysis of genetic and morphologic data collected from beach-cast, remote-biopsied and museum specimens from throughout the known Sousa range. We extracted genetic sequence data from 235 samples from extant populations and explored the mitochondrial control region and four nuclear introns through phylogenetic, population-level and population aggregation frameworks. In addition, 180 cranial specimens from the same geographical regions allowed comparisons of 24 morphological characters through multivariate analyses. The genetic and morphological data showed significant and concordant patterns of geographical segregation, which are typical for the kind of demographic isolation displayed by species units, across the Sousa genus distribution range. Based on our combined genetic and morphological analyses, there is convincing evidence for at least four species within the genus (S. teuszii in the Atlantic off West Africa, S. plumbea in the central and western Indian Ocean, S. chinensis in the eastern Indian and West Pacific Oceans, and a new as-yet-unnamed species off northern Australia).

Seascape genetics of a globally distributed, highly mobile marine mammal: the short-beaked common dolphin (genus Delphinus)

Identifying which factors shape the distribution of intraspecific genetic diversity is central in evolutionary and conservation biology. In the marine realm, the absence of obvious barriers to dispersal can make this task more difficult. Nevertheless, recent studies have provided valuable insights into which factors may be shaping genetic structure in the world's oceans. These studies were, however, generally conducted on marine organisms with larval dispersal. Here, using a seascape genetics approach, we show that marine productivity and sea surface temperature are correlated with genetic structure in a highly mobile, widely distributed marine mammal species, the short-beaked common dolphin. Isolation by distance also appears to influence population divergence over larger geographical scales (i.e. across different ocean basins). We suggest that the relationship between environmental variables and population structure may be caused by prey behaviour, which is believed to determine common dolphins' movement patterns and preferred associations with certain oceanographic conditions. Our study highlights the role of oceanography in shaping genetic structure of a highly mobile and widely distributed top marine predator. Thus, seascape genetic studies can potentially track the biological effects of ongoing climate-change at oceanographic interfaces and also inform marine reserve design in relation to the distribution and genetic connectivity of charismatic and ecologically important megafauna.

Adaptive divergence in moor frog (Rana arvalis) populations along an acidification gradient: inferences from Q(st) -F(st) correlations

Microevolutionary responses to spatial variation in the environment seem ubiquitous, but the relative role of selection and neutral processes in driving phenotypic diversification remain often unknown. The moor frog (Rana arvalis) shows strong phenotypic divergence along an acidification gradient in Sweden. We here used correlations among population pairwise estimates of quantitative trait (P(ST) or Q(ST) from common garden estimates of embryonic acid tolerance and larval life-history traits) and neutral genetic divergence (F(ST) from neutral microsatellite markers), as well as environmental differences (pond pH, predator density, and latitude), to test whether this phenotypic divergence is more likely due to divergent selection or neutral processes. We found that trait divergence was more strongly correlated with environmental differences than the neutral marker divergence, suggesting that divergent natural selection has driven phenotypic divergence along the acidification gradient. Moreover, pairwise P(ST) s of embryonic acid tolerance and Q(ST) s of metamorphic size were strongly correlated with breeding pond pH, whereas pairwise Q(ST) s of larval period and growth rate were more strongly correlated with geographic distance/latitude and predator density, respectively. We suggest that incorporating measurements of environmental variation into Q(ST) -F(ST) studies can improve our inferential power about the agents of natural selection in natural populations.