Guido J. Parra

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).

Population differentiation and hybridisation of Australian snubfin (Orcaella heinsohni) and Indo-Pacific humpback (Sousa chinensis) dolphins in North-Western Australia

Little is known about the Australian snubfin (Orcaella heinsohni) and Indo-Pacific humpback (Sousa chinensis) dolphins (‘snubfin’ and ‘humpback dolphins’, hereafter) of north-western Australia. While both species are listed as ‘near threatened’ by the IUCN, data deficiencies are impeding rigorous assessment of their conservation status across Australia. Understanding the genetic structure of populations, including levels of gene flow among populations, is important for the assessment of conservation status and the effective management of a species. Using nuclear and mitochondrial DNA markers, we assessed population genetic diversity and differentiation between snubfin dolphins from Cygnet (n = 32) and Roebuck Bays (n = 25), and humpback dolphins from the Dampier Archipelago (n = 19) and the North West Cape (n = 18). All sampling locations were separated by geographic distances >200 km. For each species, we found significant genetic differentiation between sampling locations based on 12 (for snubfin dolphins) and 13 (for humpback dolphins) microsatellite loci (F ST = 0.05–0.09; P<0.001) and a 422 bp sequence of the mitochondrial control region (F ST = 0.50–0.70; P<0.001). The estimated proportion of migrants in a population ranged from 0.01 (95% CI 0.00–0.06) to 0.13 (0.03–0.24). These are the first estimates of genetic diversity and differentiation for snubfin and humpback dolphins in Western Australia, providing valuable information towards the assessment of their conservation status in this rapidly developing region. Our results suggest that north-western Australian snubfin and humpback dolphins may exist as metapopulations of small, largely isolated population fragments, and should be managed accordingly. Management plans should seek to maintain effective population size and gene flow. Additionally, while interactions of a socio-sexual nature between these two species have been observed previously, here we provide strong evidence for the first documented case of hybridisation between a female snubfin dolphin and a male humpback dolphin.

Fine‐scale genetic population structure in a mobile marine mammal: inshore bottlenose dolphins in Moreton Bay, Australia

Highly mobile marine species in areas with no obvious geographic barriers are expected to show low levels of genetic differentiation. However, small‐scale variation in habitat may lead to resource polymorphisms and drive local differentiation by adaptive divergence. Using nuclear microsatellite genotyping at 20 loci, and mitochondrial control region sequencing, we investigated fine‐scale population structuring of inshore bottlenose dolphins (Tursiops aduncus) inhabiting a range of habitats in and around Moreton Bay, Australia. Bayesian structure analysis identified two genetic clusters within Moreton Bay, with evidence of admixture between them (FST = 0.05, P = 0.001). There was only weak isolation by distance but one cluster of dolphins was more likely to be found in shallow southern areas and the other in the deeper waters of the central northern bay. In further analysis removing admixed individuals, southern dolphins appeared genetically restricted with lower levels of variation (AR = 3.252, π = 0.003) and high mean relatedness (r = 0.239) between individuals. In contrast, northern dolphins were more diverse (AR = 4.850, π = 0.009) and were mixing with a group of dolphins outside the bay (microsatellite‐based STRUCTURE analysis), which appears to have historically been distinct from the bay dolphins (mtDNA ΦST = 0.272, P < 0.001). This study demonstrates the ability of genetic techniques to expose fine‐scale patterns of population structure and explore their origins and mechanisms. A complex variety of inter‐related factors including local habitat variation, differential resource use, social behaviour and learning, and anthropogenic disturbances are likely to have played a role in driving fine‐scale population structure among bottlenose dolphins in Moreton Bay.

At the Heart of the Industrial Boom: Australian Snubfin Dolphins in the Capricorn Coast, Queensland, Need Urgent Conservation Action

The recent industrial boom along the Australian coastline has increased concerns about the long term conservation of snubfin dolphins along the Queensland coast. National assessment of the conservation status and management of the Australian snubfin dolphin is currently hindered by the lack of adequate biological and ecological information throughout most of its range. In response to the issue of determining the conservation status of species with broad ranges, the IUCN has provided a framework for assessing the threatened status of regional populations. In this study we assessed the conservation status of a small geographically isolated population of snubfin dolphins living in the Fitzroy River region, Queensland, Australia, against the IUCN criteria for regional populations. A review of all available sightings data and stranding information indicates that this is the southernmost resident population of snubfin dolphins in Australian waters. The Fitzroy River snubfin dolphin population is composed of less than 100 individuals, with a representative range and core area of less than 400 and 300 km2 respectively. The area most often used by snubfin dolphins within the representative range and core area was estimated to be about 292 and 191 km2, respectively. A decrease in representative range, core area and preferred habitat between 14 and 25% is projected to occur if a planned industrial port development were to occur. These results are robust to uncertainty and considering the low level of formal protection and future threats, a classification of this subpopulation under the IUCN Red List as “Endangered” is appropriate.

Humpback Dolphins: S. chinensis and S. teuszii

This chapter discusses the characteristics, taxonomy, distribution, abundance, and ecology of humpback dolphins or S. chinensis and S. teuszii. Humpback dolphins are medium-sized delphinids found in coastal waters of the eastern Atlantic, Indian, and West Pacific oceans. Genetic and morphological information indicate that they are delphinids (family Delphinidae). Humpback dolphins are characterized by a robust and medium-sized body. The melon is moderate in size, slightly depressed, and in profile slopes gradually to an indistinct junction with the long, narrow rostrum. The broad flippers are rounded at the tip and the flukes are broad and full, with a deep median caudal notch. Dorsal and ventral ridges on the caudal peduncle are well developed in African and Indian Ocean populations. Overall, humpback dolphins reach a maximum total length of 2.6-2.8 m in different parts of their distribution. A few animals exceeding 3.0 m in length have been recorded in the Arabian and Indian regions. Maximum weights of 250-280 kg have been recorded for humpback dolphins in South Africa and Hong Kong. Humpback dolphins swim slowly at about 5 km/h, surfacing briefly at intervals of up to a minute. Socializing in humpback dolphins is characterized by individuals in close proximity showing high levels of physical interaction including body contact and frequent aerial behavior such as leaps and somersaults. Fins and flukes often break the surface of the water.

Monitoring Dolphins in an Urban Marine System: Total and Effective Population Size Estimates of Indo-Pacific Bottlenose Dolphins in Moreton Bay, Australia

Moreton Bay, Queensland, Australia is an area of high biodiversity and conservation value and home to two sympatric sub-populations of Indo-Pacific bottlenose dolphins (Tursiops aduncus). These dolphins live in close proximity to major urban developments. Successful management requires information regarding their abundance. Here, we estimate total and effective population sizes of bottlenose dolphins in Moreton Bay using photo-identification and genetic data collected during boat-based surveys in 2008–2010. Abundance (N) was estimated using open population mark-recapture models based on sighting histories of distinctive individuals. Effective population size (Ne) was estimated using the linkage disequilibrium method based on nuclear genetic data at 20 microsatellite markers in skin samples, and corrected for bias caused by overlapping generations (Nec). A total of 174 sightings of dolphin groups were recorded and 365 different individuals identified. Over the whole of Moreton Bay, a population size N of 554±22.2 (SE) (95% CI: 510–598) was estimated. The southern bay sub-population was small at an estimated N = 193±6.4 (SE) (95% CI: 181–207), while the North sub-population was more numerous, with 446±56 (SE) (95% CI: 336–556) individuals. The small estimated effective population size of the southern sub-population (Nec = 56, 95% CI: 33–128) raises conservation concerns. A power analysis suggested that to reliably detect small (5%) declines in size of this population would require substantial survey effort (>4 years of annual mark-recapture surveys) at the precision levels achieved here. To ensure that ecological as well as genetic diversity within this population of bottlenose dolphins is preserved, we consider that North and South sub-populations should be treated as separate management units. Systematic surveys over smaller areas holding locally-adapted sub-populations are suggested as an alternative method for increasing ability to detect abundance trends.

Conservation Status of the Australian Humpback Dolphin (Sousa sahulensis) Using the IUCN Red List Criteria.

Australian humpback dolphins (Sousa sahulensis) were recently described as a new species endemic to northern Australia and potentially southern New Guinea. We assessed the species conservation status against IUCN Red List Criteria using available information on their biology, ecology and threatening processes. Knowledge of population sizes and trends across the species range is lacking. Recent genetic studies indicate Australian humpback dolphins live in small and relatively isolated populations with limited gene flow among them. The available abundance estimates range from 14 to 207 individuals and no population studied to date is estimated to contain more than 104 mature individuals. The Potential Biological Removal method indicates populations are vulnerable to even low rates of anthropogenic mortality. Habitat degradation and loss is ongoing and expected to increase across the species range in Australia, and a continuing decline in the number of mature individuals is anticipated. Considering the available evidence and following a precautionary approach, we considered this species as Vulnerable under IUCN criterion C2a(i) because the total number of mature individuals is plausibly fewer than 10,000, an inferred continuing decline due to cumulative impacts, and each of the populations studied to date is estimated to contain fewer than 1000 mature individuals. Ongoing research efforts and recently developed research strategies and priorities will provide valuable information towards the future conservation and management of Australian humpback dolphins.

Estimates of abundance and apparent survival of coastal dolphins in Port Essington harbour, Northern Territory, Australia

Abstract Context. Three dolphin species occur in coastal waters of monsoonal northern Australia: the Australian snubfin (Orcaella heinsohni), humpback (Sousa sp.) and the bottlenose (Tursiops sp.). Their overall population size and trends are poorly known, and their conservation status has been difficult to resolve, but can be expected to deteriorate with likely increased development pressures. Aims. We sought to provide an estimate of abundance, and apparent survival, of the three dolphin species at the largely undeveloped harbour of Port Essington (325 km2), Northern Territory, with repeated sampling over a 2.9-year period. Given increasing obligations to undertake population assessments for impact studies at proposed development sites, we assess the strengths and limitations of a systematic sampling program. Methods. We used photo-identification data collected during systematic boat-based transect surveys undertaken from 2008 to 2010 and Pollock’s robust capture–recapture design model. Key results. Total abundance estimates for the three species were variable across different sampling periods. The estimated number of individuals in the sampled area varied per sampling episode from 136 (s.e. 62) to 222 (s.e. 48) for snubfin, from 48 (s.e. 7) to 207 (s.e. 14) for humpbacks and from 34 (s.e. 6) to 75 (s.e. 9) for bottlenose dolphins. Apparent survival was estimated for snubfin at 0.81 (s.e. 0.11), humpbacks at 0.59 (s.e. 0.12) and bottlenose at 0.51 (s.e. 0.17) per annum. Key conclusions. (1) The values derived here provide some of the only estimates of local population size for these species across monsoonal northern Australia; (2) population-size estimates varied considerably among seasons or sampling episodes; (3) the low apparent survival probabilities indicated that many individuals may move at scales larger than the study area; (4) density of snubfin and humpback dolphins in the present study area exceeded the few other estimates available for these species elsewhere in Australia. Implications. The present study provided the first baseline estimates of abundance and apparent survival for three coastal dolphin species in monsoonal northern Australia. Such information is becoming increasingly important as development pressures intensify in coastal areas. Sampling protocols for future monitoring and impact assessment need an enhanced consideration of seasonality and scale issues.

Observations of an Indo-Pacific humpback dolphin carrying a sponge: object play or tool use?

Wild and captive delphinids are known to carry animate and inanimate objects on their rostra, melons, fins and tail flukes. Captive bottlenose dolphins (Tursiops spp.) and pilot whales (Globicephala spp.) will often carry random objects such as seaweed, fish, and plastic toys in their tank (Brown and Norris 1956, Caldwell 1956, Tizzi et al. 2000). Free ranging bottlenose, Hector’s (Cephalorhynchus hectori, van Beneden 1881), and Atlantic spotted dolphins (Stenella frontalis, Cuvier 1829) have been observed carrying seagrass, fish, sea cucumbers and pieces of coral among others (Slooten and Dawson 1994, Mann and Smuts 1999, Miles and Herzing 2003). Most of these object carrying events are thought to be related to animal play: the motor activity directed towards the object appears to provide no obvious direct benefit to the individual(s) involved (Martin and Caro 1985). The only object manipulation activities that have been suggested as non-play in delphinids are: 1) carrying of dead calves, and 2) sponge carrying by some bottlenose dolphins in Shark Bay, Western Australia. The carrying of dead calves has been hypothesised as a manifestation of epimeletic (care-giving) behaviour (Harzen and Santos 1992, Lodi 1992, Fertl and Schiro 1994, Palacios and Day 1995). Sponge carrying by bottlenose dolphins in Shark Bay has been identified as a foraging specialisation involving tool-use (Smolker et al. 1997). It is believed that the animals involved use sponges to protect their rostrum from shells, rocks and spines and stingers from noxious organisms while looking for prey in the sea bottom. Genetic and ecological data indicate that the use of sponges as tools is culturally transmitted mainly within a matriline (Krützen et al. 2005). The use of sponges as a foraging tool has not been described in any other population of bottlenose dolphins or dolphin species, although anecdotal evidence suggests that humpback dolphins in the Dampier Archipelago, Western Australia, also carry sponges (M.Krützen, personal communication, July 2007). Indo-Pacific humpback dolphins (Sousa chinensis, Osbeck 1765) are found throughout coastal waters of the Indo-Pacific region from the eastern shores of South Africa to the northern coast of Australia (Jefferson and Karczmarski 2001, Parra et al. 2004). Two cases of epimeletic behaviour involving humpback dolphins carrying dead calves have been observed in Hong Kong (Parsons 1998). In South Africa, humpback dolphins were seen carrying and throwing sea shells for short periods of time during social-play activities (Saayman and Tayler 1979). This paper describes a sponge carrying event by an adult Indo-Pacific humpback dolphin and discusses the potential functions of this behaviour in light of the observations made. The observations were made on November 9, 2006, during boat based surveys of coastal dolphins in the Hinchinbrook Channel (188169 S, 1468049 E), northeast Queensland, Australia. The Hinchinbrook Channel, part of the Great Barrier Reef World Heritage Area, is a 44km long tidal channel that separates Hinchinbrook Island from the mainland. The channel has a maximum depth of 20 m and is fringed by one of the largest mangrove forests in Australia. During dolphin surveys, systematic data collection was carried out through focal follows, photo-identification, and scan and ad libitum behavioural sampling. Further details of survey procedures are described by Parra (2006) and Parra et al. (2006). Four adult humpback dolphins were sighted at 08:43 and followed for 2.3 h at distances ranging from 10 to 40 m. Observations took place in waters ranging from 5.1 to 9.4 m deep (means6.9, SDs1.3, ns28). The school changed later to three adults and a juvenile (see description below). All adults involved had distinctive marks on their dorsal fins. For most of the duration of the sighting, dolphins were predominantly travelling northwards slowly (2–3 km/h) within 10 m of each other. At 08:56 one of the dolphins surfaced with a large object on its rostrum (Figure 1). The object was dark brown in colour and covered the total length of the dolphin’s rostrum. At first sight the object looked like a marine sponge. Though the object could not be retrieved for further identification, Dr. John Hooper, an expert in sponge taxonomy with the Queensland Museum, inspected the sighting photographs and concluded that the object resembled a sponge-algal complex (referred to from now on as a sponge). The sponge appeared to be held in place by its apparent conformity to the shape of the rostrum and by the water pressure as the dolphin moved forward. For the next 5 min, the dolphin swam at the surface with the sponge on its rostrum following no specific direction and taking several breaths interspersed with short dives less than 1 min long. During this time the other three animals remained close to the sponger (-50 m). At 09:01 the dolphin per-

Local assessments of marine mammals in cross-cultural environments

Biodiversity assessments by research scientists are often logistically difficult and expensive to implement in remote areas. Locally-based approaches have the potential to overcome some of these challenges by capitalising on the knowledge and capacity of local people. Many Indigenous people in northern Australia are custodians of coastal areas that support globally significant populations of tropical marine mammals, including coastal dolphins and dugongs. The objective of our study was to design and implement a locally-based approach in a cross-cultural environment to assess the distribution of marine mammals in the remote waters of the Gulf of Carpentaria, Northern Territory. The study was conducted as a partnership between Yanyuwa Aboriginal families, research scientists, government officers and the li-Anthawirriyarra Sea Rangers. We conducted a series of participatory mapping workshops to share and record local observations of dolphins and dugongs. These observations provided the longitudinal information required to inform the design of the first dedicated marine mammal vessel survey in the Gulf of Carpentaria. The vessel surveys found three species of dolphins present in the area (Australian snubfin, humpback and bottlenose dolphins), even though sightings were low; dugongs being much more common. We found that the integrative and locally-based approach built the capacity of both the li-Anthawirriyarra Sea Rangers and research scientists to assess the distribution of marine mammals. If replicated over longer time-frames and coordinated over broader spatial scales, information on distribution and abundance derived from locally-based approaches has the potential to inform the status of marine mammals.