Abundance of coastal dolphins in Roebuck Bay, Western ...

Cetacean Research Unit School of Veterinary and Life Sciences

Murdoch University Murdoch WA 6150

www.mucru.org

Abundance of coastal dolphins in Roebuck Bay, Western Australia:

Updated results from 2013 and 2014 sampling periods

Report to WWF-Australia

October 2014

Alexander M. Brown, Lars Bejder, Kenneth H. Pollock and Simon J. Allen Please cite this document as:

Brown, A.M., Bejder, L., Pollock, K.H. & Allen, S.J. (2014). Abundance of coastal dolphins in Roebuck Bay, Western Australia: Updated results from 2013 and 2014 sampling periods. Report to WWF-Australia. Murdoch University Cetacean Research Unit, Murdoch University, Western Australia, 32pp. All photographs © MUCRU/WWF-Australia

Table of Contents

Non-technical summary ................................................................................................................................. 1

1. Background ................................................................................................................................................ 3

1.1. Objectives ........................................................................................................................................... 4

2. Methods .................................................................................................................................................... 4

2.1 Ethics statement .................................................................................................................................. 4

2.2 Abundance estimates ........................................................................................................................... 5

3. Results ....................................................................................................................................................... 6

3.1. Effort................................................................................................................................................... 6

3.2 Distribution of dolphin sightings and group sizes .................................................................................. 7

3.3 Encounter rates .................................................................................................................................... 9

3.4 Identification and resight rates ........................................................................................................... 10

3.5 Females and calves............................................................................................................................. 12

3.6 Abundance estimates ......................................................................................................................... 12

3.7 Potential movements of animals between study sites ........................................................................ 13

3.8 Local and indigenous engagement and data dissemination ................................................................ 14

4. Discussion ................................................................................................................................................ 14

4.1 Abundance of dolphins in Roebuck Bay .............................................................................................. 14

4.2 Apparent survival ............................................................................................................................... 15

4.3 Preliminary evidence of site fidelity .................................................................................................... 15

4.4 Temporary emigration and study design ............................................................................................ 16

4.5 Conservation and management implications ...................................................................................... 17

4.6 Recommendations for future research ............................................................................................... 17

5. Acknowledgements .................................................................................................................................. 18

6. Literature cited ........................................................................................................................................ 18

Appendix 1 - Effort maps per sampling period.............................................................................................. 21

Appendix 2 - Group sighting maps per sampling period ................................................................................ 22

Appendix 3 - Snubfin dolphin group sizes per sampling period ..................................................................... 23

Appendix 4 - Encounter rates per transect for 2013 and 2014 ...................................................................... 24

Appendix 5 - Encounter rate maps of each species per sampling period ....................................................... 25

Snubfin dolphins ...................................................................................................................................... 25

Bottlenose dolphins ................................................................................................................................. 26

Humpback dolphins ................................................................................................................................. 27

Appendix 6 - Abundance estimate model outputs ........................................................................................ 28

Appendix 7 - Dugong sightings ..................................................................................................................... 32

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Non-technical summary Murdoch University’s Cetacean Research Unit (MUCRU) is conducting research on coastal dolphins at several locations across north-western Australia. In October 2013, this research was extended to include a study area of approximately 100 km2 of Roebuck Bay with the primary objective of estimating the abundance of Australian snubfin dolphins (Orcaella heinsohni). An initial five-week survey was undertaken in October-November 2013; results were reported to WWF-Australia in February 2013 (Brown et al., 2014a). A second survey was carried out in April 2014; results for both survey periods are presented here. This report is not intended to be a stand-alone document, and the reader is encouraged to refer to Brown et al. (2014a) for further background information and a detailed description of methods adopted throughout. Over each of the survey periods, a team of MUCRU researchers, assisted by representatives of Nyamba Buru Yawuru Pty Ltd., completed multiple zig-zag transects through the study area collecting data on all groups of dolphins encountered. In both periods, snubfin dolphins were frequently encountered throughout the majority of the study area in groups of up to 17 animals, with a mean group size of 4.2 (0.32 SE). Low numbers of bottlenose dolphins (Tursiops aduncus) were occasionally encountered and humpback dolphins (Sousa sahulensis) were encountered only rarely. In 2014, snubfin group sizes were slightly smaller and encounter rates were slightly lower than those in 2013; however, no strong signal of seasonal variation was observed. A total of 114 snubfin individuals (excluding calves) were identified from distinctive markings on their dorsal fins across the two sampling periods. After two-thirds of the survey effort, very few new individuals were identified, suggesting that almost all of the animals using the study area were identified. A majority of these 114 individuals was observed in both 2013 and 2014 survey periods. A thorough cross-examination of dolphins photo-identified at Roebuck Bay with those identified previously at Beagle and Cygnet Bays did not reveal any matches. Capture-recapture population models were used to estimate the abundance of snubfin dolphins within each of the two sampling periods. There was insufficient data to estimate the abundance of bottlenose and humpback dolphins. We selected POPAN open models as the most appropriate, given evidence of movement of individuals in/out of the study area during each study period. Our best estimates of abundance for each survey period were very similar at 132 (14.5 SE, 95% Confidence Interval 107-164) snubfin dolphins (excluding calves) in 2013 and 134 (17.7 SE, 95% CI 104-174) in 2014, providing confidence in the reliability of each individual estimate. We also considered a longer study period by combining data from both 2013 and 2014 survey periods; this produced a similar, but slightly larger and more precise estimate of 143 (10.8 SE, 95% CI 123-165). These modelled abundance estimates were very similar to the total number of animals identified and are thus considered to be an accurate representation of the number of snubfin dolphins using the study area. At approximately 140 animals, the snubfin dolphin population occurring in the 100 km2 study area within Roebuck Bay is one of the largest reported in Australia to date and should be considered of regional and, indeed, national significance. Despite this relative magnitude, the population is small by conservation standards. We also provide preliminary evidence of fidelity to the study area for a majority of individuals, highlighting the importance of the area to this population and the need to minimise habitat degradation and loss. Furthermore, genetic studies indicate low levels of movement/migration between snubfin dolphins at Roebuck Bay and the nearest reported aggregation at Cygnet Bay (250 km distant) (Brown et al., 2014b). Decision makers and resource management agencies should prioritise measures to minimise anthropogenic threats to this population, including in the planning of the proposed Roebuck Bay marine protected area. We

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recommend that further research be carried out across a broader area of Roebuck Bay and adjacent waters, in order to investigate the extent of the distribution of this population and examine the relative importance of different areas within Roebuck Bay. With a density of animals suitable for capture-recapture abundance estimates at an accessible location, Roebuck Bay presents a unique opportunity in Western Australia for a longer-term study into trends in the abundance of snubfin dolphins. Such studies will play a key role in gaining the necessary data for a full assessment of the conservation status of snubfin dolphins under State and Commonwealth legislation. Furthermore, we recommend Roebuck Bay as a priority study area for the investigation of feeding ecology of snubfin dolphins.

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1. Background Murdoch University’s Cetacean Research Unit (MUCRU) is conducting research on dolphins at several locations across north-western Australia. Specifically with regard to the Kimberley region, a project funded by the Australian Federal Government through the Australian Marine Mammal Centre (AMMC) commenced in 2012 to estimate abundance, residency and genetic connectivity of snubfin and humpback dolphins1. Over the past two years, we have conducted standardised boat-based surveys of inshore dolphins at Cygnet Bay and Beagle Bay on the Dampier Peninsula, and also within the Cambridge Gulf in the eastern Kimberley (Figure 1). In October 2013, following co-investment from WWF-Australia, MUCRU’s research was extended to include a study area of approximately 100 km2 of Roebuck Bay. Over five weeks, this area was surveyed by a team of MUCRU researchers, assisted by a representative of Nyamba Buru Yawuru Pty Ltd., to collect data on the abundance of inshore dolphins within Roebuck Bay. The main objective was to produce an abundance estimate for the Australian snubfin dolphin (Orcaella heinsohni), a poorly understood species known to frequent these waters. Data were also collected on any other species of coastal dolphins encountered.

Figure 1. Study sites for boat-based surveys of inshore dolphins conducted by MUCRU 2012-2013.

The results of research conducted in 2013 were reported to WWF-Australia (Brown et al., 2014a), which was subsequently published online in May 2014. Over the five weeks of study, a total of seven transects were completed throughout the study area, over which 74 groups of snubfin dolphins were encountered, along with four groups of bottlenose dolphins and one group of humpback dolphins. A catalogue of individuals was developed, with a total of 100 distinctive snubfin dolphin individuals identified from images of sufficient quality. An abundance estimate of just over 130 snubfin dolphins (excluding calves) was found to be using the study area during the five week study period - the largest reported abundance of snubfin dolphins in Australia at the time. Results reported in Brown et al. (2014a) have provided management agencies with a baseline abundance estimate to help inform the development of a Roebuck Bay proposed marine park draft management plan.

1 http://mucru.org/research-projects/snubfin-and-humpback-dolphins-in-the-kimberley-region-western-australia/

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This document reports on the results of a second sampling period in April 2014, with results presented alongside, and in combination with, those of 2013. The objective of the second sampling period was to repeat the survey efforts of 2013 and produce a second abundance estimate of snubfin dolphins. This allows a comparison with the 2013 estimate based on data collected at a different time of year, and provides some indication of the residency of animals to the area.

1.1. Objectives For each of the sampling periods, our objectives were to: (1) Estimate the abundance of snubfin dolphins within a ca. 100 km2 area of Roebuck Bay, Western

Australia. (2) Provide quantitative information (e.g. encounter rates) on the occurrence of any other dolphin species

observed within the study area. (3) Investigate recent movements of animals between Roebuck Bay and Beagle and Cygnet Bays through

the cross-referencing of photo-identification catalogues between sites. During the 2014 sampling period, there was an additional objective to opportunistically collect biopsy samples from individuals not sampled previously, to contribute to ongoing studies of the population genetic structure of inshore dolphins in north-western Australia. This objective was secondary to the completion of line transects and collection of photo-identification data.

2. Methods Data collection and analytical methods are described in detail in the February 2014 report and remain unchanged here unless specified. The 2014 sampling period represents a repeat of the survey effort conducted in 2013. Transects were completed according to previous routes through the same study area of approximately 100 km2 (Figure 2), with the slight difference that some were completed in a west-east direction in 2014 (all done east-west in 2013) to minimise the impact of glare on observational conditions when surveying in the afternoons. Weather patterns varied throughout the data collection period such that effort took place across a range of times of day from 06:00 - 17:00.

2.1 Ethics statement

Field data collection took place under permits from the WA Department of Agriculture and Food (U6/2012-2014), WA Department of Parks and Wildlife (SF009119), with approval from Murdoch University Animal Ethics Committee (W2342/10 and R2649/14), and with the permission and active participation of Nyamba Buru Yawuru Pty Ltd. (NBY), the representative body for Traditional Owners of the area. NBY representatives assisted with data collection from the research vessel for approximately 50% of the time on the water.

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Figure 2. Study area and transect design. Depth contours are Lowest Astronomical Tide.

Encounter rates were calculated as the total number of dolphins (including dependent calves) encountered on a given transect, divided by the total survey area of the corresponding transect (assuming a 500 m wide strip around the transect line). Individual dolphins resighted within the same transect were not counted a second time; this differs from the method previously used, which included individuals observed on the same day > 1 hour after their previous sighting. Encounter rates from 2013 have been recalculated according to a one sighting per day limit and are presented alongside 2014 values below. Individuals which had undergone a change in dorsal fin appearance since 2013 were re-assessed for distinctiveness and assigned a new score applicable to 2014 data, where appropriate. The proportion of distinctive individuals was estimated for 2014 data independently, in addition to pooling data across both periods to estimate a ‘universal’ value across both sampling periods. To assess the residency of individuals between the two sampling periods, a measure of between-season resight rate was calculated. This was completed for data collected on transects only, and also for all group sightings within each study period (transect- and non-transect sightings).

2.2 Abundance estimates As described in Brown et al. (2014a), a selection of closed and open population models were fitted to capture histories of distinctive individuals to produce an abundance estimate for the 2014 sampling period. Additionally, the analysis of data from the 2013 sampling period was revisited for consistency with the methods adopted here. A full suite of eight (2*2*2) open models were fitted to data from each sampling period, with different combinations of either time-varying (t) or constant (.) parameters of apparent survival (Phi), capture probability (p) and probability of entry (pent) into the population. To investigate violation of closure, two restricted model combinations with Phi fixed at 1 and pent fixed at 0 were also fitted for comparison with the unrestricted open models. Additionally, we combined data from 2013 and 2014 to produce abundance estimates using the larger dataset representing two sampling occasions separated by

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five months. For this multi-period data, we also ran a full set of eight open models, restricted models which were closed across the entire two periods, and partially closed models with phi fixed at 1 and pent fixed at 0 within periods but left open for the longer interval between periods. Time intervals between sampling occasions (transects) were specified in days, therefore apparent survival estimates are to be interpreted as daily rates. For each sampling period, the closed model Mth was fitted, which allows for capture probability to vary with time and between individuals. The advantages of using closed models are that they provide estimates with higher precision than open models and can allow for heterogeneity of capture probabilities between individuals. However, they assume that the study site is closed to gains or losses of individuals for the duration of the sampling period; violation of this assumption may result in biased estimates of abundance. Open models allow for demographic changes in the population over the sampling period, and provide estimates for gains (births, immigration) and losses (deaths, emigration). They do not, however, allow for non-random temporary emigration. POPAN open models (Schwarz and Arnason, 1996) consider the animals encountered during the sampling events representative of a component of a larger super-population, and estimate a probability of entry of animals from the super-population into the sampled population (Carroll et al., 2013, Tyne et al., 2014). Furthermore, these models allow correction for animals which may enter and exit the study area rapidly between sampling events, therefore being unavailable for capture. The super-population estimate is particularly useful for studies where the absolute size of a population, or ‘stock’, is of more interest than the abundance or density of animals within a specific area at any given time (e.g. Constantine et al., 2012, Carroll et al., 2013). The total population size was calculated by dividing the size of the distinctive population (estimated by the models) by the proportion of distinctive animals (as described in Brown et al., 2014a).

3. Results

3.1. Effort Transect effort in 2014 took place from 04 to 25 April. As for 2013, seven transect repeats were completed over a similar number of days (or part thereof) of on-water effort (Table 1). Due to more favourable weather conditions in 2014, the seven transects were completed in a shorter total period of 22 consecutive days, compared to 32 days in 2013.

Table 1. Study period and effort summary for 2013-2014; ‘km2 effort’ corresponds to an extrapolation of ‘km effort’ to include a 500 m wide survey-strip.

2013 2014 2013-2014

Transects completed 7 7 14

Study period 04 Oct - 05 Nov (32 days)

04 Apr - 25 Apr (22 days)

-

Days of effort 19 18 37

km of effort 418.5 389.3 807.8

km2 of effort 206.5 191.1 397.6

For both periods, each individual transect took one to three days (or part thereof) of effort to complete. The majority was completed in two or three consecutive days with a minimum of 12 hours (overnight) gap before beginning the next transect. Individual transects varied in length according to the tide, ranging from 45 km to 67 km with a mean of 57.7 (SE 1.77) km. A slightly shorter length of transect was completed in 2014 compared to 2013, due to a greater coincidence between lower tides and favourable sea conditions.

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Extrapolating from the 500 m survey strip, each transect surveyed approximately 30% of the total study area. When transferred to a 1 × 1 km grid across the study area over the period 2013-2014, survey effort took place in 133 grid cells, with the effort in each ranging to a maximum of 7.4 km2 (Figure 3). Almost complete coverage of the study area was achieved, with only a few small near-shore grid cells not falling within the survey strip on any transects. Effort was relatively even across the study area, with some expected peaks at transect turns and intersections. Effort was lower along the eastern edge of the study area due to the shallow gradient preventing access close to shore on all but the higher end of the tide.

Figure 3. Effort map showing transects and total survey effort across 2013 and 2014 sampling periods combined.

3.2 Distribution of dolphin sightings and group sizes Across both sampling periods, snubfin dolphins accounted for the vast majority of dolphin groups sighted (Table 2). Small numbers of bottlenose dolphins were encountered in both periods, and one group of humpback dolphins was encountered in 2013. On four occasions, mixed-species groups of bottlenose and snubfin dolphins were observed. Table 2. Group sightings by species. Transect data only. *Two snubfin groups in 2013 also contained a single bottlenose dolphin. ** Two snubfin groups in 2014 also contained three bottlenose dolphins. 2013 2014 2013-2014

All species 79 77 156

Snubfin 74* 74** 148

Bottlenose 4 3 7

Humpback 1 0 1

The distribution of sightings in 2014 was very similar to that in 2013; maps for each of these two sampling periods are shown in Appendix 2. Group sightings from both periods combined are presented in Figure 4. Within both sampling periods, snubfin dolphins were frequently encountered in the Inner Anchorage area - a

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distinct channel of deeper water (typically 10-20 m water depth) extending ca. 10 km east from the port. Snubfin dolphins were encountered less frequently in the shallow waters over the intertidal foreshore flats to the north of the Inner Anchorage, and only occasionally to the south of Middle Ground. Three off-transect forays up Dampier Creek at high tide and one up Crab Creek did not yield any dolphin sightings, although snubfins were observed close to the mouths of these tidal creeks. Snubfin dolphins were frequently encountered throughout the study area to the east and southeast of the Inner Anchorage, where intertidal and shallow subtidal flats extend several kilometers offshore of the mangrove-fringed west-facing shore (Figure 3). The majority of groups encountered in this area were in < 5 m water depth, with many as shallow as < 2 m. The majority of bottlenose dolphin sightings occurred within the Inner Anchorage. The single sighting of humpback dolphins was in the southeast of the study area, at a water depth of 8 m.

Figure 4. Dolphin sightings and transect lines for 2013 and 2014 sampling periods combined, illustrating group sizes for snubfin (yellow circles), bottlenose (blue circles) and humpback (red circles) dolphins. Depth contours are Lowest Astronomical Tide.

Groups were defined as individuals within 100 m of each other engaged in approximately the same activity (Parra et al., 2006). Snubfin dolphin group sizes were comparable between 2013 and 2014 (Table 3). The mean group size was slightly smaller in 2014, largely due to a greater proportion of single animals observed in 2014 (36% total groups) compared to 2013 (16%). Across the two sampling periods, group sizes of one to two were the most frequently observed; when combined, they accounted for approximately half of all observations (Figure 5). Larger groups, in excess of five, were less common, although 16 groups of ten or more dolphins were observed over the course of the study. The single humpback dolphin sighting was a group of 18, including at least three dependent calves. Due to the difficulty in distinguishing between age classes of independent individuals (i.e. sexually-mature adults vs sub-adults/juveniles) in the field, no attempts are made to estimate the proportion of sub-adults/juveniles here.

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Table 3. Group sizes (including calves) of dolphin sightings in 2013, 2014 and 2013-2014 combined. SE = standard error; range = range of group sizes; n = total number of groups included in analyses; groups with calves = groups where at least one dependent calf was observed. Snubfin Bottlenose

2013 2014 2013-2014 2013 2014 2013-2014

Mean (SE) 4.5 (0.44) 4.0 (0.47) 4.2 (0.32) 3.3 (1.09) 2.8 (0.49) 3.1 (0.61)

Range 1 - 16 1 - 17 1 - 17 1 - 8 1 - 4 1 - 8

n 74 74 148 6 5 11

Groups with calves 20 (27%) 24 (32%) 44 (30%) 3 (50%) 3 (60%) 6 (55%)

Figure 5. Frequency distribution of snubfin dolphin group sizes, using 2013-2014 data combined.

3.3 Encounter rates Snubfin dolphins were by far the most frequently encountered species, with ca. 1.3 dolphins per km2 of survey effort across the two sampling periods as a whole (Table 4). The encounter rate was slightly lower in 2014 at 1.19 snubfins per km2 of survey effort, compared to 1.43 in 2013. For individual transects, the encounter rate was often similar to the mean value for the study period as a whole (Appendix 4). However, some individual transects did show exceptionally high or low encounter rates (range 0.13 - 2.31 dolphins per km2). Table 4. Survey effort (length and area) and dolphin encounter rates per sampling period, and the total for 2013-2014 combined.

Sampling

period

Total survey

length (km)

Total survey

area (km2)

Encounter rate

(number of dolphins per km2 survey effort)

Snubfin Bottlenose Humpback

2013 418.5 206.5 1.43 0.10 0.09

2014 389.3 191.1 1.19 0.07 0.00

Total 807.8 397.6 1.32 0.09 0.05

When mapped, encounter rates of snubfin dolphins were comparable in their distribution between 2013 and 2014 (Appendix 5); they both highlight the importance of the Inner Anchorage area and the shallow area in the south east of the study area (Figure 6).

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Figure 6. Encounter rates of snubfin dolphins per 1 km × 1 km grid cell for 2013-2014 combined. Depth contours are Lowest Astronomical Tide.

3.4 Identification and resight rates A total of 79 distinctive snubfin individuals (excluding calves) were observed during the 2014 study period, compared to 100 in 2013. Across both study periods, the cumulative number of photo-identified distinctive snubfin individuals was 114. A cumulative discovery curve (Figure 7) shows a plateau in the number of distinctive snubfin individuals observed over time, with 90% and 95% of total individuals observed after 21 and 26 days of effort, respectively (i.e. after just a few days of effort during the second sampling period). This suggests that the vast majority of animals that may use the study area have been observed at some stage during the study period. A further three distinctive bottlenose individuals were identified during the 2014 period (representing a single encounter of four animals), taking the total to nine over the entire study period. Of the six distinctive bottlenose dolphins observed in 2013, two were resighted in 2014. No humpback dolphins were observed during the 2014 period. The 14 distinctive individuals observed correspond to a single group encountered in the 2013 period.

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Figure 7. Cumulative number of distinctive snubfin, humpback and bottlenose dolphin individuals (excluding calves) identified for each day of effort (or part thereof) during the study period from 2013 (days 1-19) to 2014 (days 20-37). The dotted vertical line delineates the two sampling periods. Grey bars indicate daily survey effort (km). Vertical lines show points in time when 90% (dashed line) and 95% (solid line) of the total number of distinctive snubfin individuals had been observed.

The majority (84%) of the 79 distinctive individuals identified in 2014 was previously observed in 2013 (Table 5). When taken as a proportion of the total unique individuals observed, approximately 60% of distinctive individuals were observed in both sampling periods. Table 5. Distinctive individuals identified per sampling period, and those seen across both periods. *Includes one individual (OH307), which went from indistinctive in 2013 to distinctive in 2014.

Transect sightings only All sightings

Individuals identified, 2013 100* 104

Individuals identified, 2014 79 88

Individuals identified in both 2013 and 2014 66 74

Total unique individuals identified, 2013-2014 114 118

Proportion of total unique individuals identified in both 2013 and 2014

0.58 0.63

During each sampling period, the majority of distinctive snubfin individuals were only encountered on one or two of the total seven transects (Figure 8). The number of ‘per transect resights’ then dropped sharply; no individuals were encountered on more than five transects per sampling period.

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Figure 8. The total number of transects on which each snubfin dolphin individual was encountered.

3.5 Females and calves In 2013, nine distinctive snubfin individuals were identified as females with dependent calves, plus an additional two females with calves that were observed opportunistically (not on transect effort). The estimated age of these calves (based on appearance) ranged from a couple of weeks to 2-3 years; a total of six calves were estimated as < 3 months old, with several likely to be just weeks old. Nine of these females were observed again during the 2014 sampling period; of those with calves estimated as < 6 months of age, three no longer had calves and these calves can be assumed to have deceased between the 2013 and 2014 study periods. In 2014, an additional five individuals identified without calves in 2013 were observed with dependent calves, all of which were visually estimated as < 6 months of age. Of the 12 distinctive snubfin dolphins observed for the first time in 2014, one was a female with a dependent calf. In summary, we documented 11 calves which we estimate to have been born approximately between September 2013 and early March 2014, of which eight were confirmed as alive in April 2014.

3.6 Abundance estimates Data for bottlenose and humpback dolphins were too few to derive abundance estimates for either the 2013 or 2014 sampling periods. The proportion of distinctive snubfin individuals was estimated at 0.91 (0.05 SE) for the 2013 sampling period (based on 37 group sightings) and 0.88 (0.06 SE) in 2014 (based on 34 group sightings). Given the similarity between the two estimates, data were pooled and a single proportion of 0.89 (0.04 SE) was applied to abundance estimates from both sampling periods. For all models, we omitted data from the fourth transect in 2013 and the first transect from 2014, as these both showed exceptionally low capture probabilities, making it difficult to fit the more complex open models. This resulted in a reduction in the total number of distinctive individuals captured in 2013 by one to 99 and no change in 2014. Tests within MARK (Program RELEASE) indicated a degree of over-dispersion, which was corrected for in open models by specifying ĉ values of 2.44 (2013), 1.33 (2014) and 1.60 (2013-2014). Consequently, model fit and weight was assessed using QAIC values.

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2014

2013

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All possible configurations of the open models were fitted to the data for both sampling periods, including the restricted Phi = 1 and pent = 0 models (Appendix 6). For 2013 and 2013-2014 combined, the AIC weight was distributed across several models, with no single stand-out ‘best’ model. To address this, weighted model averaging was applied within program MARK across all successfully run models to produce averaged parameter estimates. This technique is considered to produce more stable estimates than selecting a single ‘best’ model from a number of closely-related models (Burnham and Anderson, 2002). The model Phi(.)p(.)pent(.) in 2013 produced spurious estimates of N with 0 SE and was omitted from model averaging. The AIC weight was also distributed across several models for 2014 data, albeit to a lesser extent than 2013; for consistency, model averaging was also applied across all models. The two restricted models with phi(fixed=1) and pent(fixed=0) carried 50% of the AIC weight combined in 2013, with one of these carrying more weight than any of the unrestricted models. In 2014 and for the 2013-2014 data combined, these restricted models carried negligible weight. Model-averaged abundance estimates were very similar between the two sampling periods (Table 6). The abundance estimate derived from the 2013-2014 data combined was also similar to those from each individual sampling period, albeit slightly larger as is to be expected when representing a longer study period. For the 2013 sampling period, closed model Mth produced a comparable estimate to that from the open models. The closed model estimate was approximately 20% lower than the open model-averaged estimate in 2014.

Table 6. Abundance estimates of snubfin dolphins, showing results for the distinctive population, and those extrapolated to the total population. POPAN estimates relate to the model averaged gross super-population.

Model

Distinctive population Total population

n Nd SE 95% CI � N SE 95% CI

2013

Open POPAN (model averaged) 99 118 12.2 94-142 0.89 132 14.5 107-164

Closed Mth 99 115 8.1 106-139 0.89 129 10.2 110-150

2014


Closed Mth 79 95 7.1 86-115 0.89 107 9.0 90-126

2013-2014 combined


n = total number of individuals captured on the six transects used (12 for 2013-2014 models); Nd = estimated size of distinctive population; SE = standard error; CI = confidence intervals; � = estimated distinctive proportion; N = estimated size of total population. Within models, phi = survival rate; p = probability of capture; pent = probability of entry; (t) = time-varying; (.) = constant with time. Closed models Mt allowing for time-varying capture probability (Darroch estimator); Mth allowing for time-varying and individual heterogeneity of capture probability (Chao estimator).

For the 2013 sampling period, capture probability was fairly stable, ranging from 0.31 (0.06 SE) to 0.36 (0.12 SE); daily apparent survival was very close to 1; probability of entry was > 0 for all sampling occasions, but low at an average of 0.04 (0.09 SE) (Table A6-4, Appendix 6). For the 2014 sampling period, capture probability ranged from 0.22 (0.07 SE) to 0.42 (0.09 SE); daily apparent survival was very close to 1 for most sampling occasions although one was lower for one interval at 0.85 (0.06 SE); probability of entry was approximately 0 for all but one sampling occasion when it was 0.31 (0.19 SE) (Table A6-4, Appendix 6).

3.7 Potential movements of animals between study sites

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Examination of all distinctive dolphins observed from 2013-2014 did not reveal any matches of individuals between Roebuck Bay and either Beagle Bay (150 km distant) or Cygnet Bay (250 km distant) for any species.

3.8 Local and indigenous engagement and data dissemination

Following on from successful indigenous participation in 2013, outcomes were presented to Nyamba Buru Yawuru Pty Ltd (NBY) and the DPaW Yawuru Rangers during an oral presentation at the NBY offices in November 2013, then through the circulation of a detailed report with non-technical summary in March 2014. NBY representatives played an active role in survey design and data collection, with Phillip Tamwoy and Ben Dolby participating in data collection on a total of 12 days (2013) and 8 days (2014), respectively. Both received training in all elements of data collection and were valued team members.

A public presentation to the community on the research took place on 9 April 2014 at Broome Public Library as part of the Science on the Broome Coast series being run by the Roebuck Bay Working Group and Yawuru Land and Sea Unit. An audience of over 70 people attended. In May 2014, a blog was posted on the MUCRU website providing a popular science account of our activities in Roebuck Bay to date and a link to the March 2014 final report. Additionally, MUCRU researchers participated in two marine fauna monitoring surveys hosted by NBY/WWF-Australia in conjunction with the DPaW Yawuru Rangers, who provided their vessel, the Jangabarri. Advice was provided on survey activities, including route selection, appropriate boating around dolphins, assessing group composition and interpreting behaviour. These surveys are scheduled to continue twice monthly throughout 2014.

4. Discussion Following the second sampling period, data are now available for both the late dry season (Oct-Nov 2013) and early dry season (April 2014). Group sightings and encounter rates were similar for both 2013 and 2014 sampling periods. Both periods showed that snubfin dolphins were frequently encountered throughout the majority of the study area in groups of up to 17 animals, low numbers of bottlenose dolphins were occasionally encountered, while humpback dolphins were encountered only rarely. While group sizes were slightly smaller and encounter rates were slightly lower in 2014, no obvious seasonality in these parameters was observed. Two areas within the study area - the Inner Anchorage and shallow waters in the east of the bay (Figure 5) - have consistently shown the highest encounter rates of snubfin dolphins across the two sampling periods, representing different times of the year.

4.1 Abundance of dolphins in Roebuck Bay Open population models for each individual sampling period and the 2013-2014 data combined yielded very similar abundance estimates in the range of 132-143 snubfin dolphins (excluding calves). These estimates represent the super-population, that being the number of animals in the population at any time over the course of the study; this does not assume that all the animals were present in the study area at any specific point in time. These weighted average estimates incorporate both unrestricted (open) and restricted (closed) model configurations, and therefore represent the model uncertainty. The similarity between the abundance estimates from different times of year and lengths of study periods, along with their comparable SEs and largely overlapping confidence intervals, adds confidence in each independent estimate as a reliable representation of the population size. Given the long-lived nature of dolphins and the evidence to suggest fidelity of snubfin dolphins to Roebuck Bay (see sections 4.2, 4.3 and Brown et al. 2014b), it seems reasonable to assume little/no mortality, permanent emigration or recruitment from outside the study area

15

of adult dolphins across the total seven months of study. As such, we consider the estimate of 143 (10.8 SE 95% CI 123-165) snubfin dolphins (excluding calves) to be the best representation of the population size within Roebuck Bay at the time of study. Further support for the accuracy of the abundance estimates can be inferred from the cumulative discovery curve (Figure 7), which reached a plateau within the second sampling period. The plateau suggests that the 114 distinctive individuals identified over the course of the study include the vast majority of individuals using the study area. Accounting for the estimated proportion of distinctive individuals in the population across 2013-2014 (114/0.892) provides an estimate of 128 snubfin individuals (excluding calves). With continued survey effort in the study area, it is likely that very few new adult individuals would be identified. The estimates from model Mth, allowing for individual heterogeneity of capture probability, were similar to those which did not allow for heterogeneity (the restricted POPAN models), suggesting that our estimates are not biased downward by heterogeneity. The strict image quality and distinctiveness criteria applied will have gone some way to minimizing this potential bias (Nicholson et al., 2012). Our revised abundance estimate for the 2013 sampling period differs slightly from that presented in Brown et al. (2014a) due to improvements to the analytical process. This difference is minor and has no influence on conclusions and management implications, although we recommend that the revised POPAN abundance estimates presented in the current report are used to inform management as they are the most statistically robust estimates available. The abundance of snubfin dolphins in Roebuck Bay reported here is one of the largest to date. An abundance of similar or larger size has recently been documented within a 325 km2 study area in Port Essington in the Northern Territory (Palmer et al., 2014). While the Port Essington estimates of 136 (62 SE) to 222 (48 SE) are subject to considerable statistical uncertainty and relate to a far larger area than the ca. 100 km2 surveyed in Roebuck Bay, they do provide further evidence that, in some locations, populations exceeding the 50-100 individuals reported elsewhere in their range may exist.

4.2 Apparent survival Time intervals between sampling occasions (transects) were specified in days, therefore apparent survival estimates are to be interpreted as daily rates. In studies of cetaceans, it is typical, and more biologically meaningful, to scale apparent survival to an annual scale. However, making such an extrapolation from just 3-5 weeks of data collection is unwise; tests of annual-scale time-intervals on the current data failed to produce sensible estimates of apparent survival. Apparent survival is defined as true survival × (1 ̶ site fidelity); on a daily scale, we can assume that true survival = 1 and, therefore, interpret any deviation from 1 in daily apparent survival estimates as emigration of animals from the study area during the study period. As such, our apparent survival estimates are of little biological value; more useful information on site fidelity can be inferred from individual resight rates between sampling periods (see below).

4.3 Preliminary evidence of site fidelity Approximately 60% of the total distinctive individuals identified across the study were observed in both the 2013 and 2014 sampling periods, providing some evidence of site fidelity across a period of approximately 6 months for the majority of animals observed. Such a pattern might be expected given studies of snubfin populations on the east coast of Australia revealing either a majority of individuals regularly using the same discrete area from year to year (Parra et al., 2006), or strong site fidelity within a resident population (Cagnazzi et al., 2013), in addition to the apparently resident population within Cygnet Bay (Brown et al., 2013). Indeed, Parra et al. (2006) reported a similar proportion (68%) of individuals observed within 400 km2

16

of Cleveland Bay, Queensland, across more than one calendar year. The ca. 40% of individuals which were only observed within one of the sampling periods can be interpreted in a number of ways. Given that the gross super-population estimates were very similar between the two sampling periods, it is more probable that these individuals were not detected/captured than absent from the population. It is likely that our study area was smaller than the home range of most individuals observed, and that the proportion of overlap between our study area and an individual’s home range varied between different individuals. Consequently, those animals with core areas within our study area were likely to have been observed more frequently, and those with only the outer edges of their range overlapping the study area were observed less frequently. It is likely that those individuals observed within only one of the two sampling periods used the study area less frequently than those observed in both periods. The potential for dolphins to be falsely identified as new individuals due to changes in fin markings between 2013 and 2014 is likely to be minimal due to the relatively short time interval between sampling occasions and the strict photo-identification procedures followed (see Brown et al., 2014a). No individuals identified at Roebuck Bay of any species had been previously observed during surveys at Beagle Bay or Cygnet Bay. The maximum reported movements of individual snubfin and humpback dolphins off the east coast of Queensland are 70 km and 130 km, respectively (Cagnazzi, 2011). It is therefore unsurprising that our relatively limited survey effort did not reveal movements of animals over the 150 km and 250 km distances to Beagle and Cygnet Bays, respectively. Furthermore, recently published genetic research revealed significant genetic differentiation and low gene flow between snubfin dolphins at Roebuck Bay and their closest reported population at Cygnet Bay - indicating low contemporary migration rates between the two areas (Brown et al., 2014b).

4.4 Temporary emigration and study design There was some evidence for a more open population during the 2014 sampling period compared to 2013: across each sampling period, daily apparent survival was estimated to be lower in 2014 compared to 2013. Additionally, the restricted models carried very little weight in 2014, while they contributed 50% of AIC weight in 2013. A possible explanation for this is the total time period over which the transects were completed: 32 days in 2013 compared to 21 days in 2014. While it seems counter-intuitive that a shorter study period would yield a more open population, we know little of the short-term movement patterns of snubfin dolphins and the potential influence this may have on their capture probability. We fitted both closed and open capture-recapture models to produce abundance estimates. Closed models assume no movement of animals in/out of the study area during the sampling period. Violation of the assumption of closure is not expected to result in biased estimates of N if the movement of animals is completely random; however, non-random temporary emigration will result in biased estimates of N (Kendall, 1999). The same is true for open models (Burnham, 1993, Kendall et al., 1997). Sources of non-random temporary emigration may include seasonal fluctuations in distribution or abundance associated with a breeding season (e.g. Smith et al., 2013), food availability or predation risk (e.g. Heithaus and Dill, 2002). Studies of snubfin dolphins on the east coast of Australia have not reported any seasonality in abundance (Parra et al., 2006, Cagnazzi, 2011), although fluctuations at shorter temporal scales (i.e. within a month) have yet to be investigated. Roebuck Bay is subject to diurnal tides of extreme range, varying from approximately 10 m range during spring tides to ca. 2 m range during neap tides, with the transition from spring to neap tides taking approximately seven days. At peak spring tides, the study area varied in surface area from ca. 110 km2 at high tide to ca. 60 km2 at low tide just six hours later. The influence of these water movements has direct implications for the availability of habitat to snubfin dolphins (which were frequently seen within intertidal areas), and quite possibly many unknown ecological influences (e.g. prey availability, predation risk,

17

energetic costs). It seems reasonable to suggest that tidal height and lunar phase may influence the habitat use of dolphins within Roebuck Bay and, therefore, their availability to capture by photo-identification. We have made no attempt to investigate these potential tide-dolphin relationships and to do so rigorously would require a survey specifically designed to address such an objective. However, future surveys for abundance estimation in areas with extreme tides may benefit from consideration of lunar phase; it may be wise to try to sample across a full lunar phase rather than sample as short a period of time as possible (which may be biased towards either spring or neap tides).

4.5 Conservation and management implications Our results provide limited, but critical baseline data on the community of inshore dolphins within Roebuck Bay. This represents an important step towards determining the importance of this area to inshore dolphins and will contribute towards our limited understanding of these species throughout their range. We have presented an example of structured, scientifically rigorous baseline data collection. This level of data collection, reproduced across months and years, should be considered an essential pre-requisite to assessing the potential impacts of coastal zone development on inshore dolphins, along with other potentially threatening activities (Allen et al., 2012, Bejder et al., 2012). At approximately 130 animals in 100 km2, the population of snubfin dolphins occurring in Roebuck Bay is one of the largest reported abundances of snubfin dolphins in Australia to date and should be considered of regional and, indeed, national significance. Despite this relative magnitude, it is small by conservation standards. We provide preliminary evidence of site fidelity to the study area among a majority of individuals, highlighting the importance of the study area to this population and the need to minimise degradation and loss of these habitats. Genetic analyses suggest a low level of gene flow between snubfin dolphins sampled within Roebuck Bay and the geographically closest documented population of snubfin dolphins at Cygnet Bay (250 km distant), and suggests that the two populations should be managed as independent units (Brown et al., 2014b). This genetic ‘stock’ definition is supported by: the high degree of site fidelity reported for the Cygnet Bay population (Brown et al., 2013); the preliminary indications of site fidelity within Roebuck Bay reported here; and also the lack of movement of animals between study sites revealed by photo-identification data to date. Inshore dolphins are vulnerable to a variety of anthropogenic stressors, including habitat degradation and loss through coastal zone development and increasing boat traffic, as well as injury and mortality through interactions with fisheries (e.g. Read, 2008, Jefferson et al., 2009, Thiele, 2010, Parra et al., 2012). It is beyond the scope of the current study to assess the range and significance of potential threats to inshore dolphins in Roebuck Bay. However, we emphasise the importance of Roebuck Bay to snubfin dolphins and the apparent vulnerability of this population to changes in the ecosystem. Decision makers and resource management agencies should be prioritising measures which minimise anthropogenic threats to this population, including in the current planning of a marine protected area.

4.6 Recommendations for future research Our results now cover two different months of the year, allowing some inferences of temporal variation in abundance and site fidelity. However, consideration should be given to the development of an ongoing, temporally structured survey effort, which could provide more useful estimates of apparent survival, temporary emigration, and may enable detection of trends in abundance. In October 2013, the Commonwealth Government published a research framework to assess the national conservation status of Australian snubfin dolphins and other tropical inshore dolphins (Department of the

18

Environment, 2013), with research methods outlined in an accompanying document (Brooks et al., 2014). A key objective outlined in the research framework was to “Conduct dedicated multi-year studies of the distribution, abundance and habitat preferences of snubfin dolphins at selected focal sites across northern Australia” (Objective 2). With a density of animals suitable for capture-recapture abundance estimates at an accessible location, Roebuck Bay presents a unique opportunity in Western Australia as a focal site for such multi-year studies. The suitability of Roebuck Bay for such study is enhanced by the capacity and interest of the Yawuru traditional owners and numerous other local stakeholders (e.g. Roebuck Bay Working Group) in the ecology and conservation of the area. Very little is known of the feeding ecology of snubfin dolphins; stomach content investigations of a limited number of animals from Queensland provide the only insights on prey items to date (Parra and Jedensjö, 2014). Information on the feeding ecology and trophic relationships of this species is an essential step in understanding their ecological role, prey requirements and preferences, and potential interactions with fisheries (Kiszka et al., 2014, Parra and Jedensjö, 2014). For reasons outlined above, Roebuck Bay presents an excellent opportunity for trophic studies of snubfin dolphin feeding ecology using stable isotopes and fatty acid analyses of tissue samples. Consideration should also be given to applying a structured, multi-stage survey design across a broader area, which encompasses the entire embayment of Roebuck Bay and some adjacent areas. While this spatial scale is unlikely to be logistically feasible for capture-recapture estimates of abundance, it will increase our understanding of the geographic range of the population, complementing genetic assessments of management unit definition. Furthermore, a broader survey area will provide information on the relative importance of areas within the population’s range.

5. Acknowledgements This research was jointly funded by WWF-Australia, the Australian Marine Mammal Centre (Project 11/23) and Murdoch University. Valuable input to the study design and logistical advice was provided by representatives of Nyamba Buru Yawuru Pty Ltd. and the DPaW Yawuru Rangers. The data collection would not have been possible without research assistants Felix Smith, Marine Quintin, Christy Harrington, Tomás Kavanagh, Hera Sengers and Cassie Chronik, who volunteered many weeks of hard work, and Elisa Chillingworth who assisted with data processing. The authors are grateful to Tanya Vernes of WWF-Australia for her efforts towards facilitating this research, in addition to the efficiency of the Murdoch University grants team. Thanks go to Arrow Pearls Pty Ltd and Sean and Frances Archer for providing the research team with subsidised accommodation within Broome, and also to Kandy Curran of Roebuck Bay Working Group for promoting the research.

6. Literature cited ALLEN, S. J., CAGNAZZI, D. D., HODGSON, A. J., LONERAGAN, N. R. & BEJDER, L. 2012. Tropical inshore

dolphins of north-western Australia: Unknown populations in a rapidly changing region. Pacific

Conservation Biology, 18, 56-63. BEJDER, L., HODGSON, A., LONERAGAN, N. & ALLEN, S. 2012. Coastal dolphins in north-western Australia:

The need for re-evaluation of species listings and short-comings in the Environmental Impact Assessment process. Pacific Conservation Biology, 18, 22-25.

BROOKS, L., CARROLL, E. & POLLOCK, K. H. 2014. Methods for assessment of the conservation status of Australian inshore dolphins. Final report to the Department of the Environment.

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BROWN, A., POLLOCK, K. H., BEJDER, L. & ALLEN, S. J. 2013. Distribution and abundance of tropical inshore dolphins in Cygnet Bay, Western Australia. Oral presentation. 20th Biennial Conference on the

Biology of Marine Mammals. University of Otago, Dunedin, New Zealand. BROWN, A. M., BEJDER, L., POLLOCK, K. H. & ALLEN, S. J. 2014a. Abundance of coastal dolphins in Roebuck

Bay, Western Australia. Report to WWF-Australia. Murdoch University Cetacean Research Unit, Murdoch University, Western Australia.

BROWN, A. M., KOPPS, A. M., ALLEN, S. J., BEJDER, L., LITTLEFORD-COLQUHOUN, B., PARRA, G. J., CAGNAZZI, D., THIELE, D., PALMER, C. & FRERE, C. H. 2014b. Population differentiation and hybridisation of Australian snubfin (Orcaella heinsohni) and Indo-Pacific humpback (Sousa chinensis) dolphins in north-western Australia. PLoS One, 9, e101427.

BURNHAM, K. P. 1993. A theory for combined analysis of ring recovery and recapture data. In: LEBRETON, J. D. & NORTH, P. M. (eds.) The study of bird population dynamics using marked individuals. Berlin: Birkhauser Verlag.

BURNHAM, K. P. & ANDERSON, D. R. 2002. Model selection and multi-model inference: a practical

information-theoretic approach, Second edition., New York, Springer-Verlag. CAGNAZZI, D. 2011. Conservation Status of Australian snubfin dolphin, Orcaella heinsohni, and Indo-Pacific

humpback dolphin, Sousa chinensis, in the Capricorn Coast, Central Queensland, Australia. PhD PhD, Southern Cross University.

CAGNAZZI, D., PARRA, G. J., WESTLEY, S. & HARRISON, P. L. 2013. At the Heart of the Industrial Boom: Australian Snubfin Dolphins in the Capricorn Coast, Queensland, Need Urgent Conservation Action. PLoS ONE, 8, e56729.

CARROLL, E. L., CHILDERHOUSE, S. J., FEWSTER, R. M., PATENAUDE, N. J., STEEL, D., DUNSHEA, G., BOREN, L. & BAKER, C. S. 2013. Accounting for female reproductive cycles in a superpopulation capture-recapture framework. Ecological Applications, 23, 1677-1690.

CONSTANTINE, R., JACKSON, J. A., STEEL, D., BAKER, C. S., BROOKS, L., BURNS, D., CLAPHAM, P., HAUSER, N., MADON, B., MATTILA, D., OREMUS, M., POOLE, M., ROBBINS, J., THOMPSON, K. & GARRIGUE, C. 2012. Abundance of humpback whales in Oceania using photo-identification and microsatellite genotyping. Marine Ecology Progress Series, 453, 249-261.

ENVIRONMENT, D. O. T. 2013. Coordinated research framework to assess the national conservation status of Australian snubfin dolphins (Orcaella heinsohni) and other tropical inshore dolphins.

HEITHAUS, M. R. & DILL, L. M. 2002. Food availability and tiger shark predation risk influence bottlenose dolphin habitat use. Ecology, 83, 480-491.

JEFFERSON, T. A., HUNG, S. K. & WÜRSIG, B. 2009. Protecting small cetaceans from coastal development: Impact assessment and mitigation experience in Hong Kong. Marine Policy, 33, 305-311.

KENDALL, W. L. 1999. Robustness of closed capture-recapture methods to violations of the closure assumption. Ecology, 80, 2517-2525.

KENDALL, W. L., NICHOLS, J. D. & HINES, J. E. 1997. Estimating temporary emigration using capture-recapture data with Pollock's robust design. Ecology, 78, 563-578.

KISZKA, J. J., MÉNDEZ-FERNANDEZ, P., HEITHAUS, M. R. & RIDOUX, V. 2014. The foraging ecology of coastal bottlenose dolphins based on stable isotope mixing models and behavioural sampling. Marine

Biology, 161, 953-961. NICHOLSON, K., BEJDER, L., ALLEN, S. J., KRÜTZEN, M. & POLLOCK, K. H. 2012. Abundance, survival and

temporary emigration of bottlenose dolphins (Tursiops sp.) off Useless Loop in the western gulf of Shark Bay, Western Australia. Marine and Freshwater Research, 63, 1059-1068.

PALMER, C., BROOKS, L., PARRA, G. J., ROGERS, T., GLASGOW, D. & WOINARSKI, J. C. Z. 2014. Estimates of abundance and apparent survival of coastal dolphins in Port Essington harbour, Northern Territory, Australia. Wildlife Research, 41, 35.

PARRA, G. J., BEASLEY, I., ALLEN, S., BROOKS, L. & POLLOCK, K. H. 2012. Draft coordinated research strategy to collect information required to assess the national conservation status of Australian tropical inshore dolphins. Final Report to the Department of Sustainability, Environment, Water, Population and Communities.

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PARRA, G. J., CORKERON, P. J. & MARSH, H. 2006. Population sizes, site fidelity and residence patterns of Australian snubfin and Indo-Pacific humpback dolphins: Implications for conservation. Biological

Conservation, 129, 167-180. PARRA, G. J. & JEDENSJÖ, M. 2014. Stomach contents of Australian snubfin (Orcaella heinsohni) and Indo-

Pacific humpback dolphins (Sousa chinensis). Marine Mammal Science, 30, 1184-1198. READ, A. J. 2008. The looming crisis: Interactions between marine mammals and fisheries. Journal of

Mammalogy, 89, 541-548. SCHWARZ, C. J. & ARNASON, A. N. 1996. A general methodology for the analysis of capture-recapture

experiments in open populations. Biometrics, 52, 860-873. SMITH, H. C., POLLOCK, K., WAPLES, K., BRADLEY, S. & BEJDER, L. 2013. Use of the robust design to estimate

seasonal abundance and demographic parameters of a coastal bottlenose dolphin (Tursiops aduncus) population. PLoS One, 8, e76574.

THIELE, D. 2010. Collision course: snubfin dolphin injuries in Roebuck Bay. Report to WWF-Australia. TYNE, J. A., POLLOCK, K. H., JOHNSTON, D. W. & BEJDER, L. 2014. Abundance and Survival Rates of the

Hawai'i Island Associated Spinner Dolphin (Stenella longirostris) Stock. PLoS One, 9, e86132.

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Appendix 1 - Effort maps per sampling period

Figure A1-1. Effort map showing transects and total survey effort in the 2013 sampling period.

Figure A1-2. Effort map showing transects and total survey effort in the 2014 sampling period.

22

Appendix 2 - Group sighting maps per sampling period

Figure A2-1. Dolphin sightings and transect lines for the 2013 sampling period, illustrating group sizes. Depth contours are Lowest Astronomical Tide.

Figure A2-2. Dolphin sightings and transect lines for the 2014 sampling period, illustrating group sizes. Depth contours are Lowest Astronomical Tide.

23

Appendix 3 - Snubfin dolphin group sizes per sampling period

Figure A3-1. Frequency distribution of snubfin dolphin group sizes observed in the 2013 sampling period.

Figure A3-2. Frequency distribution of snubfin dolphin group sizes observed in the 2014 sampling period.

0

2

4

6

8

10

12

14

16

18

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

Fre

qu

en

cy

Group size

0

5

10

15

20

25

30

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

Fre

qu

en

cy

Group size

24

Appendix 4 - Encounter rates per transect for 2013 and 2014 Table A4-1. Total and per transect encounter rate for snubfin, bottlenose and humpback dolphins in 2013.

Transect Route Transect length

(km)

Survey area

(km2)

Encounter rate



1 A 67.5 32.6 1.57 0.25 0.55

2 B 50.7 25.3 1.54 0.24 0.00

3 A 59.1 28.9 1.42 0.00 0.00

4 B 63.6 31.4 0.19 0.03 0.00

5 A 59.8 29.6 1.35 0.14 0.00

6 B 53.3 26.8 1.64 0.00 0.00

7 A 64.5 32.0 2.31 0.03 0.00

Total

(mean)

418.5

(59.8)

206.5

(29.5)

1.43

(1.43)

0.10

(0.10)

0.09

(0.08)

Table A4-2. Total and per transect encounter rate for snubfin, bottlenose and humpback dolphins in 2014.

Transect Route Transect length

(km)

Survey area

(km2)

Encounter rate



1 B 47.08 23.1 0.13 0.00 0.00

2 A 56.18 27.6 1.41 0.11 0.00

3 B 58.72 28.8 1.14 0.00 0.00

4 A 45.29 22.2 1.31 0.14 0.00

5 B 57.42 28.2 1.24 0.18 0.00

6 A 64.10 31.3 1.18 0.00 0.00

7 B 60.55 29.7 1.75 0.10 0.00

Total

(mean)

389.3

(55.62)

191.1

(29.5)

1.19

(1.17)

0.07

(0.07)

0.00

(0.00)

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Appendix 5 - Encounter rate maps of each species per sampling period

Snubfin dolphins

Figure A5-1. Encounter rates of snubfin dolphins per 1 km × 1 km grid cell in the 2013 sampling period. Depth contours are Lowest Astronomical Tide.

Figure A5-2. Encounter rates of snubfin dolphins per 1 km × 1 km grid cell in the 2014 sampling period. Depth contours are Lowest Astronomical Tide.

26

Bottlenose dolphins

Figure A5-3. Encounter rates of bottlenose dolphins per 1 km × 1 km grid cell in the 2013 sampling period. Depth contours are Lowest Astronomical Tide.

Figure A5-4. Encounter rates of bottlenose dolphins per 1 km × 1 km grid cell in the 2014 sampling period. Depth contours are Lowest Astronomical Tide.

27

Humpback dolphins

Figure A5-5. Encounter rates of humpback dolphins per 1 km × 1 km grid cell in the 2013 sampling period (no humpback dolphins were observed in 2014). Depth contours are Lowest Astronomical Tide.

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Appendix 6 - Abundance estimate model outputs Table A6-1. Results of POPAN open models applied to the 2013 sampling period, each incorporating either constant (.) or time-varying (t) parameters of phi = apparent survival; p = capture probability; pent = probability of entry. * phi(.)p(.)pent(.) model produced spurious estimates of N with 0 SE and was omitted from model averaging.

Model QAICc Delta QAICc AICc Weights Model Likelihood Num. Par

phi(fixed=1)p(.)pent(fixed=0) 180.2 0.0 0.4 1.0 2

phi(.)p(.)pent(t) 181.4 1.2 0.2 0.6 5

phi(t)p(.)pent(.) 182.1 1.9 0.1 0.4 5

phi(.)p(t)pent(t) 183.7 3.5 0.1 0.2 9

phi(.)p(t)pent(.) 183.8 3.6 0.1 0.2 8

phi(fixed =1)p(t)pent(fixed =0) 184.2 3.9 0.1 0.1 7

phi(t)p(t)pent(.) 184.7 4.4 0.0 0.1 7

phi(t)p(t)pent(t) 185.4 5.2 0.0 0.1 9

phi(t)p(.)pent(t) 186.6 6.4 0.0 0.0 8

phi(.)p(.)pent(.)* 186.7 6.5 0.0 0.0 2

Table A6-2. Results of POPAN open models applied to the 2014 sampling period, each incorporating either constant (.) or time-varying (t) parameters of phi = apparent survival; p = capture probability; pent = probability of entry.

Model QAICc Delta QAICc AICc Weights Model Likelihood Num. Par

phi(t)p(t)pent(t) 213.1 0.0 0.6 1.0 7

phi(t)p(t)pent(.) 215.7 2.7 0.2 0.3 6

phi(t)p(.)pent(t) 216.5 3.4 0.1 0.2 5

phi(.)p(t)pent(t) 217.0 3.9 0.1 0.1 8

phi(t)p(.)pent(.) 219.4 6.3 0.0 0.0 4

phi(.)p(t)pent(.) 220.9 7.9 0.0 0.0 8

phi(fixed=1)p(.)pent(fixed=0) 224.9 11.8 0.0 0.0 2

phi(fixed=1)p(t)pent(fixed=0) 225.0 11.9 0.0 0.0 7

phi(.)p(.)pent(t) 228.1 15.1 0.0 0.0 6

phi(.)p(.)pent(.) 228.3 15.3 0.0 0.0 5

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Table A6-3. Results of POPAN open models applied to the 2013-2014 sampling periods combined, each incorporating either constant (.) or time-varying (t) parameters of phi = apparent survival; p = capture probability; pent = probability of entry. ‘Globally closed models’ have phi=1 and pent=0 fixed across all sampling occasions. ‘Closed within periods’ models phi=1 and pent=0 fixed between sampling occasions within each of the two periods, but not between the two periods.

Model QAICc

Delta

QAICc

AICc

Weights

Model

Likelihood Num. Par

phi(t)p(t)pent(t) 683.6 0.0 0.5 1.0 15

phi(t)p(.)pent(t) 684.5 0.9 0.3 0.6 9

phi(t)p(t)pent(.) 686.1 2.5 0.1 0.3 15

phi(.)p(t)pent(t) 689.0 5.4 0.0 0.1 16

phi(.)p(t)pent(.) 690.5 6.9 0.0 0.0 13

phi(t)p(.)pent(.) 690.6 7.1 0.0 0.0 8

phi(.=1)p(t)pent(.=0) globally closed 691.0 7.5 0.0 0.0 12

phi(t=1)p(t)pent(t=0) closed within periods 692.5 9.0 0.0 0.0 13

phi(t=1)p(.)pent(t=0) closed within periods 692.6 9.1 0.0 0.0 2

phi(.)p(.)pent(t) 692.7 9.1 0.0 0.0 5

phi(.)p(.)pent(.) 693.1 9.5 0.0 0.0 2

phi(.=1)p(.)pent(.=0) globally closed 698.2 14.6 0.0 0.0 2

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Table A6-4. Model averaged parameter estimates from the 2013 and 2014 models listed in Table A6-1 and A6-2. phi = apparent survival; p = capture probability (per transect); pent = probability of entry; Nd = estimated abundance of distinctive animals; SE = standard error; LCI and UCI = lower and upper 95% confidence intervals respectively.

2013 2014

Parameter Estimate SE LCI UCI Estimate SE LCI UCI

Phi Group 1 Parameter 1 0.98 0.05 0.15 1.00 0.99 0.03 0.93 1.00





p Group 1 Parameter 6 0.36 0.12 0.17 0.61 0.33 0.11 0.15 0.57






pent Group 1 Parameter 12 0.02 0.04 0.00 0.52 0.00 0.01 0.00 0.03





Nd (net super-population) 117.61 12.02 94.05 141.16 107.53 15.19 77.76 137.29

Nd (gross super-population) 117.75 12.23 93.78 141.73 119.90 15.22 90.08 149.72

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Table A6-5. Model averaged parameter estimates from the 2013-2014 combined models listed in Table A6-3. phi = apparent survival; p = capture probability (per transect); pent = probability of entry; Nd = estimated abundance of distinctive animals; SE = standard error; LCI and UCI = lower and upper 95% confidence intervals respectively.

Parameter Estimate SE LCI UCI

Phi Group 1 Parameter 1 0.96 0.05 0.69 1.00











p Group 1 Parameter 12 0.31 0.06 0.21 0.43












pent Group 1 Parameter 24 0.00 0.01 0.00 0.01











Nd (net super-population) 125.46 8.32 109.16 141.77

Nd (gross super-population) 127.19 8.68 110.17 144.21

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Appendix 7 - Dugong sightings Dugong were frequently observed throughout the majority of the study area (Figure A-4). Each time they were observed, the date, time, water depth, estimated group size and location were recorded. However, groups were not approached for detailed survey, so locations, group sizes and water depths are approximate only. The definition of a group was fairly loose i.e. individuals within 100-200 m of each other. A total of 44 and 37 dugong sightings were recorded in 2013 and 2014 respectively, including those observed during survey effort and opportunistically when not on effort. Without the ability to identify individuals, some of these observations may represent resights of the same animal(s) within a single day.

Figure A7-1. Dugong sightings recorded during the 2013 and 2014 study periods. Group sizes are minimum estimates and include calves. Transect lines are shown in grey. Depth contours are in Lowest Astronomical Tide.

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