%0 Report %D 2016 %T Analysis of Approaches for Monitoring Biodiversity in Commonwealth Waters - Field work report %A Althaus, Franziska %A Neville Barrett %A Jeffrey M Dambacher %A P Davies %A Renata Ferrari %A Jessica H. Ford %A Keith R Hayes %A Nicole A. Hill %A G.R. Hosack %A Renae Hovey %A Z Huang %A J Hulls %A T Ingleton %A Alan Jordan %A Gary A. Kendrick %A Johnathan T. Kool %A E Lawrence %A Leeming, Rhys %A Vanessa L Lucieer %A Hamish A. Malcolm %A Meyer, L %A Jacquomo Monk %A Scott L Nichol %A David Peel %A Nicholas R. Perkins %A Justy P W Siwabessy %A Sherlock, M %A Martin, Tara %A Maggie Tran %A Walsh, A %A Williams, Alan %X

The overall objective of this project was to contribute to a blue-print for a sustained national environmental monitoring strategy for monitoring biodiversity in the Commonwealth Marine Areas. The approach would apply to Key Ecological Features (KEFs) and the Commonwealth Marine Reserve (CMR) Network, focusing initially on the Southeast Marine Region. CMRs and KEFs are large, remote and poorly known, so this project focussed on identifying flexible, statistically robust approaches to survey design and data collection that could result in comprehensive descriptions of the surveyed area and at the same time provide a statistical baseline for future repeat surveys in the same area. Given the conservation status and values of these areas, non-destructive sampling tools were prioritized, including remote sensing using acoustics (e.g. multibeam) that provide information on seafloor characteristics (bathymetry, hardness and texture), and direct observation using video and camera stills, taken by towed units, autonomous units or baited units. The final report is of necessity highly technical, reporting on the design and analytical issues addressed by this project. This executive summary is designed to provide an overview of the project and highlight the key findings relevant to policy makers and managers, omitting most of the technical detail. Readers interested in technical detail are referred to the main body of this report or the many research papers resulting from this work that are listed at the end of this summary.

Three field programs were undertaken. The largest survey was for the Flinders Commonwealth Marine Reserve (CMR) located offshore, northeast of Tasmania. This provided a baseline of the continental shelf, in the multiple use zone of this reserve, on which future monitoring can be built, and provides an initial characterization of the upper slope areas in the same zone of this CMR. A smaller survey targeted at known shelf reefs features in the Solitary Islands Marine Park (SIMP) and Solitary Islands Marine Reserve (SIMR) was designed to address specific sampling issues including: extending State-based research to this Commonwealth KEF, comparing autonomous and towed platforms for capturing video imagery, and examining statistical issues associated with the use of baited underwater remote videos (BRUVs). The third survey in the KEF east of the Houtman-Abrolhos islands was an exploratory survey designed to identify whether coral-kelp and other shelf reef communities in the State MPA extended into this KEF, and explore whether seabird diet could be used as a reliable indicator of pelagic ecosystem health.


 

%8 01 May 2016 %G eng %0 Journal Article %J Scientific Data %D 2015 %T Australian sea-floor survey data, with images and expert annotations %A Bewley, Michael %A Friedman, Ariell %A Renata Ferrari %A Nicole A. Hill %A Renae Hovey %A Neville Barrett %A Oscar R. Pizarro %A Figueira, Will %A Meyer, Lisa %A Russell Babcock %A Bellchambers, Lynda %A Byrne, Maria %A Williams, Stefan B. %K Biodiversity %K Coral reefs %K fisheries %K Ocean sciences %X

This Australian benthic data set (BENTHOZ-2015) consists of an expert-annotated set of georeferenced benthic images and associated sensor data, captured by an autonomous underwater vehicle (AUV) around Australia. This type of data is of interest to marine scientists studying benthic habitats and organisms. AUVs collect georeferenced images over an area with consistent illumination and altitude, and make it possible to generate broad scale, photo-realistic 3D maps. Marine scientists then typically spend several minutes on each of thousands of images, labeling substratum type and biota at a subset of points. Labels from four Australian research groups were combined using the CATAMI classification scheme, a hierarchical classification scheme based on taxonomy and morphology for scoring marine imagery. This data set consists of 407,968 expert labeled points from around the Australian coast, with associated images, geolocation and other sensor data. The robotic surveys that collected this data form part of Australia's Integrated Marine Observing System (IMOS) ongoing benthic monitoring program. There is reuse potential in marine science, robotics, and computer vision research.

%B Scientific Data %V 2 %P 150057 %8 10 Mar 2017 %G eng %U http://www.nature.com/articles/sdata201557 %! Sci. Data %R 10.1038/sdata.2015.57 %0 Journal Article %J PLOS ONE %D 2015 %T A standardised vocabulary for identifying benthic biota and substrata from underwater imagery: the CATAMI classification scheme %A Althaus, Franziska %A Nicole A. Hill %A Renata Ferrari %A Edwards, Luke %A Rachel Przeslawski %A Schönberg, Christine H. L. %A Rick D Stuart-Smith %A Neville Barrett %A Graham J. Edgar %A Jamie Colquhoun %A Maggie Tran %A Alan Jordan %A T Rees %A Karen Gowlett-Holmes %E Judi E Hewitt %X

Imagery collected by still and video cameras is an increasingly important tool for minimal impact, repeatable observations in the marine environment. Data generated from imagery includes identification, annotation and quantification of biological subjects and environmental features within an image. To be long-lived and useful beyond their project-specific initial purpose, and to maximize their utility across studies and disciplines, marine imagery data should use a standardised vocabulary of defined terms. This would enable the compilation of regional, national and/or global data sets from multiple sources, contributing to broad-scale management studies and development of automated annotation algorithms. The classification scheme developed under the Collaborative and Automated Tools for Analysis of Marine Imagery (CATAMI) project provides such a vocabulary. The CATAMI classification scheme introduces Australian-wide acknowledged, standardised terminology for annotating benthic substrates and biota in marine imagery. It combines coarse-level taxonomy and morphology, and is a flexible, hierarchical classification that bridges the gap between habitat/biotope characterisation and taxonomy, acknowledging limitations when describing biological taxa through imagery. It is fully described, documented, and maintained through curated online databases, and can be applied across benthic image collection methods, annotation platforms and scoring methods. Following release in 2013, the CATAMI classification scheme was taken up by a wide variety of users, including government, academia and industry. This rapid acceptance highlights the scheme’s utility and the potential to facilitate broad-scale multidisciplinary studies of marine ecosystems when applied globally. Here we present the CATAMI classification scheme, describe its conception and features, and discuss its utility and the opportunities as well as challenges arising from its use.

%B PLOS ONE %V 10 %P e0141039 %8 10 Apr 2017 %G eng %U http://dx.plos.org/10.1371/journal.pone.0141039 %N 10 %! PLoS ONE %R 10.1371/journal.pone.0141039 %0 Journal Article %J PLoS ONE %D 2014 %T Variable responses of benthic communities to anomalously warm sea temperatures on a high-latitude coral reef %A Tom Bridge %A Renata Ferrari %A Bryson, Mitch %A Renae Hovey %A Will F. Figueira %A Williams, Stefan B. %A Oscar R. Pizarro %A Harborne, Alastair R. %A Byrne, Maria %E Valentine, John F. %X

High-latitude reefs support unique ecological communities occurring at the
biogeographic boundaries between tropical and temperate marine ecosystems.
Due to their lower ambient temperatures, they are regarded as potential refugia for
tropical species shifting poleward due to rising sea temperatures. However, acute
warming events can cause rapid shifts in the composition of high-latitude reef
communities, including range contractions of temperate macroalgae and bleachinginduced
mortality in corals. While bleaching has been reported on numerous highlatitude
reefs, post-bleaching trajectories of benthic communities are poorly
described. Consequently, the longer-term effects of thermal anomalies on highlatitude
reefs are difficult to predict. Here, we use an autonomous underwater
vehicle to conduct repeated surveys of three 625 m2 plots on a coral-dominated
high-latitude reef in the Houtman Abrolhos Islands, Western Australia, over a fouryear
period spanning a large-magnitude thermal anomaly. Quantification of benthic
communities revealed high coral cover (.70%, comprising three main
morphospecies) prior to the bleaching event. Plating Montipora was most
susceptible to bleaching, but in the plot where it was most abundant, coral cover did
not change significantly because of post-bleaching increases in branching
Acropora. In the other two plots, coral cover decreased while macroalgal cover
increased markedly. Overall, coral cover declined from 73% to 59% over the course
of the study, while macroalgal cover increased from 11% to 24%. The significant
differences in impacts and post-bleaching trajectories among plots underline the
importance of understanding the underlying causes of such variation to improve
predictions of how climate change will affect reefs, especially at high-latitudes.

%B PLoS ONE %V 9 %P e113079 %8 11 Feb 2016 %G eng %U http://dx.plos.org/10.1371/journal.pone.0113079 %N 11 %! PLoS ONE %R 10.1371/journal.pone.0113079 %0 Generic %D 2013 %T CATAMI Classification Scheme for scoring marine biota and substrata in underwater imagery - A pictorial guide to the Collaborative and Annotation Tools for Analysis of Marine Imagery and Video (CATAMI) classification scheme %A Althaus, Franziska %A Nicole A. Hill %A Edwards, L %A Renata Ferrari %X

This is a picture-based guide designed to promote national consistency and standards for classifying marine biota and substrata captured in underwater imagery. National consistency is an important requirement for effective monitoring of benthic ecosystems in Commonwealth Marine Reserves and key ecological features (implementing Marine Bioregional Plans).

This document provides definitions and examples for the categories described in Version 1.2 of the CATAMI Classification Scheme for marine biota and substrata in underwater imagery (CATAMI Technical Working Group, 2013). It is envisaged that imagery from a range of sources, including video and digital stills and hence spanning a range in resolution and quality, will be scored using this system.

The classification scheme was designed to allow images from shallow waters to abyssal depths and from the tropics to Antarctic/ Arctic waters to be classified using the same labels, i.e. a set of consistent identifiers. For ease of tracking and data-basing, each standardised label was also assigned a CAAB ‘code’. CAAB stands for Codes for Australian Aquatic Biota and is a numerical code that is listed, described and maintained through a CSIRO website at (http://www.cmar.csiro.au/caab/). Originally CAAB were only used for taxonomic classification of biota, but the system was adapted to encompass both the physical and the biota classes of the CATAMI classification.

The publication is by CATAMI but has been facilitated through funds from CATAMI (ANDS & NECTAR), NERP and researchers  ‘in kind’ by their institutions.

Related information:

%G eng %U http://catami.github.io/catami-docs/CATAMI%20class_PDFGuide_V4_20141218.pdf