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Abundance, movements and habitat use of coastal dolphins in the Darwin region

Abundance, movements and

habitat use of coastal dolphins in

the Darwin region

Analysis of the first five primary samples (October 2011 to October 2013)

STATPLAN CONSULTING PTY LTD

March 14, 2014

Lyndon Brooks & Kenneth Pollock (2014). Abundance, movements and habitat use of

coastal dolphins in the Darwin region: Analysis of the first five primary samples (October

2011 to October 2013). Final report to the Northern Territory Government Department of

Land Resource Management.

INPEX Doc. Number: L384-AH-REP-10010_0


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Contents Contents .......................................................................................................................................................... 1

Executive Summary ........................................................................................................................................ 2

Context ........................................................................................................................................................ 2

Methods ...................................................................................................................................................... 2

Results......................................................................................................................................................... 2

Abundance .............................................................................................................................................. 3

Movements.............................................................................................................................................. 3

Apparent Survival ................................................................................................................................... 4

Habitat Use ............................................................................................................................................. 4

Conclusion .................................................................................................................................................. 5

Introduction ..................................................................................................................................................... 6

Methods .......................................................................................................................................................... 7

Sampling ..................................................................................................................................................... 7

Data analysis ............................................................................................................................................. 10

Abundance, apparent survival and movements ..................................................................................... 11

Habitat use ............................................................................................................................................ 14

Results........................................................................................................................................................... 17

Abundance, Apparent Survival and Movements ...................................................................................... 17

Humpback dolphin ................................................................................................................................ 17

Bottlenose dolphin ................................................................................................................................ 18

Snubfin dolphin ..................................................................................................................................... 20

Summary of abundance estimates ......................................................................................................... 21

Habitat use ................................................................................................................................................ 24

Summary of habitat use ........................................................................................................................ 29

Conclusion .................................................................................................................................................... 30

REFERENCES ............................................................................................................................................. 31

Appendix ......................................................................................................................................................... 0

Table A1 Dates of secondary samples by site for each primary sample ..................................................... 1

Table A2 Summary of captures by species, site and primary sample ......................................................... 2

Table A3 Model comparison results for models on each species ............................................................... 5

Table A4 Parameter estimates from selected models for each species ....................................................... 8



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Executive Summary

Context

The Darwin Harbour Coastal Dolphin Monitoring Program was initiated as part of the environmental

approvals under the Commonwealth Environment Protection and Biodiversity Conservation Act 1999 and

the Northern Territory Environmental Assessment Act 1982 for the INPEX Ichthys Gas Field Development

project. The stated aim of the program is:

“To detect change, beyond natural spatial and temporal variation, in coastal dolphin abundance and

distribution during near shore Project construction activities in Darwin Harbour, including pre- and post-

construction phase monitoring.”

Methods

The demographic parameters, abundance, apparent survival, temporary emigration and movement rates

were estimated for three species of coastal dolphin using an extension of the Robust Design model known

as the Multistate Robust Design model. This model provides an integrated analysis of the data over the

three sites sampled as part of the monitoring program (Bynoe Harbour, Darwin Harbour and Shoal Bay)

including estimates of rates of movement of dolphins between the three sites between successive pairs of

five primary samples (October/November 2011, March/April 2012, October 2012, March/April 2013 and

October/November 2013).

Sufficient data were available to build a Multistate Robust Design model for all three sites for humpback

dolphins (Sousa sp.). Conversely, for bottlenose dolphins (Tursiops sp.) there were too few data from some

sites to allow analysis, and therefore, the data for Bynoe Harbour and Shoal Bay were pooled to yield

estimates for Darwin Harbour and elsewhere in the local region. Similarly, the data for the Australian

snubfin dolphin (Orcaella heinsohni) were pooled across all three sites to yield a single set of estimates for

the whole local region.

A Binary Logistic Mixed Effects model was employed to estimate the relative rates of use of locations

(sub-sites) in the local region over the five primary samples. The model was fitted to the data for all

species combined as there were too few data on bottlenose and snubfin dolphins to support separate

models for these species.

Results

The ability to model more complex effects or to obtain estimates of demographic parameters for all sites

was limited for snubfin and bottlenose dolphins due to the small sizes of these populations. This limitation

was more acute for snubfin than bottlenose dolphins due to the irregularity of their visitation to the area

and greater difficulty of capturing and recapturing them. The population size and recapture rate for



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humpback dolphins were sufficient however to allow models to generate estimates with good precision at

all three sites.

Abundance

Humpback dolphins were the most abundant of the three species at all three sites in the region. While their

numbers have remained reasonably stable in Darwin Harbour and Shoal Bay with 40-49 using Darwin

Harbour and 15-25 using Shoal Bay in each 3-week primary sample, there was a reduction in the number

using Bynoe Harbour in the last primary sample from 23-30 in the earlier primary samples down to 14 in

primary sample five (October/November 2013). Overall, 73-97 Humpbacks use the region during a

primary sample with fewer in primary sample five (October/November 2013) than previously, due mostly

to the reduction in Bynoe Harbour.

Bottlenose dolphins rarely use Bynoe Harbour and the few data that were available for that site were

pooled with those from Shoal Bay to obtain estimates for Bynoe Harbour/Shoal Bay and Darwin Harbour.

Six to 10 bottlenose dolphins were found to use Bynoe Harbour/Shoal Bay in primary samples one to four

(October /November 2011, March/April 2012, October 2012 and March/April 2013), increasing to 18 in

the last primary sample (October/November 2013). Seventeen to 31 bottlenose dolphins were found to use

Darwin Harbour over the first four primary samples ((October /November 2011, March/April 2012,

October 2012 and March/April 2013) reducing to 12 in the last primary sample (October/November 2013).

While there has been more movement from Darwin Harbour to Bynoe Barbour/Shoal Bay than in the other

direction in between recent primary samples, overall, 26-37 bottlenose dolphins use the region during a

primary sample.

The Australian snubfin dolphin may be the least abundant or use the region in about the same numbers as

the bottlenose dolphin. Visitation of the region by this species is irregular, and their capture and recapture

rates are highly variable over time. The snubfin data were the most difficult to model and it was necessary

to pool the data over all three sites to obtain estimates for the region. There has been a marked increase in

the number of snubfin using the region from 18-31 in earlier primary samples to 68 in the last primary

sample (October/November 2013). This increase was partly due to the observation of 11 new snubfin in

Bynoe Harbour in primary sample five (October/November 2013) but also to the absence of temporary

emigration between the last two primary samples (March/April 2013 to October/November 2013), as

described below.

Movements

There were sometimes substantial movements of humpback dolphins between Bynoe Harbour and Darwin

Harbour, varying between three and 33 percent in one direction or the other between successive primary

samples. The movement of 33% of the Bynoe Harbour population in primary sample two (March/April

2012) to Darwin Harbour in primary sample three (October 2012) was by far the greatest. One movement



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was observed between Darwin Harbour and Shoal Bay between primary samples four and five

(March/April 2013 to October/November 2013) with this being the only movement ever observed between

either of Darwin Harbour or Bynoe Harbour and Shoal Bay. We found no evidence of temporary

emigration from the local region between primary samples.

Movements of bottlenose dolphins were observed between Bynoe Harbour/Shoal Bay and Darwin Harbour

between primary samples two and three (26% between March/April 2012 and October 2012), and between

Darwin Harbour and Bynoe Harbour/Shoal Bay sites between primary samples one and two (11% between

October /November 2011 and March/April 2012), three and four (23% between October 2012 and

March/April 2013) and four and five (27% between March/April 2013 and October/November 2013). We

found no evidence of temporary emigration between primary samples.

While movements of snubfin dolphins between sites were observed, it was not possible to model them.

Temporary emigration of snubfin from the local region between successive primary samples was high at

56 to 64 percent over primary samples one to four (October /November 2011, March/April 2012, October

2012, March/April 2013) but there was no temporary emigration between the last two primary samples

(i.e., none of those on site in March/April 2013 were off site in October/November 2013). Apparently,

more of the local snubfin dolphin population remained in the sample area rather than move outside it

between the last two primary samples than previously, partly accounting for the marked increase in their

abundance in the last period.

Apparent Survival

The annual apparent survival rate (alive and on site) of humpback dolphins varied markedly between

Darwin Harbour at around 0.92 and Bynoe Harbour and Shoal Bay at around 0.46 and 0.67 respectively,

suggesting substantial emigration from the latter two sites. While corresponding recruitment into these

sites as generally maintained relatively stable numbers there, reductions were observed in the last primary

sample (October/November 2013), particularly in Bynoe Harbour.

The annual apparent survival rate for bottlenose dolphins was around 0.87, which may be close to the true

biological survival rate for the species, and this suggests a relatively small rate of emigration from the local

region.

The annual apparent survival rate for snubfin dolphins was around 0.90 which may be close to the true

biological survival rate for the species, suggesting a relatively small rate of emigration from the local

region. Although there is generally substantial temporary emigration from the local region between

primary samples, most snubfin that use the area at some time are likely to return there.

Habitat Use

Significant changes over time were observed in East Arm and Middle Arm in Darwin Harbour.



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In East Arm, a significant increase in the sighting rate over primary samples from primary sample two

(March/April 2012) to primary sample five (October/November 2013), appears to be largely driven by the

very low rate in primary sample two. In Middle Arm, while there were significant decreases in the sighting

rate between highs in primary samples two (March/April 2012) and three (October 2012) to primary

sample five (October/November 2013), the rate observed in primary sample five was not as low as, and not

significantly different to, the rate observed in primary sample one (October /November 2011).

The sources of the differences in sighting rates between primary samples in East Arm and Middle Arm

detected in this report are unknown.

Conclusion

While the abundances of the three dolphin species are quite small, they have remained relatively stable

over the duration of the study so far, although there was a reduction in the number of humpback dolphins

using Bynoe Harbour and a marked increase the number of snubfin dolphins using the region in the last

primary sample. We do not speculate on the sources of the observed variation in estimated rates of use of

the habitat in East Arm and Middle Arm in Darwin Harbour between primary samples.



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Introduction

As part of the environmental approvals under the Commonwealth Environment Protection and

Biodiversity Conservation Act 1999 and the Northern Territory Environmental Assessment Act 1982 for the

INPEX Ichthys Gas Field Development Project, a monitoring program for coastal dolphins was required

for Darwin Harbour. The monitoring program includes pre- and post- construction phase monitoring.

Project dredging in Darwin Harbour East Arm and for the gas export pipeline as well as marine pile

driving for the product loading jetty and module offloading facility are considered to be the extent of

construction phase for this monitoring program.

The stated aim of the program is:

“To detect change, beyond natural spatial and temporal variation, in coastal dolphin abundance and

distribution during near shore Project construction activities in Darwin Harbour, including pre- and post-

construction phase monitoring.”

Three species of coastal dolphin inhabit the Darwin Harbour region (extending from Gunn Point to Bynoe

Harbour): Indo-Pacific humpback (Sousa sp.; hereafter referred to as humpback, see Mendez et al. 2013

for recent taxonomic results), Australian snubfin (Orcaella heinsohni, hereafter referred to as snubfin) and

bottlenose (Tursiops sp., hereafter referred to as bottlenose) dolphins. All three species are listed as Marine

and Migratory species (and hence are matters of National Environmental Significance) under the

Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act).

Monitoring of the local populations of the three species of dolphin in Darwin Harbour for the Ichthys

project commenced in October 2011. The population sizes of each species in Darwin Harbour have

previously been estimated as small, with approximately 40, 18 and eight individual humpback, bottlenose

and snubfin dolphins, respectively (Brooks and Pollock, 2012). Population sizes in Bynoe Harbour and

Shoal Bay were smaller with approximately 30 humpback, four bottlenose and 10 snubfin in Bynoe

Harbour, and 15 humpback, 11 bottlenose and a small but unknown number of snubfin in Shoal Bay.

The first two primary sample surveys may be viewed as constituting a pre-construction phase baseline as

no construction activity occurred during this period. Dredging first began in August 2012 with backhoes;

cutter suction dredging commenced in November 2012 and continued through the 2012/2013 wet season

(dredging was suspended during the 2013 dry season) which includes primary samples three (October

2012) and four (March/April 2013) and recommenced just prior to primary sample 5 in October 2013.

Construction pile driving began in July 2013 and continued through primary sample five in

October/November 2013.

The objectives for this report are, for the available data up to October 2013 (primary sample five), to:



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1. Assess changes in population dynamic parameters of the three coastal dolphin species at the three

sites, including population size, losses (mortality + emigration), gains (births + immigration) and

temporary emigration (assumes sufficient population sizes of a species at a site to yield adequate

samples for analysis) before, during and after the construction of the Ichthys LNG facility in

Darwin Harbour.

2. Assess changes in the spatio-temporal distribution (pattern of habitat use) of the three coastal

dolphin species at each of the three sites, including movements between the sites (assumes

adequate data on movements) and site fidelity before, during and after the construction of the

Ichthys LNG facility in Darwin Harbour.

Methods

Sampling

The sampling design for the Darwin Harbour Dolphin Monitoring Program is based on a Robust Design

sampling structure (Brooks and Pollock 2011, Pollock et al. 1990, Williams et al. 2002) of two primary

samples per year (wet and dry season samples), each consisting of nine secondary samples at each of three

sites (Darwin Harbour, Bynoe Harbour, Shoal Bay). Each secondary sample was defined as a complete set

of transects through a site (Brooks and Pollock 2011, Griffiths and Palmer 2011). It was planned that,

weather permitting, each secondary sample would be taken in one day using four boats in Darwin Harbour,

three in Bynoe Harbour and one in Shoal Bay. The four boats alternate each three days between all four in

Darwin Harbour, and three in Bynoe Harbour and one in Shoal Bay. Alternating between sites in this way

was intended to minimise movement between sites between secondary samples to facilitate fitting

multistate models which assume that all sites are sampled simultaneously.

The principal data collected on survey are the locations and species of dolphin groups, and photographs of

the dorsal fins of individual dolphins. The data on the locations of sighted dolphin groups were used to

model their spatial distribution, while the photographs were used to identify individuals from the nicks and

scars on their dorsal fins to yield capture-recapture data to model abundance, apparent survival and

movements.

Capture-recapture methods have been widely used to estimate demographic parameters for a number of

dolphin species including snubfin, humpback and bottlenose dolphins (Würsig and Jefferson 1990; Parra et

al. 2006; Nicholson et al. 2012, Palmer et al. 2014). Many cetaceans bear nicks and marks that allow

identification of individuals from photographs, and such identifiers provide a mechanism for population

estimation based on capture-recapture methods, where re-sightings of individuals with distinctive natural

marks constitute re-captures (Hammond and Thompson 1990). A general overview of capture-recapture

models is found in Amstrup et al. (2005) while more detailed coverage is found in Williams et al. (2002).



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The Robust Design model is described and its parameters specified in Pollock et al. (1990), Kendall and

Nichols (1995), and Kendall, et al. (1995, 1997).

Figure 1 shows a small group of bottlenose dolphins in Darwin Harbour, Figure 2 shows a group of

bottlenose dolphins surfacing in calm water, Figure 3 shows a researcher collecting photos to sort out

who’s who, and Figure 4 maps the transect lines followed nine times in each primary sample at the three

sites.

Figure 1 A small group of bottlenose dolphins in Darwin Harbour



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Figure 2 A group of bottlenose dolphins surfacing in calm water

Figure 3 Researcher taking photos to sort out who’s who



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Figure 4 Map of locations of transect lines in Bynoe Harbour, Darwin Harbour and Shoal Bay

Sampling was completed for the first five primary samples at all sites between:

20th

October and 18th

November 2011 (primary sample one – pre-construction),

26th

March and15th

April 2012 (primary sample two – pre-construction),

8th

October 2012 and 27th

October 2012 (primary sample three – dredging season one),

13th

March 2013 and 2nd

April 2013 (primary sample four – dredging season two), and

21st October 2013 and 30

th November 2013 (primary sample five – dredging season three).

The dates of the primary samples and the secondary samples of which each is composed at each site are

reported in the Appendix, Table A1.

Data analysis

The number of secondary samples with non-zero captures, the number of individuals captured,the

maximum number of captures per individual and the total number of captures of all individuals are

reported for each species at each site in each primary sample in the Appendix, Table A2.



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Abundance, apparent survival and movements

The Multistate Closed Robust Design Model (MSCRD, Nichols & Coffman 1999, Kendall & Nichols

2002, Kendall 2013) was employed for analysis of the capture-recapture data to estimate abundance,

apparent survival, and movements between sites and temporary emigration between primary samples. This

is at once an extension of the Closed Robust Design model (CRD, Pollock 1982, Kendall and Nichols

1995, Kendall et al. 1997) and the multistate model for recapture data (Arnason 1972, 1973; Brownie et al.

1993; Schwarz et al. 1993).

The CRD model was employed in a previous report (Brooks & Pollock 2013) for analysis of abundance

and apparent survival, and a multistate model based on data collapsed to primary samples (i.e., not robust

design) was employed for analysis of movements between the three sites. Here, as in the last report, these

two kinds of models are combined in the MSCRD model.

The MSCRD model provides estimates of:

1. Apparent survival between primary samples (probabilities of being alive and present in the sample

area, S parameters)

2. Movements between sites and temporary emigration between primary samples (probabilities, psi

parameters). Whereas temporary emigration is modelled in terms of gamma” and gamma’

parameters in the CRD, temporary emigration is included among the movements (psi parameters)

in the MSCRD by defining an ‘unobservable’ state for dolphins that are temporarily absent in a

primary sample.

3. Abundance at each primary sample (N parameters).

Whereas the CRD model deals with only one site (here, Bynoe Harbour, Darwin Harbour, Shoal Bay or all

considered as one regional site) at a time, the MSCRD model can simultaneously provide these estimates

for multiple states (here multiple sites, Bynoe Harbour, Darwin Harbour and Shoal Bay).

With three sites (Bynoe Harbour, Darwin Harbour and Shoal Bay) four states were defined: three

observable states (the three sites) and one unobservable state for temporary absence from all three sites.

Dolphins may move between all four states (or stay where they were) between pairs of primary samples,

with such movements being modelled as transition probabilities. The complete set of possible between-

state movements and non-movements (transition probabilities) for the intervals between primary samples

is:

1. Bynoe Harbour – remained in Bynoe Harbour.

2. Darwin Harbour – remained in Darwin Harbour.

3. Shoal Bay – remained in Shoal Bay.

4. Unobservable state – remained in unobservable state.

5. Movements between Bynoe Harbour and Darwin Harbour.



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6. Movements between Bynoe Harbour and Shoal Bay.

7. Movements between Darwin Harbour and Bynoe Harbour.

8. Movements between Darwin Harbour and Shoal Bay.

9. Movements between Shoal Bay and Bynoe Harbour.

10. Movements between Shoal Bay and Darwin Harbour.

11. Movements between Bynoe Harbour and the unobservable state (absent from Bynoe Harbour,

Darwin Harbour and Shoal Bay).

12. Movements between Darwin Harbour and the unobservable state (absent from Bynoe Harbour,

Darwin Harbour and Shoal Bay).

13. Movements between Shoal Bay and the unobservable state (absent from Bynoe Harbour, Darwin

Harbour and Shoal Bay).

14. Movements from the unobservable state to Bynoe Harbour.

15. Movements from the unobservable state to Darwin Harbour.

16. Movements from the unobservable state to Shoal Bay.

Movements between an observable and the unobservable state (temporary emigration, 4 and 11 to 16

above) may be modelled as:

1. Random, where, for each interval, the probability of staying away after an absence from the local

region is equal to the probability of leaving (i.e., is independent of previous state).

2. Markovian, where, for each interval, the probability of staying away after an absence from the

local region is not equal to the probability of leaving (i.e., depends on previous state).

3. Even flow, where, for each interval, the probability of returning to a site after an absence from the

local region is equal to the probability of leaving the site to the unobservable state.

Movements to and from the unobservable state in the MSCRD are equivalent to the temporary emigration

(gamma’’ and gamma’ parameters, for temporary absence given presence or absence respectively in the

last primary sample) in the CRD. Consequently, for Markovian models, in the MSCRD as in the CRD, if

the probability of apparent survival varies by primary sample (apparent survival varies over intervals

between primary samples), the last transition probability must be constrained to equal a transition

probability from an earlier interval. For such models we’ve set the last transition probability (primary

sample four to primary sample five) equal to the second last transition probability (primary sample three to

primary sample four).

Similarly, in the MSCRD as in the CRD, the probability of apparent survival for temporarily absent

(unobservable) dolphins must be constrained to be equal to the probability of apparent survival for

dolphins in an observable state.



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The MSCRD model estimates transitions between but not within primary samples, and requires that a

single site be identified for each individual in each primary sample. We nominated the site in which each

dolphin was last observed in a primary sample as its state for that primary sample.

The probabilities of movement between a pair of sites can only be estimated for intervals between primary

samples for which there was at least one observed movement. We’ve set the transition probabilities

between pairs of sites for intervals for which no movements were observed to zero.

The probability of capture (p) may be specified to vary by any or all of site, primary sample and secondary

sample. After elimination of poorly fitting models, we found no need to model the variation over

secondary samples within primary samples for humpback or bottlenose dolphins but this was necessary for

snubfin dolphins due to their very uneven capture rates over time. Models are reported with p varying by

site and by site by primary sample [p(site) and p(site*time] for humpbacks where there were three

observable states, by site or constant over sites [p(site) and p(constant)] for bottlenose where there were

two observable states, and by primary sample by secondary sample [p(primary*secondary)] for snubfin

where there was only one observable state.

The probability of capture (p) may be distinguished from the probability of recapture (c) following first

capture to indicate a behavioural response to first capture to persistent avoidance of recapture (‘trap-

shyness’) or to persistent seeking of recapture (‘trap-happiness’). While this sort of effect has been

observed in classic trapping studies with small mammals for example, it is considered unlikely in the

present situation where the dolphins are not actually trapped or otherwise interfered with and largely

habituated to the presence of vessels prior to their first capture. We consider only models in which the

probabilities of capture and recapture are equal on all occasions.

The modelling process involves fitting a set of models with alternative parameter structures and comparing

them for fit to data and parsimony. Models were compared with the Akaike Information Criterion

corrected for small sample sizes (AICc, Burnham and Anderson 2002), with smaller values of AICc

indicating better fitting models, and with AICc weights, which measure the relative likelihoods of the

models in the set. When one model in the set had a clearly lower AICc than all others and attracted the

major proportion of the AICc weight, the parameter estimates from this ‘best’ model are reported; when

several models have similar AICc values and shared the AICc weight, model-averaging may be applied

(Buckland et al. 1997) whereby a weighted average of the parameter estimates from several models are

reported.

The Multistate Closed Robust Design model in Program MARK (V6.1; White and Burnham 1999) was

employed for the analysis for all species of dolphin. The models, their AICc values, AICc weights,

likelihoods and numbers of parameters are reported in the Appendix, Table A3. The parameter estimates

from the best fitting model or model averaged estimates for each species at each site in each primary

sample are reported in the Appendix, Table A4..



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Habitat use

A dolphin population may change the relative frequency with which different parts of its habitat are used

according to seasonal or other variation in the environment. We used a Binary Logistic Mixed Effects

model to examine changes in spatial habitat use of dolphins in the three sites. A 3.2 km x 3.2 km grid was

placed over a map of the three sites (Bynoe Harbour, Darwin Harbour and Shoal Bay) and data on

sightings of dolphin groups and sampling intensity in each grid cell in each secondary sample were

modelled to estimate the relative probability of sighting at least one dolphin in a transect pass of a given

length in each grid cell.

The grid cells were grouped into 10 coherent locations in the three sites, with three, five and two locations

in Bynoe Harbour, Darwin Harbour and Shoal Bay respectively: in Bynoe Harbour, 19 cells were grouped

as Outer, 15 as Middle and 13 as Upper; in Darwin Harbour, nine cells were grouped as Outer, 11 as East

Arm, 12 as Middle Arm, seven as Central and nine as West Arm; and in Shoal Bay, seven cells were

grouped as Gunn Point and 10 as Hope Inlet/Buffalo Creek.

The transects through the region moved slightly between primary samples and the interaction of variable

transect locations and fixed grid cells resulted in 112 cells being sampled in at least one of the five primary

samples: 105 cells were sampled in all four primary samples, one was sampled in four and six were

sampled in only one. A map of the grid cells overlaid on the transect lines in primary sample five

(October/November 2013) is shown in Figure 5.



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Figure 5 Map of grid cells overlaid on transect lines in primary sample five (October/November 2013)



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While the data modelled were the binary response ‘dolphin sighted’ / ‘no dolphin sighted’ of each cell in

each secondary sample, the results from the model are estimated binomial means (proportions or

probabilities of sighting a dolphin) based on the binary data accumulated over secondary samples and

locations. The principal factors assessed were the primary sample and the location. Changes in habitat use

between the primary samples are modelled by the primary sample by location interaction effect which

assesses whether the relative rates of usage of the locations varies significantly between primary samples.

A non-significant interaction effect would indicate a lack of evidence of change in the relative rates of use

of the locations over the primary samples. A significant interaction effect indicates a correlation with

potential inference to impact only if the interaction involved locations closer and further way from

construction activities between primary samples.

The grid cells were sampled with different intensities, measured here in terms of the total length of transect

through a cell in each secondary sample. A single transect through and aligned with the cell would be 3.2

km long but most transects passed through cells at angles and were not aligned with them, and there was

more than one transect segment through some cells.

Primary sample, location and their interaction were initially fitted together with a linear function of

transect length through the cell to adjust for sampling intensity. Should the interaction effect not be

significant, the model was systematically reduced by eliminating non-significant effects (p≥0.05) one at a

time in order of their p-value sizes.

A model was fitted to the data for the sightings of any species of dolphin (i.e., all three species pooled). It

may be possible in future to fit a separate model for humpback dolphins but there are too few sightings of

bottlenose and snubfin to model these species separately.

The model was fitted to the sightings data with random factors for the cell and the repeated measures on

the cell with a first order autoregressive structure (AR1) fitted to the repeated measures residuals. The

‘Genlinmixed’ procedure in SPSS V22 was employed for the analysis. Genlinmixed uses a pseudo-

likelihood method to obtain estimates with fixed effects tested by F statistics.



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Results

Abundance, Apparent Survival and Movements

Humpback dolphin

Model selection

Model comparison results are reported for a set of nine of the best-fitting (smallest AICc) models in Table

A3. The best fitting model had apparent survival varying by site [S(site)], transitions between Bynoe

Harbour and Darwin Harbour and between Darwin Harbour and Bynoe Harbour varying by primary

sample, a transition between Darwin Harbour and Shoal Bay between primary samples four and five, and

no temporary emigration [psi(a_b*t, b_a*t, b4_c5, No TE] and capture probability varying by both site and

primary sample [p(site*time)]. This model attracted 94% of the AICc weight. The parameter estimates

from the best-fitting model are reported in Table A4.

Apparent survival

There was little support for variation in apparent survival (the annual probability of both remaining alive

and on site) of humpback dolphins between successive pairs of the five primary samples, but strong

support for differences among the three sites (Table A3). Apparent survival was greater in Darwin Harbour

than either of Bynoe Harbour or Shoal Bay, with estimated apparent survival in Darwin Harbour = 0.92

(95%CI = 0.80:0.97) per annum, in Bynoe Harbour = 0.46 (95%CI = 0.33:0.61) per annum, and in Shoal

Bay = 0.67 (95%CI = 0.46:0.83) per annum.

With no reason to expect differences in biological survival between sites, the lower rates of apparent

survival in Bynoe Harbour and Shoal Bay than in Darwin Harbour indicate emigration from those sites,

and with no observed movements between Bynoe Harbour and Shoal Bay, it seems likely that the

emigration from Bynoe Harbour is to the west and from Shoal Bay to the east.

Movements

Only one movement was observed between Bynoe Harbour or Darwin Harbour and Shoal Bay in either

direction, with an individual moving between Darwin Harbour in primary sample four (March/April 2013)

and Shoal Bay in primary sample five (and October/November 2013). Movements were observed between

Bynoe Harbour and Darwin Harbour in both directions between each successive pair of primary samples.

A total of eighteen such movements have been observed thus far, with most occurring between Bynoe

Harbour and Darwin Harbour between primary samples two and three (five between March/April 2012 and

October 2012), and between Darwin Harbour and Bynoe Harbour between primary samples three and four

(five between October 2012 and March/April 2013 ).



Page 18

There was significant variation in humpback dolphin movement rates between the five primary samples.

The estimated rates of movement from Bynoe Harbour to Darwin Harbour between primary samples one

and two (October/November 2011 to March/April 2012), two and three (March/April 2012 to October

2012), three and four (October 2012 to March/April 2013), and four and five (March/April 2013 to

October/November 2013) were 6% (95%CI = 1:32%), 33% (95%CI = 15:58%), 10% (95%CI =1:44%) and

9% (95%CI = 1:45%) respectively. The estimated rates of movement in the opposite direction, from

Darwin Harbour to Bynoe Harbour, between successive primary samples were 9% (95%CI = 2:29%), 3%

(95%CI = 1:19%), 15% (95%CI = 7:30%) and 5% (95%CI = 1:19%) respectively. There was a relatively

small rate of movement of 3% (95%CI = 1:20%) between Darwin Harbour and Shoal Bay between

primary samples four and five (March/April 2013 to October/November 2013).

These rates indicate movement of occasionally substantial proportions of the population between Darwin

Harbour and Bynoe Harbour in either direction, and an occasional low rate of movement between Darwin

Harbour and Shoal Bay. Movement between Bynoe and Darwin Harbours has continued through all

primary periods and now includes Shoal Bay with a movement to Shoal Bay being observed in primary

sample five.

Abundance

The estimated size of the Bynoe Harbour humpback population in primary samples one, two, three, four

and five (October /November 2011, March/April 2012, October 2012, March/April 2013 and

October/November 2013) was 29 (95%CI=26:41), 30 (95%CI=25:42), 23 (95%CI=15:45), 30 (95%CI=25-

45) and 14 (95%CI=13-23) respectively. In Darwin Harbour there were 42 (95%CI=38:53), 43

(95%CI=39:54), 49 (95%CI=43:61), 43 (95%CI=41:50) and 40 (95%CI=39:48) respectively, while in

Shoal Bay they were 15 (95%CI=13:24), 16 (95%CI=15:24), 25 (95%CI=21:38), 23 (95%CI=13:52) and

19 (95%CI=15:34) respectively.

These estimates are reasonably stable over primary samples except for the reduction in Bynoe Harbour in

primary sample five (October/November 2013). The total for all three sites varied slightly with 86, 89, 97,

96 and 73 over the five primary samples. There were fewer humpback dolphins in the region in primary

sample five (October/November 2013) than previously. The reduction appears to be largely due to

emigration from Bynoe Harbour.

Bottlenose dolphin

Very few bottlenose dolphins were ever observed in Bynoe Harbour, with four observed there in single

secondary samples in each of primary samples one (October/November 2011) and three (October 2012),

and six observed there in primary sample five (October/November 2013) (Table A2). There were too few

data to derive estimates for Bynoe Harbour and barely sufficient to derive estimates for Shoal Bay. The



Page 19

data from these two sites were pooled and Bynoe Harbour and Shoal Bay modelled as a single site

(BH&SB).

Model selection

Model comparison results from a set of six better fitting (lower AICc) models are reported in Table A3. All

models have capture probability varying by both site and primary sample [p(site*time)], and all estimate

the transitions between either Bynoe Harbour or Shoal Bay and Darwin Harbour between primary samples

two and three (March/April 2012 to October 2012), and between Darwin Harbour and either Bynoe

Harbour or Shoal Bay between primary samples one and two (October/November 2011 to March/April

2012), three and four (October 2012 to March/April 2013), and four and five (March/April 2013 to

October/November 2013) [psi(ac2_b3, b1_ac2,b3_ac4, b4_ac5,…)]. The models vary in whether they

estimate temporary emigration as time-varying and random [psi(…, Random TE)], time-varying and

Markovian [psi(…, Markovian TE)], constant and random [psi(…, Constant Random TE)], time-varying

and even flow [psi(…, Even Flow TE)] or as having no temporary emigration [psi(…, No TE)]. All

reported models had apparent survival as constant over both sites and primary samples [S(constant)].

The best fitting model had a very simple structure with apparent survival constant over both sites and

primary samples and no temporary emigration. This model attracted 89% of the AICc weight in the set.

The parameter estimates from the best-fitting model are reported in Table A4.

Apparent survival

Preliminary assessment found no evidence of apparent survival of bottlenose dolphins differing between

the intervals between primary samples or between the two sites (Bynoe and Shoal Bay combined and

Darwin Harbour). The estimated apparent survival rate was 0.87 (95%CI=0.61:0.96) per annum in both

sites over all intervals between primary samples. This may be about the rate of biological survival, or

slightly lower and indicate a small degree of emigration from the local region.

Movements

One individual was observed to have moved between Darwin Harbour in primary sample one

(October/November 2011) and either Bynoe Harbour or Shoal Bay in primary sample two (March/April

2012); two were observed to have moved between either Bynoe Harbour or Shoal Bay in primary sample

two (March/April 2012) and Darwin Harbour in primary sample three (October 2012); one was observed

to have moved between Darwin Harbour in primary sample three (October 2012) and either Bynoe

Harbour or Shoal Bay in primary sample four (March/April 2013); and three were observed to have moved

from Darwin Harbour in primary sample four (March/April 2013) and either Bynoe Harbour or Shoal Bay

in primary sample five (October/November 2013).



Page 20

There was substantial variation in the estimated bottlenose dolphin movement rates in the intervals

between the five primary samples. Eleven percent (95%CI=3%:36%) of the bottlenose dolphins in Darwin

Harbour in primary sample one (October/November 2011) were estimated to have moved to either Bynoe

Harbour or Shoal Bay in primary sample two (March/April 2012); 26% (95%CI=6%:64%) of those in

Bynoe Harbour or Shoal Bay in primary sample two (March/April 2012) were estimated to have moved to

Darwin Harbour in primary sample three (October 2012); 23% (95%CI=7%:56%) of those in Darwin

Harbour in primary sample three (October 2012) were estimated to have moved to either Bynoe Harbour

or Shoal Bay in primary sample four (March/April 2013); and 27% (95%CI=10%:55%) of those in Darwin

Harbour in primary sample four (March/April 2013) were estimated to have moved to either Bynoe

Harbour or Shoal Bay in primary sample five (October/November 2013).

There was only weak evidence for temporary emigration and none was estimated.

Abundance

The estimated size of the Bynoe Harbour/Shoal Bay population in primary samples one, two, three, four

and five (October /November 2011, March/April 2012, October 2012, March/April 2013 and

October/November 2013) was 6 (95%CI=6:11), 9 (95%CI=8:18), 6 (95%CI=5:17), 10 (95%CI=6:30) and

18 (95%CI=10:50) respectively, while in Darwin Harbour there were 20 (95%CI=20:20), 17

(95%CI=16:25), 31 (95%CI=25:48), 17 (95%CI=16:24) and 12 (95%CI=12:18) respectively.

There has been a steady increase in bottlenose abundance in Bynoe Harbour and Shoal Bay matched by a

steady decrease in Darwin Harbour from primary samples three to five (October 2012 to

October/November 2013). The total abundance for all sites has varied only slightly however, with

estimates of 26, 26, 38, 26 and 30 over primary samples. While 26-38 bottlenose dolphins use the local

region in a primary period, the trend since primary sample three (October 2012) has been towards more

use of Bynoe Harbour or Shoal Bay than Darwin Harbour.

Snubfin dolphin

There were too few data to obtain separate estimates for Darwin Harbour or Shoal Bay, and while there

were more captures in Bynoe Harbour than elsewhere, the rates of capture and recapture there were highly

irregular. The data from all three sites were combined and models fitted for the whole local region.

Model selection

Model comparison results from a set of eight better fitting (lower AICc) models are reported in Table A3.

All models have capture probability varying by both primary sample and secondary sample

[p(primary*secondary)].



Page 21

The best fitting (lowest AICc) model had apparent survival constant over primary samples and time-

varying Markovian temporary emigration (Table A3). While this model attracted 58% of the AICc weight

it estimated apparent survival at 1.000 with a tiny standard error, a sign of estimation problems, and is not

interpreted. When this model was removed from the set, the model with apparent survival constant over

primary samples and time-varying random emigration attracted 78% of the AICc weight in the remaining

set of seven models. The estimates from this model are reported in Table A4.

Apparent survival

There was no evidence of variation in apparent survival of snubfin dolphins over the intervals between

successive primary samples with 98.5% of the AICc weight on the three models with constant apparent

survival. The estimated apparent survival rate was 0.90 (95%CI=0.54:0.99) per annum. This may be about

the rate of biological survival, or slightly lower and indicate a small degree of emigration from the local

region.

Movements

The only movements in this model are movements to and from the unobservable state, or temporary

emigration estimates. While the temporary emigration rate was reasonably consistent at 0.56-0.64 (all 95%

confidence intervals within the range 0.31 to 0.79) over the first three intervals, it was estimated at zero for

the last interval indicating that the dolphins present in the sample area in primary sample four

(March/April 2013) were also there in primary sample five (October/November 2013).

Abundance

The estimated size of the local regional population in primary samples one, two, three, four and five

(October /November 2011, March/April 2012, October 2012, March/April 2013 and October/November

2013) was 164 (95%CI=65:555), 18 (95%CI=16:28), 29 (95%CI=24:48), 18 (95%CI=18:18) and 68

(95%CI=50:109), respectively. The very large estimate for primary sample one (October/November 2011)

appears to be anomalous with only one of thirty individuals recaptured. Eleven new, not-previously-

identified snubfin were observed in Bynoe Harbour in primary sample five (October/November 2013).

These entries to the population together with the number that would previously have been temporarily

absent and off the sample area but were not on this occasion probably account for the increase in the

estimated number present in primary sample five (October/November 2013).

Summary of abundance estimates

The abundance estimates at the three sites (Bynoe Harbour, Darwin Harbour, Shoal Bay) for humpback

dolphins, at two sites (Bynoe Harbour and Shoal Bay, Darwin Harbour) for bottlenose dolphins and in the

local region (Bynoe Harbour, Darwin Harbour and Shoal Bay) for snubfin dolphins by primary sample are

summarised in Table 1. The estimates are plotted in Figure 6.



Page 22

Table 1 Summary of abundance estimates for the three species over five primary samples

Species Site Primary

sample Estimate SE L95%CI U95%CI

Humpback Bynoe Harbour 1 29 3.16 26.27 40.56

2 30 3.90 25.23 42.29

3 23 6.63 15.38 44.68

4 30 4.57 24.84 44.66

5 14 1.90 13.18 23.42

Darwin Harbour 1 42 3.41 37.93 52.85

2 43 3.66 38.65 54.33

3 49 4.29 43.08 61.11

4 43 1.82 41.45 50.14

5 40 1.99 38.55 47.91

Shoal Bay 1 15 2.18 13.31 24.47

2 16 1.73 15.20 24.32

3 25 3.77 20.83 37.56

4 23 8.72 13.35 51.96

5 19 4.01 15.44 33.78

Bottlenose Bynoe Harbour 1 6 1.03 6.00 10.71

and Shoal Bay 2 9 1.76 8.12 18.03

3 6 2.13 5.15 17.08

4 10 4.82 5.91 29.73

5 18 8.70 9.79 50.11

Darwin Harbour 1 20 0.00

2 20.00 20.01

2 17 1.59 16.15 24.73

3 31 5.50 24.78 48.46

4 17 1.23 16.04 23.63

5 12 0.93 12.00 17.51

Snubfin Bynoe Harbour, 1 301 30 30

Darwin Harbour 2 18 2.20 16.24 27.90

and Shoal Bay 3 29 5.18 24.08 47.53

4 18 0.00 18.00 18.00

5 68 14.20 49.65 108.73

Notes:

1. The number captured = 30 is used as a minimum population estimate. The model estimate

of 164 (SE = 106, 95%CI = 65:555) was based on a single recapture and appears to be

anomalous.

2. This is a very small but non-zero standard error.



Page 23

Humpbacks in Bynoe Harbour Humpbacks in Darwin Harbour Humpbacks in Shoal Bay

Bottlenose in Bynoe Harbour and

Shoal Bay

Bottlenose in Darwin Harbour Snubfin in Bynoe, Darwin and

Shoal Bay

Figure 6 Abundance estimates with 95% confidence intervals over five primary samples: humpback

dolphins in Bynoe Harbour, Darwin Harbour and Shoal Bay; bottlenose dolphins in Bynoe Harbour plus

Shaol Bay, and Darwin Harbour; and snubfin dolphins in Bynoe Harbour plus Darwin Harbour plus Shoal

Bay. See notes to Table 1 for estimates without confidence intervals.

0

10

20

30

40

50

60

70

1 2 3 4 50

10

20

30

40

50

60

70

1 2 3 4 5

0

10

20

30

40

50

60

70

1 2 3 4 5

0

10

20

30

40

50

60

1 2 3 4 5

0

10

20

30

40

50

60

1 2 3 4 5

0

20

40

60

80

100

120

1 2 3 4 5



Page 24

Habitat use

A map of the sighting positions of dolphin groups over the five primary samples is shown in Figure 7.

Figure 7 Map of sighting positions of dolphin groups over the five primary samples. Group sightings in

different primary samples are plotted in different colours as indicated in the legend.



Page 25

Results of the tests of fixed effects for the binary logistic model are reported in Table 2. Only one model

was fitted as the primary sample by location interaction effect was significant.

Table 2 Tests of fixed effects for binary logistic model

Model Effect F df1 df2 p

1 transect length 134.563 1 4764 0.000

primary 1.578 4 4764 0.177

location 2.851 9 4764 0.002

primary * location 1.526 36 4764 0.023

The estimated mean probability of sighting a dolphin group from a secondary sample with the mean

transect length of 3.78 km is plotted by location by primary sample in Figure 8.

Figure 8 Estimated probability of sighting a dolphin group in a secondary sample

of transect length = 3.78 km with 95%CI by location by primary sample (P1 to P5).

Changes in the probabilities of sighting between primary samples were assessed separately for each

location with pairwise comparison tests adjusted their number by the sequential Bonferroni method.

Significant changes over time were observed in East Arm and Middle Arm in Darwin Harbour. The rate of

sighting in East Arm has steadily increased over primary samples from a low in primary sample 2

.000

.020

.040

.060

.080

.100

.120

.140

.160

.180

.200

BH outer BH

middle

BH

upper

DH outer DH East

Arm

DH

Middle

Arm

DH

central

DH West

Arm

SB Gunn

Point

SB Hope

Inlet /

Buffalo

Creek

P1

P2

P3

P4

P5



Page 26

(March/April 2012), with the increase between primary sample two and primary sample five

(October/November 2013) being significant (p = 0.024).

The rate of sighting in Middle Arm increased from a low in primary sample one (October/November 2011)

to primary sample two (March/April 2012), maintained at a relatively high rate over primary samples two,

three and four (March/April 2012, October 2012 and March/April 2013), and decreased in primary sample

five (October/November 2013) to slightly greater than in primary sample one (October/November 2011).

The increases between primary sample one (October/November 2011) and primary samples two, three and

four (March/April 2012, October 2012 and March/April 2013) were each significant (p=0.011, 0.018,

0.045 respectively). Among the decreases to primary sample five (October/November 2013) from primary

samples two, three and four (March/April 2012, October 2012 and March/April 2013), only the decreases

to the low in primary sample 5 (October/November 2013) from primary samples two and three

(March/April 2012 and October 2012) were significant (p = 0.028, p = 0.045).

In East Arm, the significance of the increase in the sighting rate over primary samples from primary

sample two (March/April 2012) to primary sample five (October/November 2013) appears to be largely

driven by the very low rate in primary sample two (March/April 2012). In Middle Arm, while there were

significant decreases in the sighting rate between highs in primary samples two (March/April 2012) and

three (October 2012) to primary sample five (October/November 2013), the rate observed in primary

sample five (October/November 2013), was not as low as, and not significantly different to, the rate

observed in primary sample one (October/November 2011).

For descriptive purposes, blending over these differences between primary samples (pooling over primary

samples), the estimated overall mean probability of sighting a dolphin group in each location from a

secondary sample with the mean transect length of 3.78 km is plotted with 95% confidence interval in

Figure 9 and mapped in Figure 10.



Page 27

Figure 9 Estimated relative probability of sighting a dolphin group in a secondary sample of transect length

= 3.78 km with 95%CI by location with 95% confidence intervals for all primary samples.

.000

.050

.100

.150

.200

.250

BH outer BH

middle

BH

upper

DH

outer

DH East

Arm

DH

Middle

Arm

DH

central

DH

West

Arm

SB Gunn

Point

SB Hope

Inlet /

Buffalo

Creek

U95%CI

L95%CI

Estimated probability



Page 28

Figure 10 Map of Darwin region showing relative rates of habitat use (probability of occurrence) over

locations for all primary samples



Page 29

Overall, that probabilities of sighting were relatively high in Shoal Bay (Gunn Point and Hope

Inlet/Buffalo Creek) and in the outer Harbours (Bynoe Outer, Darwin Outer and Gunn Point), and within

Darwin Harbour, in East Arm and West Arm.

Summary of habitat use

The statistical power to detect differences has increased with the accumulation of data. The sources of the

differences in sighting rates between primary samples in East Arm and Middle Arm detected in this report

are unknown.

Estimates of the relative rates of use of the locations and information about the natural variation in these

estimates over primary samples have been provided in this report. These estimates are for groups of any

species of dolphin but it is intended to fit a separate model for humpback dolphins in future now that

adequate data are available. It’s notable that the outer harbour areas are relatively well used and that this is

consistent with and complementary to evidence from the capture-recapture models of movement into and

out of the Darwin region: there is evidently a flow of dolphins not only across the outer Harbour areas in

the Darwin region but also to and from sites west of Bynoe Harbour and east of Shoal Bay.



Page 30

Conclusion The major constraint on obtaining estimates of abundance, movement and apparent survival was the small

sizes of the populations of bottlenose and snubfin dolphins, with the snubfin appearing to have irregular

patterns of visitation to the sampling areas. Where too few dolphins were observed to model for each site

separately, estimates were obtained by pooling the data over sites.

Adequate data were available to obtain estimates of abundance for humpback dolphins in all three sites, to

estimate their rates of movement between Bynoe Harbour and Darwin Harbour, temporary emigration

from the local region, and their apparent survival at all three sites. The number of humpback dolphins in

the sample area has declined slightly in the last primary sample (October/November 2013), with most

losses probably having been due to emigration from Bynoe Harbour.

For bottlenose dolphins, estimates were obtained of abundance, apparent survival for Bynoe

Harbour/Shoal Bay and Darwin Harbour, temporary emigration from the local region, and rates of

movement between the two sites. While their numbers in the sample area have remained relatively stable

there has been a steady net movement of bottlenose dolphins from Darwin Harbour to the other sites,

Bynoe Harbour and Shoal Bay, since primary sample three (October 2012).

For snubfin dolphins, estimates were obtained of abundance, temporary emigration and apparent survival

for the whole local region. While the numbers of snubfin dolphins in the area remained fairly stable over

the first four primary samples, the entry of new individuals into the population and lack of temporary

emigration in the last interval has seen a marked increase in the number present in the area in primary

sample five (October/November 2013).

The sources of the differences in sighting rates between primary samples in East Arm and Middle Arm

detected in this report are unknown. Over all primary samples, the outer Harbour areas (Outer Bynoe

Harbour, Outer Darwin Harbour and Shoal Bay, especially Gunn Point) are relatively well used and that

this is consistent with and complementary to evidence from the capture-recapture models of movement

into and out of the Darwin region: there is evidently a flow of dolphins not only across the outer Harbour

areas in the Darwin region but also to and from sites west of Bynoe Harbour and east of Shoal Bay.

Overall, although it was necessary to pool data over some sites for bottlenose and snubfin dolphins, the

sampling design has generated data of a quantity and structure that allows the models to generate

reasonably precise estimates of abundance, movements and other demographic parameters. Group

sightings data were also pooled to fit the habitat use model to describe the relative frequency of use of

parts of the sample area for any species of dolphin. With the accumulation of data it will be possible in

future to fit a separate model for humpback dolphins.



Page 31

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Appendix

Table A1 Dates of secondary samples by site for each primary sample Page 1

Table A2 Summary of captures by species, site and primary sample Pages 2-3

Table A3 Model comparison results for models on each species Pages 4-6

Table A4 Parameter estimates from selected models for each species Pages 7-12



Page 1

Table A1 Dates of secondary samples by site for each primary sample

Primary Secondary sample

sample Site 1 2 3 4 5 6 7 8 9

1 Darwin 02.11.2011 03.11.2011 04.11.2011 09.11.2011 10.11.2011 11.11.2011 16.11.2011 17.11.2011 18.11.2011

1 Bynoe 29.10.2011 30.10.2011 31.10.2011 05.11.2011 06.11.2011 07.11.2011 12.11.2011 13.11.2011 14.11.2011

1 Bynoe 15.11.2011

1 Shoal Bay 20.10.2011 21.10.2011 22.10.2011 05.11.2011 06.11.2011 07.11.2011 12.11.2011 13.11.2011 14.11.2011

1 Shoal Bay 08.11.2011

2 Darwin 26.03.2012 27.03.2012 28.03.2012 02.04.2012 03.04.2012 04.04.2012 09.04.2012 10.04.2012 11.04.2012

2 Darwin 12.04.2012

2 Bynoe 29.03.2012 30.03.2012 31.03.2012 05.04.2012 06.04.2012 07.04.2012 13.04.2012 14.04.2012 15.04.2012

2 Shoal Bay 29.03.2012 30.03.2012 31.03.2012 05.04.2012 06.04.2012 07.04.2013 12.04.2012 13.04.2012 14.04.2012

3 Darwin 08.10.2012 09.10.2012 10.10.2012 15.10.2012 16.10.2012 17.10.2012 22.10.2012 23.10.2012 24.10.2012

3 Bynoe 11.10.2012 12.10.2012 13.10.2012 18.10.2012 19.10.2012 20.10.2012 25.10.2012 26.10.2012 27.10.2012

3 Shoal Bay 11.10.2012 12.10.2012 13.10.2012 18.10.2012 19.10.2012 20.10.2013 25.10.2012 26.10.2012 27.10.2012

3 Shoal Bay 19.10.2012

4 Darwin 13.03.2013 14.03.2013 15.03.2013 20.03.2013 21.03.2013 22.03.2013 27.03.2013 28.03.2013 29.03.2013

4 Bynoe 16.03.2013 17.03.2013 18.03.2013 23.03.2013 24.03.2013 25.03.2013 31.03.2013 1.04.2013 2.04.2013

4 Shoal Bay 16.03.2013 17.03.2013 18.03.2013 23.03.2013 24.03.2013 25.03.2013 31.03.2013 1.04.2013 2.04.2013

5 Darwin 24.10.2013 25.10.2013 26.10.2013 01.11.2013 02.11.2013 03.11.2013 08.11.2013 09.11.2013 10.11.2013

5 Bynoe 28.10.2013 29.10.2013 30.10.2013 04.11.2013 05.11.2013 06.11.2013 11.11.2013 12.11.2013 13.11.2013

5 Shoal Bay 21.10.2013 22.10.2013 23.10.2013 28.11.2013 29.11.2013 30.11.2013 04.11.2013 05.11.2013 06.11.2013



Page 2

Table A2 Summary of captures by species, site and primary sample

Species Site Primary

sample Secondary samples

1 Individuals Max.Caps.

2 Captures

Snubfin Bynoe 1 5 25 2 26





Snubfin Darwin 1 1 5 1 5





Snubfin Shoal Bay 1 0 0 0 0





Snubfin All sites 1 5 30 2 31





Humpback Bynoe 1 9 26 4 49




Page 3




Humpback Darwin 1 9 33 4 62





Humpback Shoal Bay 1 5 11 3 18





Humpback All sites 1 9 69 4 129





Bottlenose Bynoe 1 1 4 1 4





Bottlenose Darwin 1 5 18 4 45





Page 4



Bottlenose Shoal Bay 1 3 5 3 10





Bottlenose All sites 1 6 23 4 59




Bottlenose All sites 5 6 19 4 37 1

Number of secondary samples with non-zero captures 2 Maximum number of captures per individual



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Table A3 Model comparison results for models on each species Notes:

1. S = probability of apparent survival, psi = probability of transition including temporary emigration, p = probability of capture, *t indicates variation over

primary samples.

2. a indicates Bynoe Harbour (BH), b indicates Darwin Harbour (DH), c indicates Shoal Bay (SB), ab indicates Bynoe Harbour & Shoal Bay, u indicates

unobservable (temporarily absent from region), a_b indicates transition from a to b.

3. S(…, u=b) indicates apparent survival for temporarily absent dolphins set equal to Darwin Harbour.

AICc Model Number of

Species Sites Model AICc ∆AICc Weight Likelihood Parameters

Humpback BH,DH,SB {S(site, u=b), 2281.589 0.000 0.943 1.000 42

psi(a_b*t, b_a*t, b4_c5, No TE),

p(site*time)}

Humpback BH,DH,SB {S(site*time, u=b), 2287.238 5.649 0.056 0.059 51


p(site*time)}


psi(a_b*t, b_a*t, b4_c5, Even Flow TE),

p(site*time)}



p(site)}


psi(a_b*t, b_a*t, b4_c5, Even Flow TE),

p(site*time)}




Page 6


p(site)}


psi(a_b*t, b_a*t, b4_c5, Random TE),

p(site*time)}


psi(a_b*t, b_a*t, b4_c5, Markovian TE),

p(site*time)}


psi(a_b*t, b_a*t, b4_c5, Random TE),

p(site*time)}

Bottlenose BH&SB,DH {S(constant), 662.177 0.000 0.888 1.000 25

psi(ac2_b3, b1_ac2, b3_ac4, b4_ac5, No TE),

p(site*time)}


psi(ac2_b3, b1_ac2, b3_ac4, b4_ac5, Constant Random TE),

p(site*time)}


psi(ac2_b3, b1_ac2, b3_ac4, b4_ac5, Even Flow TE),

p(site*time)}


psi(ac2_b3, b1_ac2, b3_ac4, b4_ac5, Random TE),

p(site*time)}


psi(ac2_b3, b1_ac2, b3_ac4, b4_ac5, Constant Random TE),

p(site)}




Page 7

psi(ac2_b3, b1_ac2, b3_ac4, b4_ac5, Markovian TE),

p(site*time)}

Snubfin BH&DH&SB {S(constant) 216.678 0.000 0.581 1.000 37

psi(time) Markovian TE

p(primary*secondary)}


psi(time), Random TE



psi(constant), Random TE



Psi(time) Markovian TE


Snubfin BH&DH&SB {S(time) 226.330 9.651 0.005 0.008 34

psi(constant), Random TE



psi(constant) Markovian TE



psi(time), Random TE



psi(time) Markovian TE




Page 8

Table A4 Parameter estimates from selected models for each species

Notes: Notation for the model is described above Table A3

Species Parameter Site Primary sample Secondary Estimate SE LCI UCI

Humpback Model: {S(site, u=b), psi(a_b*t, b_a*t, b4_c5, No TE), p(site*time)}

Apparent survival BH 1 to 2 = 2 to 3 = 3 to 4 = 4 to 5 0.46 0.07 0.33 0.61

Apparent survival DH 1 to 2 = 2 to 3 = 3 to 4 = 4 to 5 0.92 0.04 0.8 0.97

Apparent survival SB 1 to 2 = 2 to 3 = 3 to 4 = 4 to 5 0.67 0.1 0.46 0.83

Transition BH to DH 1 to 2 0.06 0.06 0.01 0.32




Transition DH to BH 1 to 2 0.09 0.06 0.02 0.29




Transition DH to SB 4 to 5 0.03 0.03 0.00 0.20

Capture BH 1 0.18 0.03 0.13 0.25

Capture BH 2 0.15 0.03 0.11 0.20

Capture BH 3 0.08 0.02 0.04 0.14

Capture BH 4 0.13 0.02 0.09 0.19

Capture BH 5 0.20 0.05 0.13 0.31

Capture DH 1 0.19 0.03 0.15 0.25

Capture DH 2 0.18 0.02 0.14 0.22

Capture DH 3 0.16 0.02 0.13 0.20

Capture DH 4 0.27 0.02 0.23 0.32

Capture DH 5 0.26 0.03 0.21 0.31



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Capture SB 1 0.19 0.04 0.12 0.29

Capture SB 2 0.22 0.04 0.15 0.30

Capture SB 3 0.14 0.03 0.10 0.20

Capture SB 4 0.05 0.02 0.03 0.10

Capture SB 5 0.13 0.03 0.08 0.21

Abundance BH 1 29 3.16 26.27 40.56

Abundance BH 2 30 3.90 25.23 42.29

Abundance BH 3 23 6.63 15.38 44.68

Abundance BH 4 30 4.57 24.84 44.66

Abundance BH 5 14 1.90 13.18 23.42

Abundance DH 1 42 3.41 37.93 52.85

Abundance DH 2 43 3.66 38.65 54.33

Abundance DH 3 49 4.29 43.08 61.11

Abundance DH 4 43 1.82 41.45 50.14

Abundance DH 5 40 1.99 38.55 47.91

Abundance SB 1 15 2.18 13.31 24.47

Abundance SB 2 16 1.73 15.20 24.32

Abundance SB 3 25 3.77 20.83 37.56

Abundance SB 4 23 8.72 13.35 51.96

Abundance SB 5 19 4.01 15.44 33.78

Bottlenose Model: {S(constant), psi(ac2_b3, b1_ac2, b3_ac4, b4_ac5, No TE), p(site*time)}

Apparent survival BHSB=DH All 0.87 0.08 0.61 0.96

Transition BHSB to DH 2 to 3 0.26 0.16 0.06 0.64

Transition DH to BHSB 1 to 2 0.11 0.08 0.03 0.36



Capture BHSB 1 0.33 0.10 0.17 0.54



Page 10

Capture BHSB 2 0.30 0.08 0.18 0.46

Capture BHSB 3 0.19 0.07 0.09 0.37

Capture BHSB 4 0.11 0.05 0.04 0.25

Capture BHSB 5 0.08 0.03 0.03 0.18

Capture DH 1 0.47 0.05 0.38 0.56

Capture DH 2 0.37 0.05 0.28 0.48

Capture DH 3 0.17 0.03 0.11 0.24

Capture DH 4 0.37 0.05 0.28 0.48

Capture DH 5 0.40 0.06 0.28 0.52

Abundance BHSB 1 6 1.03 6.00 10.71

Abundance BHSB 2 9 1.76 8.12 18.03

Abundance BHSB 3 6 2.13 5.15 17.08

Abundance BHSB 4 10 4.82 5.91 29.73

Abundance BHSB 5 18 8.70 9.79 50.11

Abundance DH 1 20 0.00 20.00 20.01

Abundance DH 2 17 1.59 16.15 24.73

Abundance DH 3 31 5.50 24.78 48.46

Abundance DH 4 17 1.23 16.04 23.63

Abundance DH 5 12 0.93 12.00 17.51

Snubfin Model: {S(constant), psi(time), p(primary*secondary)}

Apparent survival BH&DH&SB 1 to 2 = 2 to 3 = 3 to 4 = 4 to 5 0.90 0.09 0.54 0.99

Random TE 1 to 2 0.61 0.11 0.39 0.79

Random TE 2 to 3 0.56 0.13 0.31 0.78

Random TE 3 to 4 0.64 0.09 0.46 0.79

Random TE 4 to 5 0.00 0.00 0.00 0.00

Capture 1 2 0.09 0.06 0.02 0.31

Capture 1 3 0.02 0.02 0.00 0.11



Page 11

Capture 1 5 0.01 0.01 0.00 0.06

Capture 1 7 0.01 0.01 0.00 0.06

Capture 1 9 0.07 0.05 0.02 0.26

Capture 2 2 0.40 0.13 0.19 0.65

Capture 2 4 0.34 0.12 0.15 0.60

Capture 2 6 0.06 0.06 0.01 0.31

Capture 2 8 0.68 0.14 0.38 0.88

Capture 3 3 0.03 0.03 0.00 0.21

Capture 3 5 0.03 0.03 0.00 0.21

Capture 3 7 0.38 0.11 0.19 0.60

Capture 3 8 0.24 0.09 0.11 0.45

Capture 3 9 0.41 0.12 0.21 0.64

Capture 4 1 0.28 0.11 0.12 0.52

Capture 4 2 0.94 0.05 0.69 0.99

Capture 4 5 0.06 0.05 0.01 0.31

Capture 4 � 0.39 0.11 0.20 0.62

Capture 5 2 0.06 0.03 0.02 0.16

Capture 5 5 0.18 0.06 0.09 0.32

Capture 5 6 0.20 0.06 0.10 0.34

Capture 5 7 0.02 0.02 0.00 0.10

Capture 5 8 0.09 0.04 0.04 0.20

Capture 5 9 0.09 0.04 0.04 0.20

Abundance 1 164 106 65 555

Abundance 2 18 2 16 28



Abundance 5 68 14 50 109



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