AEBR 257 Continuous Plankton Recorder Sampling Southern Ocean 2002 2018 3347

Continuous Plankton Recorder sampling of
zooplankton in the Southern Ocean 2002–

2018: spatial, seasonal, and long-term
changes
New Zealand Aquatic Environment and Biodiversity Report No. 257
K.V. Robinson,
M. Decima,
M.H. Pinkerton,
R. Stewart
ISSN 1179-6480 (online)

ISBN 978-1-99-100357-7 (online)
April 2021
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TABLE OF CONTENTS
EXECUTIVE SUMMARY 1
1. INTRODUCTION 3
1.1 Background 3
1.2 Overall objective 4
1.3 Specific objectives 4
2. METHODS 4
2.1 CPR methodology 4
2.2 Study area 5
2.3 CPR deployments in Ross Sea region 6
2.4 Post-voyage laboratory analysis 11
2.5 SO-CPR data extract used in the present study 11
2.6 Phytoplankton Colour Index 12
2.7 Taxonomic grouping of data 13
2.8 Latitudinal variation in zooplankton abundance in the Ross Sea region 15
2.9 Spatial distribution of zooplankton abundance 15
2.10 Trends in zooplankton abundance 15
2.11 Model-based analysis of zooplankton abundance 15
2.12 Model-based analysis of zooplankton communities 18
2.13 Average Copepod Community Size (ACCS) 19
2.14 Microplastics 19
2.15 Data management and integration 20
3. RESULTS 20
3.1 Latitudinal variation in zooplankton abundance in the Ross Sea region 20
3.2 Spatial distribution of zooplankton abundance 23
3.3 Trends in zooplankton abundance 26
3.4 Model-based analysis of zooplankton abundance 28
3.5 Model-based analysis of zooplankton communities 37
3.6 Average Copepod Community Size (ACCS) 45
3.7 Microplastics 47
4. DISCUSSION 48
4.1 CPR sampling and analysis 48
4.2 Patterns in zooplankton abundances by broad taxonomic group 48
4.3 Zooplankton communities 49
4.4 Trends and long-term change 50
4.5 Average Copepod Community Size (ACCS) index 51
4.6 Comparison between Ross Sea and the rest of the Southern Ocean 52
4.7 Future effects of climate change 52
4.8 Northern hemisphere comparisons 53
4.9 Final comments 54
5. MANAGEMENT IMPLICATIONS 54
6. ACKNOWLEDGMENTS 55
7. REFERENCES 55
8. APPENDIX 1: Grouping of zooplankton data 61
9. APPENDIX 2: Environmental data used in this study 66

9.1 Environmental data 66
9.2 Trends in environmental data 75
10. APPENDIX 3: Mid-range lengths of copepod species used to calculate the Average
Copepod Community Size index 78
EXECUTIVE SUMMARY
Robinson, K.V.; Decima, M.; Pinkerton, M.H.; Stewart. R. (2021). Continuous Plankton
Recorder sampling of zooplankton in the Southern Ocean 2002–2018: spatial, seasonal, and long-
term changes.
New Zealand Aquatic Environment and Biodiversity Report No. 257. 79 p.
This report marks the end of the second phase of the New Zealand Continuous Plankton Recorder (CPR)
survey between New Zealand and the Ross Sea. The first phase was 2008–2013 (ZBD2008-15), the
second phase was 2013–2018 (ZBD2013-03), and the third phase started in 2019 (ZBD2018-01).
Through the continued collaboration with Sanford Limited, the FV San Aotea II was used to deploy the
CPR on transits between New Zealand and the Ross Sea (Antarctica) to gather zooplankton samples for
analysis. The overall objective of the project was to use these CPR samples to understand spatial,
seasonal, and long-term changes to zooplankton in New Zealand’s southern EEZ and on the transit to
the Ross Sea.
Zooplankton are small invertebrates living in the water column and are a key part of the food chain,
linking changes in primary production with consumers (such as fish, seabirds, and mammals). It is well
established that zooplankton can be effective indicators of ecosystem health and can be used for
monitoring, anticipating, and managing responses to ecosystem change, including regime shift. CPR
research in the Southern Ocean started in 1991, and over the last decade New Zealand has become the
third largest contributor of data. During the last 5 years of this project, 37 individual tows of the CPR
from the FV San Aotea II were carried out, covering a total of 11 407 nautical miles (> 20 000 km) of
towed distance. In total, 600 000 individual zooplankton specimens were counted and identified.
Zooplankton data from the circumpolar Southern Ocean CPR project were analysed in relation to
environmental measurements over the period 1997–2018, covering phytoplankton biomass, primary
productivity, water temperature, mixed layer depth, sea ice, and activity of ocean fronts. Statistical
models were used to determine relationships between key taxonomic groups of zooplankton,
zooplankton communities, and environmental conditions.
Key conclusions of this analysis:
1. Concentrations of chlorophyll-a (chl-a) in the Southern Ocean generally increased between
1997 and 2018, especially around the southern limit of the Antarctic Circumpolar Current,
around the Argentine continental shelf, and in the Subtropical Front across New Zealand. In
contrast, there were decreasing trends in chl-a over some of the Antarctic continental shelf and
in the larger Ross Sea region.
2. For 6 of the main taxonomic groups of zooplankton, statistical models could reproduce broad
spatial patterns of zooplankton abundances measured by the CPR survey. The models
developed can potentially be used in conjunction with Earth-system models to project the
effects of climate change on zooplankton in the Southern Ocean.
3. Abundances of zooplankton in general were higher in the Ross Sea region than in the Southern
Ocean as whole, by a factor of about 2 on average but varying among zooplankton taxa.
Abundances of Foraminifera and Fritillaria spp. were more than 3 times higher in the Ross Sea
region than elsewhere in the Southern Ocean. These differences are not due to the Ross Sea
region having unusual environmental conditions and are likely to be ecologically-driven.
4. Changes to environmental conditions over the last 20 years (1997–2018) are likely to lead to
increases in the abundance of most broad taxonomic groups of zooplankton in the Southern
Ocean, with copepods, Foraminifera, and Fritillaria spp. especially likely to benefit.
Fisheries New Zealand Continuous Plankton Recorder Sampling 2002–2018• 1

5. In contrast, the environmental conditions for pteropods (small marine snails living in the water
column) seem to have worsened over the last 20 years, particularly over the Ross Sea shelf. The
negative pressure on pteropod abundance may be having, and may continue to have,
implications for the Ross Sea shelf ecosystem where pteropods are major contributors to the
flow of organic matter to the benthic ecosystem.
6. Ocean warming in the Southern Ocean generally seems to be associated with a shift to larger
copepods, and cooling with a shift to smaller cold-water copepods such as Oithona spp. This
finding is contrary to the prevailing hypothesis that ocean warming favours smaller copepods.
The Average Copepod Community Size (ACCS) metric in the Ross Sea region increased
significantly during the sampling period, suggesting a shift towards larger copepod species
driven by the predominant warming signal.
7. Superimposed on the predicted changes to zooplankton abundances due to trends in
environmental conditions were shorter-term and localised (small-scale) fluctuations in
zooplankton abundances. These fluctuations were not captured by the statistical models, and
ongoing monitoring of zooplankton remains important. Regular, twice-yearly transits of a
fishing vessel on a single track provide an excellent approach for quantifying variability and
change in zooplankton and is likely superior to opportunistic sampling.
8. Microplastics, most in the form of threads, were quantified in samples collected between 2009
and 2018 and were present in 38% of the samples analysed. Distribution of microplastics in
CPR samples was similar by latitude but varied considerably among years, with between 5 and
85% of samples containing some type of thread. Numbers were higher in the last two seasons
sampled. It is not known if these samples are representative of microplastic concentrations in
the whole Southern Ocean.
2 • Continuous Plankton Recorder Sampling 2002–2018 Fisheries New Zealand

1. INTRODUCTION
1.1 Background
Zooplankton 1 are a key link in marine ecosystems, connecting oceanographic/climate drivers and higher
trophic level consumers including fish, seabirds and marine mammals (Bathmann et al. 2000, Dubischar
& Bathmann 1997). Zooplankton can be useful indicators of the state of the marine environment
(Atkinson 1998, Smetacek et al. 2004, Mackas & Beaugrand 2010) and can act as early warning
indicators of critical shifts in ecosystem function (Beaugrand 2005, Batten et al. 2016). For example,
variations in plankton abundance in the Atlantic have been linked to climatic variability, including the
North Atlantic Oscillation, Gulf Stream Index, and changing sea-surface temperatures (Reid et al. 1998,
Beare & McKenzie 1999). Zooplankton spatial analyses are also useful in the context of bio-
regionalisation and spatial management including in the context of designing and evaluating Marine
Protected Areas (Raymond & Constable 2006, Sharp et al. 2007).
Despite their fundamental importance, information on zooplankton is typically poor because the
community is diverse (hundreds of species with many developmental stages), highly variable (both in
space and time – Fasham & Pugh 1977; Mackas et al. 1985; Atkinson et al. 2008), and approaches to
observation are limited. Satellite data provide year-round data (e.g., sea-surface temperature and ocean
primary productivity) but cannot observe zooplankton. Both station-based and underway sampling
methods for zooplankton abundances (e.g., Burkill & Gallienne 2001, Davis et al. 2004, Hosie et al.
2003, Pollard et al. 2002, Postel et al. 2000) continue to rely on deployment of gear from vessels which
limits the scale and frequency of field measurements of zooplankton.
The Continuous Plankton Recorder (CPR) is a high-speed plankton sampler originally designed to be
towed behind merchant ships as they steam at cruising speed along regular shipping routes (Warner &
Hays 1994). In the North Sea and Northeast Atlantic for example, CPRs have been deployed from such
vessels for over 75 years. Such long-term marine environmental datasets are extremely rare, and the
CPR time series is globally one of the longest running monitoring programmes in the world (Hays et
al. 1993). The SCAR 2 Southern Ocean CPR survey (SO-CPR) was established in 1991 to map the
spatial and temporal patterns of zooplankton in the Southern Ocean (Hosie et al. 2003). SO-CPR is one
of nine separate CPR surveys that are now contributing data to the Global Alliance of CPR Surveys
(GACS) to understand the effects of environmental changes on plankton biodiversity, and to monitor
ecosystem health at a global level. Up until 2008 however, there were few CPR tows in the Ross Sea
region 3. New Zealand has special interest in this sector of the Southern Ocean and so, with funding
from MFish (now MPI and Fisheries New Zealand) and with the support and cooperation of Sanford
Limited, this important information gap began to be filled with the instigation of a biannual CPR survey
between New Zealand and the Ross Sea.
This report presents the combined data from the Phase 1 (2008–2013) and the Phase 2 (2013–2018)
Ross Sea region CPR projects, along with data obtained from SCAR SO-CPR Survey database. Phase
3 (2018–2023) of New Zealand SO-CPR research commenced in 2019.
1
Zooplankton are planktonic animals which drift in oceans, seas, and bodies of fresh water. In the ocean,
zooplankton range in size from nanozooplankton (2–20 µm), microzooplankton (20–200 µm), mesozooplankton
(200 µm–2 mm), and microzooplankton (> 2 mm). Zooplankton can be heterotrophic (feed on other organisms)
or detritivorous (feed on non-living detrital material) plankton.
2
Scientific Committee on Antarctic Research, https://www.scar.org/
3
Ross Sea region is often defined as lying between 160° E and 150° W, and south of 60° S.

1.2 Overall objective
To map changes in the quantitative distribution of epipelagic plankton, including phytoplankton,

zooplankton and euphausiid (krill) life stages, in New Zealand’s EEZ and transit to the Ross Sea,
Antarctica.
1.3 Specific objectives
1. Conduct annual return transits with the CPR to the Ross Sea during the austral summer in
collaboration with Sanford limited, and contribute the data collected to the SCAR Southern Ocean
CPR Survey (SO-CPR).
2. Combine the data collected during phase 1 (years 1–5) with the data collected under this project to:
i. Determine zooplankton and phytoplankton trends in the full dataset: and
ii. Compare results with datasets available through the SO-CPR Survey.
3. Characterise latitudinal and temporal changes in phytoplankton and zooplankton populations in

New Zealand’s EEZ and transit to the Ross Sea.
4. Complete coupled analysis of phytoplankton and zooplankton environmental data to investigate

causes of variations between Ross Sea and other Southern Ocean zones.
5. Describe broad similarities and differences observed between NZ, and other southern hemisphere
data with patterns of trends observed in the northern hemisphere.
2. METHODS
2.1 CPR methodology
The CPR is a robust plankton sampler that was designed in the 1920s by Sir Alister Hardy in order to
address questions regarding plankton distribution patchiness (Reid et al 2003). The design of the unit
that was deployed for both Phase 1 (2008–13) and Phase 2 (2013–18) MPI projects is based on the
original model, with some minor modifications to allow for the more extreme sea conditions in the
Southern Ocean (Hosie et al. 2003). The unit is towed horizontally at a depth of approximately 10 m
and approximately 100 m astern of the ship as it travels at cruising speed (about 10 kn.). During a tow
water enters a small aperture at the front of the CPR body where it passes through a 270 µm filtering
collecting silk (Figure 2-1). As the CPR moves through the water, an external impeller advances the
silk at a rate of ~ 1 cm per 1 nautical mile through the water irrespective of the speed of the ship over
the ground. (The speed of the ship through the water and over the ground are different because of ocean
currents and sea-state. For example, greater vertical undulation because of large swell results in shorter
distance towed over the ground, whereas a following sea can lead to longer distance towed over the
ground.) The filtering silk then gets covered by a ‘covering’ silk, with the plankton sandwiched between
the two layers. Both silks are then rolled into a storage tank, where a supply of buffered 37%
formaldehyde preserves the sample. The maximum towing distance for a silk is about 450 nautical miles
through the water.

Figure 2-1: The internal workings of the Continuous Plankton Recorder (CPR).
The sampling aperture of the CPR is 1.27 cm2 which is most effective for capturing mesozooplankton
(0.2–2 mm size). Larger organisms are unlikely to be sampled well by the CPR, particularly those such
as Antarctic krill that form swarms and have strong predator evasion responses. This size selectivity
results in under-estimates of the abundance of krill compared with large net systems such as the
Rectangular Midwater Trawl, or when compared with biological hydro-acoustic estimates. Nonetheless,
krill of all species are collected by the CPR and their smaller developmental stages (larvae) are
sometimes abundant in samples. Parallel analyses have shown that the CPR results are comparable with
plankton net systems fitted with the same mesh and sampled within a similar depth range (Hunt & Hosie
2003). However, gelatinous zooplankton, e.g., salps and jellyfish, are poorly sampled by the CPR
because their large size and soft bodies can be damaged when trapped between the silks.
2.2 Study area
The Ross Sea region is defined in this report as the area between New Zealand and the Ross Sea proper,
lying between 160° E and 150° W, and south of 60° S. The Ross Sea is wholly contained within
FAO/CCAMLR statistical area 88. This region was visited annually in the austral summer by the FV
San Aotea II from 2008–2018 and by RV Tangaroa in 2006, 2008, 2010, and 2013. The 2013 voyage
of the RV Tangaroa generated samples from both within the Ross Sea region as well as the East
Antarctic region by crossing the 160° E line. The sampling area of the FV San Aotea II extended from
just south of the port of Timaru in the South Island of New Zealand, to the Ross Sea, Antarctica (Figure
2-2). The exact route, especially in the south of the region, varied among years because this depended
on the fishing locations chosen by the master of the fishing vessel. The route in higher latitudes was
also affected by the distribution and concentration of sea ice.
CPR data from the Ross Sea region are compared in this report to those collected from the rest of the
Southern Ocean. Most CPR data in the Southern Ocean are from the East Antarctic region, defined as
between 60° E and 160° E, and south of the Subtropical Front, and largely contained within
FAO/CCAMLR statistical area 58 (between longitudes 80° and 150° E).

Figure 2-2: The geographic regions of the Southern Ocean CPR Surveys. FV San Aotea II tows are shown
in light grey and the RV Tangaroa tows are in purple. Map courtesy of the Australian Antarctic
Data Centre © Commonwealth of Australia 2018.
2.3 CPR deployments in Ross Sea region
FV San Aotea II
Sampling in this project was conducted through a collaboration with Sanford Limited, which annually
sends vessels to the Ross Sea to harvest Antarctic toothfish (Dissostichus mawsoni). The CPR was
towed by the FV San Aotea II between New Zealand and the Ross Sea annually in the austral summer
between 2008 and 2013 (Phase 1 survey) and 2013 and 2018 (Phase 2 survey). Training was provided
to the crew on deployment/recovery methodology, and one person per voyage was trained as the CPR
“handler”. The CPR handler and the assisting FV San Aotea II crew are responsible for (1) loading
internal cassettes with new silks into the main body of the CPR, deploying the CPR at regular intervals,
(2) retrieving the CPR with the sampled silks, (3) labelling and preserving the silks, and (4) recording
appropriate data. Global Positioning System (GPS) time and position data were recorded hourly (where
possible) in a logbook and later matched with the plankton data. The sampled silks were preserved in

buffered 5% formaldehyde in individually labelled jars and returned to the NIWA Christchurch
laboratory for analysis when the ship returned to port.
Between 2008 and 2018, ten transits were southward and occurred in November or December of each
year and 10 northward transits occurred in January or February of each year. Each transit consisted of
multiple individual CPR deployments (tows). A summary of all the CPR deployments for Phase 1
(2008–2013) and Phase 2 (2013–2018) is provided in Table 2-1 and Table 2-2, and Figure 2-3 and
Figure 2-4, respectively.
The very low zooplankton count in the southwards transit of the 2016–17 season was due to a complete
failure of the first tow, and a partial failure of tow 2. Seven tows in total were unable to be processed
due to a malfunction of the CPR cassette mechanism during deployment. This success rate is
comparable to Phase 1, except for the 2014–15 season, when tow failures on the southward leg
contributed to a low towed distance.
Table 2-1: Summary of FV San Aotea II CPR deployments as part of the Phase 1 project 2008–2013.
Transit: S=southward (New Zealand to Ross Sea); N=northward (Ross Sea to New Zealand). A
‘segment’ is a 5-cm section of silk representing an approximate 5 nm analysed section of the tow.
Number Distance Number

Number of towed zooplankton
Season Transit Start date End date of tows segments (nm) counts
2008–09 S 19-Dec-08 26-Dec-08 5 179 897 123 523

2008–09 N 23-Jan-09 2-Feb-09 6 282 1 413 56 242
2009–10 S 13-Dec-09 17-Dec-09 2 162 809 194 386
2009–10 N 9-Feb-10 17-Feb-10 4 306 1 527 84 154
2010–11 S 23-Nov-10 27-Nov-10 3 192 963 101 795
2010–11 N 15-Jan-11 23-Jan-11 7 349 1 740 104 557
2011–12 S 28-Nov-11 4-Dec-11 4 227 1 133 66 739
2011–12 N 22-Feb-12 26-Feb-12 2 177 884 32 329
2012–13 S 3-Dec-12 27-Jan-13 4 180 899 49 950
2012–13 N 14-Feb-13 24-Feb-13 5 324 1 614 42 980
Total 42 2 378 11 879 856 655

Figure 2-3: Ross Sea Continuous Plankton Recorder Tows. FV San Aotea II 2008–2013. The five latitudinal
zones are shown: the Subtropical Zone (STZ), the Subantarctic Zone (SAZ), the Polar Frontal
Zone (PFZ), the Permanent Open Ocean Zone (POOZ), and the Sea Ice Zone (SIZ).

Table 2-2: Summary of FV San Aotea II CPR deployments as part of the Phase 2 project 2013–2018.
Transit: S=southward (New Zealand to Ross Sea); N=northward (Ross Sea to New Zealand). A
‘segment’ is a 5-cm section of silk representing an approximate 5-nm analysed section of the tow
(though segments at the end of a tow can be of different length).
Number Total
Number of Distance zooplankton
Season Transit Start date End date of tows segments towed (nm) count
2013–14 S 30-Nov-13 9-Dec-13 4 176 878 59 452

2013–14 N 3-Feb-14 11-Feb-14 5 273 1 366 51 244
2014–15 S 6-Dec-14 8-Dec-14 2 108 539 18 558
2014–15 N 2-Feb-15 3-Mar-15 6 346 1 731 53 308
2015–16 S 24-Nov-15 28-Nov-15 2 80 402 45 210
2015–16 N 4-Feb-16 13-Feb-16 5 385 1 923 86 943
2016–17 S 25-Nov-16 2-Jan-17 2 53 267 2 469
2016–17 N 11-Jan-17 19-Jan-17 4 385 1 869 62 157
2017–18 S 18-Nov-17 24-Nov-18 2 165 826 90 514
2017–18 N 28-Jan-18 6-Feb-18 5 322 1 606 82 611
Total 37 2 293 11 407 552 466

Figure 2-4: Ross Sea Continuous Plankton Recorder Tows. FV San Aotea II 2013–2018. The five latitudinal
zones are shown: the Subtropical Zone (STZ), the Subantarctic Zone (SAZ), the Polar Frontal
Zone (PFZ), the Permanent Open Ocean Zone (POOZ), and the Sea Ice Zone (SIZ).
RV Tangaroa sampling
The CPR was also deployed during five RV Tangaroa voyages (2002, 2006, 2008, 2010, 2013) under
separate funding: (1) TAN0202, JARE43 (06/02/2002–05/03/2002); (2) TAN0602 (28/01/2006–
17/03/2006); (3) TAN0802, IPY-CAML, International Polar Year – Census of Antarctic Marine Life
(26/01/2008–21/03/2008); (4) TAN1002, Tangaroa Whale Research voyage (31/01/2010–16/03/2010);
and (5) TAN1302, RV Tangaroa Mertz Polyna Voyage (01/02/2013–14/03/2013). The locations of
CPR tows from the RV Tangaroa varied significantly among the voyages and were often distant from
the usual transit routes of the FV San Aotea II. Consequently, the CPR data from the RV Tangaroa
voyages are not as useful for assessing variability in zooplankton over time as those from the FV San
Aotea II voyages. In total, 48 individual tows of the CPR from the RV Tangaroa were carried out (Table
2-3), comprising 722 segments, with a total of 10 846 nautical miles of towed distance. Zooplankton

samples were collected between 41.48° S and 75.84° S. In the laboratory, 405 339 individual
zooplankton specimens were counted and identified. These RV Tangaroa data were also included in
the SO-CPR database during the analyses in this report.
Table 2-3: Summary of RV Tangaroa CPR data in the SO-CPR database. Transit: S=southward (New
Zealand to Ross Sea); N=northward (Ross Sea to New Zealand). A ‘tow’ is a single deployment
and retrieval of the CPR. A ‘segment’ is a 5-cm section of silk representing a 5-nm analysed section
of the tow (though segments at the end of a tow can be of different length).
Number Distance Total

Number of towed zooplankton
Voyage Transit Start date End date of tows segments (nm) count
TAN0202 S 7-Feb-02 22-Feb-2002 7 210 956 127 326

TAN0202 N 25-Feb- 02 3-Mar-2002 4 243 1 171 66 641
TAN0602 S 30-Jan-06 20-Feb-06 8 427 2 138 37 785
TAN0602 N 6-Mar-06 13-Mar-06 3 157 785 6 335
TAN0802 S 31-Jan-08 6-Feb-08 5 287 1 437 36 062
TAN0802 N 14-Mar-08 18-Mar-08 4 201 1 005 13 019
TAN1002 S 2-Feb-10 9-Feb-10 5 399 1 995 65 144
TAN1302 S 5-Feb-13 14-Feb-13 12 271 1 359 53 027
Total 48 2 195 10 846 405 339
2.4 Post-voyage laboratory analysis
In the laboratory after the voyage, each pair of silks from the Ross Sea CPR tows were unrolled and cut
into segments representing ~5 nautical miles of towed distance. The last segment at the end of a tow
was sometimes shorter than 5 nautical miles and was either included with the penultimate segment if
less than 2.5 nautical miles or retained as a short segment if more than 2.5 nautical miles. All
zooplankton were rinsed off each 5 nautical mile silk segment and counted and identified under a
dissecting microscope using the SO-CPR Survey method (Hosie et al. 2003). This method was
developed from the northern hemisphere CPR Survey’s method to be a more conservative and thorough
approach, and to eliminate the need for highly specialised equipment.
When zooplankton abundances in the SO-CPR samples were very high, subsampling using a Motoda
plankton splitter was carried out (Motoda 1959). The efficiency of the plankton splitter was tested to
ensure that each subsample was an accurate representative of the whole sample. Zooplankton were
identified to the lowest taxonomic level possible, ideally to species.
Antarctic krill (Euphausia superba) and other euphausiids were identified to developmental stage where
possible, as were copepods (adults and copepodite stages) (McLeod et al. 2010). Zooplankton that are
easily damaged, and notably gelatinous and soft bodied species, were identified to a coarser taxonomic
resolution only. Larvaceans (solitary, free-swimming tunicates) are very abundant in CPR samples, and,
although the body of the larvacean is often damaged or missing, the tails are easy to identify to genus
level and count. Other harder body zooplankton such as foraminiferans can usually be identified to an
acceptable taxonomic level and counted, although damaged individuals can only be identified to a
coarser taxonomic resolution than intact specimens.
2.5 SO-CPR data extract used in the present study
For the analysis given in this report, zooplankton data were extracted from the SO-CPR database as
current on 28 August 2018. The total number of SO-CPR observations across the Southern Ocean at
the time of the extraction is shown in Figure 2-5. It is clear that the majority of the SO-CPR samples

were in the East Antarctica and Ross Sea regions, with very few observations in other areas. The Pacific
and Atlantic Sectors of the Southern Ocean have had very little observation by the SO-CPR survey.
Figure 2-1: Number of CPR samples by area. The colours show the number of CPR segments in 81 km
pixels over the 29 years of the SO-CPR survey. Black lines are nominal positions of (from north):
Subantarctic Front (SAF, solid line), Polar Front (PF, solid line), average maximum northern
extent of seasonal sea ice (“Ice”, dashed line), and the Southern boundary of the Antarctic
Circumpolar Current (SB-ACC, solid line, Orsi et al. 1995).
2.6 Phytoplankton Colour Index
Based on the colour of the CPR silks, a Phytoplankton Colour Index (PCI) score was assigned to each
5 nautical mile segment using a Pantone colour charts (www.pantone.com) with scores of 0 = no colour,
1 = very pale green, 2 = pale green, and 3 = green. Pantone colour codes corresponding to these indices
depend on the dominant phytoplankton group and other coloured material in the water. The PCI is
indicative of the chlorophyll a (chl-a) concentration based on the Marine Biological Association
(MBA), CPR Survey method (Reid et al. 1998). Training in the use of the PCI was provided by staff at
the Australian Antarctic Division (AAD), Tasmania, as well as senior analysts at the MBA, CPR Survey
in Plymouth, England.
Spatial and temporal patterns in PCI were not analysed in this study as satellite ocean colour
observations provide a more reliable and more powerful method of exploring changes in upper ocean
phytoplankton abundance in the Southern Ocean. The coarse categorisation of PCI and the lack of
quantitative values is limiting. PCI values from the global CPR surveys were compared with satellite
data for the Southern Ocean and for the Ross Sea region alone to “ground truth” the satellite data, albeit
at the coarse 4-category level. Monthly satellite measurements of chl-a at the same point as the CPR
sample were compared, and these were logged before comparison because chl-a is close to being log-

normally distributed (Figure 2-6). Although the proportions of variance explained were modest
(R2=0.12, Southern Ocean; R2=0.14, Ross Sea region; y=ln(chl)), both regressions were significant at
p< 0.001 (F46,229=1.13 Southern Ocean; F6867=1.16, Ross Sea region). As both ln(chl) and PCI deviate
from normality, rank correlation approach (Spearman’s and Kendall’s tau) were also applied.
Spearman’s rank correlation was 0.274 and p<0.001, and Kendall’s rank correlation was 0.999, and
p<0.001. It was concluded that the satellite measurements of chl-a are, very broadly, consistent with
those from the PCI. Analysis of patterns and changes in chl-a from satellite data are shown in
Appendix 2.
a b
Figure 2-2: Phytoplankton Colour Index (PCI) showing comparison with (natural log of) satellite chl-a
concentration (mg m-3) on y-axis. PCI values are dithered by a random amount to show point
densities (colours).
2.7 Taxonomic grouping of data
CPR zooplankton samples were identified to 293 taxonomic categories in the SO-CPR database. For
the purposes of the present study, these data were further grouped into broad and fine taxonomic groups
(see Appendix 1). The broad grouping (Table 2-4) captured coarse patterns in the data and was similar
to that used in previous CPR analysis (e.g., Robinson et al. 2014).
The fine grouping of 60 taxonomic groups retained as much fine-scale taxonomic data as possible. This
double taxonomic grouping (broad and fine) was necessary because a large proportion of the
zooplankton were unidentified or unidentifiable at a fine taxonomic level, but the fine-scale data
nevertheless included important information on subtle changes in zooplankton community composition.
The fine-scale grouping was determined on a group-by-group basis considering the ambiguity caused
by unidentified specimens and included 35 separate species or genuses of calanoid copepods (see
Appendix 1). Care was taken to avoid spurious effects due to the large proportion of unidentified
copepods in the samples on the fine-scale analysis. Specifically, individuals unidentified to genus or
species (37% of all copepods) were excluded from the fine-scale analysis. The excluded copepod
samples will be one of: (1) very rare species that are not generally identified in the CPR analysis; (2)
early developmental stages (approximately C3–4 4 stages or earlier); and (3) damaged specimens. For
the 2018 data from the Ross Sea, the laboratory analysis separately recorded numbers of calanoid
copepods that could not be identified because of damage, and numbers that could not be identified for
other reasons. Within this test set of data, only 70 of 4323 unidentified calanoid copepods were damaged
or “very rare” (1.6%) with the vast majority being unidentifiable because of being early developmental
4Copepods develop in stages from eggs, to nauplii, to copepodites, and then to adults. The nauplii stages are called N1–N2,
and the copepodite stages C1–C5, where the number indicates the growing developmental life stage. “C3” is hence a
copepodite stage with 4 pairs of legs, and “C5” is the final stage before the adult.

stages (98.4%). This finding agrees with information from SO-CPR analysts internationally (Graham
Hosie pers. comm.) that most unidentified copepods are early developmental stages. This result means
that five unidentified copepod groups (“Calanoida indet [indeterminable] (small)”; “Crustacea nauplius
indet”; “Copepoda nauplius indet”; “Calanoida indet-(large)”; and “Nauplius indet”) can be safety
excluded from the fine-scale community analysis and from the copepod community size analysis (see
section 2.13).
In contrast, for euphausiids, it appears that individuals are more easily damaged by CPR collection
method, and the levels of damage are higher (Graham Hosie pers. comm.). For this reason, and until a
method is developed to use the information on euphausiid species and genuses in the CPR database, all
euphausiids were grouped together for the fine-scale analysis.
Table 2-1: “Broad” taxonomic groupings of zooplankton taxa from the CPR used in this study.
No. Group Description
1 Oithona spp. Small (1 mm) cyclopoid copepods, dominated by Oithona similis

which is generally the most numerically abundant copepod in SO-
CPR samples.
2 Copepoda All other copepods, including calanoid, cyclopoid, and harpacticoid

copepods. This group aggregates more than 90 CPR taxonomic
groups and includes more than 50 separate species. Copepods in the
Southern Ocean are taxonomically diverse, numerically abundant,
and ecologically important, being an important food source for
predators including mesopelagic fishes. This group also includes
unidentified and unidentifiable (damaged) copepods.
3 Amphipoda Order of crustaceans with no carapace and generally with laterally

compressed bodies – mostly detritivores or scavengers.
4 Chaetognatha Commonly known as arrow worms, a phylum of predatory marine

worms that are a major component of plankton worldwide.
5 Euphausiidae All adult and developmental stages of krill (generally unidentified to

species or genus).
6 Foraminifera Very abundant calcareous (calcite) zooplankton that could be affected

by ocean acidification.
7 Fritillaria spp. Two abundant larvacean genera. These are both solitary, free-
8 Oikopleura spp. swimming filter feeding tunicates.
9 Ostracoda Class of crustacea also known as “seed shrimp” – typically around

1 mm in size, with flattened bodies and bivalve-like, chitinous or
calcareous “shell”.
10 Pteropods Calcareous (aragonite) pelagic gastropod free-swimming (marine

snails) predicted to be affected by ocean acidification.
11 Other Includes remaining organisms which are rarely identified including

cephalopods, fish, fish eggs, isopods, “jellies” (salps, ctenophores,
siphonophores), mysids, polychaetes, protozoa, and shrimps.

2.8 Latitudinal variation in zooplankton abundance in the Ross Sea region
For CPR data collected along a regular north-south transect line (such as the FV San Aotea II CPR
data), the zooplankton abundances were simply shown as a stacked bar chart against latitude. Missing
data (e.g., because of failure of the CPR unit or operational issues with deployment) were identified.
This analysis is relevant to specific objective 3.
2.9 Spatial distribution of zooplankton abundance
To examine large-scale spatial patterns in zooplankton abundance the SO-CPR data were divided into
large spatial blocks, following the approach previously used for summarising CPR data (e.g., Beaugrand
et al. 2003; Beaugrand 2005; McLeod et al. 2010). Blocks of 81 km x 81 km were used so that each
block contained ~9 segments of 5 nm each time a CPR tow crossed it. This block size was chosen to be
small enough to give reasonable spatial resolution, but large enough that each contained a reasonable
amount of data. This analysis is relevant to specific objective 3.
2.10 Trends in zooplankton abundance
To investigate long-term trends in zooplankton abundances in the raw CPR data (objective 3), counts
at the broad taxonomic level were grouped into spatial blocks of 300 km x 300 km. Larger blocks were
used for the trend analysis than for the preceding spatial summary because these contain more data and
time-series must have relatively complete coverage in time for trend analysis to be useful.
Linear trends were determined using the Mann-Kendall Z statistic (Mann 1945; Kendall 1975). The
magnitude of trends was estimated using Sen’s slope (Sen 1968). Trends were identified as significant
if the p-value was less than 5% and the Sen’s slope was not equal to zero (Hipel & McLeod 1994,
Scarsbrook 2006). Such a non-parametric approach for detecting linear trends is preferred over
parametric methods (such as linear regression) because the form of the relationships is not known, and
the Sen’s slope estimator reduces the effect of outliers (Hastie et al. 2001). Data were de-seasonalised
prior to analysis by removing the climatological monthly mean from the measurements to create
monthly anomalies.
2.11 Model-based analysis of zooplankton abundance
“Block-based” abundance and trend analysis (see previous sections) is limited by the coverage of the
CPR survey and by the inherent variability of zooplankton in time and space. The most appropriate way
of overcoming complex, patchy, and time-varying ecological information is to use data-mining
approaches (Hochachka et al. 2007). In the present study, statistical models were used to investigate
spatial and temporal patterns in the abundances of the broad groups of zooplankton. This analysis was
needed to address specific objectives 4 and 5.
The multivariate statistical technique of Boosted Regression Trees (BRT: Friedman 2001; Ridgeway
2006; De'ath 2007; Elith et al. 2008) was used. BRT has been used to relate sparse measurements of
species abundance to environmental characteristics to investigate patterns of occurrence over large
spatial scales (103–105 km) and over extended periods of time (months–decades) (Guisan &
Zimmermann 2000; Leathwick et al. 2006; Elith et al. 2007, 2008; Pinkerton et al. 2010b). The
technique used in the present study broadly followed the methodology given by Pinkerton et al. (2010b)
for Oithona similis. However, the analytical approach of Pinkerton et al. (2010b) was extended by
exploring the effect of using different time scales of environmental variation in the analysis. Five
different models were used, representing a range of environmental integrations, from annual averages
to actual data at the time and point of capture (Table 2-5). Environmental data used in the present study
are shown in Appendix 2.

Table 2-2: Types of BRT models used in this study. The oceanographic environmental layers used (chl, sst,
sstgrad, SeaIce, vgpm, mld0p030, mld0p125) are explained in Appendix 2. These include: chl a
concentration; sea surface temperature, SST; spatial gradient of SST to indicate frontal activity;
vertical-generalised productivity model (ocean primary productivity), vgpm; mixed layer depth
with density different criteria of 0.030 kg/m3; mixed layer depth with density different criteria of
0.125 kg/m3). CU=cumulative (long-term average); anMean= annual mean (mean of monthly data
between April of the previous year and March of the present year inclusive); MC=monthly
climatology (e.g., average January); MO=monthly resolution; MAnom=monthly anomaly (equal to
MO minus MC). “Ecoszen” is the cosine of the solar zenith angle and gives an indication of day-
night to allow for diel variation in zooplankton. “Month” is the month of year.
Model name Description Environmental layers used
cumulative Long-term average oceanographic conditions with Ecoszen, Month,

Month provided to capture within-season {chl, sst, sstgrad, SeaIce, vgpm,
variability (see Pinkerton et al. 2010b). mld0p030, mld0p125}CU
annual Annual-average oceanographic conditions with Ecoszen, DayIndex,

Month provided to capture within-season {chl, sst, sstgrad, SeaIce, vgpm,
variability mld0p030, mld0p125}anMean
clim Monthly climatological oceanographic conditions Ecoszen,

(e.g., January average SST). {chl, sst, sstgrad, SeaIce, vgpm,
mld0p030, mld0p125}MC
climAnom Monthly climatological oceanographic conditions, Ecoszen,

and the anomaly for the actual month of sampling {chl, sst, sstgrad, SeaIce, vgpm,
provided as independent spatial data layers to the mld0p030, mld0p125}MC
BRT model separately. {chl, sst, sstgrad, SeaIce, vgpm,
mld0p030, mld0p125}MAnom
actual Actual measurements of conditions within the Ecoszen,

sampling month. {chl, sst, sstgrad, SeaIce, vgpm,
mld0p030, mld0p125}MO
combined Combination of {cumulative, annual, clim, None directly, but all above indirectly.
climAnom, actual} models as Equation 2.
It is important to use an appropriate number of trees to avoid overfitting BRT models (Elith et al. 2007,
2008). Using too few trees gives models with poor performance (i.e., ones that explain only a low
proportions of the total variance), whereas too many trees gives models with little generality
(“overfitted” models). To explore the appropriate number of trees for each BRT model, K-fold analysis
was used where data were withheld in K=10 folds, respecting CPR tows, as recommended for CPR data
previously (Pinkerton et al. 2010b). Within-bag 5 and out-of-bag comparisons were also calculated;
these are also sometimes effective at giving insights into the appropriate number of BRT trees to use.
Different BRT models were combined taking into account the relative uncertainties in estimates from
different models (Equation 1). Weighting individual model outputs by the inverse of their variance
provides the best ensemble estimate. Combining different regression tree models with different sets of
predictor variables is consistent with the approaches of Random Forest (Breiman 2001) and Gradient
Forests (Ellis et al. 2012; Stephenson et al. 2018).
5
BRT models use “bagging” where only a randomly selected subset of data is used to fit each model tree. When
the model starts to become overfitted (too many trees), there will be an increasing difference between the
performance of the model based on the “within-bag” data (that used to fit the model) and the “out-of-bag” data
(not used to fit the model).

n
∑σ zi
2
i
zbest = i =1
n
Equation 1
∑σ
i =1
1
2
Where zbest is the best ensemble estimate, generated from n separate models, where zi is the estimate
from model i, which has variance σ2.
The various BRT models were applied to predict zooplankton abundance for a particular month and
year (Table 2-6). Environmental data used for predictions are shown in Appendix 2. Predictions of
abundance were made for a standard segment length of 5 nm. Predictions will vary by time of day
because Ecoszen is used in the BRT models so three predictions representing three times of day were
averaged. For each different location and month, the value of Ecoszen used in the prediction (Epredict)
was calculated as Equation 2, where α={0.17, 0.5, 0.83}. Here, Emin and Emax are the minimum and
maximum values of Ecoszen over the middle day-of-month at a given location.
= α Emin + (1 − α ) Emax
E predict Equation 2
Table 2-3: Data used in different types of BRT models for prediction in year y and month m. The
oceanographic environmental layers used (chl, sst, sstgrad, SeaIce, vgpm, mld0p030, mld0p125) are
explained in Appendix 2 and text.
Model name Environmental layers used for prediction Comment
cumulative Ecoszen, Month, Annual means for year y

{chl, sst, sstgrad, SeaIce, vgpm, mld0p030, mld0p125}anMean(y) used instead of
cumulative (long-term)
means.
annual Ecoszen, DayIndex, Annual means for year y
{chl, sst, sstgrad, SeaIce, vgpm, mld0p030, mld0p125}anMean(y) used.
clim Ecoszen, Actual monthly means

{chl, sst, sstgrad, SeaIce, vgpm, mld0p030, mld0p125}MO(y,m) for year y and month m
used instead of
climatological months.
climAnom Ecoszen, Monthly climatologies
{chl, sst, sstgrad, SeaIce, vgpm, mld0p030, mld0p125}MC and anomalies for year y
{chl, sst, sstgrad, SeaIce, vgpm, mld0p030, mld0p125}MAnom(y,m) and month m used.
actual Ecoszen, Monthly values for year y

{chl, sst, sstgrad, SeaIce, vgpm, mld0p030, mld0p125}MO(y,m) and month m used.
Differences in zooplankton abundances between regions may arise from differences in environmental
or ecological conditions between regions, or for reasons unrelated to environmental conditions (for
example, ‘upstream’ conditions may vary). To investigate whether and why zooplankton abundances
differed between the Ross Sea region and the rest of the Southern Ocean the following analyses were
carried out. (1) The relationship between environmental conditions and zooplankton abundance was
modelled twice, first for the Southern Ocean and second for just the Ross Sea region. (2) Using the
whole Southern Ocean model, estimates of zooplankton abundances in the Ross Sea region to those
outside it were compared. (3) Again, using the whole Southern Ocean model, model residuals

(differences between the fitted model and actual CPR measurements) within the Ross Sea region were
compared with those outside it. These separate analyses were used to investigate whether environmental
properties in the Ross Sea are unusual compared with the rest of the Southern Ocean and whether
zooplankton abundances depend differently on environmental conditions in the Ross Sea region than
elsewhere.
2.12 Model-based analysis of zooplankton communities
In line with specific objectives 4 and 5, the fine taxonomic group data were used to describe zooplankton
assemblages or communities as a whole (Beaugrand 2005, Beaugrand et al. 2003, Hunt & Hosie 2005,
2006a, b). There are many alternative approaches to describing variation in multivariate communities
(e.g., Sørensen 1948, Bray & Curtis 1957, Legendre & Legendre 1998, Legendre & Gallagher 2001,
Clarke et al. 2006, De Caceres et al. 2013), but no established best practice for zooplankton community
analysis. In the present study, fine-scale SO-CPR zooplankton data from the whole Southern Ocean
were clustered along a gradient of community dissimilarity using a method that broadly followed
Beaugrand (2005) and Beaugrand et al. (2003).
There are a number of different dissimilarity measures available that emphasize different aspects of
community composition, but no standard measure for zooplankton communities. Some common
community dissimilarity measures emphasize presence/absence of species (Sørensen metric; Sørensen
1948), whereas some studies highlight the value of considering relative abundance of different species
(e.g., Clarke et al. 2006, Sharp et al. 2007). In the present analysis, dissimilarity between zooplankton
communities at location X and Y (DXY) was calculated as the product of the Euclidian distance metric
in log-space (because counts are close to log-normally distributed) for the broad group data (counts of
taxa i at site X and Y being xi and yi respectively), and the Sørensen distance metric for the fine grouped
data (Equation 3). In this equation, Nxy is the number of taxa present both at site X and at site Y, NX is
the number of taxa present at site X, and NY is the number of taxa present at site Y. Other dissimilarity
metrics were tried and gave similar results.
 2  2 N XY 
DXY  ∑ ( ln xi − ln yi )  × 1 −
=  Equation 3
 i   N X + NY 
Agglomerative hierarchical cluster analysis was used to progressively group samples along a gradient
of increasing dissimilarity. Clusters were considered to be significantly different if their group-to-group
dissimilarities were greater than a given [‘threshold’ level. Determining the appropriate threshold was
important because it determined how many significantly different clusters were identified. To determine
the threshold dissimilarity, within-group dissimilarities (pairwise averaging) from 20 neighbouring
CPR segments were calculated. This can be thought of as the ‘sampling uncertainty’ because of the
high spatial autocorrelation between CPR segments (Pinkerton et al. 2010b). Clusters were assessed as
being significantly different when their dissimilarities were more than twice the sampling uncertainty.
The analysis was repeated with other sizes of groups (10 and 30) which had little effect.
Next, BRT modelling (see previous section) was applied to explore the relationships between the
dissimilarities of each community cluster and environmental variables. Environmental data used in the
present study are shown in Appendix 3. As before, a number of different models and combinations of
environmental data were used (Table 2-5). The final models were chosen from a combination of the
cumulative, annual, clim, and climAnom models. Combining models with different independent
variables is akin to the Random Forest approach (Breiman 2001), where the ensemble approach can
provide greater robustness and performance. This approach is preferred over multivariate modelling
approaches for multinomial responses (e.g., Generalised Dissimilarity Analysis; Ferrier et al. 2007)
because it allows us to consider explicitly the dissimilarity of a point from different cluster centres. The
zooplankton community and environmental conditions within a given modelled cluster were

summarised by comparing the values within the cluster to those between clusters. This approach is
similar to methods used previously for zooplankton communities (e.g., Takahashi et al. 2010, 2011).
The BRT models were used to predict zooplankton community clusters for each month where CPR data
were available (October-March) in each year (1998–2018) which allows changes in the areas predicted
to be occupied by the communities over time to be investigated. Mann Kendall trend analysis using Sen
slopes was applied as explained in Section 2.10. Areas were first de-seasonalised by subtracting the
monthly mean over the whole time series.
2.13 Average Copepod Community Size (ACCS)
The Average Copepod Community Size (ACCS) metric (Equation 4) is the mean adult length of all
copepods in a sample, based on individual representative lengths (see Appendix 2) and can be used to
monitor changes in the dominance of large or small species in the community. The ACCS was
calculated using the mid-range length of adult female copepods (L) as an index of the relative size of a
species (i), multiplied by the number of individuals of that species (X). This is calculated for all copepod
species in a sample, summed for all species, and then divided by total number of all copepods (N) to
produce a single ACCS value (Beaugrand et al. 2003, Batten et al. 2016).
Equation 4
The ACCS was calculated for all samples in the SO-CPR dataset, covering the whole Southern Ocean
between 1991 and 2018. Only the copepod groups from the fine-scale CPR data were used for this
analysis. The mid-range lengths for adult females used were those from Beaugrand et al. (2003), with
the exception of a few species for which mid-range lengths were recalculated because these tend to be
different in the Southern Ocean compared with the global average (Appendix 3).
The ACCS metric will increase if the number of larger individuals relative to smaller species increases.
Conversely the ACCS index will decrease if there is a shift in dominance to smaller copepod species.
In the northern hemisphere, changes in the ACCS have been found to be indicative of biogeographical
changes in the copepod community due to oceanic temperature changes (Beaugrand et al. 2003,
Beaugrand et al. 2009). For example, the body size of copepods is related to water temperature, with
warmer water species tending to be smaller than those in polar oceans (Lopez & Anadon 2008). This
analysis is hence relevant to specific objective 5.
2.14 Microplastics
Microplastics were not a specific objective of this study, but there is growing interest in these particles
in the Southern Ocean as elsewhere in the world. During the zooplankton analysis process, preliminary
observations were made on samples that showed evidence of non-organic particles; items that were
believed to be microplastics, and other materials. These particles were recorded as ‘presence’ only, and
not counted. Categories of particles included single stranded filaments, flakes, or beads. The colour of
particle was also noted. These observations were not initially recorded in the 2008–09 season but were
initiated the following season and these data are available only for the 2009–2018 period. Brief results
are given in section 3.7 and Grover-Johnson (2018) gives further analysis of the data collected during
Phase 1 and Phase 2 of the MPI project.

2.15 Data management and integration
The raw zooplankton count data generated in this study and from other CPR work in the Southern Ocean
carried out by NIWA (e.g., from Tangaroa voyages) were forwarded to the marine section of the SCAR
Antarctic Biodiversity Information Facility (ANTABIF) where they can be used for the new SCAR Life
Sciences Programme State of the Antarctic Environment (AntEco) and the Antarctic Thresholds -
Ecosystem Resilience and Adaptations (AnT-ERA). The New Zealand SO-CPR data were also
transmitted to the global CPR database managed by the Global Alliance of CPR Surveys (GACS),
which produces an annual state of the environment report on ocean plankton. Data are available for use
in the Southern Ocean Observing System (SOOS), Global Ocean Observing System (GOOS), and are
available for use by the Commission for the Conservation of Antarctic Marine Living Resources
(CCAMLR). Data will be held by the Fisheries New Zealand Research Data Management team as well
as the SCAR SO-CPR Survey database hosted by the Australian Antarctic Data Centre:
https://data.aad.gov.au/aadc/cpr/.
3. RESULTS
3.1 Latitudinal variation in zooplankton abundance in the Ross Sea region
The broad (ten most abundant) zooplankton taxonomic groups enumerated on each transect of each
season sampled by F.V. San Aotea II during Phase 2 (seasons 2013–14 to 2017–18) are shown in Figure
3-1. Overall, including all years and water types, the most numerous zooplankton groups were Oithona
spp., Copepoda, Fritillaria spp., Foraminifera, pteropods, and Euphausiidae (Figure 3-1).
Zooplankton abundances were patchy, with the most consistent peak observed between latitudes 60°–
65° S, roughly coincident with the Polar Front Zone, and most noticeable during season 2013–14
(Figure 3-1a, b), 2014–15 southward transect (Figure 3-1c), and season 2017–18 (Figure 3-1i, j). The
southward transects (first one of the season) do not typically sample the area south of 65° S due to sea
ice, whereas the northward transects occur late enough in the season to provide data on the zooplankton
community closer to the Ross Sea shelf, between 70° and 78° S. Although the composition of the
community in this area does vary by year, the presence of Fritillaria spp. (2014–15, 2015–16, and
2017–18; Figure 3-1d, f, & j), and pteropods (2014–15, 2015–16; Figure 3-1d, f) were notable in some
years.
Based on the latitudinal plots from the FV San Aotea II transects only (Figure 3-1), the relative
abundances of different groups varied between years, yet no broad zooplankton taxon was
overwhelmingly more abundant during any particular sampling season, in contrast to the bloom of
Fritillaria spp. observed during the 2009–10 season in Phase 1 (Robinson et al. 2014). Although these
larvaceans were always present in significant numbers in the samples, order-of-magnitude higher
abundances during any of the seasons sampled during Phase 1 were not observed.

b
c d
Figure 3-1: Abundance of zooplankton taxa in broad taxonomic groups, plotted by year and transect
(S=southward, N=northward). a) 2013–14 S, b) 2013–14 N, c) 2014–15 S, d) 2014–15 N. Note that
zero total abundance indicates no data. “nm” = nautical mile. Missing data (e.g., because of failure
of the CPR unit or operational issues with deployment) are shown grey. Dashed lines indicate
boundaries between oceanographic zones (see section 2.9, Figure 2-3, Figure 2-4). (Continued on
next page)

e f
g h
Figure 3-1: continued. Abundance of zooplankton taxa in broad taxonomic groups, plotted by year and
transect (S=southward, N=northward). e) 2015–16 S, f) 2015–16 N, g) 2016–17 S, h) 2016–17 N.
Note that zero total abundance indicates no data. “nm” = nautical mile. Missing data (e.g., because
of failure of the CPR unit or operational issues with deployment) are shown grey. Dashed lines
indicate boundaries between oceanographic zones (see section 2.9, Figure 2-3, Figure 2-4).
(Concluded on next page)

i j
Figure 3-1: continued and concluded. Abundance of zooplankton taxa in broad taxonomic groups, plotted
by year and transect (S=southward, N=northward). i) 2017–18 S, j) 2017–18 N. Note that zero total
abundance indicates no data. “nm” = nautical mile. Missing data (e.g., because of failure of the CPR unit
or operational issues with deployment) are shown grey. Dashed lines indicate boundaries between
oceanographic zones (see section 2.9, Figure 2-3, Figure 2-4).
3.2 Spatial distribution of zooplankton abundance
Spatial patterns of total zooplankton abundance were driven largely by variations in copepod and
Oithona spp. numbers which were numerically dominant (Figure 3-2). Amphipoda, Chaetognatha, and
Ostracoda were most abundant south of the southern limit of the Antarctic Circumpolar Current (ACC)
near the Antarctic continent. Euphausiidae abundances were higher to the north, especially around the
south of New Zealand. The other groups (copepods, Oithona spp., Foraminifera, Fritillaria spp.,
Oikopleura spp., pteropods) generally had higher abundances in the frontal area separating Subantarctic
waters from the sea ice zone around the Antarctic continent, though substantial variability and
heterogeneity in the spatial distributions is clear in Figure 3-2. Some “hotspots” in pteropods abundance
are seen over the Ross Sea shelf and offshore of Prydz Bay. Abundances of several groups (copepods,
Oithona spp., Foraminifera, Fritillaria spp.) and total abundance of zooplankton were substantially
higher in the Ross Sea region compared with the rest of the Southern Ocean (Figure 3-2).

a b
c d
e f
Figure 3-2: Long-term average total abundance and abundances of the broad groups. a) total abundance,
b) Amphipoda, c) Chaetognatha, d) Copepoda, e) Euphausiidae, f) Foraminifera. Missing data are
shown as white. (Continued on next page)

g h
i j
Figure 3-3: continued. Long-term average total abundance and abundances of the broad groups. g)
Fritillaria spp., h) Oikopleura spp., i) Oithona spp., j) Ostracoda, k) Pteropods. Missing data are
shown as white.

3.3 Trends in zooplankton abundance
Relatively few significant long-term trends in abundances (Figure 3-3) were found from the raw CPR
data, which was likely because of the lack of consistent CPR sampling in any given location even at
this relatively-coarse spatial resolution (300-km blocks). For example, in the case of total abundance,
isolated locations with high positive trends (+20%/y) and high negative trends (-12%/y) were found,
but a predominance of no significant trend. There were also no widespread, spatially coherent patterns
in long-term trends for the other taxonomic group.
a b
c d
e f
Figure 3-4: Long-term trends in total abundance and broad groups. a) total abundance, b) Amphipoda, c)
Chaetognatha, d) Copepoda, e) Euphausiidae, f) Foraminifera. Fewer than 2 measurements at
different times at a given pixel are shown as grey. Trends which are not significant at the 0.05 level
are shown as white. (Continued on next page)

g h
i j
Figure 3-3: concluded. Long-term trends in total abundance and broad groups. g) Fritillaria spp., h)
Oikopleura spp., i) Oithona spp., j) Ostracoda, k) Pteropods. Fewer than 2 measurements at
different times at a given pixel are shown as grey. Trends which are not significant at the 0.05
level are shown as white.

3.4 Model-based analysis of zooplankton abundance
Using the BRT method, four broad groups of zooplankton could not be modelled adequately
(Amphipoda, Chaetognatha, Oikopleura spp., Ostracoda), but modelling the abundances of remaining
six groups (Oithona spp., Copepoda, Euphausiidae, Foraminifera, Fritillaria spp., pteropods) was
successful (Table 3-1). “Success” was defined as well-behaved K-fold analysis, R2 values greater than
0.3, and significant model performance (p<0.01). Overall, the separate BRT models explained 0.35 of
the variance (0.33–0.37), whereas the combined model explained on average 0.46 of the variance. The
climAnom model performed best across all groups and the actual model the worst, though the difference
in performance across the models was small. The CVs were relatively high (mean of 1.04 for the
combined model), but all models gave significant reductions in variance than a null model at better than
the 0.05% level for all taxonomic groups (F>1.28, p < 0.0005, for N=45 489).
In terms of the relative importance of the environmental variables for the models, across all taxonomic
groups, SST was the most important variable, explaining 11.4% of the total variance (Table 3-2). The
other variables in decreasing order of overall importance were mixed layer depth, time of day (Ecoszen),
primary productivity (vgpm), chl-a concentration (chl), month, SST gradient (sstgrad, indicative of
frontal activity), and sea ice concentration (seaIce).
Table 3-1: Performances of fitted models for all broad taxonomic groups from each Boosted Regression
Tree (BRT) model. The proportion of variation explained (R2) and coefficients of variation (CV =
root mean square differences as a proportion of the mean) are shown.
cumulative annual clim climAnom actual combined

Model R2 CV R2 CV R2 CV R2 CV R2 CV R2 CV
Total abundance 0.43 0.38 0.44 0.36 0.40 0.39 0.44 0.37 0.43 0.37 0.54 0.34
Oithona spp. 0.44 0.82 0.46 0.77 0.43 0.83 0.45 0.78 0.42 0.80 0.54 0.74
Copepoda 0.41 0.73 0.44 0.67 0.42 0.72 0.44 0.69 0.42 0.70 0.53 0.65
Euphausiidae 0.26 0.77 0.27 0.77 0.25 0.78 0.27 0.76 0.25 0.77 0.32 0.75
Foraminifera 0.31 3.42 0.32 3.96 0.30 3.55 0.34 3.64 0.27 3.83 0.46 3.12
Fritillaria spp. 0.40 1.82 0.38 2.09 0.33 1.95 0.36 1.96 0.31 2.04 0.52 1.71
Pteropods 0.35 0.66 0.36 0.67 0.32 0.68 0.40 0.63 0.35 0.66 0.47 0.61
Table 3-2: Dependencies on sampling and environmental variables of the combined Boosted Regression
Tree (BRT) model for each univariate model. Values shown are the proportions of variance
explained by each of the variables (%). Ecoszen represents the time of day of sampling in terms of
the cosine of the solar zenith angle. Environmental variables include all components (i.e., month,
climatological month, climatological year average, and annual anomaly). mld includes both
mld0p030 and mld0p125 variables.
Sampling and environmental variables

Cluster Month Ecoszen SeaIce chl sst mld sstgrad vgpm all
Total abundance 5.1 8.1 3.3 4.9 14.8 8.2 3.4 6.4 54.2
Oithona spp. 5.3 1.5 4.4 3.5 20.9 10.4 3.1 5.1 54.1
Copepoda 4.5 15.9 2.2 4.0 12.7 6.2 2.4 5.0 53.0
Euphausiidae 1.5 15.0 0.1 2.4 4.6 2.9 1.7 3.9 32.2
Foraminifera 4.4 0.4 1.2 5.9 10.1 13.9 4.2 6.2 46.2
Fritillaria spp. 5.6 0.9 1.7 7.6 11.7 12.5 6.2 5.9 52.2
Pteropods 2.9 7.4 1.3 8.4 10.0 7.2 4.6 5.1 46.8

Although the spatial predictions varied between models (Figure 3-4), the general characteristics were
very similar, i.e., higher zooplankton abundances in the frontal zone (i.e., between the Subantarctic front
and southern limit of the Antarctic Circumpolar Current), and lower total abundances to the north and
south. The combined model predictions over the 2011 austral summer months October-March (Figure
3-5) showed some seasonal variation, but the overall pattern of high zooplankton abundance in the
frontal zone was consistent between months. The models predict higher zooplankton abundances in
December, especially in the Polar Frontal area in the Ross Sea and Amundsen Sea regions.
The predicted abundances of the separate broad groups of zooplankton (Oithona spp., Copepoda,
Euphausiidae, Foraminifera, Fritillaria spp., and pteropods) (Figure 3-6) show differences in their
distributions. Copepoda in general and Oithona spp. were predicted to have a broad latitudinal
distribution with maximum abundances to the south of the Polar Front. Predicted maximum abundances
of Foraminifera occupied a narrower latitudinal range which was further north than that of copepods.
Fritillaria spp. also have a narrow latitudinal range of high abundances which is located further south
than that of copepods. The predicted abundances of Euphausiidae were higher to the north of the
Southern Ocean, and lower further south. This group included all euphausiids and not just Antarctic
krill (Euphausia superba).

a b
c d
e f
Figure 3-5: Total abundance of Southern Ocean zooplankton for February based on separate BRT models
and oceanographic environmental information. a: cumulative; b: annual c: clim; d: climAnom; e:
actual; f: combined. Different models cover different total areas because predictions were not made
when the environmental conditions were outside the range of the training data.

a b
c d
e f
Figure 3-6: Total zooplankton abundances (log scale) predicted using the combined BRT model and
oceanographic environmental information for months: a: October; b: November; c: December; d:
January; e: February; f: March. Areas with environmental conditions outside the range of the
training data were excluded from the prediction.

a b
c d
e f
Figure 3-7: Abundances of broad zooplankton taxonomic groups predicted using the combined BRT model
and oceanographic environmental information (long-term average). Areas with environmental
conditions outside the range of the training data were excluded from the prediction. a: Copepoda;
b: Euphausiidae; c: Foraminifera; d: Fritillaria spp.; e: Oithona spp.; f: Pteropods.

Zooplankton abundances were predicted to be significantly higher in the Ross Sea region than in the
Southern Ocean as a whole when a regional model of the Ross Sea region was used (Table 3-3).
Fritillaria spp. was predicted to be more than three times as abundant on average in the Ross Sea region
than in the Southern Ocean as a whole, whereas pteropods were predicted to be only 10% more abundant
in the Ross Sea region than in the rest of the Southern Ocean. Total zooplankton abundance was
estimated to be twice as high in the Ross Sea region than in the Southern Ocean as a whole. Comparing
average abundances of taxa in these broad groups predicted by the same Southern Ocean model inside
and outside the Ross Sea region (Table 3-3, column “RSR/all [1]”) showed that this difference was not
due to different environmental conditions in the Ross Sea region compared with the rest of the Southern
Ocean. In fact, environmental conditions led to slightly lower predictions of total zooplankton
abundance in the Ross Sea region than elsewhere when the same Southern Ocean model was used.
Analysis of model residuals showed that the Southern Ocean BRT model underestimated zooplankton
abundances in the Ross Sea region by 24% on average whereas the Ross Sea combined model
underestimated abundances by only 2% on average. This means that it was regional variation in the
relationship between abundances and environmental properties and/or differences in unobserved and
unmodelled environmental conditions that led to differences in zooplankton abundances between the
Ross Sea region and the rest of the Southern Ocean.
Table 3-3: Comparison between zooplankton abundances (numbers per 5 nm segment) in the Ross Sea
region (RSR) and the rest of the Southern Ocean. Information from the combined BRT model
developed on all Southern Ocean data is shown in the left part of the table (“Southern Ocean
model”). Information on the Ross Sea region based on the BRT combined model fitted to only Ross
Sea region data is shown on the right (“Ross Sea model”). A two-sided t-test (N=120) was used to
assess whether zooplankton abundances in the Ross Sea region were significantly different to those
in the rest of the Southern Ocean, evaluated over the months October-March and years 1998–2018:
* p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001. Non-significant differences are shaded grey.
Southern Ocean model Ross Sea model

RSR/All RSR/All
Taxa or index All RSR t80 p [1] RSR t80 p [2]
Total abundance 67.7 57.7 4.29 0.000*** 0.9 136.3 11.65 0.000*** 2.0
Oithona spp. 15.2 11.3 4.38 0.000*** 0.7 23.9 5.31 0.000*** 1.6
Copepoda 23.5 20.5 3.54 0.001*** 0.9 40.2 10.77 0.000*** 1.7
Euphausiidae 1.3 1.4 1.59 0.115 1.0 2.1 21.78 0.000*** 1.6
Foraminifera 2.8 2.8 0.09 0.931 1.0 9.1 11.38 0.000*** 3.2
Fritillaria spp. 1.4 1.3 0.69 0.493 0.9 4.9 8.01 0.000*** 3.5
Pteropods 0.5 0.4 4.88 0.000*** 0.8 0.5 1.43 0.155 1.1
Across the Southern Ocean, significant, positive long-term trends in total zooplankton abundance, and
for most broad taxonomic groups (except pteropods; Table 3-4), were found. Based on the circumpolar
modelling, similar significant, positive long-term trends in abundance were also predicted for the Ross
Sea region. The mean rate of increase was 0.62% per year in the period 1997–2018 (range +0.19%/y to
+0.83%/y), or a mean 12% increase over the modelled 20-year period. The models developed
specifically for the Ross Sea region predicted higher rates of increase for the same groups compared
with the Southern Ocean models (mean +0.91%/y, range +0.56%/y to +1.52%/y).
Spatial plots of statistically significant long-term trends are shown in Figure 3-7 for the abundances of
broad taxonomic groups of zooplankton, and in Figure 3-8 for total zooplankton abundance. The models
predict that total zooplankton abundance is increasing in the zone closest to the Antarctic continent in
the sea ice zone south of the Polar Front, especially in the East Antarctic, Indian, and Atlantic sectors.
Decreases in total abundance are predicted around the Polar Front and Subantarctic Front. Similar
spatial patterns in long-term trends are seen for Copepoda and Oithona spp. Temporal trends in
euphausiids are smaller, with trends being positive, and higher trends in the area of the Polar Front and

Subantarctic Front. Foraminifera temporal trends are also most pronounced between the Polar Front
and Subantarctic Front, but there is a “patchwork” mixture of positive and negative trends. Trends in
the abundance of Fritillaria spp. are also mixed, with increases and decreases. The highest temporal
trends in Fritillaria spp. are in East Antarctica close to the continent. Pteropods showed small
significant increases over the study period in many areas south of the Polar Front, but there is an area
of significant decreases (-6% per year) over the Ross Sea shelf.
Table 3-4: Trends in abundances of zooplankton taxa (total and in broad taxonomic groups) from the
combined BRT models of the Southern Ocean and Ross Sea. The de-seasonalised Mann-Kendall
statistic (Z) and probability (p) are shown. Significance of Mann-Kendall trend: * p ≤ 0.05,
** p ≤ 0.01, *** p ≤ 0.001, with non-significant trends shaded grey. The Sen’s slope trend in the
area is shown as a proportion of the mean area.
Sen slope
Taxa or index Z p
(%/y)
Southern Ocean (Southern Ocean combined model)
Total abundance 7.46 0.000*** +0.64
Oithona spp. 6.09 0.000*** +0.59
Copepoda 8.18 0.000*** +0.65
Euphausiidae 4.40 0.000*** +0.19
Foraminifera 8.19 0.000*** +0.83
Fritillaria spp. 7.12 0.000*** +0.82
Pteropods 1.38 0.169 +0.13
Ross Sea (Southern Ocean combined model)
Total abundance 3.02 0.002** +0.38
Oithona spp. 1.09 0.275 +0.15
Copepoda 4.00 0.000*** +0.40
Euphausiidae 5.55 0.000*** +0.40
Foraminifera 4.22 0.000*** +0.62
Fritillaria spp. 2.62 0.009** +0.42
Pteropods -0.65 0.515 -0.05
Ross Sea (Ross Sea combined model)
Total abundance 3.57 0.000*** +0.56
Oithona spp. 4.72 0.000*** +1.16
Copepoda 4.50 0.000*** +0.76
Euphausiidae 6.01 0.000*** +0.59
Foraminifera 4.57 0.000*** +1.52
Fritillaria spp. 3.45 0.001*** +0.87
Pteropods -5.31 0.000*** -0.63

a b
c d
e f
Figure 3-8: Predicted long-term trends in abundances of broad zooplankton taxonomic groups predicted using the
combined BRT model and oceanographic environmental information. The coloured data shown are the Sen’s
slope trends (average change per year for the period 1998–2018) where these trends were significant at better
than the 5% level assessed using the de-seasonalised Mann-Kendall test. a: Oithona spp.; b: Copepoda; c:
Euphausiidae; d: Foraminifera; e: Fritillaria spp.; f: pteropods.

Figure 3-9: Predicted long-term trends in total zooplankton abundance predicted using the combined BRT
model and oceanographic environmental information. The coloured data shown are the Sen’s slope
trends (average change per year for the period 1998–2018) where these trends were significant at
better than the 5% level assessed using the de-seasonalised Mann-Kendall test.

3.5 Model-based analysis of zooplankton communities
The hierarchical dendrogram (Figure 3-9) suggested a total of 56 clusters were significantly different
based on a dissimilarity of 1.25 (twice the mean within-group distance of 0.62). The 11 largest clusters
were selected. These together represent more than 90% of the clustered data. These were Clusters 1, 4,
6, 9, 10, 22, 24, 37, 39, 40, and 43, and these cluster groups were considered to represent zooplankton
communities. Note that some clustered community groups were much larger (contained more points)
than others (Figure 3-10). In particular, Clusters 6, 22, and 24 were very small, whereas Clusters 1 and
4 represented a substantial amount of the space.
Figure 3-10: Dendrogram of agglomerative hierarchical clustering applied to the whole SO-CPR dataset as
described in the text. Between-cluster dissimilarity is shown on the x-axis (note that the axis is
reversed to show more similar clusters on the right). Significant differences are those greater than
twice the mean dissimilarity in the 20-segment subsets (shown as the vertical red line at
dissimilarity of 1.25). Significant clusters (= communities) are shown as different colours on the
furthest right bar. The largest clusters are numbered. The three coloured bars (see colour scales)
show the distribution of data by three variables: season, day, and latitude. “Season” here is the
later year of an Antarctic summer (e.g., 2000 for December 1999 and January 2000). “Day” is the
number of days after 1 January within a season.

Figure 3-11: Clusters, representing distinct zooplankton communities, based on the agglomerative
hierarchical clustering of the CPR data as described in the text.
The optimum number of trees to use to avoid overfitting based on the K-fold analysis was 161 (range
of 57–699), with best R2 values of 0.18 (0.06–0.28). Hence, 150 trees were used for all BRT models of
cluster distances to obtain models with a high degree of generality. The separate BRT models explained
0.38 of the variance (range of 0.28–0.45), whereas the combined model explained on average 0.50 of
the variance (Table 3-5). The climAnom model performed best across all clusters and the actual model
the worst, though the difference in performance across the models was small. The CVs were relatively
high (mean of 0.48 for the combined model), but all models gave significant reductions in variance than
a null model at better than the 0.05% level for all clusters (F>1.34, p < 0.0005, for N=47 574). In terms
of dependencies on environmental variables, across all clusters, mixed layer depth was the most
important variable, explaining 12.5% of the total variance in cluster distances (Table 3-5). The other
variables in decreasing order of overall importance were SST, primary productivity (vgpm), time of day
(solar zenith angle, Ecoszen), chl-a concentration (chl), month, SST gradient (indicative of frontal
activity), and sea ice concentration (seaIce). The fact that month explained a low proportion of variance
(4.2% overall) means that cluster or community membership is primarily determined from the
oceanographic conditions rather than the date, which gives more likelihood that these models can be
used to understand the effects of oceanographic change on zooplankton communities.

Table 3-5: Dependencies on sampling and environmental variables of the combined Boosted Regression
Tree (BRT) model for each cluster. Values shown are the proportions of variance explained by
each of the variables (%). Ecoszen represents the time of day of sampling in terms of the cosine of
the solar zenith angle. Environmental variables include all components (i.e. month, climatological
month, climatological year average and annual anomaly). mld includes both mld0p030 and
mld0p125 variables.
% of variance explained by sampling and environmental variables

Cluster Month Ecoszen SeaIce chl sst mld sstgrad vgpm all
1 3.9 1.1 7.6 3.4 8.1 15.8 3.0 3.8 46.7

4 3.8 4.8 6.6 4.1 11.3 14.0 3.2 3.8 51.6
6 2.8 13.0 5.1 4.0 10.5 10.1 2.3 2.6 50.5
9 3.7 1.5 3.4 5.0 5.9 15.2 4.1 5.0 43.9
10 3.3 2.2 2.9 2.5 12.4 11.2 3.3 5.4 43.3
22 3.1 10.4 4.6 3.5 10.7 12.5 2.4 4.6 51.8
24 4.3 4.2 4.6 4.1 13.5 13.1 2.9 5.3 52.0
37 6.4 1.1 1.4 4.5 12.9 12.9 6.9 7.3 53.3
39 4.3 4.8 2.2 5.5 8.9 8.9 5.2 7.7 47.4
40 4.7 4.2 1.7 6.2 9.4 12.9 5.1 7.1 51.4
43 5.6 4.6 1.7 5.0 13.0 10.8 4.2 7.3 52.2
All 4.2 4.8 3.8 4.4 10.7 12.5 3.9 5.5 49.7
After BRT modelling of cluster dissimilarities, Clusters 6, 22, and 24 had few or no members and were
excluded from further consideration. One cause of these changes is that the initial zooplankton
clustering was based on pooled data (20 CPR data points to establish cluster significance), whereas the
BRT modelling was based on individual CPR data points (not pooled), and this affected dissimilarity
based on the fine-scale Sørensen distance metric. Comparing results from different block sizes indicated
that this is a relatively minor effect, however. The second and more important factor is that the original
clustering was based exclusively on CPR data (i.e., zooplankton counts), and these clusters overlapped
considerably in environmental space. In other words, zooplankton communities in a given cluster
substantially shared the same environmental conditions as different clusters. The BRT analysis
attempted to separate out these different zooplankton communities based on environmental conditions.
Because many points in different clusters were closer in environmental space than those in the same
cluster, this environmental-based analysis led to changes in cluster memberships. Three Clusters (6, 22,
and 24) did not occupy distinct environmental space so using environmental conditions to separate
clusters meant that these clusters could not be resolved and were subsumed into other clusters.
Two analyses were used to show that, despite these changes, the remaining eight clusters (Clusters 1,
4, 9, 10, 37, 39, 40, and 43) remained significantly different from each other when measured by the
original cluster distances and, crucially, retained the characteristics (in terms of the zooplankton
communities) as the original clusters. First, within cluster dissimilarities were always significantly
smaller than between cluster dissimilarities (one-sided t-test, p<0.01). Second, analysis showed that
after the BRT analysis, clusters had the same key characteristics as in the original clustering. Cluster
(zooplankton community) characteristics (Table 3-6) did not change significantly after the BRT
modelling from the original clustering. The post-BRT cluster characteristics explained 90% of the
variance in the original cluster characteristics for the broad taxonomic groups, 77% of the variance for
the fine taxonomic groups, and 76% of the variance for the environmental data across all environmental
variables.

Table 3-6: Characteristics of clusters determined from fitted Boosted Regression Tree (BRT) models
(combined model) showing comparison between values within the cluster and outside the cluster.
Only the highest magnitude 6 characteristics are shown here, with negative differences (i.e., lower
values in the clusters than outside) shaded grey. The cluster characteristics are grouped into three
categories: (1) Log abundance of zooplankton taxa in broad groups; (2) probability of presence of
zooplankton taxa in fine groups; (3) standardised difference (difference divided by standard
deviation of variable over whole data set) for environmental variables. Log-normally distributed
environmental variables (chl, vgpm, sstgrad) were logged before comparison. AnMean= annual
mean; monthClim=monthly climatology. Significance of t-test for within-cluster to outside cluster:
* p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001.
Standardised difference
Cluster Log abundance (broad taxa) Probability of presence (fine taxa) (environmental)
1 Foraminifera +0.86 *** Rhincalanus gigas +0.41 *** mld0p125_mP +0.82 ***
1 Oithona +0.85 *** Ctenocalanus citer +0.15 *** mld0p125_mPClim +0.80 ***
1 Total abundance +0.72 *** Clausocalanus sp. +0.08 *** mld0p030_mP +0.76 ***
1 Fritillaria sp. +0.69 *** Ostracoda indet -0.09 *** mld0p030_mPClim +0.75 ***
1 Copepoda +0.46 *** Neocalanus tonsus -0.09 *** sst_mPClim -0.61 ***
1 Ostracoda -0.23 *** Metridia sp. -0.10 *** sst_mP -0.61 ***
4 Copepoda +1.02 *** Calanus simillimus +0.42 *** SeaIce_cum -0.37 ***
4 Total abundance +0.93 *** Clausocalanus sp. +0.31 *** SeaIce_anMean -0.37 ***
4 Oithona +0.77 *** Rhincalanus gigas +0.28 *** chl_mPClim -0.41 ***
4 Pteropods +0.68 *** Ostracoda indet +0.22 *** chl_cum -0.42 ***
4 Ostracoda +0.58 *** Ctenocalanus citer +0.20 *** vgpm_anMean -0.48 ***
4 Amphipoda +0.46 *** Calanoides acutus +0.15 *** vgpm_cum -0.57 ***
9 Copepoda +0.06 *** Oithona sp. +0.06 *** mld0p030_anMean -0.35 ***
9 Oithona +0.04 *** Metridia sp. +0.05 *** mld0p030_cum -0.35 ***
9 Total abundance -0.05 *** Calanoides acutus +0.03 *** mld0p125_anMean -0.35 ***
9 Pteropods -0.09 *** Neocalanus tonsus +0.03 *** mld0p125_cum -0.37 ***
9 Fritillaria sp. -0.14 *** Ctenocalanus citer -0.05 *** mld0p125_mPClim -0.46 ***
9 Foraminifera -0.50 *** Rhincalanus gigas -0.08 *** mld0p125_mP -0.47 ***
10 Foraminifera +1.15 *** Metridia sp. +0.18 *** mld0p125_mP +1.08 ***
10 Euphausiidae +0.31 *** Clausocalanus sp. +0.14 *** mld0p125_mPClim +1.08 ***
10 Chaetognatha +0.19 *** Thalicidae +0.12 *** mld0p030_mP +0.94 ***
10 Pteropods -0.17 *** Ostracoda indet +0.12 *** mld0p030_mPClim +0.92 ***
10 Fritillaria sp. -0.46 *** Calanoides acutus -0.14 *** sst_cum +0.81 ***
10 Oithona -0.55 *** Rhincalanus gigas -0.26 *** sst_anMean +0.78 ***

Table 3-6: continued and concluded.
Standardised difference
Cluster Log abundance (broad taxa) Probability of presence (fine taxa) (environmental)
37 Pteropods -0.40 *** Neocalanus tonsus +0.36 *** sst_anMean +1.58 ***
37 Copepoda -0.41 *** Calanoides acutus -0.12 *** sst_cum +1.58 ***
37 Foraminifera -0.47 *** Ctenocalanus citer -0.14 *** vgpm_cum +1.47 ***
37 Fritillaria sp. -0.67 *** Oithona sp. -0.21 *** sst_mP +1.38 ***
37 Total abundance -0.76 *** Rhincalanus gigas -0.32 *** sst_mPClim +1.37 ***
37 Oithona -1.14 *** Calanus simillimus -0.40 *** vgpm_anMean +1.34 ***
39 Euphausiidae -0.29 *** Ctenocalanus citer -0.14 *** sst_mP +0.67 ***
39 Fritillaria sp. -0.31 *** Metridia sp. -0.14 *** sst_mPClim +0.67 ***
39 Ostracoda -0.33 *** Calanoides acutus -0.14 *** sst_anMean +0.62 ***
39 Oithona -0.75 *** Calanus simillimus -0.22 *** sst_cum +0.61 ***
39 Total abundance -0.77 *** Clausocalanus sp. -0.28 *** vgpm_cum +0.51 ***
39 Copepoda -0.93 *** Rhincalanus gigas -0.29 *** vgpm_anMean +0.46 ***
40 Oikopleura sp. -0.29 *** Metridia sp. -0.11 *** SeaIce_cum +1.24 ***
40 Ostracoda -0.31 *** Ostracoda indet -0.12 *** SeaIce_anMean +1.22 ***
40 Foraminifera -0.48 *** Ctenocalanus citer -0.18 *** chl_cum +1.06 ***
40 Oithona -0.74 *** Rhincalanus gigas -0.27 *** chl_mPClim +0.99 ***
40 Total abundance -0.88 *** Clausocalanus sp. -0.33 *** SeaIce_mPClim +0.86 ***
40 Copepoda -0.96 *** Calanus simillimus -0.35 *** SeaIce_mP +0.81 ***
43 Foraminifera -0.66 *** Ostracoda indet -0.16 *** SeaIce_cum +2.75 ***
43 Oikopleura sp. -0.67 *** Ctenocalanus citer -0.28 *** SeaIce_mPClim +2.72 ***
43 Fritillaria sp. -0.71 *** Rhincalanus gigas -0.33 *** SeaIce_anMean +2.69 ***
43 Copepoda -1.61 *** Clausocalanus sp. -0.42 *** SeaIce_mP +2.41 ***
43 Oithona -1.70 *** Calanus simillimus -0.45 *** sstgrad_cum -1.91 ***
43 Total abundance -1.99 *** Oithona sp. -0.54 *** sstgrad_anMean -1.98 ***
Cluster characteristics are shown in Table 3-6. Clusters 1 and 4 had high total zooplankton abundance.
Cluster 1 was characterised by high Foraminifera, Oithona spp., and Fritillaria spp. abundances, high
probability of presence of Rhincalanus gigas, and deep mixed layer depths. Cluster 4 was characterised
by high copepod (and total zooplankton) abundance, high probability of presence of Calanus simillimus,
and low sea ice concentrations. Cluster 9, which covered the largest area, was characterised by
“average” conditions in most variables apart from low foraminifera abundance and shallow mixed layer
depths. Cluster 10 had high abundances of foraminifera, euphausiids, and Metridia spp., warm water,
and a deep mixed layer. Cluster 37 had low abundances of Oithona spp., low overall zooplankton
abundances, high probability of presence of Neocalanus tonsus, and very warm productive waters.
Cluster 39 had low zooplankton abundances (especially low copepod abundances), and warm and
productive water. Cluster 40 was also characterised by low total zooplankton abundance, low copepod
abundance, and had high sea ice and high chl-a concentration. Cluster 43 had the lowest overall
zooplankton abundances (especially for Oithona spp. and calanoid copepods) and the greatest effect of
sea ice. A brief title defines each cluster: Cluster 1, “Polar Front-Rhincalanus gigas zone”; Cluster 4,
“Polar Front-Calanus simillimus zone”; Cluster 9, “Open ocean zone”; Cluster 10, “Polar Front-
foraminifera zone”; Cluster 37, “warm Subantarctic zone”; Cluster 39, “cool Subantarctic zone”;
Cluster 40, “seasonal sea ice zone”; Cluster 43, “extreme sea ice zone”.

The combined BRT models for climatological months October-March are shown in Figure 3-11. Across
the six months of the study (October-March) and averaging over all years, the largest community in
both the Southern Ocean was Cluster 9 (open ocean zone) with 37.6% of the area (Table 3-7). Cluster
37 (warm Subantarctic zone) was next with 22.1%, then Cluster 1 (Polar Front-Rhincalanus gigas zone)
with 17.7%, and Cluster 39 (cool Subantarctic zone) with 10.2% of the area. The smallest area occupied
by a community was by Cluster 43 (extreme sea ice zone), which accounted for <1% of the observable
area in the Southern Ocean as a whole. However, this area is likely to be under-represented in the
analysis because it occurred at the highest latitudes where satellite data (especially ocean colour
observation) are relatively scarce. In the Ross Sea region, the relative sizes of the clusters were in
consistent proportions to those in the Southern Ocean.
Based on the Mann-Kendall trend analysis, statistically significant long-term changes in the areas
occupied by many communities over time were found (Table 3-7), and these were very largely
consistent between the different BRT models. Changes to the areas occupied by the communities in the
Ross Sea region (160°E to 150°W) very closely followed those in the rest of the Southern Ocean. In
particular, Cluster 1 (Polar Front-Rhincalanus gigas zone) was predicted to have increased in area
significantly between 1998 and 2018 at the average rate of about 2.6% per year. In the Southern Ocean
as a whole, Cluster 4 (Polar Front-Calanus simillimus zone) was also predicted to have increased in
area significantly (1.5% per year), but not so in the Ross Sea region where there was no significant
long-term trend. In the Southern Ocean as a whole, the areas of communities represented by Cluster 9
(open ocean zone), Cluster 10 (Polar Front-foraminifera zone), and Cluster 37 (warm Subantarctic zone)
were predicted to have not changed significantly between 1998 and 2018. The area of Cluster 10 (Polar
Front-foraminifera zone) showed a cyclical pattern, with expansion in the middle of the time series
(2006–2011) and contraction before and after, and this was especially pronounced in the Ross Sea
region. In the Southern Ocean, the analysis found that Cluster 39 (cool Subantarctic zone) had
contracted in area (-0.7% per year), but not in the Ross Sea region (no trend). The area of Cluster 37
(warm Subantarctic zone) was predicted to have increased in the Ross Sea region but not in the Southern
Ocean. The area of Cluster 40 (seasonal sea ice zone) showed no trend in the Southern Ocean or Ross
Sea region. The area predicted to be occupied by the communities representing the extreme sea ice
zooplankton community (Cluster 43) showed the highest rates of change in both the Southern Ocean as
a whole and the Ross Sea region (predicted decrease in area of Cluster 43 at 7% per year on average in
the Southern Ocean and 3% per year in the Ross Sea region).

a b
c d
e f
Figure 3-12: Zooplankton communities based on predicted cluster distances using the combined BRT model
and oceanographic environmental information for climatological months. a: October; b:
November; c: December; d: January; e: February; f: March. Colours show the different
zooplankton communities (clusters). Areas with environmental conditions outside the range of the

Table 3-7: Cluster sizes and trends for the Southern Ocean and Ross Sea from the combined BRT model.
“Area” is the average proportion (%) of the observable area for each cluster. The de-seasonalised
Mann-Kendall Z statistic and probability (p) are shown. Significance of Mann-Kendall trend:
* p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001, with non-significant trends shaded grey. The Sen’s slope
trend in the area is shown as a proportion of the mean area. “PF” = Polar Front.
Sen’s slope
Cluster Description Area (%) Z p
(% per y)
Southern Ocean
1 PF-Rhincalanus gigas zone 17.7 6.36 0.000*** +2.65
4 PF-Calanus simillimus zone 5.7 3.84 0.000*** +1.49
9 Open ocean zone 37.6 -2.02 0.043* -0.39
10 PF-Foraminifera zone 1.1 1.52 0.129 +0.73
37 Warm Subantarctic zone 22.1 0.76 0.447 +0.08
39 Cool Subantarctic zone 10.2 -3.71 0.000*** -0.72
40 Seasonal sea ice zone 4.7 -0.90 0.368 -0.29
43 Extreme sea ice zone 0.9 -5.56 0.000*** -7.04
Ross Sea
1 PF-Rhincalanus gigas zone 12.9 4.53 0.000*** +2.54
4 PF-Calanus simillimus zone 2.0 0.80 0.423 +0.68
9 Open ocean zone 33.9 -1.44 0.148 -0.42
10 PF-foraminifera zone 1.1 0.46 0.642 +0.41
37 Warm Subantarctic zone 29.4 3.38 0.001*** +0.76
39 Cool Subantarctic zone 13.6 -1.54 0.124 -0.49
40 Seasonal sea ice zone 6.6 -2.37 0.018* -1.08
43 Extreme sea ice zone 0.4 -3.88 0.000*** -3.08

3.6 Average Copepod Community Size (ACCS)
In the Ross Sea region, based on raw CPR measurements (Figure 3-12a), the ACCS was highest in the
Polar Frontal Zone (mean 1.8 mm) and slightly lower to the north and south, but the index was very
heterogenous. The BRT model of ACCS was acceptable (combined model of R2=0.33, F=1.31, p<0.05).
The BRT model dependency was greatest on mld and sst, and least on SeaIce.
The predicted spatial pattern of the ACCS index across the Southern Ocean (Figure 3-12b) suggested
that this index is generally lower south of the Polar Front and higher in the frontal region. The BRT
combined model of ACCS also show a pronounced seasonal variation in the index (Figure 3-13), with
higher values in October/November (especially in Subantarctic Water in East Antarctica) than in other
months. On average, the BRT combined model suggested that the ACCS was significantly lower in the
Ross Sea region than for the Southern Ocean as whole (1.43 compared with 1.53) meaning that the Ross
Sea region zooplankton assemblage had more small species compared with larger species than average,
but this difference was small.
Few long-term trends in ACCS were seen in raw CPR data (Figure 3-14a). However, the BRT combined
model suggested that increases in ACCS had occurred mainly in the South Atlantic region near the
Polar Front, with modelled patchy decreases in ACCS in higher latitude waters (Figure 3-14b).
a b
Figure 3-13: Average copepod community size (ACCS) index. a: Spatial average ACCS from the raw CPR
data. b: Predicted using the combined BRT model and oceanographic environmental information
(6-month, long term average). Areas with environmental conditions outside the range of the

a b
c d
e f
Figure 3-14: Predicted average copepod community size (ACCS) index by month. a: October; b:
November; c: December; d: January; e: February; f: March. Areas with environmental conditions
outside the range of the training data were excluded from the prediction.

a b
Figure 3-15: Long-term trends in Average Copepod Community Size (ACCS) index. Sen’s slope trends
(average change per year for the period 1998–2018) a: Long-term trends in ACCS from the raw
CPR data. White indicates no significant trend; grey indicates not enough data for trend analysis.
b: Trends in ACCS predicted using the combined BRT model and oceanographic environmental
information. White indicates no significant trend. “Significant” means at better than the 0.05
confidence level assessed using the de-seasonalised Mann-Kendall test. Note that the colour scales
are different (a: -0.10 to +0.10 mm/y; b: -0.02 to +0.02 mm/y).
3.7 Microplastics
Microplastics, primarily in the form of threads, were present in 1597 of the 4159 samples analysed
between 2009 and 2018. The percentage of samples with microplastics varied little among the different
water masses, between ~25 to 40% containing at least one thread (Figure 3-15). Variability among years
was higher, with ~5 to 85% of the samples collected during a given season containing microfibres and
higher percentages in the most recent two seasons (2016–2017 and 2017–2018).
Figure 3-16: a: percentage of samples with microplastics by water type, and b: percentage of samples with
microplastics by season.
Different types of threads, as indicated by thread colour (called ‘thread diversity’), present in different
water masses and seasons were investigated. This metric varied little between water masses (Figure
3-16a) or season (Figure 3-16b). There did seem to be a prevalence of blue and red threads, with higher

counts of these (~700 and 850, respectively) compared with the other coloured thread (Figure 3-16c).
At present the origin of these threads is not known, but further work into the specific plastic composition
of these will provide further understanding as to the origin and potential accumulation of these
micropollutants. Note that the thread colour information was only collected for the last 6 years of the
time series, because the methodology to quantify these items was still developing.
Finally, other types of plastics present in samples were identified as flakes, but only 9 of these items
were found, and threads seem to be the dominant type of microplastics retained on the CPR silk.
Figure 3-17: a: thread ‘diversity’ (types of different coloured threads) by water mass; b: thread ‘diversity’
by season, and c: colour of threads found throughout the whole time series.
4. DISCUSSION
4.1 CPR sampling and analysis
There are well-known advantages and disadvantages to sampling zooplankton communities by the CPR
rather than using vertical, depth-resolved, or oblique net hauls from research ships (e.g., Reid et al.
2003, Hosie et al. 2003, Pinkerton et al. 2010b). The main disadvantages include surface-only sampling,
more damaged specimens, greater ability to avoid capture, and poorer retention of small zooplankton
species for the CPR versus research nets. However, for long-term monitoring of zooplankton over large
areas, it is generally accepted that the advantage of sampling consistently and cost-effectively over large
areas and over extended periods of time (decades) outweighs the disadvantages of CPR sampling.
This report has used a dual broad- and fine-scale grouping of SO-CPR data for analysis. These
groupings were chosen to maximise the useful information content of the dataset whilst being minimally
affected by uncertainties caused by the different levels of taxonomic identification possible in different
samples. Retaining unidentified taxa in the broad grouping enabled the best analysis of spatial, seasonal,
and long-term changes in Southern Ocean zooplankton generally. Excluding poorly-identified
specimens and using the finely-grouped data allowed more detailed examination of the composition of
the zooplankton community.
4.2 Patterns in zooplankton abundances by broad taxonomic group
These analyses of the raw CPR data in the Southern Ocean confirmed the expectation that zooplankton
abundances had high spatial and temporal variability at the broad taxonomic level. This variability
meant that trend analysis of the raw CPR data, even at a coarse spatial scale of 300 km, had limited
power to identify spatially-coherent, long-term changes. Using a data-mining analysis consistent with
best practice (e.g., Hochachka et al. 2007), the underlying spatial and temporal patterns in the CPR data
for many of the broad groups was revealed. The BRT models effectively allowed regionally-restricted
CPR sampling to be extrapolated to the whole Southern Ocean using satellite observations and data-
assimilating hindcasts of ocean primary productivity, phytoplankton biomass, surface water
temperature, mixed layer depth, sea ice, and frontal activity.

The CPR data were related to environmental data at a number of different timescales. The performance
of the models based on the different timescales were similar; no one model did much better than the
others. The different models were hence combined, taking into account their different uncertainty
characteristics. The models represent the average environmental conditions associated with particular
taxonomic groups of zooplankton. Within this “zooplankton environmental envelope”, there were high
levels of variability in the zooplankton because of small-scale heterogeneity and ecological factors such
as predation that are not included in the models. The environmental data used here were not sufficient
to explain this small-scale variability in zooplankton abundances.
At the broad scale, however. the spatial patterns of key zooplankton groups in the Southern Ocean
predicted by the combined BRT models were consistent with previous analyses of zooplankton
distributions (e.g., Pinkerton et al. 2010b, McLeod et al 2010, Takahashi et al. 2011, Stevens et al.
2014). In particular, the modelled abundances of pteropods showed a hotspot over the Ross Sea shelf
and around South Georgia. Based on a global analysis of net samples, Hunt et al. (2008) concluded that
South Georgia, East Antarctica south of Australia, and the Ross Sea were hotspots in terms of both
pteropod densities and proportional contribution to zooplankton communities. It is remarkable that
despite no CPR data being collected from the South Georgia area, this SO-CPR analysis also predicted
a hotspot in pteropod numbers in this region. This provides some independent validation of the results
shown here.
The highest total zooplankton abundances were found in the vicinity of the Polar Front, with lower
abundances to the north and south, broadly following the pattern of primary production in the Southern
Ocean which would be expected if zooplankton populations were subject to bottom-up trophic control
(Ainley et al. 2007). However, peak latitudinal abundances of different zooplankton groups are
separated spatially around the frontal zone: the highest abundances of Foraminifera are to the north of
the peak copepod abundance, whereas the highest Fritillaria spp. and Oithona spp. abundances are to
the south of that of copepods. Partly this spatial segregation will arise from the direct differences in the
physical environment. Given the interacting nature of dependences captured by BRT analysis, these
environmental dependences are not easily summarised. However, this analysis shows that SeaIce more
strongly affected the distribution of Copepoda than for Foraminifera or Fritillaria spp., whereas the
reverse is true for sstgrad (frontal activity). The strength and nature of the dependence on primary
production also varied between the groups, with Fritillaria spp. (low trophic level) having a much
stronger dependence on vgpm (primary productivity) than Copepoda (higher trophic level in general)
which seems consistent with more grazing compared with carnivory. Trophic interactions, as well as
environmentally-driven responses, contributed to spatial distributions of zooplankton in the Southern
Ocean. Trophic niche separation could arise from carnivorous zooplankton feeding on different prey
(bottom-up niche segregation), or through the presence of top-down control within zooplankton
communities (prey zooplankton are depleted in some areas by their predators).
4.3 Zooplankton communities
No standard method is available for zooplankton community analysis and the approach developed in
the present study is a step forward in this kind of analysis. Our method appropriately captured the
combination of broad-scale and fine-scale variability in zooplankton communities from the CPR data
and robustly obtained the number of significantly-different clusters.
Using cluster analysis, 11 “clusters” in the CPR data were identified as distinct zooplankton
communities in the Southern Ocean. Of these, 8 could be resolved using environmental properties: two
communities in the Subantarctic water (Cluster 37, warm Subantarctic zone and Cluster 39, cool
Subantarctic zone); the largest open ocean zone (Cluster 9); three frontal zone communities (Cluster 1,
Polar Front-Rhincalanus gigas zone; Cluster 4, Polar Front-Calanus simillimus zone; and Cluster 10:
Polar Front-foraminifera zone); and two se -ice communities (Cluster 40, seasonal sea ice zone; Cluster
43, extreme sea ice).
Cluster 40 is the least well resolved cluster based on environmental properties, and in March becomes
split latitudinally making its interpretation problematic. Otherwise, the positions and characteristics of

these communities broadly agree with those from similar previous studies (e.g., Hunt & Hosie 2005,
2006a, b). For example, Hunt & Hosie (2005) identified high total abundances in their Cluster 2 at
around 64° S corresponding to our Clusters 1 and 4, and these had high Oithona spp. abundances.
Cluster 3 of Hunt & Hosie (2005) had high numbers of foraminifera and corresponded to Cluster 10 in
the present study. The ability to investigate zooplankton communities based on the combination of their
broad-scale characteristics (like total abundance) and fine taxonomic-scale characteristics (particular
species and genus of zooplankton), and combined with their environmental properties, is a major step
forward. This approach provides a means in the future to compare zooplankton communities as a whole
in different areas without assuming a simple dependence of zooplankton community on geographic
regions as done previously (Robinson et al. 2014, Hunt & Hosie et al. 2006a, b).
4.4 Trends and long-term change
The CPR data in broad taxonomic groups were analysed by oceanographic zone in the Ross Sea region
and in large (300 km) spatial blocks. From analysis of the “raw” CPR data, only a few significant trends
were found, and the magnitudes of these significant trends tended to be very high (>10% y-1), especially
for Fritillaria spp. These results contrasted with those from the model-based analysis; the BRT models
showed significant trends in the abundances of almost all broad zooplankton groups, but with very low
rates of change (less than 1% y-1).
The fact that month explained a relatively low proportion of variance in the abundances of the broad
taxonomic groups (4.0% overall) means that predicted values based on the BRT models are primarily
determined from the oceanographic conditions rather than the date per se. This result gave more
likelihood that the BRT model-based analysis can be used to understand the effects of oceanographic
change on zooplankton communities. The fact that the same types of changes were predicted by
different BRT models (cumulative, annual, etc.) based on different sets of environmental variables also
supported the conclusion that the predictions of long-term changes from the BRT modelling were robust
to the particular type of model developed.
What seemed to be occurring is that the environmental conditions have generally changed in a way
likely to be beneficial (in terms of leading to higher abundances) for most broad taxonomic groups of
zooplankton (Oithona spp. and calanoid copepods, euphausiids, foraminifera, Fritillaria spp.) over the
last 20 years (1997–2018). The environmental changes were likely to have been especially beneficial
in the area between the Subantarctic Front and the southern boundary of the ACC, though the changes
were “patchy” geographically. Positive trends in zooplankton abundances tended to follow increased
ocean productivity (higher chl), warmer water (higher sst), and deeper mixed layers (higher mld0p125).
In contrast, the environmental conditions for pteropods had worsened over the last 20 years over the
Ross Sea shelf especially, and this corresponded to lower phytoplankton biomass (chl) in the region of
decrease.
Superimposed on these environmentally-driven changes in zooplankton communities was a very large
amount of spatial and short-term variability which was not captured by the models. This intrinsic
variability in zooplankton abundances and the limited nature of the sampling prevents the underlying
changes to zooplankton abundances being apparent in simple analysis of the CPR data alone. Hence,
occasional, spatially-incoherent, high-magnitude, significant trends were identified from the “raw” CPR
data, but the large-area, relatively small-magnitude, environmentally-driven trends that are likely to be
present were not resolved. As the time series of observation increases, the power to observe these long-
term changes above the short-term fluctuations will improve.
Corresponding to the change in the abundances of broad taxonomic groups of zooplankton, the analysis
showed that the environmental properties have been changing in a way this is likely to lead to significant
long-term changes in the spatial extent of many zooplankton communities over time. Based on the
environmental change and model relationships between the environment and communities, two zones
in the vicinity of the Polar Front (Cluster 1, Polar Front-Rhincalanus gigas zone; Cluster 4, Polar Front-
Calanus simillimus zone) are predicted to have increased in area between 1997 and 2018. In contrast,
Cluster 39 (cool Subantarctic zone) and southernmost community (Cluster 43) are predicted to have

contracted over the last 20 years. The rapid contraction (-7% y-1 generally and -3% y-1 in the Ross Sea
region) of the main sea ice associated community (Cluster 43) occurred along with the reductions in
pteropod abundance suggested by the BRT models over the Ross Sea shelf.
4.5 Average Copepod Community Size (ACCS) index
BRT modelling was used to investigate changes in the average size of copepods in the Southern Ocean.
An updated average size for groups of zooplankton (at the genus level or above) in the Southern Ocean
was used (Appendix 3). Based on the BRT model, this analysis suggested that the ACCS is decreasing
at high latitudes in the Southern Ocean (approximately south of the southern limit of the ACC). These
high latitude areas showed no trends, or slightly cooling trends, in SST. In contrast, north of the southern
limit of the ACC, surface waters were warming strongly in most areas. The warming of the surface
ocean in the Southern Ocean seems to be associated with a shift to larger zooplankton and, in contrast,
cooling with a shift to smaller zooplankton.
A caveat to these results arises from the factors involved in calculating the ACCS. Because the average
female adult size is used and not a measurement of each specimen within the sample which could
include other developmental stages, the estimate will be more ‘true’ if the real catch comprised more
adults. More importantly, the catchability of a zooplankter by the CPR varies with size, with small
organisms like Oithona spp. likely to be under-sampled because of net efficiencies, and larger copepods
and euphausiids under-sampled because larger organisms tend to live deeper in the water column, with
more pronounced diel vertical migration (De Robertis 2002; Steinberg et al. 2002). If communities are
shifting significantly into the size-spectral area that is under-sampled by the CPR (either too large or
too small), this effect could reduce the reliability of trends in the ACCS. In addition, because most of
the sampling occurs within a restricted time-frame (November-February), ocean-warming induced
changes in phenology could result in our CPR sampling missing (or under-sampling) the abundance of
species which have pronounced seasonal peaks, e.g., Calanoides acutus (Atkinson 1998).
Notwithstanding these caveats, these results are contrary to the expectation that warming oceans would
see a shift to warm-water species that tend to be smaller (Lopez & Anadon 2008). The rationale for this
premise is that tropical species are typically very small, temperate species tend to be bigger, and the
largest species are usually found in sub-polar/polar waters or in deeper cooler waters. However, iron-
limited Subantarctic waters also tend to have phytoplankton communities dominated by small cells,
which is similar to tropical systems, and thus have the same effect of reducing zooplankton species size
(Bradford-Grieve et al. 2003). The near surface Antarctic waters, notably in higher latitudes, are
typically characterised by large species such as Calanoides acutus, Calanus propinquus, Rhincalanus
gigas, and several species of Paraeuchaeta. However, the Southern Ocean also has quite a broad size
range of numerous abundant small species of 1–2 mm common in the CPR samples, e.g., species of
Clausocalanus, Ctenocalanus, and then there is the numerically most abundant species, the
cosmopolitan Oithona spp. at < 1 mm. Given that the BRT model predicts that total zooplankton
abundances are generally increasing, especially just to the north of the seasonal limit of sea ice (Figure
3-8), it is likely that decreases in ACCS in these high latitude areas are driven by the increasing
abundance of small zooplankton taxa. Of the broad groups, Oithona spp. shows the greatest increasing
trend at these high latitudes and is likely responsible for some or much of the decreases in ACCS.
Areas of increasing trends in ACCS are mainly located between the Subantarctic Front and the Polar
Front and correspond with increases in the abundance of Foraminifera (Figure 3-8). Foraminifera
abundances were not used to calculate the ACCS, which is restricted to abundances of copepods. The
hypothesis from this analysis therefore is that large copepod species are increasing in abundance faster
than smaller copepod species in the Subantarctic Front and Polar Front areas and that this is ecologically
associated with increasing abundances of Foraminifera in these areas. It is possible that increasing
abundances of Foraminifera in these areas are fueling (i.e., as prey) increases in the abundance of large,
carnivorous zooplankton species, or that the underlying ecological drivers increasing copepod
abundances are also positively affecting Foraminifera, perhaps linked to increases in productivity or
more palatable phytoplankton.

4.6 Comparison between Ross Sea and the rest of the Southern Ocean
There is interest in considering whether zooplankton abundances are different in the Ross Sea region
than in the rest of the Southern Ocean. Some studies have suggested that mesozooplankton biomass in
the Ross Sea is unusually low (Tagliabue & Arrigo 2003), which was not confirmed by later analysis
(e.g., Stevens et al. 2014, Pinkerton et al. 2010a, b, Robinson et al. 2014). In this study, spatial statistical
models were used to explore large-area differences in abundances between the regions and whether this
could be due to differences in environmental conditions between the regions or different ecological
characteristics.
Overall, analysis presented in this report showed that zooplankton abundances were higher in the Ross
Sea region than the Southern Ocean as whole, by a factor of about 2 on average, but this factor varied
between zooplankton taxa. Foraminifera and Fritillaria spp. were more than 3 times as abundant in the
Ross Sea region than elsewhere in the Southern Ocean. The reasons for these differences in abundances
are not known, but they are not related to the environmental conditions considered here (primary
productivity, phytoplankton biomass, SST, mixed layer depth, sea ice, or frontal activity). The spatial
differences in zooplankton could be related to factors including (but not restricted to): (1) different types
of phytoplankton in the Ross Sea region; (2) different microbial communities; and (3) different grazing
pressure by higher trophic level consumers. Seeking large-area information on these factors would be
a useful next step from this study and is underway elsewhere (e.g., under the Ross-RAMP project 6).
Interestingly, long-term trends in the abundances of zooplankton groups in the Ross Sea region were
very similar irrespective of whether a Southern Ocean or specific Ross Sea region model was used
(Table 3-4) indicating the changes to the environmental envelopes of zooplankton are likely to be
changing at similar rates inside and outside the Ross Sea region.
4.7 Future effects of climate change
The data and results developed in this report pave the way to explore the effects of climate change on
Southern Ocean zooplankton populations. A large global effort is focussed on forecasting the effects of
increasing carbon dioxide levels in the atmosphere on atmospheric and oceanographic conditions. For
example, the CMIP5 7 and CMIP6 programmes bring together more than 14 Earth-system models from
leading research groups around the world in a way in which the results can be examined and re-used
(Bopp et al. 2013). Previous work has examined which of the many Earth system models work best in
the New Zealand and in the Ross Sea regions by comparing model results with observational data from
satellites (Rickard & Behrens 2016).
Less developed are methods to use these predicted changes in physical and chemical characteristics to
explore the potential effects on living organisms. Zooplankton, although a key part of ocean ecosystems
worldwide, are particularly problematic because they are ecologically diverse (hundreds of taxa),
poorly-observed, and spatially and temporally variable. The relationships developed in the present study
provide a step forward by enabling the forecasting of the effect of climate change on key taxonomic
groups of zooplankton and zooplankton communities. Although carrying out this analysis is beyond the
scope of this report, this analysis will continue under funding from the MBIE-Endeavour RAMP 8
programme and potentially the Antarctic Science Platform.
6
Ross-RAMP (Ross Sea region Research and Monitoring Programme): MBIE Endeavour Fund programme,
2017–2023. Pinkerton PI (NIWA).
7
Coupled Model Intercomparison Project - https://cmip.llnl.gov/.
8
Ross Sea Research and Monitoring programme associated with the Ross Sea region MPA.

4.8 Northern hemisphere comparisons
A formal comparison between Northern Hemisphere and Southern Hemisphere CPR datasets was not
possible because of methodological differences in the way CPR zooplankton samples were analysed,
which means that treating the two datasets in the same way would be inappropriate (Beaugrand et al.
2001, 2003). Also, the CPR survey in the North Atlantic started in 1948, so there is less ability to track
long-term (decadal) changes in zooplankton in the Southern Ocean because the SO-CPR survey started
in 1991.
Trends in zooplankton in the North Atlantic show communities shifting polewards, accompanying
warming ocean temperatures (Beaugrand et al. 2002), with once-tropical species now found in more
temperate latitudes, and temperate species shifting to polar waters (Beaugrand et al. 2002, Beaugrand
et al. 2001, Beaugrand et al. 2003). These changes in the North Atlantic are not necessarily forced by
the local phytoplankton communities, because these seem to be responding to decadal, rather than
longer-term, forcing (Harris et al. 2014, Harris et al. 2015). The changes would tend to lead to a
decreasing ACCS index in the North Atlantic over time.
The zooplankton community (cluster) analysis of Southern Ocean zooplankton data showed a similar
pattern of temperate zooplankton communities (especially in the Polar Front region) expanding
polewards and the high-latitude polar zooplankton communities (Antarctic “sea ice” zooplankton
communities, Cluster 43) being squeezed out. The decline in abundance of pteropods over the Ross Sea
shelf is also notable (Figure 3-7). Analysis of the ACCS patterns in the SO-CPR data also suggested
more smaller copepods compared with more sizeable polar species at high latitudes. There were
corresponding negative (decreasing) long-term trends in ACCS in the Southern Ocean at high latitudes.
What is different between hemispheres is that the negative trends in ACCS in the high-latitude Southern
Ocean correspond to increases in SST (warming) rather than cooling in the North Atlantic. Also, the
drivers of the changes in zooplankton communities between the two hemispheres may be different; in
the Southern Ocean, the increases in abundances of small copepods are tentatively interpreted as
resulting from improved food-conditions (given positive relationships with chl-a) rather than the longer-
term (potentially physical) forcing in the North Atlantic.
It is important to discuss both the different latitudinal range sampled as part of each of these
programmes, and the inherent differences in the oceanography of the southern versus the northern
hemisphere. The North Atlantic CPR coverage spans a slightly different latitudinal range, with the bulk
of measurements carried out between 40°–65° N (Beaugrand & Ibanez 2002), i.e., slightly more
temperate than the SO-CPR sampling. The oceanography of the North Atlantic basin is also quite
different from the Southern Ocean, with large portions of land that prohibit a circumpolar water
circulation pattern being established. This means the copepod communities sampled as part of the North
Atlantic programme inhabit large areas of somewhat homogenous oceanic conditions, e.g., large areas
of Subtropical waters not structured by the Subtropical Front, or polar waters without the strong
Antarctic Polar Front. These fundamental oceanographic differences between hemispheres mean that
the differences in zooplankton abundance patterns might not be so surprising. Furthermore, there have
been differences in ocean heat absorption between hemispheres. Since 2006, an estimated 60–90% of
global ocean heat content change associated with global warming has occurred in the Southern Ocean
(Roemmich et al. 2015, Llovel & Terray 2016, Sallée 2018), suggesting that changes in the Southern
Hemisphere would be expected to be more dramatic than in the Northern Hemisphere.
The time series analysed here is presently too short to determine these long-term changes with certainty,
but the BRT model results suggest that the large-scale pattern of Southern Hemisphere warming is likely
the cause in changing communities, with higher total abundances and relative increases in key
taxonomic groups of zooplankton which are not paralleled by changes in the North Atlantic time series.
Longer time series and enhanced spatial resolution will allow us to confirm these patterns.

4.9 Final comments
This report has explored the relation between zooplankton abundance, zooplankton communities, and
environmental conditions in the Southern Ocean, with a focus on the Ross Sea region. It seems that
changes to the environmental conditions have already occurred and are likely to continue to cause long-
term change in Southern Ocean zooplankton. The effect of these changes on higher trophic level species
like fish, seabirds, and marine mammals is not known. The data and analyses presented here are suitable
to underpin multi-trophic studies to see if changes to zooplankton can help explain changes to larval
fishes, mesopelagics, seabirds, and marine mammals across the Southern Ocean. Continued collection
of zooplankton data in the future will provide an ability to confirm empirically whether these patterns
and trends are genuine, and how zooplankton taxonomic groups and communities change in the future.
5. MANAGEMENT IMPLICATIONS
Key conclusions of this study:
1. Concentrations of chl-a in the Southern Ocean (likely indicative of changes to oceanic primary
production) are generally increasing, especially around the southern limit of the Antarctic
Circumpolar Current (particularly in East Antarctica), around the Argentine continental shelf,
and in the Subtropical Front around New Zealand. In the Ross Sea region (especially over the
continental shelf), however, chl-a concentrations show significant negative long-term trends
(decreases).
2. Abundances of zooplankton are higher in the Ross Sea region than in the Southern Ocean as
whole, by a factor of about 2 on average but varying between zooplankton taxa. Abundances
of Foraminifera and Fritillaria spp. were the most different in the Ross Sea region than
elsewhere. These differences are not due to the Ross Sea region having unusual environmental
conditions and are more likely to be ecologically-driven.
3. Predictions of abundances and distributions of key zooplankton groups based on environmental
conditions (phytoplankton biomass, primary productivity, water temperature, mixed layer
depth, sea ice, or frontal activity) are generally good at representing average spatial patterns in
occurrence of particular broad groups of zooplankton taxa. The models developed in this study
can be used in conjunction with Earth-system models to forecast the effects of climate change
on zooplankton in the Southern Ocean. This has relevance to anticipating, understanding, and
managing change in Antarctic ecosystems because variability in zooplankton will affect other
parts of the marine food-web, including fishes, seabirds, and mammals.
4. Environmental conditions for most broad taxonomic groups of zooplankton in the Southern
Ocean have generally improved over the last 20 years (1997–2018) and these environmental
changes are likely to drive increases in abundances of most zooplankton groups in the future.
5. In contrast, the environmental conditions for pteropods (small marine snails living in the water
column) seems to have worsened over the last 20 years over the Ross Sea shelf especially. The
negative pressure on pteropod abundance may have implications for the Ross Sea shelf
ecosystem where pteropods are a major contributor to the flow of organic matter to the seabed.
6. There were significant increases in the Average Copepod Community Size (ACCS) metric in
the Ross Sea region during the sampling period, suggesting a shift towards larger copepod
species. Ocean warming in the Southern Ocean generally seems to be associated with a shift to
larger zooplankton, and cooling with a shift to smaller cold-water copepods such as Oithona
spp. This finding is contrary to the prevailing hypothesis that ocean warming favours smaller
copepods.
7. Superimposed on these predicted changes to zooplankton due to trends in environmental
conditions were shorter-term and localised fluctuations in zooplankton abundances. These

fluctuations were not captured by the models developed here and ongoing monitoring of
zooplankton remains important. Regular, twice-yearly transits of a fishing vessel on a single
track provide an excellent approach for quantifying variability in zooplankton between New
Zealand and the Ross Sea and, for tracking long-term change, is likely superior to opportunistic
CPR sampling.
8. The comparison between results of studies conducted in the Southern Hemisphere and Northern
Hemisphere suggested similarities and differences between the hemispheres. In both areas,
there is evidence of poleward shifting zooplankton communities, but these changes seem to be
in response to different oceanographic and environmental drivers.
9. The presence of plastic microfibre threads was ubiquitous across water types and years, with
the last two seasons showing a higher abundance of threads. Although the nature of these
particles is not known, or even if they are a homogenous type of particle, red and blue threads
were by far the most abundant, and future study into their composition would shed more light
into their origin. No trend with water type would suggest that the source of these particles is
not restricted to land. It is not known how many of the plastic microfibres sampled by the CPR
had a local source (i.e., from the ship towing the CPR) rather than a far-field source (i.e.,
representing the concentration of plastic in the Southern Ocean generally).
6. ACKNOWLEDGMENTS
This work was completed under Ministry for Primary Industries project ZBD2013-03 Objective 10.
Additional resources for CPR sample and data analysis were provided by NIWA Strategic Science
Investment Fund (SIFF) Coasts & Oceans, Programme 4: Structure and function of marine ecosystems,
and MBIE Endeavour Fund programme Ross-RAMP (C01X1710). The work would not have been
possible without the assistance of Sanford Limited, Dave Bilton, Monique Messina, and the officers
and crew of FV San Aotea II. We acknowledge the scientists, officers, and crew of RV Tangaroa for
CPR data collection on voyages between 2006 and 2013. CPR equipment and training were provided
by Graham Hosie and John Kitchener from the SO-CPR survey (Australian Antarctic Division, Hobart,
Australia) and The Marine Biological Association CPR Survey (formerly SAHFOS), Plymouth, UK.
We thank Ashley Rowden (NIWA) for statistical discussions and for review of this report which helped
improve it. We also thank Barb Hayden (NIWA) for review.
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8. APPENDIX 1: Grouping of zooplankton data
Table 8-1. Groupings of the standard CPR identification groups used in the analysis. Two levels of grouping
were used: “broad” and “fine”. In a small number of fine groups, subgroups were also used; these
subgroups are shown separated with ‘|’. In these cases, counts were partitioned pro rata amongst subgroups
on a sample-by-sample basis unless none of the subgroup counts were greater than zero, in which case the
average proportions in the tow were used. Broad and fine groups marked “other” were excluded from
analysis.
CPR group Broad group Fine group

1 Acartia (Acartia) danae Copepoda Acartia spp.
2 Acartia (Acartiura) tranteri Copepoda Acartia spp.
3 Acartia (Odontacartia) pacifica Copepoda Acartia spp.
4 Acartia spp. Copepoda Acartia spp.
5 Aetideus australis Copepoda OtherCopepod
6 Aetideus spp. Copepoda OtherCopepod
7 Calanoides spp. Copepoda OtherCopepod
8 Calanoides acutus Copepoda Calanoides acutus
9 Calanoides brevicornis Copepoda Calanoides brevicornis
10 Calanus spp. Copepoda Calanus australis|Calanus propinquus|Calanus simillimus
11 Calanus australis Copepoda Calanus australis
12 Calanus propinquus Copepoda Calanus propinquus
13 Calanus simillimus Copepoda Calanus simillimus
14 Calocalanus plumulosus Copepoda Calocalanus spp.
15 Calocalanus spp. Copepoda Calocalanus spp.
16 Calocalanus styliremis Copepoda Calocalanus spp.
17 Candacia bipinnata Copepoda Candacia spp.
18 Candacia cheirura Copepoda Candacia spp.
19 Candacia falcifera Copepoda Candacia spp.
20 Candacia maxima Copepoda Candacia spp.
21 Candacia spp. Copepoda Candacia spp.
22 Centropages aucklandicus Copepoda Centropages spp.
23 Centropages bradyi Copepoda Centropages spp.
24 Centropages furcatus Copepoda Centropages spp.
25 Centropages spp. Copepoda Centropages spp.
26 Clausocalanus spp. Copepoda Clausocalanus spp.
27 Clausocalanus arcuicornis Copepoda OtherCopepod
28 Clausocalanus brevipes Copepoda Clausocalanus spp.
29 Clausocalanus ingens Copepoda Clausocalanus spp.
30 Clausocalanus laticeps Copepoda Clausocalanus spp.
31 Clausocalanus pergens Copepoda Clausocalanus spp.
32 Ctenocalanus spp. Copepoda Ctenocalanus spp.
33 Ctenocalanus spp. Copepoda Ctenocalanus spp.
34 Drepanopus spp. Copepoda Drepanopus spp.
35 Euaugaptilus spp. Copepoda Euaugaptilus spp.
36 Eucalanus hyalinus Copepoda Eucalanus spp.
37 Eucalanus spp. Copepoda Eucalanus spp.
38 Euchirella rostrata Copepoda Euchirella spp.
39 Euchirella rostromagna Copepoda Euchirella spp.
40 Euchirella spp. Copepoda Euchirella spp.
41 Haloptilus oxycephalus Copepoda Haloptilus oxycephalus
42 Heterorhabdus austrinus Copepoda Heterorhabdus spp.
43 Heterorhabdus lobatus Copepoda Heterorhabdus spp.
44 Heterorhabdus spp. Copepoda Heterorhabdus spp.
45 Heterorhabdus spinifrons Copepoda Heterorhabdus spp.
46 Lucicutia flavicornis Copepoda Lucicutia spp.
47 Lucicutia spp. Copepoda Lucicutia spp.
48 Mecynocera clausi Copepoda Mecynocera spp.
49 Mecynocera spp. Copepoda Mecynocera spp.

50 Mesocalanus spp. Copepoda Mesocalanus spp.
51 Mesocalanus tenuicornis Copepoda Mesocalanus spp.
52 Metridia spp. Copepoda Metridia spp.
53 Metridia gerlachei Copepoda Metridia spp.
54 Metridia lucens Copepoda Metridia spp.
55 Microcalanus pygmaeus Copepoda Microcalanus pygmaeus
56 Nannocalanus minor Copepoda OtherCopepod
57 Neocalanus gracilis Copepoda OtherCopepod
58 Neocalanus tonsus Copepoda Neocalanus tonsus
59 Onchocalanus spp. Copepoda OtherCopepod
60 Paracalanus aculeatus Copepoda Paracalanus spp.
61 Paracalanus indicus Copepoda Paracalanus spp.
62 Paracalanus spp. Copepoda Paracalanus spp.
63 Paraeuchaeta barbata Copepoda Paraeuchaeta spp.
64 Paraeuchaeta spp. Copepoda Paraeuchaeta spp.
65 Paraeuchaeta antarctica Copepoda Paraeuchaeta spp.
66 Paraeuchaeta biloba Copepoda Paraeuchaeta spp.
67 Paraeuchaeta exigua Copepoda Paraeuchaeta spp.
68 Paraheterorhabdus farrani Copepoda OtherCopepod
69 Paralabidocera antarctica Copepoda Paralabidocera antarctica
70 Pleuromamma abdominalis Copepoda Pleuromamma spp.
71 Pleuromamma spp. Copepoda Pleuromamma spp.
72 Pleuromamma borealis Copepoda Pleuromamma spp.
73 Pleuromamma gracilis Copepoda Pleuromamma spp.
74 Pleuromamma piseki Copepoda Pleuromamma spp.
75 Pleuromamma robusta Copepoda Pleuromamma spp.
76 Pleuromamma xiphias Copepoda Pleuromamma spp.
77 Rhincalanus gigas Copepoda Rhincalanus gigas
78 Rhincalanus gigas nauplius Copepoda Rhincalanus gigas
79 Rhincalanus nasutus Copepoda OtherCopepod
80 Rhincalanus spp. Copepoda Rhincalanus gigas
81 Scaphocalanus echinatus Copepoda OtherCopepod
82 Scaphocalanus farrani Copepoda OtherCopepod
83 Scolecithricella minor Copepoda Scolecithricella minor
84 Scolecithricella spp. Copepoda Scolecithricella minor
85 Stephos longipes Copepoda Stephos longipes
86 Subeucalanus longiceps Copepoda Subeucalanus longiceps
87 Subeucalanus spp. Copepoda Subeucalanus longiceps
88 Sulcanus conflictus Copepoda OtherCopepod
89 Temora turbinata Copepoda Temora turbinata
90 Calanoida indet (small) Copepoda Calanoida indet (small)
91 Crustacea nauplius indet Copepoda Calanoida indet-(large)
92 Copepoda nauplius indet Copepoda Calanoida indet-(large)
93 Calanoida indet-(large) Copepoda Calanoida indet-(large)
94 Calanoida indet-(large) damaged Copepoda Calanoida indet-(large) DAMAGED
95 Nauplius indet Copepoda Nauplius indet
96 Farranula spp. Copepoda OtherCopepod
97 Lubbockia spp. Copepoda OtherCopepod
98 Oncaea curvata Copepoda Oncaea spp.
99 Oncaea mediterranea Copepoda Oncaea spp.
100 Oncaea spp. Copepoda Oncaea spp.
101 Oncaea venusta typica Copepoda Oncaea spp.
102 Sapphirina nigromaculata Copepoda Sapphirina spp.
103 Sapphirina spp. Copepoda Sapphirina spp.
104 Triconia antarctica Copepoda Triconia antarctica
105 Cyclopoida nauplius indet Copepoda Cyclopoida nauplius indet
106 Clytemnestra scutellata Copepoda Harpacticoida
107 Clytemnestra spp. Copepoda Harpacticoida
108 Euterpina spp. Copepoda Harpacticoida
109 Microsetella norvegica Copepoda Harpacticoida
110 Microsetella rosea Copepoda Harpacticoida

111 Microsetella spp. Copepoda Harpacticoida
112 Oculosetella gracilis Copepoda Harpacticoida
113 Harpacticoida indet Copepoda Harpacticoida
114 Oithona spp. Oithona Oithona spp.
115 Oithona atlantica Oithona Oithona spp.
116 Oithona frigida Oithona Oithona spp.
117 Oithona longispina Oithona Oithona spp.
118 Oithona similis Oithona Oithona spp.
119 Thysanoessa spp. furcilia Euphausiidae Euphausiidae
120 Euphausia crystallorophias Euphausiidae Euphausiidae
121 Euphausia crystallorophias calyptopis Euphausiidae Euphausiidae
122 Euphausia crystallorophias furcilia Euphausiidae Euphausiidae
123 Euphausia frigida Euphausiidae Euphausiidae
124 Euphausia frigida calyptopis Euphausiidae Euphausiidae
125 Euphausia frigida furcilia Euphausiidae Euphausiidae
126 Euphausia hanseni furcilia Euphausiidae Euphausiidae
127 Euphausia longirostris Euphausiidae Euphausiidae
128 Euphausia longirostris calyptopis Euphausiidae Euphausiidae
129 Euphausia longirostris furcilia Euphausiidae Euphausiidae
130 Euphausia lucens Euphausiidae Euphausiidae
131 Euphausia recurva Euphausiidae Euphausiidae
132 Euphausia similis Euphausiidae Euphausiidae
133 Euphausia similis furcilia Euphausiidae Euphausiidae
134 Euphausia spinifera Euphausiidae Euphausiidae
135 Euphausia spinifera calyptopis Euphausiidae Euphausiidae
136 Euphausia spinifera furcilia Euphausiidae Euphausiidae
137 Euphausia superba Euphausiidae Euphausiidae
138 Euphausia superba C1 Euphausiidae Euphausiidae
141 Euphausia superba calyptopis Euphausiidae Euphausiidae
142 Euphausia superba F1 Euphausiidae Euphausiidae
148 Euphausia superba furcilia Euphausiidae Euphausiidae
149 Euphausia triacantha Euphausiidae Euphausiidae
150 Euphausia triacantha calyptopis Euphausiidae Euphausiidae
151 Euphausia triacantha furcilia Euphausiidae Euphausiidae
152 Euphausia vallentini Euphausiidae Euphausiidae
153 Euphausia vallentini calyptopis Euphausiidae Euphausiidae
154 Euphausia vallentini furcilia Euphausiidae Euphausiidae
155 Nematoscelis megalops Euphausiidae Euphausiidae
156 Nyctiphanes australis Euphausiidae Euphausiidae
157 Nyctiphanes australis calyptopis Euphausiidae Euphausiidae
158 Nyctiphanes australis furcilia Euphausiidae Euphausiidae
159 Thysanoessa gregaria Euphausiidae Euphausiidae
160 Thysanoessa gregaria calyptopis Euphausiidae Euphausiidae
161 Thysanoessa gregaria furcilia Euphausiidae Euphausiidae
162 Thysanoessa macrura Euphausiidae Euphausiidae
163 Thysanoessa macrura C1 Euphausiidae Euphausiidae
166 Thysanoessa macrura calyptopis Euphausiidae Euphausiidae
167 Thysanoessa macrura F1 Euphausiidae Euphausiidae

173 Thysanoessa macrura furcilia Euphausiidae Euphausiidae
174 Thysanoessa macrura metanauplius Euphausiidae Euphausiidae
175 Thysanoessa spp. Euphausiidae Euphausiidae
176 Euphausiidae calyptopis indet Euphausiidae Euphausiidae
177 Euphausiidae furcilia indet Euphausiidae Euphausiidae
178 Euphausiidae indet Euphausiidae Euphausiidae
179 Euphausiidae metanauplius indet Euphausiidae Euphausiidae
180 Euphausiidae nauplius indet Euphausiidae Euphausiidae
181 Brachyscelus crusculum Amphipoda Amphipoda
182 Cyllopus lucasii Amphipoda Amphipoda
183 Cyllopus magellanicus Amphipoda Amphipoda
184 Dairella californica Amphipoda Amphipoda
185 Hemityphis spp. Amphipoda Amphipoda
186 Hyperia spp. Amphipoda Amphipoda
187 Hyperia spinigera Amphipoda Amphipoda
188 Hyperiella antarctica Amphipoda Amphipoda
189 Hyperiella dilatata Amphipoda Amphipoda
190 Hyperiella spp. Amphipoda Amphipoda
191 Hyperoche medusarum Amphipoda Amphipoda
192 Hyperoche spp. Amphipoda Amphipoda
193 Phronima spp. Amphipoda Amphipoda
194 Primno macropa Amphipoda Amphipoda
195 Scina spp. Amphipoda Amphipoda
196 Themisto australis Amphipoda Amphipoda
197 Themisto gaudichaudii Amphipoda Amphipoda
198 Themisto spp. Amphipoda Amphipoda
199 Vibilia antarctica Amphipoda Amphipoda
200 Vibilia armata Amphipoda Amphipoda
201 Vibilia spp. Amphipoda Amphipoda
202 Platysceloidea indet Amphipoda Amphipoda
203 Hyperiidae indet Amphipoda Amphipoda
204 Amphipoda indet Amphipoda Amphipoda
205 Branchiopoda indet Other Other
206 Teuthida indet Other Other
207 Eukrohnia hamata Chaetognatha Chaetognatha
208 Pseudosagitta gazellae Chaetognatha Chaetognatha
209 Pseudosagitta spp. Chaetognatha Chaetognatha
210 Solidosagitta marri Chaetognatha Chaetognatha
211 Sagittidae indet Chaetognatha Chaetognatha
212 Chaetognatha indet Chaetognatha Chaetognatha
213 Tintinnina indet Other Tintinnina indet
214 Cirripedia cyprid Other Cirripedia
215 Cirripedia nauplius Other Cirripedia
216 Evadne spp. Other Cladocera
217 Podon spp. Other Cladocera
218 Abylidae indet Other Cnidaria
219 Chelophyes spp. Other Cnidaria
220 Lensia spp. Other Cnidaria
221 Siphonophora nectophore Other Cnidaria
222 Siphonophora spp. Other Cnidaria
223 Solmundella bitentaculata Other Cnidaria
224 Cnidaria indet Other Cnidaria
225 Ctenophora indet Other Ctenophora indet
226 Cumacea indet Other Other
227 Munida gregaria Other Decapoda
228 Nematocarcinus longirostris Other Decapoda
229 Sergestidae indet Other Decapoda
230 Squilla spp. Other Decapoda
231 Decapoda (natant) indet juv Other Decapoda
232 Decapoda megalopa indet Other Decapoda

233 Decapoda nauplius indet Other Decapoda
234 Decapoda phyllosoma indet Other Decapoda
235 Decapoda zoea indet Other Decapoda
236 Noctiluca scintillans Other Noctiluca scintillans
237 Echinoidea larvae Other Echinoidea larvae
238 Egg indet Other Other
239 Egg mass Other Other
240 Clio pyramidata pteropods pteropods
241 Clio spp. pteropods pteropods
242 Clione limacina antarctica pteropods pteropods
243 Clione spp. pteropods pteropods
244 Spongiobranchaea australis pteropods pteropods
245 Pteropods indet pteropods pteropods
246 Gastropoda indet pteropods pteropods
247 Limacina cf helicina pteropods pteropods
248 Limacina cf helicina antarctica forma rangi pteropods pteropods
249 Limacina cf retroversa pteropods pteropods
250 Limacina spp. pteropods pteropods
251 Isopoda indet Other Isopoda
252 Bivalvia larvae Other Bivalvia larvae
253 Mysidae indet Other Mysidae indet
254 Ostracoda indet Ostracoda Ostracoda indet
255 Myctophidae indet Other Other
256 Pisces egg Other Other
257 Pisces larvae Other Other
258 Pleuragramma antarctica Other Other
259 Protomyctophum spp. Other Other
260 Alciopidae indet Other Polychaeta
261 Iospilidae indet Other Polychaeta
262 Lopadorrhynchidae indet Other Polychaeta
263 Maupasia spp. Other Polychaeta
264 Pelagobia longicirrata Other Polychaeta
265 Phalacrophorus pictus Other Polychaeta
266 Phalacrophorus spp. Other Polychaeta
267 Tomopteris carpenteri Other Polychaeta
268 Tomopteris spp. Other Polychaeta
269 Travisiopsis levinseni Other Polychaeta
270 Travisiopsis spp. Other Polychaeta
271 Typhloscolex muelleri Other Polychaeta
272 Vanadis antarctica Other Polychaeta
273 Vanadis longissima Other Polychaeta
274 Polychaeta indet Other Polychaeta
275 Polychaeta larvae Other Polychaeta
276 Globigerina bulloides Foraminifera Foraminifera
277 Globigerinita uvula Foraminifera Foraminifera
278 Globorotalia spp. Foraminifera Foraminifera
279 Neogloboquadrina incompta Foraminifera Foraminifera
280 Neogloboquadrina pachyderma Foraminifera Foraminifera
281 Turborotalita quinqueloba Foraminifera Foraminifera
282 Foraminifera indet Foraminifera Foraminifera
283 Radiozoa indet Other Radiozoa indet
284 Appendicularia indet Fritillaria spp. Fritillaria spp.
285 Fritillaria spp. Fritillaria spp. Fritillaria spp.
286 Oikopleura spp. Oikopleura spp. Oikopleura spp.
287 Salpa fusiformis Other Thalicidae
288 Salpa thompsoni Other Thalicidae
289 Soestia zonaria Other Thalicidae
290 Thalia spp. Other Thalicidae
291 Salpidae indet Other Thalicidae
292 Doliolidae indet Other Thalicidae
293 Pyrosomatidae indet Other Thalicidae

9. APPENDIX 2: Environmental data used in this study
9.1 Environmental data

A variety of satellite data were assembled in order to provide information needed to explore
relationships between CPR zooplankton data and environmental conditions. The environmental data
chosen are a subset of those used for Southern Ocean bio-regionalisation (Grant et al. 2006) and
zooplankton-specific spatial modelling (e.g., Pinkerton et al. 2010b). It was decided to use only
environmental data that met two criteria. First, the environmental data should be clearly and directly
related to the environment in which zooplankton live and so most likely to have direct influence on
zooplankton abundances (e.g., Atkinson 1998, Ducklow et al. 2006, Atkinson et al. 2008, Harris et al.
2014, 2015). Second, consistent time series of the environmental properties are needed so the effect of
seasonal and long-term environmental change on zooplankton populations can be investigated. These
fundamental and well-observed ocean properties were surface temperature, frontal activity (via the
proxy of SST spatial gradient), phytoplankton abundance, primary production rate, sea ice
concentration, and two measures of mixed-layer depth.
All data were projected onto a circumpolar, polar stereographic grid with nominal 9 km resolution.
Monthly climatologies were generated by averaging all data in a given month. All data were produced
at monthly resolution, because shorter timespans than this lead to large data gaps in the Southern Ocean.
Annual climatological averages are the mean of all data from each complete year. “Cumulative” average
data are the average of all data at a given location between 1997 and 2018. Because sampling occurred
midway through a month, the conditions in the month of sampling were combined with those in the
previous month. Two months is likely to be the shortest timescale over which abundances of the species
of meso- and macro-zooplankton considered in this study would respond significantly to changes in
environmental conditions.

Table 9-1: Environmental data used in analysis.
Variable Units Description Figure Reference(s)
chl mg m-3 Near surface concentration of chl a estimated Figure 9-1 Pinkerton et al. (2018); Hooker et
from the default (case 1) processing of MODIS- al. (1992); Murphy et al. (2001);
Aqua (version R2018.0) and SeaWiFS (version NASA (2018a, b)
R2018.0) satellite sensors, blended using overlap
period 2002-2010. The data set spans the period
September 1997 to August 2018.
sst °C Sea Surface Temperature (SST). The dataset used Figure 9-2 Reynolds et al. (2002)
is the Optimum Interpolation Sea Surface
Temperature (OISST), version 2, based on
satellite measurements by the Advanced Very
High Resolution Radiometer series, operated by
NOAA (National Oceanic and Atmospheric
Administration of the USA) The data set spans
the period 1981 to August 2018.
sstgrad °C km-1 Spatial gradient of SST obtained from a 20 pixel Figure 9-3 NIWA unpublished data
(180 km) smoothed version of OISST, extended
beyond the analysis domain to avoid edge effects.
SeaIce % Sea ice concentration data set derived using Figure 9-4 Cavalieri et al. (1990), updated
measurements from the Scanning Multichannel 2007; https://nsidc.org/
Microwave Radiometer (SMMR) on the Nimbus-
7 satellite and from the Special Sensor
Microwave/Imager (SSM/I) sensors on the
Defense Meteorological Satellite Program's
(DMSP) -F8, -F11, and -F13 satellites.
Measurements from the Special Sensor
Microwave Imager/Sounder (SSMIS) aboard
DMSP-F17 are also included. The data set has
been generated using the Advanced Microwave
Scanning Radiometer - Earth Observing System
(AMSR-E) Bootstrap Algorithm with daily
varying tie-points.
vgpm mgC m-2 d-1 Net primary productivity from the Vertically Figure 9-5 Behrenfeld & Falkowski (1997);
Generalized Production Model (VGPM). Based O’Reilly & Sherman (2016)
on www.science.oregonstate.edu/
ocean.productivity/
mld0p030 m Mixed layer depth calculated from numerical Figure 9-6 Unpublished data:
oceanographic model data using a potential orca.science.oregonstate.edu
density difference of 0.030 kg m-3 from the 1080.by.2160.
surface. Models used are: (1) hycom: from day monthly.hdf.mld.hycom.php
265 (2008) to present; (2) fnmoc: from day 169
(2005) to present; (3) soda: from day 249 (1997)
to end of 2004; (4) tops: from day 001 (2005) to
225 (2010).
mld0p125 m As above but using a potential density difference Figure 9-7 Unpublished data:
of 0.125 kg m-3 orca.science.oregonstate.edu
1080.by.2160.
monthly.hdf.mld.hycom.php
As context to the analysis of the CPR zooplankton data, long-term trends in environmental properties
in the Southern Ocean were investigated by applying Mann Kendall (Mann 1945, Kendall 1975) and
Sen’s slope analysis to each pixel in the dataset. Statistical significance was assessed using unadjusted
Mann-Kendall p values; trends were identified as significant when the p-value was less than 5%. The
magnitude of any statistically significant trends was estimated using the Sen’s slope (Sen 1968). The
Mann-Kendall trend is preferred over linear regression analysis because it is non-parametric
(distribution free) and does not require an assumption that the data are normally distributed. The
insensitivity of the Sen’s slope to outliers means that it is generally the preferred non-parametric method
for estimating a linear trend (Hipel & McLeod 1994).
Example environmental data are shown below: chl (Figure 9-1), sst (Figure 9-2), sstgrad (Figure 9-3),
SeaIce (Figure 9-4), vgpm (Figure 9-5), mld0p030 (Figure 9-6), mld0p125 (Figure 9-7).

a b
c d
Figure 9-1: Chl-a concentration (chl): Example of chl-a environmental data used in this study. a: Long-
term average (CU, “cumulative”); b: Annual average (anMean); c: Monthly climatology (MC), February;
d: Monthly average (MO), February 2011; e: Monthly anomaly (MAnom), February 2011.

a b
c d
Figure 9-2: Sea surface temperature (sst): Example of sst environmental data used in this study. a: Long-
term average (CU, “cumulative”); b: Annual average (anMean); c: Monthly climatology (MC), February;
d: Monthly average (MO), February 2011; e: Monthly anomaly (MAnom), February 2011.

a b
c d
Figure 9-3: Sea surface temperature spatial gradient (sstgrad): Example of sstgrad environmental data used
in this study. a: Long-term average (CU, “cumulative”); b: Annual average (anMean); c: Monthly
climatology (MC), February; d: Monthly average (MO), February 2011; e: Monthly anomaly (MAnom),
February 2011.

a b
c d
Figure 9-4: Sea ice concentration (SeaIce): Example of SeaIce environmental data used in this study. a:
Long-term average (CU, “cumulative”); b: Annual average (anMean); c: Monthly climatology (MC),
February; d: Monthly average (MO), February 2011; e: Monthly anomaly (MAnom), February 2011.

a b
c d
Figure 9-5: Oceanic primary productivity by the vertically generalised production model (vgpm): Example
of vgpm environmental data used in this study. a: Long-term average (CU, “cumulative”); b: Annual
average (anMean); c: Monthly climatology (MC), February; d: Monthly average (MO), February 2011; e:
Monthly anomaly (MAnom), February 2011.

a b
c d
Figure 9-6: Mixed layer depth with a 0.030 kg/m3 density different criterion (mld0p030): Example of
mld0p030 environmental data used in this study. a: Long-term average (CU, “cumulative”); b: Annual

a b
c d
Figure 9-7: Mixed layer depth with a 0.125 kg/m3 density different criterion (mld0p125): Example of
mld0p125 environmental data used in this study. a: Long-term average (CU, “cumulative”); b: Annual

9.2 Trends in environmental data
The temporal analysis of the environmental data showed that concentrations of chl-a in the Southern
Ocean are generally increasing, especially south of the southern limit of the Antarctic Circumpolar
Current (particularly in East Antarctica), and around the Argentine continental shelf (Figure 9-8). In the
Ross Sea and Weddell Sea regions, however, chl-a concentrations show significant negative long-term
trends (decreases). These trends in phytoplankton biomass broadly match those reported by Gregg &
Rousseaux (2014) for the Southern Ocean, which showed increasing trends in chl-a off South America
and in the Indian sector and decreasing trends in chl-a in the Ross Sea region.
Trends in sea surface temperature (SST) were found to be generally positive, and trends were higher
north of the Subantarctic Front than in Subantarctic Water. Surface warming extends further south in
East Antarctica and the South Atlantic. There were areas of significant surface cooling (1997–2018)
apparent around the south of Patagonia and south of South Africa. Small but significant and widespread
cooling of the surface ocean was found between the southern boundary of the Antarctic Circumpolar
Current and the Antarctic continent. A similar high-latitude cooling in the Southern Ocean to that
reported here has been noted in analyses of the full satellite SST record (e.g., Maheshwari et al. 2013,
Kostov et al. 2016, Sallée 2018). The spatial patterns of warming and cooling of the Southern Ocean
seem to be related to the way in which large-scale geographic patterns of delayed and accelerated
warming are related to the climatological background ocean circulation (Kostov et al. 2016).
Sea ice concentration is decreasing to the immediate west of the Ross Sea region, in the Amundsen Sea,
at rates of ~1% per year. This contrasts to smaller areas of long-term increases in sea ice concentration
at the tip of the Antarctic Peninsula, in the Weddell Sea, around Prydz Bay in East Antarctica, and in
parts of the Bellinghausen Sea. These sea ice trends were broadly consistent with those presented to
IPCC in 2013 (Vaughan et al. 2013), though the underlying reasons for these patterns are still uncertain
(Zhang et al. 2018).
Mixed layer depths (using the 0.125 kg m-3 density-difference criteria) showed positive and negative
trends between 1997 and 2018. Mixed layers are getting deeper around most of the Polar Front but are
becoming shallower just to the north of the Antarctic continental shelves of the Ross Sea and Weddell
Sea. Significant long-term trends in sea ice concentration between 1997 and 2018 are seen in the satellite
data. The authors are not aware of wide-area analysis of trends in the depth of mixing in the Southern
Ocean. Mismatched timescales and small-area studies makes comparisons difficult (e.g., Lecomte et al.
2017). Measurements of mixed layer depth off the Antarctic Peninsula between 1993 and 2017
(Schofield et al. 2018) showed a mixture of significant decreasing and no significant trends in mixed-
layer depth whereas our analysis in the same location showed no significant trend in either mld0p030
or mld0p125. It appears that the mixed layer depth estimates from HyCOM have been validated over
much of the world’s oceans, but not at all in the Southern Ocean. It is hence not known to what extent
these trends and patterns in the model mixed layer depths are genuine.

a b
c d
Figure 9-8: Long-term trends (Sen’s slope values) in environmental properties of the Southern Ocean. a:
chl a concentration (chl, mg/m3/y); b: net primary production by the VGPM model (vgpm, mgC/m2/d/y); c:
sea-surface temperature (sst, °C per decade); d: seaice concentration (SeaIce, %/y). [Figure continued
below] Only trends assessed as being significant at better than 5% by the Mann-Kendall trend test are
shown coloured. Nominal positions of (from north) the Subantarctic Front, Polar Fronts, Southern
boundary of the Antarctic Circumpolar Current (Orsi et al. 1995), and the average maximum northern
extent of the sea ice are also shown.

e f
Figure 9-8: continued and concluded. e: mixed layer depth (mld0p0030, m/y); f: mixed layer depth
(mld0p0125, m/y); g: sea surface temperature spatial gradient (sstgrad, m°C/km/y).

10. APPENDIX 3: Mid-range lengths of copepod species used to calculate the
Average Copepod Community Size index
Table 10-1: Indicative mid-range length of adult females used to calculate the Average Copepod
Community Size index (ACCS) from Beaugrand et al. (2003) and with recalculated indicative values
appropriate for the Southern Ocean.
Recalculated indicative total length

Indicative total length of adult female of adult female based on the
(mm) in global waters from Southern Ocean CPR data (this
Copepod species Beaugrand et al. (2003). study) (mm)
Acartia danae 1.18

Acartia spp 1.18
Calanoid cope & copepodites 1.00
Calanoides acutus 4.60
Calanoides macrocarinatus 3.55
Calanus australis 3.10
Calanus propinquus 5.38
Calanus simillimus 3.23
Calanus spp. 3.90 3.29
Calocalanus spp. 0.85
Candacia cheirura 2.63
Candacia falcifera 3.81
Candacia maxima 3.72
Candacia spp. 3.39 3.66
Centropages aucklandicus 1.65
Centropages bradyi 2.25 1.77
Clausocalanus brevipes 1.43
Clausocalanus laticeps 1.46
Clausocalanus sp 1.45 1.44
Ctenocalanus sp cf citer 1.11
Drepanopus spp. 2.29
Euaugaptilus sp 3.86
Eucalanus sp 4.00
Euchirella rostromagna 6.05
Haloptilus oxycephalus 3.56
Heterorhabdus austrinus 3.36
Heterorhabdus farrani 3.94
Heterorhabdus spinifrons 2.35
Heterorhabdus lobatus 3.10
Heterorhabdus sp 3.22 3.34
Lubbockia sp 1.70
Lucicutia sp 2.33
Mecynocera clausi 1.07
Mesocalanus tenuicornis 2.10
Metridia gerlachei 3.82
Metridia lucens 2.66
Metridia sp 3.24 2.74
Microcalanus pygmaeus 0.86
Microsetella rosea 0.85
Microsetella spp. 0.85
Neocalanus gracilis 3.22
Neocalanus tonsus 3.75
Oithona frigida 1.22
Oithona similis 0.82
Oithona spp. 1.02 0.82
Oncaea antarctica 1.21
Oncaea curvata 0.63
Oncaea sp 0.90 0.64
Onchocalanus spp. 7.54

Paracalanus sp 1.08
Paraeuchaeta antarctica 9.15
Paraeuchaeta barbarta 9.00
Paraeuchaeta biloba 5.85
Paraeuchaeta exigua 6.85
Paraeuchaeta sp 7.71 7.23
Paralabidocera antarctica 2.01
Pleuromamma abdominalis 3.05
Pleuromamma borealis 2.03
Pleuromamma gracilis 2.08
Pleuromamma piseki 1.85
Pleuromamma robusta 3.65
Pleuromamma spp. 2.53 2.47
Rhincalanus gigas 7.88
Rhincalanus gigas nauplius 7.88
Rhincalanus sp copepodite 7.88
Sapphirina sp 4.41
Scolecithricella minor 1.27
Scolecithricella sp 1.27
Stephos longipes 0.84
Subeucalanus longiceps 4.55
Sulcanus conflictus 1.55
Temora turbinata 1.33

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AEBR 257 Continuous Plankton Recorder Sampling Southern Ocean 2002 2018 3347

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Continuous Plankton Recorder sampling of

zooplankton in the Southern Ocean 2002–

ISSN 1179-6480 (online)

Publications Logistics Officer

© Crown Copyright – Fisheries New Zealand

8. APPENDIX 1: Grouping of zooplankton data 61

9. APPENDIX 2: Environmental data used in this study 66

New Zealand Aquatic Environment and Biodiversity Report No. 257. 79 p.

Fisheries New Zealand Continuous Plankton Recorder Sampling 2002–2018• 1

2 • Continuous Plankton Recorder Sampling 2002–2018 Fisheries New Zealand

Fisheries New Zealand Continuous Plankton Recorder Sampling 2002–2018• 3

To map changes in the quantitative distribution of epipelagic plankton, including phytoplankton,

1.3 Specific objectives

3. Characterise latitudinal and temporal changes in phytoplankton and zooplankton populations in

4. Complete coupled analysis of phytoplankton and zooplankton environmental data to investigate

2.1 CPR methodology

4 • Continuous Plankton Recorder Sampling 2002–2018 Fisheries New Zealand

2.2 Study area

Fisheries New Zealand Continuous Plankton Recorder Sampling 2002–2018• 5

2.3 CPR deployments in Ross Sea region

6 • Continuous Plankton Recorder Sampling 2002–2018 Fisheries New Zealand

Number Distance Number

2008–09 S 19-Dec-08 26-Dec-08 5 179 897 123 523

Fisheries New Zealand Continuous Plankton Recorder Sampling 2002–2018• 7

8 • Continuous Plankton Recorder Sampling 2002–2018 Fisheries New Zealand

2013–14 S 30-Nov-13 9-Dec-13 4 176 878 59 452

Fisheries New Zealand Continuous Plankton Recorder Sampling 2002–2018• 9

10 • Continuous Plankton Recorder Sampling 2002–2018 Fisheries New Zealand

Number Distance Total

TAN0202 S 7-Feb-02 22-Feb-2002 7 210 956 127 326

2.4 Post-voyage laboratory analysis

2.5 SO-CPR data extract used in the present study

Fisheries New Zealand Continuous Plankton Recorder Sampling 2002–2018• 11

2.6 Phytoplankton Colour Index

12 • Continuous Plankton Recorder Sampling 2002–2018 Fisheries New Zealand

2.7 Taxonomic grouping of data

Fisheries New Zealand Continuous Plankton Recorder Sampling 2002–2018• 13

No. Group Description

1 Oithona spp. Small (1 mm) cyclopoid copepods, dominated by Oithona similis

2 Copepoda All other copepods, including calanoid, cyclopoid, and harpacticoid

3 Amphipoda Order of crustaceans with no carapace and generally with laterally

4 Chaetognatha Commonly known as arrow worms, a phylum of predatory marine

5 Euphausiidae All adult and developmental stages of krill (generally unidentified to

6 Foraminifera Very abundant calcareous (calcite) zooplankton that could be affected

9 Ostracoda Class of crustacea also known as “seed shrimp” – typically around

10 Pteropods Calcareous (aragonite) pelagic gastropod free-swimming (marine

11 Other Includes remaining organisms which are rarely identified including

14 • Continuous Plankton Recorder Sampling 2002–2018 Fisheries New Zealand

2.9 Spatial distribution of zooplankton abundance

2.10 Trends in zooplankton abundance

2.11 Model-based analysis of zooplankton abundance

Fisheries New Zealand Continuous Plankton Recorder Sampling 2002–2018• 15

Model name Description Environmental layers used

cumulative Long-term average oceanographic conditions with Ecoszen, Month,

annual Annual-average oceanographic conditions with Ecoszen, DayIndex,

clim Monthly climatological oceanographic conditions Ecoszen,

climAnom Monthly climatological oceanographic conditions, Ecoszen,

actual Actual measurements of conditions within the Ecoszen,