Australian Marine Mammal Centre Final Report

Season 2015

Title - Satellite tagging of blue whales in southern Australian waters: examining movements and occupancy patterns to inform management decision-making

Chief Investigator – Assoc Prof Luciana Moller, Dr Catherine Attard Co-Investigator – Dr Mike Double, Dave Paton, Dr Kerstin Bilgmann Organisation – Flinders University

Activity Period – 3 November 2014 – 30 October 2015 Table of contents 1. Activity Summary 2. The Outcomes/Objectives 3. Appropriateness 4. Effectiveness 1. Activity Summary A clear summary of approximately 500 words outlining the work undertaken and any significant findings (for publication on the Department's web site) We undertook a satellite telemetry study to investigate the movements and occupancy patterns of blue whales that seasonally inhabit the Bonney Upwelling region. This is important for identifying biologically important areas for these whales, such as potentially the Great Australian Bight, and when and where anthropogenic activities may disrupt them. The Bonney Upwelling off the coast of southern Australia is a known feeding area for pygmy blue whales (Balaenoptera musculus brevicauda) and little is known about occupancy patterns and movements of these whales in this region and adjacent waters. During January-March 2015 we satellite tagged 13 whales (5 with depth/location SPLASH MK10 and 8 with location-only SPOT transmitters; Wildlife Computers, USA) in the Bonney Upwelling. The tags and deployment method were those previously used and refined by the Australian Antarctic Division (e.g. Double et al. 2014) involving a modified version of the Air Rocket Transmitter System (ARTS; Heide-Jørgensen et al. 2001). Telemetry data were collected using the Argos satellite system. Tagged whales were also biopsy sampled to determine subspecies and sex. Photo-ID images (right and/or left side) were obtained for 29 blue whales, including 12 of the satellite tagged whales, and uploaded to the electronic Southern Hemisphere Blue Whale Catalogue (SHBWC). Up to the date of submission of this report, tags transmitted from a range of 2 days and 4 hrs to 200 days and 12 hours (mean=72.4 days±14). Whales performed square-, U- and V-shape dives, dives recorded to a maximum of 492 m (mean=59.5 m±94.3), and for a maximum of 112 min (mean=6.1 min±5.2). Dives were on average deeper at

night (mean=87 m±1.5) than during the day (mean=32.6 m±1.5). Whale movements in the Bonney Upwelling region ranged from eastern South Australia, over the continental shelf south of Kangaroo Island, to between mainland Australia and Tasmania. Four whales were tracked leaving the Bonney Upwelling region between April and June 2015. They travelled west into the Great Australian Bight where tags stopped, except one whale that continued transmitting while migrating northward along the western Australian coast to Indonesia (Banda Sea). This tag was still sending intermittently by the time of submission of this report (31 October 2015). One of the 13 tags had failed to transmit after tagging, but started transmitting seven months later when the whale was south of the Indonesian islands of Bali and Java. The tag was still sending intermittently by the time of preparation of this report. The distances travelled by the tagged whales ranged from 237 km for the tag (#131124) that transmitted for 2 days and 4 hrs, to 17,042 km for the tag (#123229) that transmitted for 200 days and 12 hours (mean=5588.3 km ±1223.6). We analysed the Argos location data by fitting a hierarchical switching state-space model (hSSSM) with the R package ‘bsam’ (Jonsen et al. 2007) to correct for Argos location error and to determine behavioural states (area restricted search (ARS) versus transiting). Over the time periods the tags were transmitting, the whales showed ARS behaviour 76% of the time, and transiting 24% of the time. Genetic analysis of biopsy samples, using 20 microsatellite markers, revealed that all tagged whales that were biopsied were of the pygmy blue whale subspecies (see Attard et al. 2012 for details of analysis). Of the 10 biopsied whales, four were genetically sexed as female and six as male. Altogether, results confirm the importance of the Bonney Upwelling as a feeding area for blue whales in Australia, and indicate the whales’ migratory route along the southern and western Australian coastlines. Results also inform about the location and timing of potential impacts from anthropogenic activities; these can be used for management decision-making under Australia’s EPBC Act 1999, for the Blue Whale Conservation Management Plan and Marine Bioregional Planning, and for developing inter-governmental collaborations to protect the species. 2. The Outcomes/Objectives The degree to which the Activity has achieved the objectives Objective The objective is to determine the occupancy patterns and movements of blue whales in the Bonney Upwelling region, and potentially also movements of blue whales from the Bonney Upwelling region to adjacent areas in the Great Australian Bight and Bass Strait, to other feeding/suspected feeding areas, and/or to breeding areas. This is to be conducted by deploying up to 15 satellite tags (and concurrently obtaining genetic samples and photo-IDs) on blue whales in the Bonney Upwelling region between January and March 2015. Degree of Achievement: Successful

Outcomes Summary of field work A total of 13 satellite tags (Wildlife Computers) were deployed on blue whales in the Bonney Upwelling region of South Australia during two field trips between January and March 2015 (Table 1; Figure 1). All 13 whales were adults, and one of them had an accompanying calf. Five of the deployed tags were Mk10 SPLASH tags that recorded geo-location, dive behaviour, dive depth and dive duration. The remaining eight tags deployed were light level SPOT tags that recorded geo-location, temperature and light levels. One of the Mk10 tags was deployed on the adult whale with an accompanying calf. All blue whales were satellite tagged off South Australia (off towns of Robe, Beachport and Port MacDonnell) between longitudes 139.6 and 140.9 (Figure 1), in continental shelf waters. Field work was conducted in continental shelf areas of up to 130 m water depth and as far as 23 nautical miles from shore. The boat effort equated to 2,287 nautical miles (tagging and support vessels combined) during the 21 days that weather permitted working on the water (out of 40 days in the field locations). Of the 13 tagged whales, 10 were successfully biopsy sampled and 12 were successfully photo-identified. Table 1 Details of satellite tags deployed on 13 blue whales in the Bonney Upwelling region between January and March 2015. The details shown for each tag are the tag number, tag type, date deployed, % tag implantation (estimated visually), tag status at date of submission of this report, photo-ID (photos are accessible through the Southern Hemisphere Blue Whale Catalogue (SHBWC)), biopsy ID and sex of individual (M = male; F = female; and U = unknown sex). *tag deployed on adult whale with accompanying calf.

Tag ID/ Ptt No. Tag Type Date Deployed % Implant Date stopped Photo-ID SHBWC Alias Biopsy ID Sex

131124 SPLASH (Mk10) 21-Jan-15 100 23-Jan-15 FLBW001 BU1-15 F 131125 SPLASH (Mk10) 22-Jan-15 95 14-Apr-15 FLBW003 BU2-15 M 131123 SPLASH (Mk10) 22-Jan-15 90 24-Apr-15 no photo-ID BU3-15 M 131122 SPLASH (Mk10) 27-Feb-15 80-85 5-Apr-15 FLBW007 no biopsy U 131139 SPLASH* (Mk10) 2-Mar-15 100 23-Apr-15 FLBW010 BU4-15 F 123227 SPOT (light level) 2-Mar-15 100 25-Apr-15 FLBW012 no biopsy U 123233 SPOT (light level) 3-Mar-15 100 28-Jun-15 FLBW016 BU5-15 M 123235 SPOT (light level) 7-Mar-15 95 + oblique 2-May-15 FLBW017 BU6-15 M 123234 SPOT (light level) 10-Mar-15 100 9-Jul-15 FLBW022 BU7-15 M 131177 SPOT (light level) 10-Mar-15 100 Still sending FLBW024 BU8-15 M 123230 SPOT (light level) 13-Mar-15 95-98 stopped 7-Apr-15 FLBW020 BU9-15 F

123229 SPOT (light level) 13-Mar-15 95 Still sending FLBW028 BU10-15 F 131174 SPOT (light level) 13-Mar-15 90-95 30-Apr-15 FLBW015 no biopsy U

Figure 1 Locations of 13 satellite tag deployments on blue whales in the Bonney Upwelling region, between January and March 2015. Deployment locations are marked with X and labelled with tag numbers. Argos data collection Argos data was downloaded once a week and collated over the time period the tags were transmitting, between 21 January 2015 and the submission of the report on 30 October 2015. By the time of the submission of this report two tags were still transmitting. The weekly download will continue until all tags stop transmitting, and data checked for up to one year after last transmission in case a tag resumes transmitting.

SA VIC

Robe

Beachport

Port MacDonnell

Portland

100m 200m

123227

123229 123230

123233

123234 123235

131122

131123

131124 131125

131139

131174 131177

Australia

Argos data analysis Location correction and behavioural states Data analysis was performed for 13 tagged whales for the time period since tagging (Jan-Mar) until the cut-off date on 28 September 2015 to allow enough time for data analyses before submission of this report. Two SPOT tags (#123229 and #131177) continued to transmit past this cut-off date. For the analysis time period, transmission from tags was intermittent for some of the whales and tracks were split into segments when gaps in transmission exceeded 48 hours (2 days) (Jonsen, personal communication). Tracks shorter than five location transmissions were excluded from the data analysis. The splitting of tracks resulted in a total of 26 tracks for 13 tagged whales (Appendices A and B). We also excluded the first three locations of each track segment to remove outlier locations in the data set (locations that were unrealistic because distances were larger than possible considering the maximum swimming speed of blue whales in relation to the locations). Unrealistic locations up to 3,400 km away or locations that logged on land occurred for some of the tags when they initially turned on, or turned back on after they had temporarily stopped. We fitted a hierarchical switching state-space model (hSSSM) in R (R Development Core Team 2006) using the R package ‘bsam’ (Jonsen et al. 2007) to correct raw Argos-acquired surface locations for location error and to determine behavioural states: 1 = transiting behaviour, and 2 = area restricted search (ARS) behaviour (presumably feeding (Jonsen et al. 2007, Bailey et al. 2009) or breeding (Bailey et al. 2009). We ran two chains, each for a total of 10,000 Markov Chain Monte Carlo (MCMC) samples. We discarded the first 30,000 samples as a burn-in and thinned the remaining samples by retaining every 10th sample to reduce autocorrelation. We used a time step of three hours (tstep=0.125). Mean time step/ hour averaged for the 13 whales was 2.3 hours, and therefore we chose a time step slightly larger than the mean (Jonsen, personal communication). Analysis was performed in a high capacity computer (20 cores; 520 GB RAM). Diagnostic tests and inspection of lag-auto-correlation and trace plots suggested that MCMC chains converged, and thus provided representative samples from posterior distributions (Appendices C and D). Maps displaying geolocation of whales, tracks and behavioural states as obtained from the analysis in ‘bsam’ were created in ArcMap 10.2 (Esri Inc. 1999-2013). The results from fitting the state-space model showed that 76% of the blue whale locations were inferred as ARS (presumably foraging or breeding), and 24% as transiting. Whales spent the majority of their time in the Bonney Upwelling (Appendix E) and in Indonesia (Banda Sea; and south of Bali and Java) performing ARS behaviour (presumably foraging in the Bonney Upwelling region and foraging and/or breeding in Indonesia). Other areas where ARS behaviour was estimated included two areas north of Exmouth Gulf and southeast of Timor. Transiting behaviour was generally characteristic of whales between the Bonney Upwelling region and Indonesia (Appendices F1 – F13). Spatio-temporal movements by whales are displayed in Appendix G, colour coded by month.

Table 2 Details of satellite transmissions from 13 blue whales in the Bonney Upwelling region between January and March 2015, and estimated behavioural state proportions per whale. The details shown for each tag are the tag number, overall track duration for each whale, number of Argos locations received, mean number of locations per day, mean time step, distance travelled, % transiting behaviour, and % area restricted search (ARS) behaviour (behavioural state estimated using the hierarchical switching state-space models (hSSSM) (Jones et al. 2007) with a time step of 3 hours).

Tag ID Track duration (days)

No. of locations received Mean no. of locations/ day Mean time step (hour)

Distance travelled (km) ARS (%) Transiting (%) 131124 2.2 35 16.1 1.5 237 0 100 131125 81.8 939 11.5 2.1 5192 85.2 14.8 131123 92.7 1835 19.8 1.2 8650 75.3 24.7 131122 37.7 538 14.3 1.7 3841 67.7 32.3 131139 52.3 974 18.6 1.3 5231 67.2 32.8 123227 62.8 314 5.0 4.8 2479 88.7 11.3 123233 107.1 1579 14.7 1.6 10022 82.1 17.9 123235 56.5 691 12.2 2.0 4912 67.8 32.2 123234 121.3 1033 8.5 2.8 7057 82.7 17.3 131177 52.3 349 6.7 3.6 3767 86 14 123230 25.4 177 7.0 3.4 1221 86.9 13.1 123229 200.5 2080 10.4 2.3 17042 60 40 131174 48.6 767 15.8 1.5 2997 90.7 9.3

Diving behaviour An initial analysis of diving behaviour was performed using data from the five Mk10/SPLASH tags. Dives were defined as submergences > 5 metres depth and surfacing bouts of > 20 seconds in length. The start and end time of surfacing bouts between qualifying dives was determined by the tag’s transition of wet and dry at the surface. Dive shapes were classified as square-shaped, V-shaped and U-shaped based on the percentage of time (T) spent in bottom phase of dive (B) (square: B > 50% T; V: 20% T < B <= 50% T; U: B <= 20% T; dive shapes are pre-defined by Wildlife Computers). A total of 6,631 hours of dive and surfacing bouts were obtained, which accounted for 12,402 classified dives and 12,397 surfacing bouts. Whales performed mostly square-shaped dives that were shallow in depth and short in duration (Figure 2, 3 and 4). However, the deepest dive recorded was 492 m, and the longest dive was 112 min. Recorded surfacing bouts lasted between 3 sec and 68 min. Dives were significantly deeper at night (mean=87 m±1.5) than during the day (mean=32.6 m±1.5) (Mann-Whitney rank sum test, p < 0.001) (considering daylight hours as between 7:00-19:29).

Figure 2 Dive behaviour of five blue whales in the Bonney Upwelling region derived from Mk10 tags between January and March 2015. Summary of overall percentage of dive types performed (square-, U- and V-shaped dives).

Figure 3 Dive behaviour of five blue whales in the Bonney Upwelling region derived from Mk10 tags between January and March 2015. Percentage of square-, U- and V-shaped dives are displayed for each dive depth class bin (m).

Figure 4 Dive behaviour of five blue whales in the Bonney Upwelling region derived from Mk10 tags between January and March 2015. Percentage of square-, U- and V-shaped dives are displayed for each dive duration class bin (min). Genetic data collection and analyses Data were collected at 20 microsatellites from the tagged whales that were biopsy sampled. The subspecies identity of these individuals was genetically confirmed to be pygmy blue whales using these microsatellites by following the method of Attard et al. (2012). Tagged individuals that were previously sampled in our genetic dataset of 125 individuals from Australia were identified by identical multilocus genotypes or genotypes with up to two allele mismatches using EXCEL MICROSATELLITE TOOLKIT 3.1 (Park 2001). The 125 individuals comprised of 38 from the Bonney Upwelling region, 72 from the Perth Canyon, and 15 from Geographe Bay. The sex of the individuals was determined by PCR amplification of a fragment of the genes ZFX/ZFY and SRY using primers designed by Aasen and Medrano (1990) and Fain and LeMay (1995), respectively, and following the method of Gilson et al. (1998). All whales were genetically confirmed to be pygmy blue whales. Sexing analyses showed there were four female and six male individuals (Table 1). Female whale #131124 (tagged and biopsied off Port MacDonnell on 23 January 2015) was previously biopsied on 15 January 2012 south of Port Phillip Bay in VIC (38.5341°S, 144.7615°E), male whale #131123 (tagged and biopsied off Port MacDonnell on 23 January 2015) was previously biopsied on 25 March 2009 off Portland in VIC (38.4844°S, 141.5939°E), and female whale #123230 (tagged and biopsied off Beachport on 13 March 2015) was previously biopsied on 25 March 2010 off Beachport in SA (37.6020°S, 139.7642°E) (Table 1, Figure 1). There were no mismatches in the genotypes of resampled individuals. Photo-ID collection and upload to the SHBWC Photo-identification images of whales were taken from both the tagging vessel and the support vessels during field work. Where possible, right and left dorsal sides of the

whales were photographed, including the dorsal fin. All photo-identification images were screened for quality, sorted and whales were compared with each other. A total of 29 individual whales could be identified. Identification images of these 29 whales were uploaded to the Marine Vertebrate Lab (MARVEL) section of the Southern Hemisphere Blue Whale Catalogue (SHBWC) using Flinders University Blue Whale (FLBW) Aliases (FLBW1 – FLBW29). For each whale we also included the following information: feature (left side/right side), date of sighting, quality of image (excellent/good/average), pigmentation (light coloured/dark coloured), skin lesions (blister lesions/cookie cutter shark bites/other lesions or rare marks), geolocation information of the sighting, sex of whale (male/female/unidentified) and if a biopsy was obtained. For the tagged whales, we reported the tagging location as the sighting location since photo-ID images were taken immediately prior to tagging. The tag IDs (PTT numbers), FLBW Aliases, biopsy sample IDs and sex of whale for the 13 tagged whales are displayed in Table 1. Two of the three tagged whales that were also biopsied years prior to this study (identical microsatellite genotypes and sex) had matching photo-IDs. For the third whale with matching genotypes, photo-ID could not be obtained during tagging and therefore photo-ID matching could not be performed. Overlaying whale tracks with SST and chlorophyll a We produced examples of ArcGIS maps overlaying whale tracks from ‘bsam’ and Sea Surface Temperature (SST) or chlorophyll a for a chosen time window when cloud cover was reduced (14 March – 21 March and 30 March – 6 April 2015) in the Bonney Upwelling region to explore associations between whale movements and environmental variables. We extracted SST and chlorophyll a using the Marine Geospatial Ecology Tool (MGET) 0.8a60 (Duke University Laboratory, USA) to create NASA MODIS Global Level 3 SST 4x4 km grid cells, and NASA OceanColor L3 SMI Chlorophyll a 4x4 km grid cells, using ArcToolbox. We created SST and chlorophyll a maps averaged over 8 days (to account for missing data due to cloud cover) and overlayed corresponding whale tracks (Appendices H1-H4). Maps suggest that there may be an association of tracks with cold upwelling waters, temperature fronts and higher levels of chlorophyll a, but this needs to be further investigated. Future data analyses Future additional data analyses will involve a comprehensive analysis of how Argos whale locations relate to environmental variables (e.g. satellite derived sea surface temperature and chlorophyll a). We will do this by extracting environmental variables using MGET to create 4x4 km and/or 9x9 km grid cells from which point data will be extracted (for each whale location). We will then fit Generalized Additive Models (GAMs) and/or Generalized Linear Mixed Models (GLMMs) to the data, using R. In addition we will estimate weighted utilisation distributions to assess occupancy patterns in the Bonney Upwelling region and investigate potential differences in dive profiles by inferred behavioural mode.

Discussion and conclusions Our study assisted in elucidating pygmy blue whale diving behaviour, movements and occupancy patterns, including migratory routes in state, Australian and international waters. Most blue whales remained over the continental shelf while in the Bonney Upwelling, and utilised the area from at least January-June. In April-June some whales migrated westwards; two continued north reaching waters of the Banda Sea and Bali/Java in July and August, respectively, where they stayed until at least September. In the Bonney Upwelling, whales predominantly carried out area-restricted search (presumably foraging) with generally shallow and short dives. However, dives were generally deeper at night compared to during the day. Between the Bonney Upwelling region and Indonesia, whales displayed mainly transiting behaviour, with the exception of two areas north of Exmouth Gulf and southeast of Timor where ARS behaviour was observed. In Indonesian waters, whales carried out predominantly area-restricted search (possibly breeding, and potentially also feeding). The proportion of track time spent in area restricted search and transiting behaviour was similar to that reported for blue whales in the Northeast Pacific that migrate annually from Baja California to waters off Washington (Bailey et al. 2009). Blue whale movements of this study corroborated with previous findings that blue whales aggregate to feed in the Bonney Upwelling region during November-May between the Great Australian Bight and Bass Strait (Gill et al. 2011). Whale movements from this study further corroborate previous findings based on tagging at the Perth Canyon that whales migrate north along the western Australian coast to potential breeding grounds in Indonesia (Banda Sea) (Double et al. 2014). Our study therefore shows for the first time that whales from the Bonney Upwelling region travel west along the southern Australian coast to then use a similar migratory pathway north to Indonesia as whales that feed seasonally at the Perth Canyon. Results from this project confirm the importance of the Bonney Upwelling as a feeding area for pygmy blue whales in Australia, and indicate the whales’ migratory route along the southern and western Australian coastlines to their likely breeding grounds in Indonesia. Results also inform about the location and timing of potential impacts from anthropogenic activities. These can be used for management decision-making under Australia’s EPBC Act 1999, for the Blue Whale Conservation Management Plan and Marine Bioregional Planning, and for developing inter-governmental collaborations to protect the species. References Aasen E, Medrano JF (1990) Amplification of the ZFY and ZFX genes for sex

identification in humans, cattle, sheep and goats. Nature Biotechnology. 8:1279-1281.

Attard CRM, Beheregaray LB, Jenner KCS, Gill PC, Jenner M-N, Morrice MG, Robertson KM, Möller LM (2012) Hybridization of Southern Hemisphere blue whale subspecies and a sympatric area off Antarctica: impacts of whaling or climate change? Molecular Ecology. 21: 5715-5727.

Bailey H, Mate BR, Palacios DM, Irvine L, Bograd SJ, Costa DP (2009) Behavioural estimation of blue whale movements in the Northeast Pacific from state-space model analysis of satellite tracks. Endangered Species Research. 10:93-106.

Double MC, Andrews-Goff V, Jenner KCS, Jenner MN, Laverick, SM, Branch TA, Gales NJ (2014) Migratory movements of pygmy blue whales (Balaenoptera musculus brevicauda) between Australia and Indonesia as revealed by satellite telemetry. PLoS One. 9(4): e93578. doi: 10.1371/journal.pone.0093578

Fain SR, LeMay JP (1995) Gender identification of humans and mammalian wildlife species from PCR amplified sex-linked genes. Proceedings of the American Academy of Forensic Science. 1:34.

Gill PC, Morrice MG, Page B, Pirzl R, Levings AH, Coyne M (2011) Blue whale habitat selection and within-season distribution in a regional upwelling system of southern Australia. Marine Ecology Progress Series. 421:243-263.

Gilson A, Syvanen M, Levine K, Banks J (1998) Deer gender determination by polymerase chain reaction: validation study and application to tissues, bloodstains, and hair forensic samples from California. California Fish and Game. 84(4): 159-169.

Heide-Jorgensen MP, Kleivane L, Oien N, Laidre KL, Jensen MV (2001) A new technique for deploying satellite transmitters on baleen whales: tracking a blue whale (Balaenoptera musculus) in the North Atlantic. Marine Mammal Science 17:949-954.

Jonsen ID, Myers RA, James MC (2007) Identifying leatherback turtle foraging behaviour from satellite-telemetry using a switching state-space model. Marine Ecology Progress Series 337:255-264.

Park SDE (2001) Trypanotolerance in West African cattle and the population genetic effects of selection. PhD dissertation, University of Dublin.

3. Appropriateness The appropriateness of the approaches used in the development and implementation of the Activity All approaches were appropriate for carrying out the objectives of the project. Satellite tagging: appropriate approach and successful tagging of 13 blue whales. Photo-identification: appropriate approach and successful identification of 29 blue whales. Biopsy sampling: appropriate approach and successful biopsying of 10 of the 13 tagged whales. Three of the whales could not be biopsied during tagging due to rapid submergence after tagging or technical issue.

Argos data collection and analysis: appropriate approach, successful (with two tags still transmitting). Genetic data collection and analyses: appropriate approach and successful sex determination and subspecies identification for all 10 biopsied blue whales. Photo-ID collection and upload to the SHBWC: appropriate approach and successful submission of photo-ID images to the SHBWC for 29 individual blue whales. Maps of whale locations, tracks and behavioural states in ArcGIS: appropriate approach and successful display of whale tracks and behavioural states on maps created in ArcGIS. Overlaying whale tracks with SST and chlorophyll a: appropriate approach and successful display. 4. Effectiveness The degree to which the Activity has effectively met its stated objectives All research activities have been effectively met at the time of writing this report. The methods applied for data collection have all been successful resulting in extensive telemetry data. The project objectives were therefore fulfilled within the running time of the project with a one month extension for submission of the final report. We will continue the analysis of the data with the aim of publishing the findings in international peer-reviewed journals.

Signature of Chief Investigator

Name

A/Prof Luciana Moller

Date

31/10/15

Signature of Organisation Representative

Name

Date

Please forward 4 hard copies, and one electronic Word document of this report to:

Robyn Goyen Coordinator

Australian Marine Mammal Centre Australian Antarctic Division 203 Channel Highway KINGSTON TAS 7050 ammccoordinator@aad.gov.au

Appendix A. Table of tracks used for the analysis in bsam (hSSSM). Tracks were split into segments when gaps in transmission exceeded 48 hours. The day of tag deployment is displayed in black. Track sections for each whale are displayed in dark grey. Days in orange were excluded from the analysis due to different issues (e.g. exclusion of tracks shorter than five location transmissions).

Appendix B. Individual hierarchical switching state-space model (hSSSM) derived tracks of 13 pygmy blue whales, satellite tagged in the Bonney Upwelling region, South Australia, between 21 January and 13 March 2015. Individual whale tracks are colour coded.

WA

Banda Sea INDONESIA

AUSTRALIA

SA NSW

NT

VIC

QLD

TAS

Legend131177131174131139131125131124131123131122123235123234123233123230123229123227

Appendix C. Output from ‘bsam’, suggesting that MCMC chains converged.

Appendix D. Output from ‘bsam’, suggesting that MCMC chains converged.

Appendix E. Hierarchical switching state-space model (hSSSM) derived locations and behavioural states of 13 pygmy blue whales in the Bonney Upwelling region, South Australia.

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3000 4000 5000 Area Restricted Search

Transiting

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VIC

Appendix F1. Hierarchical switching state-space model (hSSSM) derived track and behavioural states of pygmy blue whale #131124 (female).

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Area Restricted Search Transiting

SA VIC

Appendix F2. Hierarchical switching state-space model (hSSSM) derived track and behavioural states of pygmy blue whale #131125 (male).

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Area Restricted Search Transiting

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Appendix F3. Hierarchical switching state-space model (hSSSM) derived track and behavioural states of pygmy blue whale #131123 (male).

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Appendix F4. Hierarchical switching state-space model (hSSSM) derived track and behavioural states of pygmy blue whale #131122 (unknown sex).

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Area Restricted Search Transiting

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Appendix F5. Hierarchical switching state-space model (hSSSM) derived track and behavioural states of pygmy blue whale #131139 (female with accompanying calf).

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Area Restricted Search Transiting

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Appendix F6. Hierarchical switching state-space model (hSSSM) derived track and behavioural states of pygmy blue whale #123227 (unknown sex).

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Area Restricted Search Transiting

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Appendix F7. Hierarchical switching state-space model (hSSSM) derived track and behavioural states of pygmy blue whale #123233 (male).

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Area Restricted Search Transiting

SA NSW

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Appendix F8. Hierarchical switching state-space model (hSSSM) derived track and behavioural states of pygmy blue whale #123235 (male).

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Appendix F9. Hierarchical switching state-space model (hSSSM) derived track and behavioural states of pygmy blue whale #123234 (male).

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Appendix F10. Hierarchical switching state-space model (hSSSM) derived track and behavioural states of pygmy blue whale #131177 (male).

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Appendix F11. Hierarchical switching state-space model (hSSSM) derived track and behavioural states of pygmy blue whale #123230 (female).

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Area Restricted Search Transiting

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Appendix F12. Hierarchical switching state-space model (hSSSM) derived track and behavioural states of pygmy blue whale #123229 (female).

Area Restricted Search Transiting SA

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Banda Sea

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Appendix F13. Hierarchical switching state-space model (hSSSM) derived track and behavioural states of pygmy blue whale #131174 (unknown sex).

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20

Appendix G. Individual hierarchical switching state-space model (hSSSM) derived locations of 13 pygmy blue whales, satellite tagged in the Bonney Upwelling region, South Australia, between 21 January and 13 March 2015. Locations are colour coded by month.

WA

Banda Sea INDONESIA

AUSTRALIA

SA NSW

NT

VIC

QLD

TAS

Legend January February March April May June July August September

Appendix H1. Individual hierarchical switching state-space model (hSSSM) derived tracks of 13 pygmy blue whales for an 8-day period between 14 March and 21 March 2015, overlaying corresponding 8-day averaged SST in the Bonney Upwelling region. Whale tracks are displayed in black.

- 2 – 0 0 – 16 16 – 16.2 16.2 – 16.4 16.4 – 16.6 16.6 – 16.8 16.8 – 17.0 17.0 – 17.2 17.2 – 17.4 17.4 – 17.6 17.6 – 17.8 17.8 – 18.0 18.0 – 18.2 18.4 – 18.6 18.6 – 18.8 18.8 – 19.0 19.0 – 19.2 19.2 – 19.4 19.4 – 19.6 19.6 – 35

SST [C°]

SA

Appendix H2. Individual hierarchical switching state-space model (hSSSM) derived tracks of 13 pygmy blue whales for an 8-day period between 30 March and 6 April 2015, overlaying corresponding 8-day averaged SST in the Bonney Upwelling region. Whale tracks are displayed in black.

- 2 – 0 0 – 16 16 – 16.2 16.2 – 16.4 16.4 – 16.6 16.6 – 16.8 16.8 – 17.0 17.0 – 17.2 17.2 – 17.4 17.4 – 17.6 17.6 – 17.8 17.8 – 18.0 18.0 – 18.2 18.4 – 18.6 18.6 – 18.8 18.8 – 19.0 19.0 – 19.2 19.2 – 19.4 19.4 – 19.6 19.6 – 35

Chlorophyll a [mg/m3]

SA

- 2 – 0 0 – 16 16 – 16.2 16.2 – 16.4 16.4 – 16.6 16.6 – 16.8 16.8 – 17.0 17.0 – 17.2 17.2 – 17.4 17.4 – 17.6 17.6 – 17.8 17.8 – 18.0 18.0 – 18.2 18.4 – 18.6 18.6 – 18.8 18.8 – 19.0 19.0 – 19.2 19.2 – 19.4 19.4 – 19.6 19.6 – 35

SST [C°]

SA

Appendix H3. Individual hierarchical switching state-space model (hSSSM) derived tracks of 13 pygmy blue whales for an 8-day period between 14 March and 21 March 2015, overlaying corresponding 8-day averaged chlorophyll a in the Bonney Upwelling region. Whale tracks are displayed in black.

0 - 0.05 0.05 – 0.06 0.06 – 0.07 0.07 – 0.08 0.08 – 0.09 0.09 – 0.1 0.1 – 0.11 0.11 – 0.12 0.12 – 0.13 0.13 – 0.14 0.14 – 0.15 0.15 – 0.16 0.16 – 0.17 0.17 – 0.18 0.18 – 0.19 0.19 – 0.2 0.2 – 0.3 0.3 – 0.4 0.4 – 0.5 0.5 – 99.9

Chlorophyll a [mg/m3]

SA

Appendix H4. Individual hierarchical switching state-space model (hSSSM) derived tracks of 13 pygmy blue whales for an 8-day period between 30 March and 6 April 2015, overlaying corresponding 8-day averaged chlorophyll a in the Bonney Upwelling region. Whale tracks are displayed in black.

0 - 0.05 0.05 – 0.06 0.06 – 0.07 0.07 – 0.08 0.08 – 0.09 0.09 – 0.1 0.1 – 0.11 0.11 – 0.12 0.12 – 0.13 0.13 – 0.14 0.14 – 0.15 0.15 – 0.16 0.16 – 0.17 0.17 – 0.18 0.18 – 0.19 0.19 – 0.2 0.2 – 0.3 0.3 – 0.4 0.4 – 0.5 0.5 – 99.9

Chlorophyll a [mg/m3]