The use of carcasses for the analysis of cetacean population genetic structure: a comparative study in two dolphin species

Genetic Analysis as a Tool to Improve the Monitoring of Stranded Cetaceans in Chile

Cetacean strandings are a valuable source of information for several studies from species richness to conservation and management. During the examination of strandings, taxonomic and sex identification might be hindered for several reasons. Molecular techniques are valuable tools to obtain that missing information. This study evaluates how gene fragment amplification protocols can support the records of strandings done in the field in Chile by identifying, corroborating, or correcting the identification of the species and sex of the recorded individuals. Through a collaboration between a scientific laboratory and government institution in Chile, 63 samples were analyzed. Thirty-nine samples were successfully identified to the species level. In total, 17 species of six families were detected, including six species of conservation interest. Of the 39 samples, 29 corresponded to corroborations of field identifications. Seven corresponded to unidentified samples and three to corrected misidentifications, adding up to 28% of the identified samples. Sex was successfully identified for 58 of the 63 individuals. Twenty were corroborations, 34 were previously unidentified, and four were corrections. Applying this method improves the stranding database of Chile and provides new data for future management and conservation tasks.

Aerial abundance estimates for two sympatric dolphin species at a regional scale using distance sampling and density surface modeling

Monitoring wildlife populations over scales relevant to management is critical to supporting conservation decision-making in the face of data deficiency, particularly for rare species occurring across large geographic ranges. The Pilbara region of Western Australia is home to two sympatric and morphologically similar species of coastal dolphins—the Indo-pacific bottlenose dolphin (Tursiops aduncus) and Australian humpback dolphin (Sousa sahulensis)—both of which are believed to be declining in numbers and facing increasing pressures from the combined impacts of environmental change and extensive industrial activities. The aim of this study was to develop spatially explicit models of bottlenose and humpback dolphin abundance in Pilbara waters that could inform decisions about coastal development at a regional scale. Aerial line transect surveys were flown from a fixed-wing aircraft in the austral winters of 2015, 2016, and 2017 across a total area of 33,420 km2. Spatio-temporal patterns in dolphin density were quantified using a density surface modeling (DSM) approach, accounting for imperfect detection as well as both perception and availability bias. We estimated the abundance of bottlenose dolphins at 3,713 (95% CI = 2,679–5,146; average density of 0.189 ± 0.046 SD individuals per km2) in 2015, 2,638 (95% CI = 1,670–4,168; 0.159 ± 0.135 individuals per km2) in 2016 and 1,635 (95% CI = 1,031–2,593; 0.101 ± 0.103 individuals per km2) in 2017. Too few humpback dolphins were detected in 2015 to model abundance, but their estimated abundance was 1,546 (95% CI = 942–2,537; 0.097 ± 0.03 individuals per km2) and 2,690 (95% CI = 1,792–4,038; 0.169 ± 0.064 individuals per km2) in 2016 and 2017, respectively. Dolphin densities were greatest in nearshore waters, with hotspots in Exmouth Gulf, the Dampier Archipelago, and Great Sandy Islands. Our results provide a benchmark on which future risk assessments can be based to better understand the overlap between pressures and important dolphin habitats in tropical northwestern Australia.

The first study of genetic diversity and population structure of Indo- Pacific bottlenose dolphin (Tursiops aduncus) and pantropical spotted dolphin (Stenella attenuata) in the Thai Andaman Sea based on ISSR

Background and Aim:

The Indo-Pacific bottlenose dolphin, Tursiops aduncus, and the pantropical spotted dolphin, Stenella attenuata, are protected marine mammals in Thailand; however, knowledge regarding the populations of both species in Thai seas is minimal. We aimed to reveal the genetic diversity and population structure of two species, T. aduncus, and S. attenuata, based on inter-simple sequence repeats (ISSRs).

Materials and Methods:

Samples of stranded T. aduncus (n = 30) and S. attenuata (n = 23) found along Thai Andaman Sea coasts from 1998 to 2018 were used in this study. A total of 17 and 16 ISSR primers that produced clear and polymorphic bands were selected for T. aduncus and S. attenuata, respectively.

Results:

The highest percentages of polymorphic bands for T. aduncus and S. attenuata were 93.750% and 92.857%, respectively. Phylogenetic dendrograms indicated that the population of each species was clustered into three groups. This outcome was consistent with the genetic population structure, as both suggested three genetic clusters (DK = 3). Genetic diversity analysis revealed that the average Shannon’s information index (I) was 1.926 ± 0.066 for T. aduncus and 1.714 ± 0.090 for S. attenuata, which indicate a high level of genetic variation. Further, low fixation index (F) values were observed for T. aduncus and S. attenuata at −0.231 ± 0.024 and −0.312 ± 0.042, respectively, suggesting that inbreeding is unlikely to have occurred for both species over the past decades.

Conclusion:

At least three genetic clusters of both species were found in the Thai Andaman Sea, and the diversity indices of each species indicated that these species are not at a critical level for extinction. However, monitoring their population status should be prioritized to observe any future changes in the level of diversity.

Abundance estimates and habitat preferences of bottlenose dolphins reveal the importance of two gulfs in South Australia

Informed conservation management of marine mammals requires an understanding of population size and habitat preferences. In Australia, such data are needed for the assessment and mitigation of anthropogenic impacts, including fisheries interactions, coastal zone developments, oil and gas exploration and mining activities. Here, we present large-scale estimates of abundance, density and habitat preferences of southern Australian bottlenose dolphins (Tursiops sp.) over an area of 42,438km² within two gulfs of South Australia. Using double-observer platform aerial surveys over four strata and mark-recapture distance sampling analyses, we estimated 3,493 (CV = 0.21; 95%CI = 2,327-5,244) dolphins in summer/autumn, and 3,213 (CV = 0.20; 95%CI = 2,151-4,801) in winter/spring of 2011. Bottlenose dolphin abundance and density was higher in gulf waters across both seasons (0.09-0.24 dolphins/km²) compared to adjacent shelf waters (0.004-0.04 dolphins/km²). The high densities of bottlenose dolphins in the two gulfs highlight the importance of these gulfs as a habitat for the species. Habitat modelling associated bottlenose dolphins with shallow waters, flat seafloor topography, and higher sea surface temperatures (SSTs) in summer/autumn and lower SSTs in winter/spring. Spatial predictions showed high dolphin densities in northern and coastal gulf sections. Distributional data should inform management strategies, marine park planning and environmental assessments of potential anthropogenic threats to this protected species.

Genetic diversity of bottlenose dolphin (Tursiops sp.) populations in the western North Pacific and the conservation implications

The evolutionary processes that shape patterns of diversity in highly mobile marine species are poorly understood, but important towards transferable inference on their effective conservation. In this study, bottlenose dolphins (Tursiops sp.) are studied to address this broader question. They exhibit remarkable geographical variation for morphology, life history, and genetic diversity, and this high level of variation has made the taxonomy of the genus controversial. A significant population structure has been reported for the most widely distributed species, the common bottlenose dolphin (T. truncatus), in almost all ocean basins, though no data have been available for the western North Pacific Ocean (WNP). The genetic diversity of bottlenose dolphins in the WNP was investigated based on 20 microsatellite and one mitochondrial DNA markers for samples collected from Taiwanese, Japanese, and Philippine waters (9°-39°N, 120°-140°E) during 1986-2012. The results indicated that there are at least four genetically differentiated populations of common bottlenose dolphins in the western and central North Pacific Ocean. The pattern of differentiation appears to correspond to habitat types, resembling results seen in other populations of the same species. Our analyses also showed that there was no evident gene flow between the two "sister species", the common bottlenose dolphins, and the Indo-Pacific bottlenose dolphins (T. aduncus) occurring sympatrically in our study region.

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.