Glossary and appendices

Here we provide definitions of te reo Māori terms, technical terms and abbreviations used throughout the report. You can also find appendices to accompany the main report content.

Some key technical terms and how we use them
Te reo Māori terms
Technical terms and abbreviations
Appendices
References and footnotes

Some key technical terms and how we use them

A report of this breadth is necessarily cross-disciplinary, incorporating input from a wide variety of people with different expertise, who may use terms in very specific (and sometimes rather different) ways. Here we lay out definitions of some key terms and how we use them in this report. A full glossary of technical terms and abbreviations with definitions can be found below. Approximate translations of all Māori words and phrases are also provided below.

This report is about commercial fishing: taking fish, aquatic life or seaweed in circumstances where a fishing permit is required as per section 89 of the Fisheries Act 1996. We use the term ‘commercial fisheries’ to refer to wild-caught marine life that is harvested to sell. We did not include seaweed in this report.

In this report, sustainability or sustainable use usually refers to sustainability as defined in the Fisheries Act 1996 – that is, (a) maintaining the potential of fisheries resources to meet the reasonably foreseeable needs of future generations, and (b) avoiding, remedying or mitigating any adverse effects of fishing on the aquatic environment. Sometimes, we use a narrower definition referring to the long-term maintenance of a single fish stock without considering the wider ecosystem impacts. At other times, we use a broader meaning of sustainability that encompasses ecological and social factors, including but not limited to biodiversity (genetic, species and ecosystem diversity), environmental and ecosystem impacts.

In this report, a stock or fish stock usually describes a management unit of a species as defined by Fisheries New Zealand (FNZ). A stock may be a discrete biological population, with little to no reproductive mixing with other stocks of the same species. In other cases, there may be migration or mixing between stocks.

Biodiversity refers to the variety of life. It pertains to the variety of different species present, the variability of ecosystems themselves, and diversity within species. Biodiversity is a critical part of ecosystem and planetary health but not the major focus of this report.

An ecosystem approach to fisheries management (EAFM) and ecosystem-based fisheries management (EBFM) are different terms used widely in the literature. Both involve moving beyond single-species measures to incorporate wider ecosystem effects into management. We generally use EAFM, unless referring to specific literature which uses EBFM. They differ from ecosystem-based management (EBM) which refers to management of the ocean more broadly – not just fisheries.

Threatened species are those assessed according to the New Zealand Threat Classification System as facing imminent extinction because of their small total population size and/or rapid rate of population decline. This includes three sub-categories: ‘Nationally Critical’, ‘Nationally Endangered’ and ‘Nationally Vulnerable’. Protected species are defined under the Wildlife Act 1953. In the marine environment, all marine mammals, seabirds (except black-backed gulls), all sea turtles, some corals and some fish are protected species. A species may be protected but not threatened, or it may be both protected and threatened.

People from different disciplines use the term marine protected area (MPA) as an umbrella term for spatial areas in the marine environment where restrictions exist in order to conserve nature or maintain biodiversity values. There are a range of legal tools that offer differing levels of protection in the marine environment. Protected areas in the marine environment include marine reserves (as defined in the Marine Reserves Act 1971), benthic protection areas (BPAs), mātaitai and taiāpure reserves, and others. Different marine protection tools are discussed in detail here. The term MPA is often conflated with ‘marine reserve’ in everyday use, but is uses a wider definition in this report.

Te reo Māori terms

The translations are described based on the Māori Dictionary, and as they are used in this report. Other sources are noted in footnotes.

Māori	English
hapū	kinship group, clan, subtribe
īnanga/īnaka	whitebait, juvenile freshwater fish of several species
iwi	tribe
kaimoana	seafood
kaitiaki	guardian
kaitiakitanga[1]	guardianship and conservation or protection; managing the environment based on a Māori worldview
kaumātua	elder, a person of status within the whānau
kaupapa Māori	Māori approach, ideology, topic or principles
ki uta ki tai[2]	from the mountains to the sea
kōhanga	nursery, birthplace
(te) korowai	cloak; the name of a group of marine guardians in Kaikōura
mahinga kai/mahika kai	food-gathering place, natural resources
mana	prestige, authority
mana whenua	power associated with possession and occupation of tribal land
manaakitanga	hospitality, kindness, generosity
mātaitai reserve[3]	recognise and provide for traditional fishing through local management. They allow customary and recreational fishing but usually don't allow commercial fishing; areas closed to commercial fishing that may also restrict recreational and customary fishing
mātauranga Māori	the body of knowledge originating from Māori ancestors, including the Māori worldview and perspectives, Māori creativity, and cultural practices
mauri	life force, vital essence
(te) moana	(the) ocean
rāhui	a temporary closure or prohibition; in the fisheries context, this generally involves restricting use of a fisheries area
rangatahi	younger generation, youth
rangatira	chief, supervisor
rangatiratanga	chieftainship, the right to exercise self-determination and sovereignty
rohe	district, region, area
rohe moana[4]	customary fishing area of tangata whenua
Tai Timu Tai Pari[5]	The tidal cycle, from low tide to high tide; Sea Change
taiāpure	local fisheries that are significant for food, spiritual, or cultural reasons; managed by local communities, which may have additional fishing rules
Tangaroa	the Māori god of the sea and fish; also the name of one of NIWA’s research vessels
tangata whenua	local people, people born of the whenua
taonga (species)	treasure; a native species of special cultural significance to Māori
tauiwi	non-Māori, foreigner, colonist
te hā o Tangaroa kia ora ai tāua	the breath of Tangaroa sustains us
Te Moutere o Motiti	Motiti Island
Te Ohu Kaimoana[6]	a statutory organisation dedicated to future advancement of Māori interests in the marine environment; this term is defined in the Māori Fisheries Act 2004 and the Fisheries Act 1996
Te Wahipounamu	a World Heritage site incorporating four national parks including Fiordland National Park
tiaki	protect, conserve, look after
tikanga	correct procedure, custom, protocol, the customary system of values and practices that have developed over time and are deeply embedded in the social context
tūpuna/tīpuna	ancestors
wāhi taonga[7]	places of sacred or extreme importance to Māori
wāhi tapu[8]	a place sacred to Māori in the traditional, spiritual, religious, ritual, or mythological sense
wairua	spirit
waka	canoe
whānau	family
whanaungatanga	relationship, kinship, sense of family connection forged through shared experiences

Technical terms and abbreviations

Since this is a report on commercial fishing, where applicable, we have used the Fisheries New Zealand definition for technical terms and abbreviations in this glossary. We note that there are other definitions of many terms and discuss this for some key terms above.

Term	Meaning	Also called
abundance	the amount of something as measured by number of individuals
ACE	annual catch entitlement; an entitlement to harvest a quantity of fish, aquatic life, seaweed or other stock, taken in accordance with a fishing permit and any conditions and limitations imposed by or under the Fisheries Act 1996	annual catch entitlement
AEBAR	aquatic environment and biodiversity annual review; a review produced each year by Fisheries New Zealand that presents scientific information on the effects of fishing on the environment, marine biodiversity, and aquatic environments	aquatic environment and biodiversity annual review
AFMA	Australian Fisheries Management Authority
AI	artificial intelligence
AIS	automatic ship identification system
annual catch entitlement	an entitlement to harvest a quantity of fish, aquatic life, seaweed or other stock, taken in accordance with a fishing permit and any conditions and limitations imposed by or under the Fisheries Act 1996	ACE
ANZBS	Aotearoa New Zealand Biodiversity Strategy	Te Mana o Te Taiao
AOS	acoustic-optical system
aquaculture	the farming of fish or shellfish
aquatic environment and biodiversity annual review	a review produced each year by Fisheries New Zealand that presents scientific information on the effects of fishing on the environment, marine biodiversity, and aquatic environments	AEBAR
B	biomass; the size of the stock in units of weight; often, biomass refers to only one part of the stock (e.g. spawning biomass, recruited biomass or vulnerable biomass, the latter two of which are essentially equivalent)	biomass
B₀	unfished biomass; the theoretical carrying capacity of the recruited or vulnerable biomass of a fish stock. In some cases, it refers to the average biomass of the stock in the years before fishing started more generally, it is the average over recent years of the biomass that theoretically would have occurred if the stock had never been fished B₀ is often estimated from stock modelling and various percentages of it (e.g. 40% B₀) are used as biological reference points to assess the relative status of a stock	original biomass, unfished biomass
B_MSY	the average stock biomass that results from taking an average catch of maximum sustainable yield under various types of harvest strategies often expressed in terms of spawning biomass, but may also be expressed as recruited or vulnerable biomass B_MSY is a common fisheries management target
ballast	water taken in to a tank in the hull of vessels for stability
bathymetry	the measurement of depth
benthic	pertaining to the bottom of the ocean or the seafloor
benthic protection area	any area established by the Fisheries (Benthic Protection Areas) Regulations 2007 as being a BPA	BPA
BERL	Business and Economic Research Ltd
biodiversity	the variety and diversity of all life on land, in freshwater and in the sea, including the places where they live it pertains to the variety of different species present, the variability of ecosystems themselves and diversity within species	biological diversity
biofouling	the accumulation of microorganisms, plants, algae, or small animals on surfaces such as pipes or vessel hulls
biogenic	produced by living organisms e.g. a coral reef is a biogenic structure
biological diversity	the variety and diversity of all life on land, in freshwater and in the sea, including the places where they live it pertains to the variety of different species present, the variability of ecosystems themselves and diversity within species	biodiversity
biomass	the size of the stock in units of weight; often, biomass refers to only one part of the stock (e.g. spawning biomass, recruited biomass or vulnerable biomass, the latter two of which are essentially equivalent)	B
blue economy	a term that is sometimes used to capture a holistic approach to managing human use of the oceans, including biological, social and economic dimensions	ocean economy, marine economy
BOMEC	benthic-optimised marine environment classification
BPA	any area established by the Fisheries (Benthic Protection Areas) Regulations 2007 as being a BPA	benthic protection area
BRUVS	baited remote underwater video station
bryozoan	a family of aquatic invertebrate animals that form colonies
bycatch	species not targeted by a fishery but caught incidentally during fishing operations	non-target species
calcareous	composed of calcium carbonate
cartilaginous	made of cartilage, i.e. the skeletons of sharks
CASAL	a fish stock assessment model
catch per unit effort	the quantity of fish caught with one standard unit of fishing effort e.g. the number of fish taken per 1,000 hooks per day; or the weight of fish taken per hour of trawling CPUE is often assumed to be an abundance index a declining CPUE may mean that more effort e.g. metres of net set and/or length of soak time, is required to catch a given volume of fish; this in turn may indicate that a fish stock has declined (although other factors can also influence rates of CPUE, particularly the method used to catch the fish)	CPUE
catchability	catchability is the proportion of fish that are caught by a defined unit of fishing effort
catchment	area of land in which rainfall drains towards a common watercourse, stream, river, lake or estuary
CBD	Convention on Biological Diversity
CCSBT	Commission for Conservation of Southern Bluefin Tuna
cetacean	aquatic mammals including dolphins, whales and porpoises
chemoautotroph	organism that produces organic molecules by fixation of carbon dioxide, using energy derived from the oxidation of inorganic substances such as iron
chimaera	a family of cartilaginous fish	ghost sharks
chondrichthyans	the family of cartilaginous fish including sharks, rays and ghost sharks
CNN	convolutional neural network; a deep neural network inspired by the human vision system often used for image analysis	convolutional neural network
cod-end	the end of a trawl net which retains the catch and the part of the net where the most size selection takes place
commercial fishing	taking fish, aquatic life, or seaweed in circumstances where a fishing permit is required; this term is defined in the Fisheries Act 1996
convolutional neural network	a deep neural network inspired by the human vision system often used for image analysis	CNN
CPR	continuous plankton recorder
CPUE	the quantity of fish caught with one standard unit of fishing effort e.g. the number of fish taken per 1,000 hooks per day; or the weight of fish taken per hour of trawling CPUE is often assumed to be an abundance index a declining CPUE may mean that more effort e.g. metres of net set and/or length of soak time, is required to catch a given volume of fish; this in turn may indicate that a fish stock has declined (although other factors can also influence rates of CPUE, particularly the method used to catch the fish)	catch per unit effort
CRI	Crown Research Institute; crown-owned companies that carry out scientific research
CSIRO	Commonwealth Scientific and Industrial Research Organisation; Australia’s national science agency, similar to New Zealand’s CRIs
customary fishing	the traditional rights confirmed by the Treaty of Waitangi and the Treaty of Waitangi (Fisheries Claims) Settlement Act 1992, being the taking of fish, aquatic life, or seaweed or managing of fisheries resources, for a purpose authorised by Tangata Kaitiaki / Tiaki, to the extent that such purpose is consistent with Tikanga Māori and is neither commercial in any way nor for monetary gain or trade this term is defined in the Fisheries (Kaimoana Customary Fishing) Regulations 1998
demersal	pertaining to the seafloor and deep water column affected by the seafloor
discards	any fish or other organisms that are landed but subsequently returned to the ocean
DOC	Department of Conservation
dredging	a fishing method where a steel net (a dredge) is towed along the seafloor by a vessel and scrapes up all the shellfish living there
DTIS	deep towed imaging system
EAFM	ecosystem approach to fisheries management; fisheries management that moves beyond single-species measures to incorporate wider ecosystem effects. Also called ecosystem-based fisheries management (EBFM); this differs from ecosystem-based management (EBM) which refers to management of the ocean more broadly – not just fisheries.	ecosystem approach to fisheries management, EBFM, ecosystem-based fisheries management
EBFM	ecosystem-based fisheries management; fisheries management that moves beyond single-species measures to incorporate wider ecosystem effects; also called ecosystem approach to fisheries management (EAFM); this differs from ecosystem-based management (EBM) which refers to management of the ocean more broadly – not just fisheries.	ecosystem-based fisheries management, EAFM, ecosystem approach to fisheries management
EBM	ecosystem-based management; using a holistic approach to management of the whole ocean taking into account the ecosystems	ecosystem-based management
ecosystem	an area where plants, animals, and other organisms, as well as weather and landscape, interact as a system
ecosystem approach to fisheries management	EAFM; fisheries management that moves beyond single-species measures to incorporate wider ecosystem effects; also called ecosystem-based fisheries management (EBFM); this differs from ecosystem-based management (EBM) which refers to management of the ocean more broadly – not just fisheries	EAFM, EBFM, ecosystem-based fisheries management
ecosystem-based fisheries management	EBFM; fisheries management that moves beyond single-species measures to incorporate wider ecosystem effects, also called ecosystem approach to fisheries management (EAFM); this differs from ecosystem-based management (EBM) which refers to management of the ocean more broadly – not just fisheries	EBFM, ecosystem approach to fisheries management, EAFM
ecosystem-based management	EBM; using a holistic approach to management of the whole ocean taking into account the ecosystems	EBM
ecosystem thinking	a holistic perspective that moves beyond single-species measures to consider the whole ecosystem and its interconnections, including biodiversity
echogram	the 2D output from an echosounder
echosounder	a device that uses sound and echoes to detect organisms underwater
eDNA	environmental DNA
EEZ	Exclusive Economic Zone; a maritime zone over which the coastal state has sovereign rights over the exploration and use of marine resources usually, a state's EEZ extends to a distance of 200 nautical miles (nm) (approx. 370 km) out from its coast, except where resulting points would be closer to another country Aotearoa New Zealand has a 200 nm EEZ that was declared in 1978; the EEZ formally extends from the territorial sea at 12 nm (from the coastline) to 200 nm; this term is defined in the territorial sea and Exclusive Zone Act 1977	Exclusive Economic Zone
EM	electronic monitoring
EPA	Environment Protection Authority
epigenetics	the study of changes in gene expression (active vs inactive genes) rather than the underlying DNA sequence
ER	electronic reporting
ERA	ecosystem risk assessment
ESP3	open-source software to process large hydro-acoustic datasets
ESR	New Zealand’s Institute of Environmental Science and Research; a CRI
Exclusive Economic Zone	Exclusive Economic Zone; a maritime zone over which the coastal state has sovereign rights over the exploration and use of marine resources usually, a state's EEZ extends to a distance of 200 nautical miles (nm) (approx. 370 km) out from its coast, except where resulting points would be closer to another country Aotearoa New Zealand has a 200 nm EEZ that was declared in 1978; the EEZ formally extends from the territorial sea at 12 nm (from the coastline) to 200 nm; this term is defined in the territorial sea and Exclusive Zone Act 1977	EEZ
eutrophic	overly enriched with nutrients and/or minerals, resulting in excessive plant and algal growth (e.g. an algal bloom) and corresponding depletion in oxygen levels that may kill other organisms living in the water such as fish
EwE	Ecopath with Ecoism; a type of ecosystem model
FAD	fish aggregating device
FAO	Food and Agriculture Organization, part of the United Nations
finfish	a bony, jawless or cartilaginous fish with fins, as opposed to shellfish
FINZ	Fisheries Inshore New Zealand
fish stock	in this report, a stock or fish stock usually describes a management unit of a species as defined by Fisheries New Zealand; a stock may be a discrete biological unit, with little to no reproductive mixing with other stocks of the same species in other cases, there may be migration or mixing between stocks	stock
Fisheries New Zealand	the government agency that regulates fishing in Aotearoa New Zealand, part of the Ministry for Primary Industries	FNZ
Fisheries Settlement 1992	the Treaty of Waitangi (Fisheries Claims) Settlement Act became law in late 1992, and gave effect to the Deed of Settlement, signed in September 1992 this deed (1) settled Māori claims to commercial fishing; (2) clarified Māori rights to customary or non-commercial fishing; and (3) discharged the Crown’s obligations in respect of Māori commercial fishing interests under the Treaty of Waitangi	Treaty of Waitangi (Fisheries Claims) Settlement Act 1992; Māori Fisheries Settlement 1992
Fishery Management Area	Fishery Management Area; the New Zealand 200 nautical mile EEZ is divided into 10 areas, each known as a Fishery Management Area FMAs are based on likely stock boundaries as well as administrative considerations; the standard FMAs are the basis of QMAs for most fish stocks; this term is defined in the Fisheries Act 1996	FMA
FishServe	a subsidiary of Seafood New Zealand that provides administrative services to the Aotearoa New Zealand commercial fishing industry
FMA	Fishery Management Area; the New Zealand 200 nm EEZ is divided into 10 areas, each known as a Fishery Management Area FMAs are based on likely stock boundaries as well as administrative considerations; the standard FMAs are the basis of QMAs for most fish stocks; this term is defined in the Fisheries Act 1996	Fishery Management Area
FNZ	Fisheries New Zealand, the government agency that regulates fishing in Aotearoa New Zealand, part of the Ministry for Primary Industries	Fisheries New Zealand
Gazette	the New Zealand Gazette is the official government newspaper, published weekly; regulations are notified in the Gazette after they are made but before they come into force
ghost gear	abandoned, lost or discarded fishing gear
ghost shark	a family of cartilaginous fish	chimaera
gillnet	vertical panels of netting held in place by regularly spaced floats and weights, catches sea life by entanglement
GIS	geographical information system; an organised collection of computer hardware, software, geographic data, and personnel designed to efficiently capture, store, update, manipulate, analyze, and display all forms of geographically referenced information a GIS can combine relational databases with spatial interpretation and outputs often in form of maps
GPR	geospatial position reporting
GPS	global positioning system
habitat	the place or environment that provides everything an organism needs to live and grow
hard limit	biomass limit below which fisheries should be considered for closure
HMS	highly migratory species
HPSFM	habitats of particular significance to fisheries management
hydroacoustic	the study and application of sound in water
ikijime	a humane method of quickly killing fish originating in Japan, where a spike is quickly inserted just behind the fish’s eye
individual transferable quota	a property right that represents the quota owners’ share of a fishery; ITQs can be bought or sold there are 100 million shares in each fish stock; the number of shares owned determines the amount of ACE generated each fishing year	ITQ
IOC	intergovernmental oceanographic commission
ITQ	a property right that represents the quota owners’ share of a fishery; ITQs can be bought or sold there are 100 million shares in each fish stock; the number of shares owned determines the amount of ACE generated each fishing year	individual transferable quota
IUCN	International Union for Conservation of Nature
IUU	illegal, unreported and unregulated (of fishing)
jigging	using a line with multiple baits, moving it up and down vertically to attract target species
lacustrine	related to lakes
landing	an amount of fish (or other marine life) harvested from the sea and brought onshore
LAWA	Land Air Water Aotearoa
LINZ	Land Information New Zealand
longlining	using a very long fishing line with shorter lines and baited hooks every few feet
machine learning	an application of AI where algorithms learn and improve from experience, rather than being explicitly programmed
Māori Fisheries Settlement 1992	the Treaty of Waitangi (Fisheries Claims) Settlement Act became law in late 1992, and gave effect to the Deed of Settlement, signed in September 1992 this deed (1) settled Māori claims to commercial fishing; (2) clarified Māori rights to customary or non-commercial fishing; and (3) discharged the Crown’s obligations in respect of Māori commercial fishing interests under the Treaty of Waitangi	Fisheries Settlement 1992; Treaty of Waitangi (Fisheries Claims) Settlement Act 1992
marine economy	a term that is sometimes used to capture a holistic approach to managing human use of the oceans, including biological, social and economic dimensions	blue economy, ocean economy
marine protected area	an area of the marine environment especially dedicated to, or achieving, through adequate protection, the maintenance and/or recovery of biodiversity at the habitat and ecosystem level in a healthy functioning state	MPA
marine reserve	marine reserves are specified areas of the sea and foreshore that are managed to preserve them in their natural state for scientific study or other purposes marine reserves may be established in areas that contain underwater scenery, natural features or marine life, of such distinctive quality, or so typical, or beautiful, or unique, that their continued preservation is in the national interest; within a marine reserve, all marine life is protected and fishing and the removal or disturbance of any living or non-living marine resource is prohibited, except as necessary for permitted monitoring or research; this includes dredging, dumping or discharging any matter or building structures
marine trophic index	a measure of the mean trophic level of fish caught
maw	swim bladder
maximum sustainable yield	MSY, the largest long-term average catch or yield that can be taken from a stock under prevailing ecological and environmental conditions; it is the maximum use that a renewable resource can sustain without impairing its renewability through natural growth and reproduction For most quota management stocks, the total allowable catch is set at a level that either moves the stock towards, or maintains the stock at or above a biomass level that can support the maximum sustainable yield (section 13 of the Fisheries Act 1996);this term is defined in the Fisheries Act 1996	MSY
MBIE	Ministry of Business, Innovation and Employment
MEC	marine environment classification
mesopelagic	inhabiting the intermediate depths of the sea around 200-1,000 m
MfE	Ministry for the Environment
MICE	models of intermediate complexity; a type of ecosystem model
microchemical	analytical chemistry for studying small samples
micronekton	group or organisms intermediate in size between zooplankton and nekton; consists mainly of crustaceans, small cephalopods and small fishes
MPA	marine protected area; an area of the marine environment especially dedicated to, or achieving, through adequate protection, the maintenance and/or recovery of biodiversity at the habitat and ecosystem level in a healthy functioning state	marine protected area
MPI	Ministry for Primary Industries
MSC	Marine Stewardship Council
MSY	MSY, maximum sustainable yield, is the largest long-term average catch or yield that can be taken from a stock under prevailing ecological and environmental conditions; it is the maximum use that a renewable resource can sustain without impairing its renewability through natural growth and reproduction for most quota management stocks, the total allowable catch is set at a level that either moves the stock towards, or maintains the stock at or above a biomass level that can support the maximum sustainable yield (section 13 of the Fisheries Act 1996); this term is defined in the Fisheries Act 1996	maximum sustainable yield
neural network	a type of machine learning system inspired by the structure of a human brain
NGS	next-generation sequencing
NIWA	National Institute of Water and Atmospheric Research; a CRI that carries out a large amount of fisheries research under contract to MPI
NOAA	National Oceanic Atmospheric Administration (US)
nominal stock	stocks that represent less than one percent of catch
non-target species	species that are unintentionally caught or not routinely assessed for fisheries management	bycatch
nutraceutical	a substance that is a food or derived from food that provides medical or health benefits including the prevention and treatment of disease
observer	a person placed onboard a fishing vessel to independently confirm catch and record a range of information such as bycatch species
observer effect	observed trips do not represent unobserved trips as the presence of an observer changes fisher behaviour
ocean economy	a term that is sometimes used to capture a holistic approach to managing human use of the oceans, including biological, social and economic dimensions	blue economy, marine economy
OIA	Official Information Act
olfactory	related to the sense of smell
oligotrophic	water bodies characterised by nutrient deficiency that can support few forms of life
OOS/GOOS	Ocean Observing System; Global Ocean Observing System
OPMCSA	Office of the Prime Minister’s Chief Science Advisor
original biomass	B₀; the theoretical carrying capacity of the recruited or vulnerable biomass of a fish stock; in some cases, it refers to the average biomass of the stock in the years before fishing started More generally, it is the average over recent years of the biomass that theoretically would have occurred if the stock had never been fished. B0 is often estimated from stock modelling and various percentages of it (e.g. 40% B0) are used as biological reference points to assess the relative status of a stock	B₀, unfished biomass
otolith	part of the inner ear of fish important for balance and hearing; this grows from the centre out in a series of daily rings and seasonal bands or growth zones; otoliths can be used to identify the age of fish
PCE	Parliamentary Commissioner for the Environment
pelagic	pertaining to the open ocean; neither close to the shore nor near to the seafloor
phylodynamics	the study of population dynamics and evolutionary processes as it relates to the relationships between organisms of different species
phytoplankton	microscopic marine algae
pinger	an active sound emitter used to deter bycatch from net entanglement
pinniped	family of semi-aquatic marine mammals including seals and sea lions
plenary	Fisheries New Zealand holds fisheries assessment working groups throughout the year to discuss and review stock assessments; the working group meetings are open to the public, and include researchers, FNZ staff, commercial, customary, recreational and environmental stakeholders every year in May ‘plenary sessions’ are held to assess the fisheries managed within the QMS, as well as other important fisheries in the New Zealand EEZ, and to discuss various matters that pertain to fishery assessment a plenary report is then released by 31 May that summarises the conclusions and recommendations from the meetings of the Fishery Assessment Working Groups held during the previous months, as well as the Fishery Assessment Plenary session
polyp	an individual belonging to the Cnidaria family which includes coral-forming organisms and sea anemones
potting	a method of catching some marine species such as crayfish where a pot-like trap attached to a long rope is baited, dropped in the water and retrieved later; once entered, the target marine organism can’t escape	trapping
protected species	(a) any marine wildlife as defined in section 2 of the Wildlife Act 1953 that is absolutely protected under section 3 of that Act; (b) any marine mammal as defined in section 2(1) of the Marine Mammals Protection Act 1978; this term is defined in the Fisheries Act 1996
PVC	polyvinyl chloride; a type of plastic
QMA	species within the QMS are managed by QMAs; QMAs are geographic areas within the EEZ the standard fishery management areas are the basis of quota management areas for most fish stocks	quota management area
QMS	the QMS controls the overall catches for virtually all the main fish stocks found within Aotearoa New Zealand’s 200 nautical mile EEZ	quota management system
quota	quota is a right which allows people to own a share of the 100 million shares available for a particular species in a defined area ownership of quota generates an annual catch entitlement to catch that stock; within the commercial catch limit, access is determined by ownership of ACE and the possession of a fishing permit
quota management area	species within the QMS are managed by QMAs; QMAs are geographic areas within the EEZ the standard fishery management areas are the basis of quota management areas for most fish stocks	QMA
quota management system	the QMS controls the overall catches for virtually all the main fish stocks found within Aotearoa New Zealand’s 200 nautical mile EEZ	QMS
recruitment	the addition of new individuals to the fished component of a stock; this is determined by the size and age at which fish are first caught
RFID	radio-frequency identification
RFMO	regional fisheries management organisation
rhodolith	calcareous nodules formed by marine algae found on the seafloor
RMA	Resource Management Act 1991
ROV	remotely operated vehicle
SDG	sustainable development goal
seamount	a geological formation rising from the seafloor that does not reach the sea surface – essentially, an underwater mountain
sediment	particles or clumps of soil, sand, clay, silt or other matter suspended in water
SEFRA	spatially explicit fisheries risk assessment
seine/seining	a fishing method using a net that hangs vertically and encircles a school of fish
SFFF	sustainable food and fibre futures
ShiPCC	sea-going high-performance computing cluster
SIL	Seafood Innovations Ltd
SLED	sea lion exclusion device
SNP	single nucleotide polymorphism; a variation at a single site in a DNA sequence
SNP-ChIP	a microarray to measure genetic variation
soft limit	a biomass limit below which the requirement for a formal, time-constrained rebuilding plan is triggered
spat	shellfish larvae attached to a surface
spawning	the production or depositing of large quantities of eggs in water
spawning biomass	the total weight of sexually mature fish in a stock that spawn in a given year
SPM	spatial population model
SSIF	strategic science investment fund
SST	satellite surface temperature
stock	in this report, a stock or fish stock usually describes a management unit of a species as defined by Fisheries New Zealand; a stock may be a discrete biological unit, with little to no reproductive mixing with other stocks of the same species in other cases, there may be migration or mixing between stocks	fish stock
stock assessment	the application of statistical and mathematical tools to relevant data in order to obtain a quantitative understanding of the status of the stock relative to defined benchmarks or reference points (e.g. BMSY) the results may include (1) an estimate of the current biomass relative to biomass targets; (2) an estimate of current and recent exploitation rates relative to optimum exploitation rates; (3) a determination of changes in the biomass of fish stocks in response to fishing; and/or (4) to the extent possible, a prediction of future trends in stock biomass stock assessments are based on (1) surveys; (2) knowledge of the habitat requirements, life history, and behaviour of the species; (3) likely environmental impacts on stocks; and (4) catch and effort statistics
stock structure	(1) The geographical boundaries of the stocks assumed for assessment and management purposes (e.g. albacore tuna may be assumed to be comprised of two separate stocks in the North Pacific and South Pacific). (2) The boundaries that define self-contained populations in a genetic sense. (3) Known, inferred or assumed patterns of residence and migration for stocks that mix with one another
sustainability / sustainable use	In this report, sustainability or sustainable use usually refers to sustainability as defined in the Fisheries Act 1996 – that is, (a) maintaining the potential of fisheries resources to meet the reasonably foreseeable needs of future generations, and (b) avoiding, remedying or mitigating any adverse effects of fishing on the aquatic environment. Sometimes, we use a narrower definition referring to the long-term maintenance of a single fish stock without considering the wider ecosystem impacts. At other times, we use a broader meaning of sustainability that encompasses ecological and social factors, including but not limited to biodiversity (genetic, species and ecosystem diversity), environmental and ecosystem impacts.
TAC	total quantity of each fish stock that can be taken by commercial, customary Māori interests, recreational fishery interests and other sources of fishing-related mortality, to ensure sustainability of that fishery in a given period, usually a year; this term is defined in the Fisheries Act 1996	total allowable catch
TACC	total quantity of each fish stock that the commercial fishing industry can catch in a given year; the TACC is a portion of the TAC that is set after allowances have been made for customary and recreational fishing, and for other sources of fishing-related mortality; this term is defined in the Fisheries Act 1996	total allowable commercial catch
telson	the last segment in the abdomen or terminal appendage to the abdomen found in crustaceans such as rock lobsters
tipping point	a point at which an ecosystem makes an abrupt shift between different states, driven by environmental change
tori line	a type of bird-scaring fishing line with coloured streamers that is deployed behind a longline fishing vessel to deter seabirds from accessing baited hooks
total allowable catch	total quantity of each fish stock that can be taken by commercial, customary Māori interests, recreational fishery interests and other sources of fishing-related mortality, to ensure sustainability of that fishery in a given period, usually a year; this term is defined in the Fisheries Act 1996	TAC
total allowable commercial catch	total quantity of each fish stock that the commercial fishing industry can catch in a given year; the TACC is a portion of the TAC that is set after allowances have been made for customary and recreational fishing, and for other sources of fishing-related mortality; this term is defined in the Fisheries Act 1996	TACC
trapping	a method of catching some marine species such as crayfish where a pot-like trap attached to a long rope is baited, dropped in the water and retrieved later; once entered, the target marine organism can’t escape	potting
trawling	a fishing method where a net is dragged through the water behind a vessel
Treaty of Waitangi (Fisheries Claims) Settlement Act 1992	the Treaty of Waitangi (Fisheries Claims) Settlement Act became law in late 1992, and gave effect to the Deed of Settlement, signed in September 1992 this deed (1) settled Māori claims to commercial fishing; (2) clarified Māori rights to customary or non-commercial fishing; and (3) discharged the Crown’s obligations in respect of Māori commercial fishing interests under the Treaty of Waitangi	Fisheries Settlement 1992; Māori Fisheries Settlement 1992
trolling	a fishing method using a line, sometimes with multiple lures, and dragging it horizontally through the water to simulate prey movement
trophic cascade	flow of changes in an ecosystem and relative abundance of prey species, triggered by the removal or addition of a top predator
trophic level	the position an organism occupies in a food web
turbidity	a measure of the murkiness of water due to the presence of suspended particles
UAV	unmanned aerial vehicle
UBA	underwater breathing apparatus
UNCLOS	United Nations Convention on the Law of the Sea
UNEP	United Nations Environment Programme
unfished biomass	B₀; the theoretical carrying capacity of the recruited or vulnerable biomass of a fish stock; in some cases, it refers to the average biomass of the stock in the years before fishing started More generally, it is the average over recent years of the biomass that theoretically would have occurred if the stock had never been fished. B₀ is often estimated from stock modelling and various percentages of it (e.g. 40% B₀) are used as biological reference points to assess the relative status of a stock	B₀, original biomass
UNFSA	United Nations Fish Stocks Agreement
UNGA	United Nations General Assembly
UTF	underwater topographical feature
VIAME	video and image analytics for marine environments
VME	vulnerable marine ecosystem; a marine ecosystem is classified as 'vulnerable' based on the characteristics that it possesses, such as uniqueness or rarity; functional significance of the habitat; fragility; life-history traits of component species that make recovery difficult; and structural complexity’ examples are seamounts and deepwater coral forests.	vulnerable marine ecosystem
vulnerable marine ecosystem	vulnerable marine ecosystem; a marine ecosystem is classified as 'vulnerable' based on the characteristics that it possesses, such as uniqueness or rarity; functional significance of the habitat; fragility; life-history traits of component species that make recovery difficult; and structural complexity’ examples are seamounts and deepwater coral forests.	VME
WCPFC	Western and Central Pacific Fisheries Commission
WGS	whole genome sequencing
WWF	World Wildlife Fund
xenophyphore	single-celled organisms that live on the seafloor, extracting minerals from their surroundings to construct an exoskeleton

Appendices

Appendix 1: EAFM principles and relevant Fisheries Act 1996 provisions

Table taken directly from the Fathom report, ‘EAFM and the Fisheries Act 1996’ [9]

Usually we refer to sections of the Fisheries Act 1996 as section X. In this table, these are abbreviated to sX.

Principles	Key Fisheries Act provisions
1. Ensuring the sustainability of fish stocks	s11 sustainability measures; s13 total allowable catch (TAC); s14 and s14A alternative TACs.
2. Rebuilding depleted stocks	s11 sustainability measures; s13 TAC
3. Ecosystem integrity: safeguarding biodiversity and ecosystem structure and functioning	s8 purpose; s9 environmental principles; s11 sustainability measures.
4. Taking account of species interactions	s9 environmental principles; s13 TAC; s15 fishing-related mortality of marine mammals and other wildlife.
5. Minimising impacts on non-target species	s9 environmental principles; s11 sustainability measures; s15 fishing-related mortality of marine mammals and other wildlife; s72 dumping of fish prohibited.
6. Protecting fisheries habitats	s9 environmental principles; s11 sustainability measures.
7. Managing at appropriate spatial scale	s19 (QMS introduction); s11 sustainability measures; s11A fisheries plans; Part 9 taiāpure-local fisheries and customary fishing.
8. Considering trans-boundary effects	s5 application of international obligations; s17A highly migratory species taken outside NZ fisheries waters; Part 6A high seas fishing; Schedule 1A (fish stocks agreement).
9. Managing at appropriate temporal scale	s8 purpose; s9 environmental principles; s13 TAC; s11 sustainability measures; s11A fisheries plans.
10. Adopting a precautionary approach	s5 application of international obligations; s8 purpose; s9 environmental principles; s10 information principles; s13 TAC.
11. Using science and diverse forms of knowledge	s12 consultation; Part 10 record keeping and reporting; Part 12 observer programme.
12. Broadening stakeholder participation	s12 consultation; various specific consultation provisions; s11A fisheries plans; various provisions enabling active stakeholder involvement; s5 application of Treaty of Waitangi (Fisheries Claims) Settlement Act 1992.
13. Recognising and providing for Indigenous rights	s5 application of Treaty of Waitangi (Fisheries Claims) Settlement Act 1992; s12 consultation; s44 (settlement allocation); Part 9 taiāpure-local fisheries and customary fishing.
14. Balancing utilisation and sustainability	s8 purpose.
15. Taking account of social and economic factors	s8 purpose; s13 TAC; s14A alternative TAC; Part 9 taiāpure-local fisheries and customary fishing; s123 dispute resolution; Part 14 cost recovery.
16. Taking account of environmental influences on fisheries	s11 sustainability measures; s13 TAC; s16 emergency measures.
17. Encouraging integrated management	s6 application of RMA; s11 sustainability measures; s15 fishing-related mortality of marine mammals and other wildlife.

Appendix 2: Climate change data

The table below highlights environmental areas of concern and summarises the Ministry for the Environment’s marine environmental reporting in these areas (taken from Our Marine Environment 2019). This is not a comprehensive summary of all environmental information available – it is to show what information is analysed and presented within the current environmental reporting framework.

Climate and oceans

Indicator	Measurement	2018/2019 summary
Sea-level rise	National mean trends in annual sea-level rise at four long-term monitoring sites (Auckland, Wellington, Lyttelton and Dunedin).	The rate of sea-level rise has increased (the average rate in the past 60 years was more than double the rate of the previous 60 years).
Ocean sea-surface temperature	Average temperature recorded by satellite since 1981.	The seas are warming – satellite data recorded an average increase of 0.2°C per decade since 1981.
Extreme wave events	Extreme wave events from 2008.	Frequency of extreme wave events is increasing to the east and south of New Zealand and decreasing on the North Island’s west coast and to the north of the Bay of Plenty. The short time period makes it too early to definitively separate this trend from longer-term climate cycles.
Ocean acidity	pH of New Zealand subantarctic surface waters along from the Munida Transect, from 1998. New dataset for coastal water pH for nine sites across NZ.	Long-term measurements of subantarctic waters off the Otago coast show an increase of 7.1% in ocean acidity in the past 20 years. More data is needed before role of climate change can be separated from other factors that may be affecting coastal water acidity.
Primary productivity	Abundance of phytoplankton (measured as chlorophyll-a) measured by satellite near the sea surface from 1997.	The abundance of phytoplankton has increased and decreased in different New Zealand waters. Changing oceanic productivity is specific to the location; an increase or decrease in one area may not have the same impacts as in another area.
Marine heatwaves	High sea-surface temperatures over significant area and for significant duration.	Marine heatwaves are increasing in frequency. A marine heatwave occurring in the Tasman Sea and south of the Chatham Rise in 2017/18 was unprecedented (based on data since 1981).

Appendix 3: Estimates for newly trawled area

Tables reproduced from [10].

For the deepwater fish stocks, the number of cells contacted in a year, that had not been contacted in previous years, and the aggregate area and footprint within those cells. A base of 25,103 cells were contacted in 1990-94, and, for example, 1,316 cells were contacted in 1995 (but not in 1990-94), with an aggregate area of 1,201 km² and footprint of 1,022 km². The table shows the equivalent data for Tier 1 and Tier 2 fish stocks.

Fishing year	No. new cells	Aggregate area (km²)	Footprint (km²)
No. cells contacted in 1990-4 = 25,103
1995	1,316	1,201.5	1,022.3
1996	1,420	1,032.1	948.8
1997	1,185	916.0	868.5
1998	1,543	1,892.8	1,538.1
1999	1,388	1,360.6	1,172.7
2000	1,227	1,517.1	1,363.2
2001	737	715.7	614.1
2002	1,173	1,050.2	1,007.5
2003	633	703.5	629.7
2004	328	319.8	294.9
2005	557	587.0	519.9
2006	266	134.0	129.3
2007	251	153.4	143.7
2008	279	191.0	177.7
2009	220	99.7	96.6
2010	165	60.3	59.5
2011	167	59.1	58.7
2012	106	36.9	36.7
2013	74	35.6	35.0
2014	94	34.4	34.2
2015	178	171.8	157.7
2016	172	108.6	104.5
2017	100	60.8	59.4
2018	117	32.8	32.8
2019	73	89.9	85.7

For the inshore fish stocks, the number of cells contacted in a year, that had not been contacted in previous years, and the aggregate area and footprint within those cells. A base of 9,459 cells were contacted in 2008 (the fishing year that tow-level data were first collected for all inshore fisheries), and, for example, 1,497 cells were contacted in 2009 (but not in 2008), with an aggregate area of 819.3 km² and footprint of 775.9 km².

Fishing year	No. new cells	Aggregate area (km²)	Footprint (km²)
No. cells contacted in 2008 = 9,459
2009	1,497	819.3	775.9
2010	934	657.8	576.4
2011	771	304.1	296.9
2012	484	151.7	148.3
2013	384	145.4	142.4
2014	400	167.9	161.0
2015	316	133.0	130.2
2016	285	79.1	79.1
2017	275	80.6	80.5
2018	198	66.1	65.9
2019	196	63.5	62.3

Appendix 4: Land-based effects data

Fisheries New Zealand, as reported in the trends and indicators section of the Aquatic Environment and Biodiversity Annual Review:

Indicator	Measurement	2018/2019 summary
Land-based effects on the coastal environment
A national view of the impacts of land‐based influences upon seafood production does not exist.	N/A	N/A

The table below highlights environmental areas of concern and summarises the Ministry for the Environment’s marine environmental reporting in these areas. This is not a comprehensive summary of all environmental information available – it is to show what information is analysed and presented within the current environmental reporting framework.

Human land use and sediment impacts

Indicator	Measurement	2018/2019 summary
Sediment	Focus on sediment accumulation in estuaries.	Accumulation rates have increased. Intertidal sedimentation rates have generally increased and become highly variable since European settlement.
Biogenic habitats	Review of the state of key biogenic habitats using nationally available data.	Most have decreased (e.g. mussel beds, seagrass meadows).
Litter and contaminants	Beach litter density, monitoring of contaminants limited and inconsistent.	Have increased in the habitat and food webs, particularly plastic.
Water quality	Nutrients (phosphorus and nitrogen), phytoplankton, oxygen, water clarity, and pH monitoring.	It is difficult to assess the overall state of coastal water quality.

Appendix 5: New Zealand fisheries legal instruments

New Zealand fisheries legal instruments: Acts and regulations

Instrument	Purpose	Lead
Fisheries Act 1996 & residual parts of Fisheries Act 1983	Provides for the utilisation of fisheries resources while ensuring sustainability. Ensuring sustainability means: Maintaining the potential of fisheries resources to meet the reasonably foreseeable needs of future generations, and Avoiding, remedying, or mitigating any adverse effects of fishing on the aquatic environment. Utilisation means conserving, using, enhancing, and developing fisheries resources to enable people to provide for their social, economic, and cultural wellbeing.	MPI
Treaty of Waitangi (Fisheries Claims) Settlement Act 1992	Gives effect to settlement of claims relating to Māori commercial fishing rights: Makes better provision for Māori non-commercial traditional and customary fishing rights and interests, and Makes better provision for Māori participation in the management and conservation of New Zealand’s fisheries.	MPI
Māori Fisheries Act 2004	Implements agreements made in the Deed of Settlement dated 23 September 1992, and Provides for development of the collective and individual interests of iwi in fisheries, fishing, and fisheries-related activities in a manner that is ultimately for the benefit of all Māori. Provision is made to establish a framework for the allocation and management of settlement assets through: allocation and transfer of specified settlement assets to iwi as provided for by or under this Act, and central management of the remainder of those settlement assets.	MPI
Māori Commercial Aquaculture Claims Settlement Act 2004	Provide a full and final settlement of Māori claims to commercial aquaculture on or after 21 September 1992. Provides for the allocation and management of aquaculture settlement assets.	MPI
Aquaculture Reform (Repeals and Transitional Provisions) Act 2004 (provides only for transitional matters for aquaculture)	Repeals Marine Farming Act 1971 and provides for transitional matters relating to the repeal; and Repeals certain provisions in Part 4A of the Fisheries Act 1983 and provides for transitional matters relating to the repeal. Provides for transitional matters relating to the ending of the moratorium under the Resource Management Act 1991. Provides for transitional matters relating to amendments made in 2011 to the Fisheries Act 1996, Resource Management Act 1991, and Māori Commercial Aquaculture Claims Settlement Act 2004 to further reform the law relating to aquaculture, including the removal of requirements relating to aquaculture management areas.	MPI
Driftnet Prohibition Act 1991	Prohibits driftnet fishing activities and implements the Convention for the Prohibition of Fishing with Long Driftnets in the South Pacific.	MPI
Antarctic Marine Living Resources Act 1981	Gives effect to the Convention on the Conservation of Antarctic Marine Living Resources: No person shall in the Convention Area take any marine organism, whether alive or dead, without first obtaining a permit to do so.	MFAT
Wildlife Act 1953	Consolidates and amends the law relating to the protection and control of wild animals and birds, the regulation of game shooting seasons, and the constitution and powers of acclimatisation societies.	DOC
Marine Mammals Protection Act 1978	Makes provision for the protection, conservation, and management of marine mammals within New Zealand and within New Zealand fisheries waters.	DOC
Marine Reserves Act 1971	Provides for the setting up and management of areas of the sea and foreshore as marine reserves for the purpose of preserving them in their natural state as the habitat of marine life for scientific study.	DOC
Conservation Act 1987	Promotes the conservation of New Zealand’s natural and historic resources, and for that purpose to establish a Department of Conservation.	DOC
Resource Management Act 1991	Restates and reforms the law relating to the use of land, air, and water.	MfE
Exclusive Economic Zone and Continental Shelf (Environmental Effects) Act 2012	Promotes sustainable management of the natural resources of the EEZ and the continental shelf. In relation to the EEZ, the continental shelf, and the waters above the continental shelf beyond the outer limits of the EEZ, to protect the environment from pollution by regulating or prohibiting the discharge of harmful substances and the dumping or incineration of waste or other matter.	MfE
Environmental Reporting Act 2015	Requires regular reports on New Zealand’s environment.	MfE
Biosecurity Act 1993	An Act to restate and reform the law relating to the exclusion, eradication, and effective management of pests and unwanted organisms.	MPI
Crown Minerals Act 1991	The purpose of this Act is to promote prospecting for, exploration for, and mining of Crown-owned minerals for the benefit of New Zealand.	MBIE
Maritime Transport Act 1994	The functions of the Minister under this Act are: to promote safety in maritime transport; to promote protection of the marine environment; to administer New Zealand’s participation in the conventions and any other international maritime or marine protection convention, agreement, or understanding to which the Government of New Zealand is a party; to ensure New Zealand’s preparedness for, and ability to respond to, marine oil pollution spills; and to make maritime rules and marine protection rules under this Act.	MoT
Marine and Coastal Area (Takutai Moana) Act 2011	Establishes a durable scheme to ensure the protection of the legitimate interests of all New Zealanders in the marine and coastal area of New Zealand; Recognises the mana tuku iho exercised in the marine and coastal area by iwi, hapū, and whānau as tangata whenua; Provides for the exercise of customary interests in the common marine and coastal area; and Acknowledges the Treaty of Waitangi (te Tiriti o Waitangi).	MoJ
Fisheries (Reporting) Regulations 2017	Regulations made under the Fisheries Act 1996.	MPI
Fisheries (Commercial Fishing) Regulations 2001	Sets out measures for governing administrative matters including the registration and marking of vessels. Places restrictions on take of certain species. Outlines conditions governing use of fishing equipment, reporting obligations, communication requirements etc. Sets out fees, offenses and penalties.	MPI
Fisheries (Auckland and Kermadec Areas Commercial Fishing) Regulations 1986	Places restrictions on types of fishing, fishing gear and permitted catch in areas around Auckland, Northland and the Kermadecs.	MPI
Fisheries (Challenger Area Commercial Fishing) Regulations 1986	Places restrictions on types of fishing, fishing gear and permitted catch in the Challenger FMA.	MPI
Fisheries (Southland and Sub-Antarctic Areas Commercial Fishing) Regulations 1986	Places restrictions on types of fishing, fishing gear and permitted catch in Southland and the subantarctic.	MPI
Fisheries (South-East Area Commercial Fishing) Regulations 1986	Places restrictions on types of fishing, fishing gear and permitted catch in the South-East FMA.	MPI
Fisheries (Central Area Commercial Fishing) Regulations 1986	Places restrictions on types of fishing, fishing gear and permitted catch in the Central FMA.	MPI
Fisheries (Infringement Offences) Regulations 2001	Sets out infringement offences, fees and notices.	MPI
Fisheries (Foreign Fishing Vessel) Regulations 2001	Outlines licensing, control and enforcement of foreign vessels operating in New Zealand’s EEZ.	MPI
Fisheries (Recordkeeping) Regulations 1990	Sets out who must keep records within the fishing industry, what records must be kept, and how they must be kept.	MPI
Fisheries (South Island Customary Fishing) Regulations 1999 and Fisheries (Kaimoana Customary Fishing) Regulations 1998	Tangata kaitiaki/tiaki (guardians) can be appointed for a specific rohe moana. Tangata kaitiaki/tiaki are proposed by tangata whenua and confirmed by the Minister. They authorise and manage customary activities within the rohe moana. The South Island Customary Fishing Regulations apply to the South Island and Stewart Island. The Kaimoana Customary Fishing Regulations apply to the North Island and Chatham Islands.	MPI
Ngā Rohe Moana o Ngā Hapū o Ngāti Porou Act 2019	Contributes to the legal expression, protection, and recognition of the continued exercise of mana by ngā hapū o Ngāti Porou in relation to ngā rohe moana o ngā hapū o Ngāti Porou. Gives effect to the deed of agreement between ngā hapū o Ngāti Porou and the Crown.
Submarine Cables and Pipelines Protection Act 1996	Protection of New Zealand’s undersea cables.	MoT
Fisheries (Amateur Fishing) Regulations 2013	Applies to people taking fish or other aquatic life who are not licensed fishers and not taking for customary purposes. Sets out restrictions on minimum sizes, mesh sizes, gear types, daily quotas and take of certain species. Outlines offences and penalties.	MPI

Appendix 6: Key regulators in Aotearoa New Zealand’s marine fisheries space

Fisheries New Zealand (Ministry for Primary Industries)

Fisheries New Zealand is the key regulator tasked with guiding the sustainable use of fisheries resources to the greatest overall benefit to New Zealanders.

This focus includes the sustainability of New Zealand’s wild fish stocks, aquaculture, and the wider aquatic environment.

Key legislation Fisheries New Zealand administers includes:

Department of Conservation

The Department of Conservation is the key regulator for species protection and biodiversity in the marine space.

This includes marine reserves and parks, protection of protected or threatened species, and protection of biodiversity.

Key legislation the Department of Conservation administers includes:

Ministry for the Environment

The Ministry for the Environment is responsible for national environmental reporting, including the marine environment, and promoting the sustainable management of natural resources in our EEZ and continental shelf.

Key legislation the Ministry for the Environment administers includes:

Regional councils

Our 11 regional councils are responsible for managing the territorial sea (out to 12 nautical miles).

This includes land use and its impacts on the marine environment.

Regional councils are empowered in the marine space through the:

Other regulators

Ministry of Foreign Affairs and Trade represents Aotearoa New Zealand in global discussions to ensure successful implementation of international agreements on ocean governance and fisheries management.

Ministry of Business, Innovation and Employment is responsible for health and safety in the marine environment. This includes managing permits and licences for oil, gas and minerals (via New Zealand Petroleum and Minerals).

Environmental Protection Authority is responsible for consenting, monitoring and enforcement under the EEZ Act.

Ministry of Transport is responsible for the Maritime Transport Act 1994.

Maritime New Zealand is responsible for managing maritime transport and its effects.

National Maritime Coordination Centre is responsible for managing Aotearoa New Zealand’s maritime surveillance. It is part of the New Zealand Customs Service.

Many other ministries have adjacent or supporting roles: Te Arawhiti, Department of Prime Minister and Cabinet, Te Puni Kōkiri, Ministry for Culture and Heritage, New Zealand Defence Force, Ministry of Health, Ministry of Justice, Stats NZ, and Land Information New Zealand.

Appendix 7: Fisheries Act 1996 schematic

As provided by industry:

This schematic breaks down the Fisheries Act into the following components: purpose, sustainability measures, fisheries access, the QMS, customary fishing, amateur fishing, compliance and enforcement, and offences and penalties

Appendix 8: Specific marine management acts

Hauraki Gulf Marine Park Act 2000

Integrates management of the natural, historic, and physical resources of the Hauraki Gulf, its islands, and catchments.
Establishes the Hauraki Gulf Marine Park.
Establishes objectives for the management of the Hauraki Gulf, its islands, and catchments.
Recognises the historic, traditional, cultural, and spiritual relationship of the tangata whenua with the Hauraki Gulf and its islands.
Establishes the Hauraki Gulf Forum.

Admin: Department of Conservation.

Fiordland (Te Moana o Atawhenua) Marine Management Act 2005

Establishes the Fiordland (Te Moana o Atawhenua) Marine Area and eight marine reserves in that area.
Implements measures to assist in the preservation, protection, and sustainable management of the marine environment and biological diversity of the Fiordland (Te Moana o Atawhenua) Marine Area.
Establishes the Fiordland Marine Guardians to provide advice on fisheries management, biosecurity, sustainable management, and marine preservation and protection.
Facilitates and promotes co-operation between the Guardians and management agencies, to assist in achieving the integrated management of the Fiordland (Te Moana o Atawhenua) Marine Area.
Acknowledges the importance of kaitiakitanga.

Admin: Ministry for the Environment.

Kaikōura (Te Tai ō Marokura) Marine Management Act 2014

Recognises the local, national, and international importance of the coast and sea around Kaikōura (Te Tai ō Marokura) as a consequence of its unique coastal and marine environment and distinctive biological diversity and cultural heritage.
Provides measures to assist the preservation, protection, and sustainable and integrated management of the coastal and marine environment and biological diversity of Te Tai ō Marokura.
Acknowledges the importance of kaitiakitanga and local leadership.
Establishes an advisory committee to provide advice regarding biosecurity, conservation, and fisheries matters within a marine management area.
Establishes, within Te Tai ō Marokura:
- a marine reserve,
- a whale sanctuary,
- a New Zealand fur seal sanctuary, and
- various mātaitai reserves and taiāpure-local fisheries.
Amends the Fisheries (Amateur Fishing) Regulations 2013 to provide specific regulation of amateur fishing in the marine management area.

Sugar Loaf Islands Marine Protected Area Act 1991

Ensures that the scenery, natural features, and ecosystems of the Protected Area that should be protected and conserved by reason of their distinctive quality, beauty, typicality, or uniqueness are conserved.

Admin: Department of Conservation.

Subantarctic Islands Marine Reserves Act 2014

Provides for the setting up and management of the Subantarctic Islands Marine Reserves, so as to conserve and protect its scenery, natural features and ecosystem.

Admin: Department of Conservation.

Appendix 9: New Zealand international obligations

Instrument	Purpose	Admin
United Nations Convention on the Law of the Sea (UNCLOS)	UNCLOS is a comprehensive regime of law and order in the world's oceans and seas establishing rules governing all uses of the oceans and their resources.	MFAT
United Nations Fish Stocks Agreements	Sets out principles for the conservation and management of straddling fish stocks and highly migratory fish stocks and establishes that such management must be based on the precautionary approach and the best available scientific information.
United Nations Sustainable Development Goals (SDGs)	A collection of 17 global goals set by the 2015 UN General Assembly and adopted by all member states. Of particular relevance is SDG 14: Life below water – Conserve and sustainably use the oceans, seas and marine resources for sustainable development.
Convention on the Conservation of Migratory Species of Wild Animals (CMS)	As an environmental treaty of the United Nations, CMS provides a global platform for the conservation and sustainable use of migratory animals and their habitats. Migratory species threatened with extinction are listed on Appendix I of the Convention. CMS Parties strive towards strictly protecting these animals, conserving or restoring the places where they live, mitigating obstacles to migration and controlling other factors that might endanger them.
Convention on Biological Diversity (CBD)	This intentional legal instrument is for the conservation of biological diversity, the sustainable use of its components and the fair and equitable sharing of the benefits arising out of the utilisation of genetic resources. Overall objective is to encourage actions, which will lead to a sustainable future. See also: Aichi Biodiversity Targets Aotearoa New Zealand reports every four years (see New Zealand’s Sixth National Report to the United Nations Convention on Biological Diversity (2014-2018)).
Aichi Biodiversity Targets	At the CBD meeting in November 2010, a Strategic Plan for Biodiversity 2011-2020 was agreed and published. This included the Aichi Biodiversity Targets, 20 targets that would move towards a world where “pressures on biodiversity are reduced, ecosystems are restored” and “biological resources are sustainably used”. The international community failed to achieve any of the targets by 2020, with progress made on only six of the 20 goals.
South Pacific Regional Fisheries Management Organisation (SPRFMO)	An inter-governmental organisation that is committed to the long-term conservation and sustainable use of the fishery resources of the South Pacific Ocean and in so doing safeguarding the marine ecosystems in which the resources occur. The SPRFMO Convention applies to the high seas of the South Pacific.
Convention on the International Trade in Endangered Species of Wild Fauna and Flora (CITES)	The aim is to ensure that international trade in specimens of wild animals and plants does not threaten their survival.	DOC/MPI
International Whaling Commission (IWC)	In addition to regulation of whaling, today's IWC works to address a wide range of conservation issues including bycatch and entanglement, ocean noise, pollution and debris, collision between whales and ships, and sustainable whale watching.	MPI
Wellington Convention	Multilateral treaty to prohibit the use of fishing driftnets longer than 2.5 km in the South Pacific. See appendix 5: Driftnet Prohibition Act 1991.
Noumea Convention	Aims to address the accelerating degradation of the world’s oceans and coastal areas through the sustainable management and use of marine and coastal environments.
Food and Agriculture Organisation – Code of Conduct for Responsible Fisheries	Sets out principles and international standards of behavior for responsible practices with a view to ensuring the effective conservation, management and development of living aquatic resources, with due respect for the ecosystem and biodiversity.
Food and Agriculture Organisation – International Plan of Action for Seabirds (IPOA-Seabirds)	The objective of the IPOA-Seabirds is to reduce the incidental catch of seabirds in longline fisheries where this occurs. See also New Zealand’s National Plan of Action – Seabirds 2020: Reducing the incidental catch of seabirds in fisheries.	MPI/DOC
Agreement on the Conservation of Albatrosses and Petrels (ACAP)	The objective of this agreement is to achieve and maintain a favourable conservation status for albatrosses and petrels.
Food and Agriculture Organisation – International Plan of Action for Sharks (IPOA-Sharks)	The objective of the IPOA-Sharks is to ensure the conservation and management of sharks and their long-term sustainable use. See also New Zealand’s National Plan of Action for the conservation and management of Sharks 2013 (was to be reviewed in 2018).	MPI
Convention for the Conservation of Southern Bluefin Tuna (CCSBT)	Objective to ensure, through appropriate management, the conservation and optimum utilisation of southern bluefin tuna.
Convention on the Conservation and Management of Highly Migratory Fish Stocks in the Western and Central Pacific Ocean (WCPFC)	The objective of the Convention is to ensure, through effective management, the long-term conservation and sustainable use of highly migratory fish stocks in the western and central Pacific Ocean in accordance with the 1982 United Nations Convention on the Law of the Sea and the 1995 UN Fish Stocks Agreement.
South Tasman Rise Orange Roughy Arrangement	Arrangement between Government of Australia and Government of New Zealand for the conservation and management of orange roughy on the South Tasman Rise. In New Zealand see the Fisheries (South Tasman Rise Orange Roughy Fishery) Regulations 2000.
Convention for the Conservation of Antarctic Marine Living Resources (CCAMLR)	Applies to all Antarctic populations of finfish, molluscs, crustacean and seabirds found south of the Antarctic Convergence.	MFAT/MPI
Convention on the Conservation and Management of High Seas Fishery Resources in the South Pacific Ocean	The objective is to ensure, through effective management, the long-term conservation and sustainable use of highly migratory fish stocks in the south Pacific Ocean in accordance with the 1982 Convention and the Agreement.
World Heritage Convention	The Convention sets out the duties of States Parties in identifying potential sites and their role in protecting and preserving them. By signing the Convention, each country pledges to conserve not only the World Heritage sites situated on its territory, but also to protect its national heritage. The States Parties are encouraged to integrate the protection of the cultural and natural heritage into regional planning programmes, set up staff and services at their sites, undertake scientific and technical conservation research and adopt measures which give this heritage a function in the day-to-day life of the community.

Appendix 10: National fisheries plans management objectives

Management objectives of the National Fisheries Plan for Deepwater and Middle-depth Fisheries.[11]

Management objectives
Use	1	Ensure the deepwater and middle-depth fisheries resources are managed so as to provide for the needs of future generations.
	2	Ensure excellence in the management of New Zealand’s deepwater and middle-depth fisheries, so they are consistent with, or exceed, international best practice.
	3	Ensure effective management of deepwater and middle-depth fisheries is achieved through the availability of appropriate, accurate and robust information.
	4	Ensure deepwater and middle-depth fish stocks and key bycatch fish stocks are managed to an agreed harvest strategy or reference points.
Environmental outcome	5	Ensure that maintenance of biological diversity of the aquatic environment and protection of habitats of particular significance for fisheries management are explicitly considered in management.
	6	Manage deepwater and middle-depth fisheries to avoid, remedy or mitigate the adverse effects of these fisheries on associated or dependent and incidentally caught fish species.
	7	Manage deepwater and middle-depth fisheries to avoid, remedy or mitigate the adverse effects of these fisheries on the benthic habitat.
	8	Manage deepwater and middle-depth fisheries to avoid, remedy or mitigate the adverse effects of these fisheries on the long-term viability of endangered, threatened and protected species populations.
Governance conditions	9	Ensure the management of New Zealand’s deepwater and middle-depth fisheries meets the Crown’s obligations to Māori.
	10	Ensure there is consistency and certainty of management measures and processes in the deepwater and middle-depth fisheries.
	11	Ensure New Zealand’s deepwater and middle-depth fisheries are transparently managed.

Management objectives of the National Fisheries Plan for Highly Migratory Species (HMS).[12]

Management objectives
Use	1	Support viable and profitable commercial tuna fisheries in New Zealand
	1.1	Support initiatives to add value to HMS fisheries.
	1.2	Negotiate favourable country allocations for New Zealand fishers.
	1.3	Reduce administrative barriers to profitability in HMS fisheries.
	1.4	Recognise importance of access to fisheries resources in New Zealand and the South Pacific region, and identify potential threats and opportunities.
	2	Maintain and enhance world class game fisheries in New Zealand fisheries waters.
	2.1	Maintain and enhance recreational catch rates for HMS game fisheries.
	3	Māori interests (including customary, commercial, recreational, and environmental) are enhanced.
	3.1	Take into account the views of relevant iwi and hapū in management of HMS.
	3.2	Ensure abundant HMS for customary use.
Environmental	4	Maintain sustainable HMS fisheries within environmental standards.
	4.1	Encourage management of HMS at specified target reference points.
	4.2	Support the objectives of the National Plan of Action for Sharks.
	4.3	Promote sustainable management of HMS fisheries through RFMOs.
	5	Implement an ecosystem approach to fisheries management, taking into account associated and dependent species.
	5.1	Recognise value of HMS and their ecosystems, including predators, prey, and protected species.
	5.2	Improve the quality of information available on the capture of protected species.
	5.3	Avoid, remedy, or mitigate the adverse effects of fishing on associated and dependent species (including protected species), using a risk assessment approach.
	5.4	Support the objectives of the National Plan of Action for Seabirds.
	6	Protect, maintain, and enhance fisheries habitat.
	6.1	Identify and, where appropriate, protect habitats of particular significance to HMS, especially within New Zealand fisheries waters.
Governance	7	Maintain an effective fisheries management regime.
	7.1	Ensure transparency by providing stakeholders with relevant information and performance indicators for HMS fisheries.
	8	Recognise and provide for Deed of Settlement obligations.
	8.1	Implement Deed of Settlement obligations as they relate to HMS.
	9	Ensure New Zealand interests are taken into account internationally.
	9.1	Influence international fora and ensure New Zealand interests are taken into account.
	9.2	Build and maintain strong relationships with other fishing nations, in order to influence international fora governance.
	10	Contribute to Pacific capacity development.
	10.1	Contribute to the implementation of MPI’s Memorandum of Understanding with NZAID on Pacific capacity development.

Appendix 11: Some history surrounding an Oceans Strategy in Aotearoa New Zealand

The idea of an Oceans Strategy has been around for a long time. In 1998, Australia explored its own Ocean Policy to set ‘in place the framework for integrated and ecosystem-based planning and management for all of Australia’s marine jurisdictions’.

Shortly after, in 2000, the New Zealand Government announced plans for development of their own Oceans Policy. Then Fisheries Minister, Pete Hodgson, stated in the announcement:

“We begin simply with a recognition of the value of our oceans, a recognition of the growing pressures on the marine environment, and a determination to address problems before they become crises…. Vast or not, ecological strains have begun to show in our oceans. Conflicts in their use are erupting more and more frequently… If there is one simple reason why an Oceans Policy is a good idea, it is that those strains and conflicts will increase. That’s a certainty…

But do we have overarching goals well defined? What are the points of reference for this complex mixture of law and practice? Have we ever collectively identified and expressed the range of cultural, economic, environmental or social values that apply? Or the range of interests?

Have we ever looked forward 20 years, and identified the opportunities and threats we might encounter?”

The vision created to support the Oceans Policy was:

Healthy Oceans: wisely managed for the greatest benefit of all New Zealanders, now and in the future.[13]

The Oceans Policy was never completed. Some of the delays were reportedly so that it could take account of government decisions on public access and customary rights to the foreshore and seabed.

Another strategy of mention is the Strategy for Managing the Environmental Effects of Fishing (known as SMEEF) developed by the then Ministry of Fisheries in 2005, which proposed the development of a set of standards for defining acceptable limits of effects of fishing on the aquatic environment. Challenges to setting limits identified included:[14]

“The scale of impact that fishing is having on aspects of the aquatic environment
The biological consequences of that impact
The utilisation value associated with that impact, or the cost of avoiding it
The value placed on that impact by society
The value likely to be placed on that impact by future generations”

In practice, much of the work on developing standards has been superseded by the development of National Plans of Action.

Over the subsequent years there have been various calls for greater development of maritime strategy.[15, 16] In 2014, NIWA’s Marine Futures project funded by MBIE sought to enable stakeholders to develop an agreed decision making framework to facilitate ‘economic growth, improve marine stewardship and ensure that cumulative stresses placed on the environment do not degrade the ecosystem beyond its ecological adaptive capacity’. It was hoped the research would help decision making where there were conflicting resource uses and different trade-offs, allowing improved integrative management activities (like marine spatial planning and ecosystem-based management).

In 2014, the McGuiness Institute Te Hononga Waka (a ‘non-partisan think tank’) held a structured discussion on ocean management as part of their OneOceanNZ project. The project looks at how public policy solution around ocean governance can support best practice ocean management. In the discussion they found that the ineffective aspect of the existing framework most commonly cited was a fragmented political and policy process, followed by fragmented legislation, lack of scientific information, lack of a clear national goal, and imbalance of economic/social/environmental objectives.[17] Nationally holistic strategic considerations are not able to be made in a consistent and considered way.[18]

Appendix 12: Methods and applications of genetic technology in fisheries

There are a range of methods for generating genetic data and numerous ways to apply these methods to glean information that can inform fisheries management decisions. Looking to the future in fisheries management, we are better to focus on the application of genomic approaches rather than traditional genetic methods, though there will still be applications where older methods are appropriate. The table below highlights key methods that are available for genomic studies.

Whole genome sequencing (WGS)

What it is
Sequencing all of the DNA found in the nucleus of the cell.

Strengths

Captures majority of genetic variation in a population and is typically summarised as SNP differences.
Can delineate differences based on fine-scale similarities and differences.
High throughput, so can sequence many samples at once.
Can detect both genome-wide (neutral) and allele-specific (adaptive) patterns of diversity.

Limitations

Price.
Production of large volumes of genome sequence data can be challenging for the transfer, storage and analysis of datasets.
Data capture improved by the presence of a reference genome.

Best suited applications/uses

Delineating stock structure.
Developing reference SNP marker sets that can be used for a SNP chip to delineate stocks/species/provenance/sexes.
Understanding of population structure and the evolutionary process.
Identifying species for conservation efforts, detecting pathogens, compliance surveillance etc.
Identifying individuals for conservation efforts (e.g. through genetic tagging).
Stock size (note: best for species with small population sizes).
Understanding age demographics of population (with epigenomics) or for biopsied samples through telomere length (though this is not validated for most species).
Can be combined with eDNA and ancient DNA applications.
Traceability.

Gene-tagging

What it is
Sequencing the genes from a biopsied sample and using their unique genetic fingerprint as a tag to track that individual in the future.

Strengths

Allows estimating real-time migration rates and dispersal.
Could replace physical tagging as it is permanent and cannot get lost.
Data can be used for other applications.
Can identify the species or the population of origin of exploited fish, as well as their associated pathogens.
Doesn’t rely on self-reporting from fishers.

Limitations

Invasive technique.
May not be better than conventional approaches if samples are from dead specimens or sampling is lethal.

Best suited applications/uses

See case study: Genetic tagging to understand bluefin tuna population dynamics.
Can provide information about stock biomass and growth and how these change through time.
Best used for species where the biopsy is low-risk.
Use WGS to have the power to identify unique individuals.

Mitochondrial DNA (mtDNA) sequencing

What it is
Sequencing the short, circular DNA found in the mitochondria of the cell.

Strengths

Cheaper than WGS techniques.
Methods well established.
More species have had their mtDNA sequenced so there are more reference genomes.

Limitations

Limited statistical power to identify unique individuals.
Often fails to detect population differences.
Limited value as a gene-tagging marker.

Best suited applications/uses

eDNA applications because it can be used to identify species and many have reference barcodes for it.
Ancient DNA applications because it is abundant in the cell so remains after degradation.
Identifying species.
Detect mixed species stocks.
Useful for preliminary stock structure analyses.

Sequencing genetic markers

What it is
Sequencing a select number of genetic markers, typically SNPs.

Strengths

Cheaper than WGS techniques.
Method well established.

Limitations

Have to know what genetic markers can provide the information you are after (e.g. delineate stocks) to design the test.
Cannot be used to identify unique individuals if a limited number of markers are used.

Best suited applications/uses

Detect mixed species stocks. See case study: Real-time genetic management of a marine fishery.

Microsatellite DNA

What it is
Detecting variation in length of specific repetitive stretches of DNA.

Strengths
Cheaper than WGS techniques.

Limitations

Limited statistical power to identify unique individuals.
Often fails to detect population differences.

Best suited applications/uses

Species identification.
Understanding genetic variation and stock structure.

RNA sequencing

What it is
Measuring gene expression.

Strengths
Tells us about responsiveness to environmental conditions if baseline data is available.

Limitations

Requires specific sample collection and storage to ensure results are valid because the RNA degrades.
Cost – as it is usually more expensive than DNA-based methods per individual.

Best suited applications/uses

Support conservation management of species by understanding responses to environmental change.[19]

DNA methylation

What it is
Detecting variation in epigenetic patterns which can impact gene expression.

Strengths

Tells us about responsiveness to environmental conditions.
Can provide information about sample age.
More stable to measure than RNA.

Limitations

Need to understand the association between DNA methylation signatures and the outcome for this to be applicable – limited data on age-related epigenetic signatures for fish so requires study first but proof-of-principle exists.[20]
Requires baseline data.

Best suited applications/uses

Understanding age demographics of population or for biopsied samples.
Support conservation management of species by understanding responses to environmental change.

Environmental DNA (eDNA)

What it is
Collecting DNA from the environment (e.g. collection of seawater) and sequencing it to identify the different species that have been in that area recently.

Strengths

Non-invasive sampling.
Can provide a high-level overview of genetic biodiversity, including presence/absence data.
Can detect ecosystem changes over time.
Can identify elusive species or detect low-density or pelagic species.
Can be used to estimate species abundance (not yet precise numbers of fish but this may improve in the future with analytical advances).[21–23]
Overcomes limitations in more complex biological survey methods e.g. time-consuming microscopy, difficulties identifying different life stages and sexes, and cryptic species.

Limitations

Methods are relatively new and still require sampling and analytical consistency to make sure results are robust (e.g. weather conditions or recent trawling could impact findings).[24]
Relies on species having reference DNA in databases to match the sample. These databases will continue to grow making this application more powerful.
Quick degradation of DNA in marine environment.[21]
Potential for contamination from fishing gear or lab contamination.[23]
No direct information on numbers, age, weight, life-stage or fecundity.[23]

Best suited applications/uses

Use in conservation and biosecurity by detecting specific species. See case study: Managing great white shark conservation through environmental DNA.
Monitoring ecosystems through species detection, determining species diversity and further details about ecosystem function e.g. diet, pathogens, invasive species.[24, 25]
Potential to provide abundance data and input into management decisions.
Potential to collect samples now for future use with technological advances. Need to ensure these are collected correctly so that DNA does not degrade.[23]

Ancient DNA

What it is
Extracting and sequencing DNA from ancient samples (e.g. over 100 years old).

Strengths

Provides genetic information from a snapshot in history which can be compared to modern samples.

Limitations

Degradation of DNA over time means DNA may not be able to be retrieved from all samples, but technological advances are reducing this issue.[26]

Best suited applications/uses

Answering evolutionary ecology questions which can inform management and conservation decisions. See case study: What does ancient DNA tell us about the snapper population?

Appendix 13: Genetics in fisheries in Aotearoa New Zealand

The local genetics work in the fisheries sector includes:

A recently funded SIL project led by the Deepwater Group and Plant & Food Research investigates the stock structure of hoki in Aotearoa New Zealand waters. The study employs WGS of individuals from 10 locations and will assemble the genome of hoki (contact person Dr Maren Wellenreuther).
Dr Maren Wellenreuther and Dr Peter Ritchie together oversee projects on ancient DNA in snapper to study fisheries-induced evolution (Marsden-funded) and tarakihi stock structure (MBIE-supported). Both projects apply WGS methods, and use genome assemblies.
Dr Maren Wellenreuther leads a project investigating the role of epigenomic versus genomic variation in enabling rapid adaptation to a changing climate (Marsden-funded). The data will be produced using whole genome and epigenome sequencing and use the snapper genome.
Together with researchers in Australia (led by Professor Beheregaray), Dr Maren Wellenreuther investigates the stock structure of snapper in Australia and Aotearoa New Zealand using genome-wide markers (ARC Linkage Program-funded) using reduced representation libraries and some WGS and the snapper genome.
The Ira Moana – Genes of the Sea project is enabling a collaborative network of scientists to deliver a searchable meta-database for genetic and genomic data (from both old and next-generation sequencing techniques) for terrestrial and marine species, as well as environmental samples.
A study at the Cawthron Institute taking seabed samples from beneath fish farms to detect bacterial DNA to check whether these farms are meeting best practice management practice. This could be an alternative or complementary method and is considered to be cost-effective (contact person is Xavier Ponchon).
A group led by Dr Peter Ritchie at the Victoria University of Wellington researches the population genetics of the New Zealand scampi.
Genomics Aotearoa have provided funding in this area to allow the development of new shallow sequencing methods in marine fisheries species (contact Dr Maren Wellenreuther) and to trial improved sequencing and assembly methods for key species, and this is being trialled on the blue cod genome.
A special issue focused on eDNA is coming out in 2021 New Zealand Journal of Zoology.
A review on the use of genetics on Aotearoa New Zealand fisheries was published in late 2020.[27]

Appendix 14: Further examples of models

A non-exhaustive list of additional models for application in the marine domain.

BayesNet model

How was is developed?

Expert workshop and elicitation process.

How can we use it?

It can be used to demonstrate how different management decisions lead to varying outcomes, the importance of which will vary among stakeholders. It can be used to gain consensus around management decisions.

Further development required?

The existing model and user interface requires revisiting through a proper stakeholder- and iwi-run process, whereby they are participants in the model’s construction and use.

Plastic tracker

How was is developed?

Coding for efficient post-processing of data generated by hydrodynamic models.

How can we use it?

To visualize connectivity of our coastal waters. The tool is easily accessed and used with any device capable of logging onto the internet through browser (other than Internet Explorer).

Further development required?

No further development required, however, the tool can be expanded to the whole of the EEZ.

Contamination nowcasting tool

How was is developed?

Integration of catchment, river flow, coastal hydrodynamic, and bacterial survivorship models, with using real data for validation and tuning.

How can we use it?

To obtain ‘nowcasts’ of the spatial extent of river plumes and levels of faecal indicator bacteria. Aquaculture farmers and council staff can use the tool to assist in managing shellfish harvest and beach closures. It can also serve as a wider communication tool for highlighting land-sea connectivity.

Further development required?

Full validation process and trials are required prior to roll out.

System mapping

How was is developed?

Series of workshops and interviews with experts, stakeholders and iwi.

How can we use it?

Facilitating decision making; for example in helping communities to prioritise, rationalise and implement management interventions that will assist in restoring seabed health and fisheries.

Further development required?

Two systems maps have been completed (one pilot and one Māori-led). A full systems mapping exercise would be warranted to use to inform decisions.

SeaSketch

How was is developed?

Developed at UC Santa Barbara, and parameterised/ populated by Sustainable Seas and DOC scientists.

How can we use it?

The mapping tool can be used to share spatial information and data layers widely with non-GIS experts, and has embedded participatory functions around surveying, sharing data and knowledge (safely) and collaborative spatial planning (drawing on maps).

Further development required?

Tool is functional for the region. Requires time/workshop(s) to train users and someone to manage and load additional data layers.

Appendix 15: Ocean acidification studies underway

Infographic highlighting the range of acidification studies underway. Infographic and further information available on the NIWA website

Appendix 16: Plan for a New Zealand ocean observing system

New Zealand Ocean Observing System (NZ-OOS)[28]

Year one plan

A pan-New Zealand steering committee and governance board.
Four working groups focused on estuaries to shelf, bluewater, data systems, and communications. The scope of each group will be expansive to overcome organization and science discipline silos.
A catalogue of observational assets and existing marine data for New Zealand.
A strategy for implementing mātauranga Māori in an NZ-OOS.
Draft strategic plan built on a well-designed framework and collaborative governance structure.
Business case for funding an NZ-OOS.
Many of the elements, both observational and modelling, already exist in New Zealand.

Five year vision

A widely subscribed data system built around the NZ-Ocean Data Network providing data to a wide range of users.
A network of coastal monitoring assets in key regions across a range of organisations that follow standardised data exchange protocols.
Access to model hindcast and reanalysis products for simulating and visualising New Zealand’s EEZ.
The ability for rapid response for forecasting coastal hazards, oil spill trajectories, and biosecurity risk.
Implementation of a network of sentinel sites for observing ecological outcome verifications along latitudinal and anthropogenic gradients.
Develop and implement sentinel fish and marine megafauna data collection programs that indicate ecosystem change.

Ten year vision

Widely accessible OOS visualisation system that enables society to engage with ocean data in new and exciting ways.
Data assimilating operational models providing near real time forecasting of our entire EEZ.
Commitment from the seafood industry, with the entire fishing fleet and aquaculture farms established as observing platforms.
Integration of ecological layers and the inclusion of biogeochemical and molecular ocean data through aligned sampling programs.
Successful integration of mātauranga Māori into a national OOS framework.

References and footnotes

[1] Te Ahukaramū Charles Royal (2007) Kaitiakitanga – guardianship and conservation, Te Ara – the Encyclopedia of New Zealand.

[2] Parliamentary Commissioner for the Environment (2020) Managing our estuaries. Wellington, New Zealand.

[3] Ministry for Primary Industries. Managing customary fisheries.

[4] Ministry for Primary Industries. About Māori customary fisheries.

[5] Sea change – Tai Timu Tai Pari. Acronyms and Māori terms.

[6] See Te Ohu Kaimoana.

[7] Environment Canterbury. Canterbury Regional Policy Statement, p 246.

[8] Heritage New Zealand Pouhere Taonga Act 2014, section 6.

[9] Fathom (2019) EAFM and the Fisheries Act 1996.

[10] Baird, S.J. and Mules, R. (2021, in review). Extent of bottom contact by commercial trawling and dredging in New Zealand waters, 1990-2019. New Zealand Aquatic Environment and Biodiversity Report, pending.

[11] Fisheries New Zealand (2019) National Fisheries Plan for Deepwater and Middle-Depth Fisheries 2019.

[12] Fisheries New Zealand (2019) National Fisheries Plan for Highly Migratory Species 2019. Fisheries New Zealand Technical Paper No: 2018/08.

[13] A longer vision is also given of: “Healthy Oceans: New Zealanders understand marine life and marine processes and, accordingly take responsibility for wisely managing the health of the ocean and its contribution to the present and future social, cultural, environmental and economic wellbeing of New Zealand.”

[14] Clubb, S. and Helson, J. (2006) Pragmatism and principles: The challenges of delivering a strategy to manage the environmental effects of fishing in the face of uncertainty, in proceedings of the 13^th biennial conference of the International Institute of Fisheries Economics & Trade, Portsmouth, UK.

[15] Peart, R. et al. (2011) Governing our oceans: Environmental reform for the exclusive economic zone, p. 72.

[16] Cozens, P. (2014) Commentary: Some reflections on recent oceans policy and oceans governance issues in New Zealand, Australian Journal of Maritime & Ocean Affairs, 6(1), pp. 41–48.

[17] Tremlett, A. J. (2015) Working Paper 2015/01: Ocean Management in New Zealand: Findings from a structured discussion, pp. 1–20.

[18] McGuinness, W. and Hett, S. (2015) Proposal for the creation of an oceans institution, Think piece 22.

[19] Connon, R. E. et al. (2018) The utility of transcriptomics in fish conservation, Journal of Experimental Biology, 221(2).

[20] Anastasiadi, D. and Piferrer, F. (2019) Data from: A clockwork fish. Age-prediction using DNA methylation-based biomarkers in the European seabass, v5, Dataset, Molecular Ecology Resources, 20(2), 387-397.

[21] Thomsen, P. F. et al. (2016) Environmental DNA from seawater samples correlate with trawl catches of subarctic, deepwater fishes, PLoS One, 11(11), pp. 1–22.

[22] Jerde, C. L. (2019) Can we manage fisheries with the inherent uncertainty from eDNA?, Journal of Fish Biology, 1, pp. 1–13.

[23] Hansen, B. K. et al. (2018) The sceptical optimist: Challenges and perspectives for the application of environmental DNA in marine fisheries, Fish and Fisheries, 19(5), pp. 751–768.

[24] Zaiko, A. et al. (2018) Advantages and limitations of environmental DNA/RNA tools for marine biosecurity: Management and surveillance of non-indigenous species, Frontiers in Marine Science, 5.

[25] Ficetola, G. F. et al. (2008) Species detection using environmental DNA from water samples, Biology Letters, 4(4), pp. 423–425.

[26] Oosting, T. et al. (2019) Unlocking the potential of ancient fish DNA in the genomic era, Evolutionary Applications, (12) p. 1513–1522.

[27] Papa et al. (2020) Genetic stock structure of New Zealand fish and the use of genomics in fisheries management: An overview and outlook, New Zealand Journal of Zoology, pp. 1-31.

[28] O’Callaghan, J. et al. (2019) Developing an integrated ocean observing system for New Zealand, Frontiers in Marine Science, 6, pp. 1–7.

Glossary and appendices

Contents

Some key technical terms and how we use them

Te reo Māori terms

Technical terms and abbreviations

Appendices

Appendix 1: EAFM principles and relevant Fisheries Act 1996 provisions

Appendix 2: Climate change data

Climate and oceans

Appendix 3: Estimates for newly trawled area

Appendix 4: Land-based effects data

Human land use and sediment impacts

Appendix 5: New Zealand fisheries legal instruments

New Zealand fisheries legal instruments: Acts and regulations

Appendix 6: Key regulators in Aotearoa New Zealand’s marine fisheries space

Fisheries New Zealand (Ministry for Primary Industries)

Department of Conservation

Ministry for the Environment

Regional councils

Other regulators

Appendix 7: Fisheries Act 1996 schematic

Appendix 8: Specific marine management acts

Hauraki Gulf Marine Park Act 2000

Fiordland (Te Moana o Atawhenua) Marine Management Act 2005

Kaikōura (Te Tai ō Marokura) Marine Management Act 2014

Sugar Loaf Islands Marine Protected Area Act 1991

Subantarctic Islands Marine Reserves Act 2014

Appendix 9: New Zealand international obligations

Appendix 10: National fisheries plans management objectives

Appendix 11: Some history surrounding an Oceans Strategy in Aotearoa New Zealand

Appendix 12: Methods and applications of genetic technology in fisheries

Whole genome sequencing (WGS)

Gene-tagging

Mitochondrial DNA (mtDNA) sequencing

Sequencing genetic markers

Microsatellite DNA

RNA sequencing

DNA methylation

Environmental DNA (eDNA)

Ancient DNA

Appendix 13: Genetics in fisheries in Aotearoa New Zealand

Appendix 14: Further examples of models

BayesNet model

Plastic tracker

Contamination nowcasting tool

System mapping

SeaSketch

Appendix 15: Ocean acidification studies underway

Appendix 16: Plan for a New Zealand ocean observing system

New Zealand Ocean Observing System (NZ-OOS)[28]

References and footnotes