Ancestry testing of "Old Tom," a killer whale central to mutualistic interactions with human whalers.

Cooperative hunting between humans and killer whales (Orcinus orca) targeting baleen whales was reported in Eden, New South Wales, Australia, for almost a century. By 1928, whaling operations had ceased, and local killer whale sightings became scarce. A killer whale from the group, known as "Old Tom," washed up dead in 1930 and his skeleton was preserved. How these killer whales from Eden relate to other populations globally and whether their genetic descendants persist today remains unknown. We extracted and sequenced DNA from Old Tom using ancient DNA techniques. Genomic sequences were then compared with a global dataset of mitochondrial and nuclear genomes. Old Tom shared a most recent common ancestor with killer whales from Australasia, the North Atlantic, and the North Pacific, having the highest genetic similarity with contemporary New Zealand killer whales. However, much of the variation found in Old Tom's genome was not shared with these widespread populations, suggesting ancestral rather than ongoing gene flow. Our genetic comparisons also failed to find any clear descendants of Tom, raising the possibility of local extinction of this group. We integrated Traditional Custodian knowledge to recapture the events in Eden and recognize that Indigenous Australians initiated the relationship with the killer whales before European colonization and the advent of commercial whaling locally. This study rectifies discrepancies in local records and provides new insight into the origins of the killer whales in Eden and the history of Australasian killer whales.

Seascape genomics of coastal bottlenose dolphins along strong gradients of temperature and salinity.

Heterogeneous seascapes and strong environmental gradients in coastal waters are expected to influence adaptive divergence, particularly in species with large population sizes where selection is expected to be highly efficient. However, these influences might also extend to species characterized by strong social structure, natal philopatry and small home ranges. We implemented a seascape genomic study to test this hypothesis in Indo-Pacific bottlenose dolphins (Tursiops aduncus) distributed along the environmentally heterogeneous coast of southern Australia. The data sets included oceanographic and environmental variables thought to be good predictors of local adaptation in dolphins and 8081 filtered single nucleotide polymorphisms (SNPs) genotyped for individuals sampled from seven different bioregions. From a neutral perspective, population structure and connectivity of the dolphins were generally influenced by habitat type and social structuring. Genotype-environment association analysis identified 241 candidate adaptive loci and revealed that sea surface temperature and salinity gradients influenced adaptive divergence in these animals at both large- (1000 km) and fine-scales (<100 km). Enrichment analysis and annotation of candidate genes revealed functions related to sodium-activated ion transport, kidney development, adipogenesis and thermogenesis. The findings of spatial adaptive divergence and inferences of putative physiological adaptations challenge previous suggestions that marine megafauna is most likely to be affected by environmental and climatic changes via indirect, trophic effects. Our work contributes to conservation management of coastal bottlenose dolphins subjected to anthropogenic disturbance and to efforts of clarifying how seascape heterogeneity influences adaptive diversity and evolution in small cetaceans.

Longitudinal monitoring of neutral and adaptive genomic diversity in a reintroduction.

Restoration programs in the form of ex-situ breeding combined with reintroductions are becoming critical to counteract demographic declines and species losses. Such programs are increasingly using genetic management to improve conservation outcomes. However, the lack of long-term monitoring of genetic indicators following reintroduction prevents assessments of the trajectory and persistence of reintroduced populations. We carried out an extensive monitoring program in the wild for a threatened small-bodied fish (southern pygmy perch, Nannoperca australis) to assess the long-term genomic effects of its captive breeding and reintroduction. The species was rescued prior to its extirpation from the terminal lakes of Australia's Murray-Darling Basin, and then used for genetically informed captive breeding and reintroductions. Subsequent annual or biannual monitoring of abundance, fitness, and occupancy over a period of 11 years, combined with postreintroduction genetic sampling, revealed survival and recruitment of reintroduced fish. Genomic analyses based on data from the original wild rescued, captive born, and reintroduced cohorts revealed low inbreeding and strong maintenance of neutral and candidate adaptive genomic diversity across multiple generations. An increasing trend in the effective population size of the reintroduced population was consistent with field monitoring data in demonstrating successful re-establishment of the species. This provides a rare empirical example that the adaptive potential of a locally extinct population can be maintained during genetically informed ex-situ conservation breeding and reintroduction into the wild. Strategies to improve biodiversity restoration via ex-situ conservation should include genetic-based captive breeding and longitudinal monitoring of standing genomic variation in reintroduced populations.

Monitoreo Longitudinal de la Diversidad Genómica Neutral y Adaptativa en una Reintroducción Marshall et al. 21-643 Resumen Los programas de restauración a manera de reproducción ex situ combinada con reintroducciones se están volviendo críticos para contrarrestar las declinaciones demográficas y la pérdida de especies. Dichos programas usan cada vez más la gestión genética para mejorar los resultados de conservación. Sin embargo, la falta de monitoreo a largo plazo de los indicadores genéticos posteriores a la reintroducción evita que se realicen evaluaciones de la trayectoria y la persistencia de las poblaciones reintroducidas. Se rescató un pez de talla pequeña (percha pigmea del sur [Nannoperca australis]) previo a su extirpación de los lagos terminales de la Cuenca Murray-Darling en Australia para después reproducirlo en cautiverio con información genética y reintroducirlo. Realizamos monitoreos anuales o bianuales de la abundancia, aptitud y ocupación en vida silvestre durante once años, además de un muestreo genético posterior a la reintroducción. Analizamos los datos genómicos de los grupos originales rescatados, los nacidos en cautiverio y los reintroducidos. Nuestro objetivo era evaluar los efectos genómicos a largo plazo de la reproducción en cautiverio y la reintroducción de esta especie. Esto reveló baja endogamia y el sólido mantenimiento de la diversidad genómica neutral y adaptativa durante varias generaciones. Encontramos una coherencia entre la tendencia creciente en el tamaño de la población efectiva de la población reintroducida y los datos de campo que demostraron el restablecimiento exitoso de la especie. Nuestro estudio proporciona un raro ejemplo empírico de cómo el potencial adaptativo de una población localmente extinta puede mantenerse durante la reproducción de conservación ex situ genéticamente informada y su reintroducción. Las estrategias para mejorar la restauración de la biodiversidad por medio de la conservación ex situ deberían incluir la reproducción en cautiverio basada en la genética y el monitoreo longitudinal de la variación genómica actual de las poblaciones reintroducidas.

Whole genomes reveal multiple candidate genes and pathways involved in the immune response of dolphins to a highly infectious virus.

Wildlife species are challenged by various infectious diseases that act as important demographic drivers of populations and have become a great conservation concern particularly under growing environmental changes. The new era of whole genome sequencing provides new opportunities and avenues to explore the role of genetic variants in the plasticity of immune responses, particularly in non-model systems. Cetacean morbillivirus (CeMV) has emerged as a major viral threat to cetacean populations worldwide, contributing to the death of thousands of individuals of multiple dolphin and whale species. To understand the genomic basis of immune responses to CeMV, we generated and analysed whole genomes of 53 Indo-Pacific bottlenose dolphins (Tursiops aduncus) exposed to Australia's largest known CeMV-related mortality event that killed at least 50 dolphins from three different species. The genomic data set consisted of 10,168,981 SNPs anchored onto 23 chromosome-length scaffolds and 77 short scaffolds. Whole genome analysis indicated that levels of inbreeding in the dolphin population did not influence the outcome of an individual. Allele frequency estimates between survivors and nonsurvivors of the outbreak revealed 15,769 candidate SNPs, of which 689 were annotated to 295 protein coding genes. These included 50 genes with functions related to innate and adaptive immune responses, and cytokine signalling pathways and genes thought to be involved in immune responses to other morbilliviruses. Our study characterised genomic regions and pathways that may contribute to CeMV immune responses in dolphins. This represents a stride towards clarifying the complex interactions of the cetacean immune system and emphasises the value of whole genome data sets in understanding genetic elements that are essential for species conservation, including disease susceptibility and adaptation.

Phylogenomics of the genus Tursiops and closely related Delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers.

Phylogeographic inference has provided extensive insight into the relative roles of geographical isolation and ecological processes during evolutionary radiations. However, the importance of cross-lineage admixture in facilitating adaptive radiations is increasingly being recognised, and suggested as a main cause of phylogenetic uncertainty. In this study, we used a double digest RADseq protocol to provide a high resolution (~4 Million bp) nuclear phylogeny of the Delphininae. Phylogenetic resolution of this group has been especially intractable, likely because it has experienced a recent species radiation. We carried out cross-lineage reticulation analyses, and tested for several sources of potential bias in determining phylogenies from genome sampling data. We assessed the divergence time and historical demography of T. truncatus and T. aduncus by sequencing the T. aduncus genome and comparing it with the T. truncatus reference genome. Our results suggest monophyly for the genus Tursiops, with the recently proposed T. australis species falling within the T. aduncus lineage. We also show the presence of extensive cross-lineage gene flow between pelagic and European coastal ecotypes of T. truncatus, as well as in the early stages of diversification between spotted (Stenella frontalis; Stenella attenuata), spinner (Stenella longirostris), striped (Stenella coeruleoalba), common (Delphinus delphis), and Fraser's (Lagenodelphis hosei) dolphins. Our study suggests that cross-lineage gene flow in this group has been more extensive and complex than previously thought. In the context of biogeography and local habitat dependence, these results improve our understanding of the evolutionary processes determining the history of this lineage.

Low genetic diversity in pygmy blue whales is due to climate-induced diversification rather than anthropogenic impacts.

Unusually low genetic diversity can be a warning of an urgent need to mitigate causative anthropogenic activities. However, current low levels of genetic diversity in a population could also be due to natural historical events, including recent evolutionary divergence, or long-term persistence at a small population size. Here, we determine whether the relatively low genetic diversity of pygmy blue whales (Balaenoptera musculus brevicauda) in Australia is due to natural causes or overexploitation. We apply recently developed analytical approaches in the largest genetic dataset ever compiled to study blue whales (297 samples collected after whaling and representing lineages from Australia, Antarctica and Chile). We find that low levels of genetic diversity in Australia are due to a natural founder event from Antarctic blue whales (Balaenoptera musculus intermedia) that occurred around the Last Glacial Maximum, followed by evolutionary divergence. Historical climate change has therefore driven the evolution of blue whales into genetically, phenotypically and behaviourally distinct lineages that will likely be influenced by future climate change.

Recent diversification of a marine genus (Tursiops spp.) tracks habitat preference and environmental change.

Understanding the evolution of diversity and the resulting systematics in marine systems is confounded by the lack of clear boundaries in oceanic habitats, especially for highly mobile species like marine mammals. Dolphin populations and sibling species often show differentiation between coastal and offshore habitats, similar to the pelagic/littoral or benthic differentiation seen for some species of fish. Here we test the hypothesis that lineages within the polytypic genus Tursiops track past changes in the environment reflecting ecological drivers of evolution facilitated by habitat release. We used a known recent time point for calibration (the opening of the Bosphorus) and whole mitochondrial genome (mitogenome) sequences for high phylogenetic resolution. The pattern of lineage formation suggested an origin in Australasia and several early divisions involving forms currently inhabiting coastal habitats. Radiation in pelagic environments was relatively recent, and was likely followed by a return to coastal habitat in some regions. The timing of some nodes defining different ecotypes within the genus clustered near the two most recent interglacial transitions. A signal for an increase in diversification was also seen for dates after the last glacial maximum. Together these data suggest the tracking of habitat preference during geographic expansions, followed by transition points reflecting habitat shifts, which were likely associated with periods of environmental change.

Predicting suitable habitats for foraging and migration in Eastern Indian Ocean pygmy blue whales from satellite tracking data.

BACKGROUND: Accurate predictions of animal occurrence in time and space are crucial for informing and implementing science-based management strategies for threatened species. METHODS: We compiled known, available satellite tracking data for pygmy blue whales in the Eastern Indian Ocean (n = 38), applied movement models to define low (foraging and reproduction) and high (migratory) move persistence underlying location estimates and matched these with environmental data. We then used machine learning models to identify the relationship between whale occurrence and environment, and predict foraging and migration habitat suitability in Australia and Southeast Asia. RESULTS: Our model predictions were validated by producing spatially varying accuracy metrics. We identified the shelf off the Bonney Coast, Great Australian Bight, and southern Western Australia as well as the slope off the Western Australian coast as suitable habitat for migration, with predicted foraging/reproduction suitable habitat in Southeast Asia region occurring on slope and in deep ocean waters. Suitable foraging habitat occurred primarily on slope and shelf break throughout most of Australia, with use of the continental shelf also occurring, predominanly in South West and Southern Australia. Depth of the water column (bathymetry) was consistently a top predictor of suitable habitat for most regions, however, dynamic environmental variables (sea surface temperature, surface height anomaly) influenced the probability of whale occurrence. CONCLUSIONS: Our results indicate suitable habitat is related to dynamic, localised oceanic processes that may occur at fine temporal scales or seasonally. An increase in the sample size of tagged whales is required to move towards developing more dynamic distribution models at seasonal and monthly temporal scales. Our validation metrics also indicated areas where further data collection is needed to improve model accuracy. This is of particular importance for pygmy blue whale management, since threats (e.g., shipping, underwater noise and artificial structures) from the offshore energy and shipping industries will persist or may increase with the onset of an offshore renewable energy sector in Australia.

Genomic Divergence and the Evolution of Ecotypes in Bottlenose Dolphins (Genus Tursiops).

Climatic changes have caused major environmental restructuring throughout the world's oceans. Marine organisms have responded to novel conditions through various biological systems, including genomic adaptation. Growing accessibility of next-generation DNA sequencing methods to study nonmodel species has recently allowed genomic changes underlying environmental adaptations to be investigated. This study used double-digest restriction-site associated DNA (ddRAD) sequence data to investigate the genomic basis of ecotype formation across currently recognized species and subspecies of bottlenose dolphins (genus Tursiops) in the Southern Hemisphere. Subspecies-level genomic divergence was confirmed between the offshore common bottlenose dolphin (T. truncatus truncatus) and the inshore Lahille's bottlenose dolphin (T. t. gephyreus) from the southwestern Atlantic Ocean (SWAO). Similarly, subspecies-level divergence is suggested between inshore (eastern Australia) Indo-Pacific bottlenose dolphin (T. aduncus) and the proposed Burrunan dolphin (T. australis) from southern Australia. Inshore bottlenose dolphin lineages generally had lower genomic diversity than offshore lineages, a pattern particularly evident for T. t. gephyreus, which showed exceptionally low diversity. Genomic regions associated with cardiovascular, musculoskeletal, and energy production systems appear to have undergone repeated adaptive evolution in inshore lineages across the Southern Hemisphere. We hypothesize that comparable selective pressures in the inshore environment drove similar adaptive responses in each lineage, supporting parallel evolution of inshore bottlenose dolphins. With climate change altering marine ecosystems worldwide, it is crucial to gain an understanding of the adaptive capacity of local species and populations. Our study provides insights into key adaptive pathways that may be important for the long-term survival of cetaceans and other organisms in a changing marine environment.

Sociogenetic structure, kin associations and bonding in delphinids.

Social systems are the outcomes of natural and sexual selection on individuals' efforts to maximize reproductive success. Ecological conditions, life history, demography traits and social aspects have been recognized as important factors shaping social systems. Delphinids show a wide range of social structures and large variation in life history traits and inhabit several aquatic environments. They are therefore an excellent group in which to investigate the interplay of ecological and intrinsic factors on the evolution of mammalian social systems in these environments. Here I synthetize results from genetic studies on dispersal patterns, genetic relatedness, kin associations and mating patterns and combine with ecological, life history and phylogenetic data to predict the formation of kin associations and bonding in these animals. I show that environment type impacts upon dispersal tendencies, with small delphinids generally exhibiting female-biased philopatry in inshore waters and bisexual dispersal in coastal and pelagic waters. When female philopatry occurs, they develop moderate social bonds with related females. Male bonding occurs in species with small male-biased sexual size dimorphism and male-biased operational sex ratio, and it is independent of dispersal tendencies. By contrast, large delphinids, which live in coastal and pelagic waters, show bisexual philopatry and live in matrilineal societies. I propose that sexual conflict favoured the formation of these stable societies and in turn facilitated the development of kin-biased behaviours. Studies on populations of the same species inhabiting disparate environments, and of less related species living in similar habitats, would contribute towards a comprehensive framework for the evolution of delphinid social systems.

Hybridization of Southern Hemisphere blue whale subspecies and a sympatric area off Antarctica: impacts of whaling or climate change?

Understanding the degree of genetic exchange between subspecies and populations is vital for the appropriate management of endangered species. Blue whales (Balaenoptera musculus) have two recognized Southern Hemisphere subspecies that show differences in geographic distribution, morphology, vocalizations and genetics. During the austral summer feeding season, the Antarctic blue whale (B. m. intermedia) is found in polar waters and the pygmy blue whale (B. m. brevicauda) in temperate waters. Here, we genetically analyzed samples collected during the feeding season to report on several cases of hybridization between the two recognized blue whale Southern Hemisphere subspecies in a previously unconfirmed sympatric area off Antarctica. This means the pygmy blue whales using waters off Antarctica may migrate and then breed during the austral winter with the Antarctic subspecies. Alternatively, the subspecies may interbreed off Antarctica outside the expected austral winter breeding season. The genetically estimated recent migration rates from the pygmy to Antarctic subspecies were greater than estimates of evolutionary migration rates and previous estimates based on morphology of whaling catches. This discrepancy may be due to differences in the methods or an increase in the proportion of pygmy blue whales off Antarctica within the last four decades. Potential causes for the latter are whaling, anthropogenic climate change or a combination of these and may have led to hybridization between the subspecies. Our findings challenge the current knowledge about the breeding behaviour of the world's largest animal and provide key information that can be incorporated into management and conservation practices for this endangered species.

Influences of past climatic changes on historical population structure and demography of a cosmopolitan marine predator, the common dolphin (genus Delphinus).

Climatic oscillations during the Pleistocene have greatly influenced the distribution and connectivity of many organisms, leading to extinctions but also generating biodiversity. While the effects of such changes have been extensively studied in the terrestrial environment, studies focusing on the marine realm are still scarce. Here we used sequence data from one mitochondrial and five nuclear loci to assess the potential influence of Pleistocene climatic changes on the phylogeography and demographic history of a cosmopolitan marine predator, the common dolphin (genus Delphinus). Population samples representing the three major morphotypes of Delphinus were obtained from 10 oceanic regions. Our results suggest that short-beaked common dolphins are likely to have originated in the eastern Indo-Pacific Ocean during the Pleistocene and expanded into the Atlantic Ocean through the Indian Ocean. On the other hand, long-beaked common dolphins appear to have evolved more recently and independently in several oceans. Our results also suggest that short-beaked common dolphins had recurrent demographic expansions concomitant with changes in sea surface temperature during the Pleistocene and its associated increases in resource availability, which differed between the North Atlantic and Pacific Ocean basins. By proposing how past environmental changes had an effect on the demography and speciation of a widely distributed marine mammal, we highlight the impacts that climate change may have on the distribution and abundance of marine predators and its ecological consequences for marine ecosystems.

Species tree of a recent radiation: the subfamily Delphininae (Cetacea, Mammalia).

Lineages undergoing rapid radiations provide exceptional opportunities for studying speciation and adaptation, but also represent a challenge for molecular systematics because retention of ancestral polymorphisms and the occurrence of hybridization can obscure relationships among lineages. Dolphins in the subfamily Delphininae are one such case. Non-monophyly, rapid speciation events, and discordance between morphological and molecular characters have made the inference of phylogenetic relationships within this subfamily very difficult. Here we approach this problem by applying multiple methods intended to estimate species trees using a multi-gene dataset for the Delphininae (Sousa, Sotalia, Stenella, Tursiops, Delphinus and Lagenodelphis). Incongruent gene trees obtained indicate that incomplete lineage sorting and possibly hybridization are confounding the inference of species history in this group. Nonetheless, using coalescent-based methods, we have been able to extract an underlying species-tree signal from divergent histories of independent genes. This is the first time a molecular study provides support for such relationships. This study further illustrates how methods of species-tree inference can be very sensitive both to the characteristics of the dataset and the evolutionary processes affecting the evolution of the group under study.

Male reproductive success increases with alliance size in Indo-Pacific bottlenose dolphins (Tursiops aduncus).

1. Determining the extent of variation in male mating strategies and reproductive success is necessary to understand the fitness benefits of social and cooperative behaviour. 2. This study assesses the reproductive success of male Indo-Pacific bottlenose dolphins in a small embayment population where different behavioural strategies of males have previously been identified. Parentage for 44 sampled calves was examined using 23 microsatellite loci and one mitochondrial DNA marker. Our candidate parent pool of 70 males and 64 females contained individuals sampled from both the embayment and adjacent coastal populations. 3. A moderate level of polygyny was detected in our sample. We assigned paternity of 23 calves to 12 males at the strict 95% confidence level and an additional nine calves to two males at the 80% confidence level. The majority (92%) of successful males were identified as residents to the embayment, and 46% of offspring were located within the same social group or community as their father. 4. Our results suggest that the size of alliances was the best predictor of reproductive success for males in this population, while the strength of association among allied males, alliance stability and male ranging patterns had little influence. In line with predictions for male alliances formed between unrelated individuals, we found that reproductive skew within alliances was not large. 5. Together, our genetic and behavioural analyses demonstrate that alliance formation between male dolphins is a successful strategy to enhance reproductive output.

How does Australia's largest dolphin-watching industry affect the behaviour of a small and resident population of Indo-Pacific bottlenose dolphins?

The small, genetically distinct population of Indo-Pacific bottlenose dolphins (Tursiops aduncus) in Port Stephens, New South Wales (NSW), is the target of the largest dolphin-watching industry in Australia and is located within the Port Stephens - Great Lakes Marine Park that was created in 2005. The effects of this industry have been identified as of significant management importance by the Marine Parks Authority NSW. Accordingly, the impact of commercial dolphin-watching boats was investigated from boat-based surveys from August 2008 to August 2009. Presence of dolphin-watching boats altered both the dolphins' behavioural states and activity budgets. Dolphins spent 66.5% less time feeding and 44.2% less time socialising, spent four times more milling, and were never observed to rest in the presence of dolphin-watching boats. Moreover, dolphin groups were more cohesive during dolphin-watching boat encounters and dolphins tended to avoid tour boats. These effects were exacerbated as the number of boats increased and the distance from boats decreased. The rate of approach was high with boats approaching each dolphin group three times per day in winter and six times in summer. Moreover, groups of dolphins with newborns were approached closer than state regulated minimum approach distances in nine out of ten encounters. Globally, dolphin-watching industries frequent small resident groups of coastal dolphins and effects are likely to be similar. We suggest that existing controls are inadequate and that these together with additional regulations be enforced by a regular presence of authorities. We suggest no more than one dolphin-watching boat within 50 m of a group of dolphins, or 100 m if calves are present. Operating times of dolphin-watching boats should be restricted in numbers after 1 pm, i.e., during preferred foraging times for dolphins. Additionally, exclusion zones should be considered to reduce pressure on dolphins undertaking critical activities such as feeding and resting. We recommend monitoring the effectiveness of new regulations that are incorporated in the reviewed marine park management plan in 2012 for a period of three years.

Seascape genomics of common dolphins (Delphinus delphis) reveals adaptive diversity linked to regional and local oceanography.

BACKGROUND: High levels of standing genomic variation in wide-ranging marine species may enhance prospects for their long-term persistence. Patterns of connectivity and adaptation in such species are often thought to be influenced by spatial factors, environmental heterogeneity, and oceanographic and geomorphological features. Population-level studies that analytically integrate genome-wide data with environmental information (i.e., seascape genomics) have the potential to inform the spatial distribution of adaptive diversity in wide-ranging marine species, such as many marine mammals. We assessed genotype-environment associations (GEAs) in 214 common dolphins (Delphinus delphis) along > 3000 km of the southern coast of Australia. RESULTS: We identified 747 candidate adaptive SNPs out of a filtered panel of 17,327 SNPs, and five putatively locally-adapted populations with high levels of standing genomic variation were disclosed along environmentally heterogeneous coasts. Current velocity, sea surface temperature, salinity, and primary productivity were the key environmental variables associated with genomic variation. These environmental variables are in turn related to three main oceanographic phenomena that are likely affecting the dispersal of common dolphins: (1) regional oceanographic circulation, (2) localised and seasonal upwellings, and (3) seasonal on-shelf circulation in protected coastal habitats. Signals of selection at exonic gene regions suggest that adaptive divergence is related to important metabolic traits. CONCLUSION: To the best of our knowledge, this represents the first seascape genomics study for common dolphins (genus Delphinus). Information from the associations between populations and their environment can assist population management in forecasting the adaptive capacity of common dolphins to climate change and other anthropogenic impacts.

Evolution of 2 reproductive proteins, ZP3 and PKDREJ, in cetaceans.

The rapid evolution of proteins involved in reproduction has been documented in several animal taxa. This is thought to be the result of forces involved in sexual selection and is expected to be particularly strong in promiscuous mating systems. In this study, a range of cetacean species were used to analyze the patterns of evolution in 2 reproductive proteins involved in fertilization: the zona pellucida 3 (ZP3), present in the egg coat, and PKDREJ, localized in the sperm head. We targeted exons 6 and 7 of ZP3 and a part of the REJ domain in PKDREJ for a total of 958 bp in 18 species. We found very low levels of amino acid sequence divergence in both proteins, a very weak signal of positive selection in ZP3 and no signal in PKDREJ. These results were consistent with previous reports of a slow rate of molecular evolution in cetaceans but unexpected due to the existence of promiscuous mating systems in these species. The results raise questions about the evolution of reproductive isolation and species recognition in whales and dolphins.

Kinship and reproductive condition correlate with affiliation patterns in female southern Australian bottlenose dolphins.

Social relationships in female mammals are usually determined by an interplay among genetic, endogenous, social and ecological factors that ultimately affect their lifetime reproductive success. However, few studies have attempted to control for, and integrate these factors, hampering our understanding of drivers underlying female sociality. Here, we used generalized affiliation indices, combined with social networks, reproductive condition, and genetic data to investigate drivers of associations in female southern Australian bottlenose dolphins. Our analysis is based on photo-identification and genetic data collected through systematic boat surveys over a two-year study period. Female dolphins formed preferred associations and social clusters which ranged from overlapping to discrete home ranges. Furthermore, matrilineal kinship and biparental relatedness, as well as reproductive condition, correlated with the strength of female affiliations. In addition, relatedness for both genetic markers was also higher within than between social clusters. The predictability of resources in their embayment environment, and the availability of same-sex relatives in the population, may have favoured the formation of social bonds between genetically related females and those in similar reproductive condition. This study highlights the importance of genetic, endogenous, social and ecological factors in determining female sociality in coastal dolphins.

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.