Benthic Biodiversity Model Outputs for Campbell Plateau and Chatham Rise

Using seafloor image data to build single-taxon and community distribution models for seabed fauna in New Zealand waters.

Understanding the spatial distributions of seabed biodiversity is essential for effective management of the effects of human activities. However, existing knowledge of seabed faunal distributions comes overwhelmingly from records of museum specimens and fisheries and research trawl bycatch. Data from such sources have been used to build models that predict species and community distributions on the basis of correlations with environmental gradients but because these models are based on presence-only data from disparate sources and times, their predictions are considered uncertain. To improve understanding of seabed fauna distributions around New Zealand, we are developing a new database of occurrences and population densities based entirely on quantitative data from seabed photographic surveys designed to sample these fauna. By modelling the spatial relationships between taxon occurrences and environmental gradients across the region, we are able to predict the likelihood of individual taxa and communities being present in as-yet unsampled areas. In the first phase of the project, we concentrated on Chatham Rise; a region of high importance to commercial fisheries and with the highest density of existing seabed imagery. The models developed here were the first abundance-based models of benthic distributions in the New Zealand region at these spatial scales. In the second phase, we expanded the domain of the predictive models to encompass Campbell Plateau, in the south-eastern sector the EEZ. Combining data from Chatham Rise and Campbell Plateau in a single dataset of benthic invertebrate taxon occurrences and population densities enabled development of up-dated predictive distribution models for a range of individual invertebrate taxa, as well as models of the spatial variability in overall community composition.

Rasters are in a geotiff format at a 1000 m resolution cell size and have their relevant projections written in their files.

Date (Publication): 2021-11-04T02:30:00

Cited responsible party

Organisation name	Individual name	Electronic mail address	Role
National Institute of Water and Atmospheric Research (NIWA)		enquiries@niwa.co.nz	Resource provider

Other citation details: The citation in a list of references is: "NIWA [year-of-data-download], [Title], [data-access-URL], accessed [date-of-access]."

Purpose: We developed a new, spatially extensive, fully quantitative, and taxonomically consistent dataset of benthic invertebrate occurrence by merging data from five seabed photographic surveys on Chatham Rise (Bowden et al. 2019) and two on Campbell Plateau (Bowden et al. in press). We then used this dataset to inform development of improved predictive species-distribution models (SDM) for the entire south-eastern sector of New Zealand’s EEZ in depths from 100 to 1500 m. Predictions were developed both for a range of individual taxa and for variations in whole-community composition, yielding maps of predicted population densities, beta-diversity (rate of change of community composition), and hard-boundary community classifications. Modelling methods for individual taxa included Boosted Regression Trees (BRT, De’ath 2007), Random Forests (RF, Breiman 2001), and Generalised Additive Modelling (GAM), which were combined in ensembles, and Joint Species Distribution Modelling (jSDM, Ovaskainen et al. 2017), while for communities we used Regions of Common Profile (RCP, Foster et al. 2013) and Gradient Forests (GF, Ellis et al. 2012). For single-taxon ensemble models, the ‘hurdle’ technique was used, combining predictions from presence-absence and abundance models to reduce bias associated with zero-inflated data. Explanatory environmental variables were selected from an initial set of 58 candidate layers and the total of 354 invertebrate taxa identified from the seabed image surveys were condensed into a set of 69 taxa by aggregation to higher taxonomic levels and exclusion of rarer and non-benthic taxa.

Outputs from the single-taxon models are presented as maps showing predicted occurrences as abundances (individuals 1000 m-2) with associated estimates of model precision (CV). Outputs from the community models are presented as either continuous gradients of predicted change in community composition, or spatial classifications of the study area at a range of class-levels (e.g., GF outputs range from 5 to 75 classes across the study area).

All model predictions are downloadable as raster files in geotiff format at 1000 m grid cell size and and have their relevant projections written in their files.

These predictions are the best-informed representations of seabed distributions at regional scales in the New Zealand Exclusive Economic Zone to date and provide a resource that will have applications in marine environmental management and ecosystem research. Potential applications include quantification of benthic impacts from bottom-contact fishing gear and other anthropogenic agencies, informing spatial management of biodiversity through, for example, the design of marine protected areas, and informing research into ecosystem linkages between water-column and seabed processes. The dataset developed here has also enabled objective evaluation of the credibility of predictions from earlier SDM initiatives for the region, which were based on museum and bycatch data (see Bowden et al. 2021).

Acknowledgements

This study was funded by Fisheries New Zealand (FNZ) under projects ZBD2016-11 and ZBD2019-01, with governance at FNS by Mary Livingston. The Principal investigator is David Bowden ( David.Bowden@niwa.co.nz ) and the full team includes: Owen Anderson; Ashley Rowden; Fabrice Stephenson; Caroline Chin; Malcolm Clark; Niki Davey; Alan Hart, and Brent Wood.

References

Anderson, O.F.; Pallentin, A.; Bowden, D.A.; Chin, C.; Davey, N.; Eton, N.; Fenwick, M.; George, S.; Macpherson, D. (2020). Quantifying Benthic Biodiversity - Phase II: a factual voyage report from RV Tangaroa voyage TAN2004 to Campbell Plateau 17 May - 7 June 2020. No. 44 p.

Bowden, D.A.; Rowden, A.A.; Anderson, O.F.; Clark, M.R.; Hart, A.; Davey, N., . . . Chin, C. (2019a). Quantifying Benthic Biodiversity: developing a dataset of benthic invertebrate faunal distributions from seabed photographic surveys of Chatham Rise. Aquatic Environment and Biodiversity Report No. 221. 35 p.

Bowden, D.A.; Anderson, O.F.; Escobar-Flores, P.; Rowden, A.A.; Clark, M.R. (2019b). Quantifying benthic biodiversity: using seafloor image data to build single-taxon and community distribution models for Chatham Rise, New Zealand. Aquatic Environment and Biodiversity Report No. 235. 67 p.

Bowden, D.A.; Anderson, O.F.; Rowden, A.A.; Stephenson, F.; Clark, M.R. (2021). Assessing Habitat Suitability Models for the Deep Sea: Is Our Ability to Predict the Distributions of Seafloor Fauna Improving? Frontiers in Marine Science 8(239). < http://dx.doi.org/10.3389/fmars.2021.632389 >

Bowden, D.A.; Anderson, O.F.; Rowden, A.A.; Stephenson, F. (in press). Assessing the utility of habitat suitability models developed for Chatham Rise when applied to Campbell Plateau. Aquatic Environment and Biodiversity Report No. p.

Breiman, L. (2001). Random forests. Machine Learning 45(1): 5-32

De'ath, G. (2007). Boosted trees for ecological modelling and prediction. Ecology 88(1): 243-251.

Ellis, N.; Smith, S.J.; Pitcher, C.R. (2012). Gradient forests: calculating importance gradients on physical predictors. Ecology 93(1): 156-168.

Foster, S.D.; Givens, G.H.; Dornan, G.J.; Dunstan, P.K.; Darnell, R. (2013). Modelling biological regions from multi-species and environmental data. Environmetrics 24(7): 489-499.

Ovaskainen, O.; Tikhonov, G.; Norberg, A.; Blanchet, F.G.; Duan, L.; Dunson, D.; Roslin, T.; Abrego, N. (2017). How to make more out of community data? A conceptual framework and its implementation as models and software. Ecology Letters 20(5): 561-576. < http://dx.doi.org/10.1111/ele.12757 >

Credit: NIWA

See:

Bowden, D.A.; Anderson, O.F.; Rowden, A.A.; Stephenson, F.; Clark, M.R. (2021). Assessing Habitat Suitability Models for the Deep Sea: Is Our Ability to Predict the Distributions of Seafloor Fauna Improving? Frontiers in Marine Science 8(239). http://dx.doi.org/10.3389/fmars.2021.632389

Bowden, D.A.; Anderson, O.F.; Rowden A.A.; Stephenson F. (in press). Assessing the utility of habitat suitability models developed for Chatham Rise when applied to Campbell Plateau. New Zealand Aquatic Environment and Biodiversity Report.

Stephenson, F.; Bowden, D.A.; Finucci, B.; Anderson, O.F.; Rowden, A.A. (in press). Developing updated predictive models for benthic taxa and communities across Chatham Rise and Campbell Plateau using photographic survey data. New Zealand Aquatic Environment and Biodiversity Report.

Anderson, O.F.; Pallentin, A.; Bowden, D.A.; Chin, C.; Davey, N.; Eton, N.; Fenwick, M.; George, S.; Macpherson, D. (in press). Quantifying Benthic Biodiversity – Phase II: a factual voyage report from RV Tangaroa voyage TAN2004 to Campbell Plateau 17 May – 7 June 2020. New Zealand Aquatic Environment and Biodiversity Report.

Status: Completed

Point of contact

Organisation name	Individual name	Electronic mail address	Role
National Institute of Water and Atmospheric Research (NIWA)	Dr David Bowden	enquires@niwa.co.nz	Principal investigator

Maintenance and update frequency: Not planned

AODN Geographic Extents Vocabulary

Global / Oceans | South West Pacific Ocean

Place

Countries | New Zealand
Chatham Rise
Campbell Plateau

Theme

Biodiversity
Taxon
Habitat
Seabed fauna
Distribution models

Distance: 1000 1000 m

Language: eng

Topic category

Biota

Description: New Zealand regional waters, encompassing the Exclusive Economic Zone and the Continental Shelf

Distribution format

Name	Version
GeoTIFF	1.0
CSV-file	1.0
MS Excel	Version 2002
Text	Ascii

OnLine resource

Protocol	Linkage	Name
WWW:LINK-1.0-http--metadata-URL	https://nzodn.nz/geonetwork/srv/en/metadata.show?uuid=28e841e3-19e9-4473-a1ed-f112bca5ac1a
OGC:WMS-1.1.1-http-get-map	https://nzodn.nz/geoserver/nzodn/wms	nzodn:bio_campbell_chatham_map
IMOS:AGGREGATION--bodaac	https://nzodn.nz/geoserver/ows	bio_campbell_chatham_map#url

Metadata

File identifier: 28e841e3-19e9-4473-a1ed-f112bca5ac1a XML

Metadata language: eng

Character set: UTF8

Hierarchy level: Dataset

Date stamp: 2021-11-04T21:45:57

Metadata standard name: ISO 19115:2003/19139

Metadata standard version: 1.0

Metadata author

Organisation name	Individual name	Electronic mail address	Role
National Institute of Water and Atmospheric Research (NIWA)		enquiries@niwa.co.nz	Distributor

Overviews

thumbnail

large_thumbnail

Spatial extent

Provided by

Access to the catalogue

Read here the full details and access to the data.

Simple

Metadata

Overviews

Spatial extent

Keywords

Provided by