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Funded research


Understanding the Links Between Habitat and Fisheries

The research program focused on understanding the links between habitat and fisheries within the Eastern Scotian Shelf Integrated Management (ESSIM) area. More specifically, research was conducted in an attempt to answer questions regarding how different life stages of demersal fish utilize benthic habitat and associated epibenthic organisms, what kinds of habitats are required to support them, how these habitats are spatially distributed, how much of these habitats are required to support sustainable fish communities and how vulnerable these habitats or species interactions are to human disturbance. Answers to these questions aid Fisheries and Oceans Canada (DFO) in dealing with issues associated with the Integrated Management Initiative, ecosystem management, biodiversity and productive capacity. The three-year program builded upon previous DFO and National Research Council of Canada (NRCan) experience including the following steps:


Catch and effort data

Fisheries and Oceans Canada catch and effort data from annual groundfish surveys was analyzed by species and age class to determine specific locations where demersal fish congregate in the ESSIM area. Furthermore, general maps of habitat type were prepared utilizing previous DFO/NRCan and NGO studies with overlays of the fish distribution.

Hot spot information

Information on fish, physical habitat, and associated epibenthic organisms was collected at identified 'hot spots' within and outside the closed area. Sampling tools included acoustic fish counters, Towcam video, Campod video and photography, QTC View, and sidescan sonar for identification of fish composition and its association with habitat type. A temporal component to the field observations was used to determine the fidelity of fish to habitat, including comparisons both within and outside the closed area. The data was used to describe fish assemblages, physical habitat, associated epibenthic organisms, and to investigate the interrelationships toward identification of potential areas of preferred habitat in the ESSIM.

Multibeam and seismic surveys

Multibeam and seismic surveys of the closed area were conducted in order to develop a preliminary benthic habitat map. The results of the field surveys of fish, epibenthic organisms and habitat was overlayed on to multibeam imagery and interrelationships were analyzed. Accepted methodology was applied to classify benthic habitat, with a focus on preferred habitat for demersal species. Using the multibeam imagery as a planning tool, directed acoustic data and imagery of benthic habitat and associated epibenthic organisms were obtained at specific targets. Further, the amount and distribution of preferred habitat for different species of demersal fish in the study area was determined.

Scientific fishing

Scientific fishing was performed to confirm the reported 'hot spot's for demersal fish and to obtain information on species composition. Using the new habitat map, predictions were made concerning additional locations where demersal fish are expected to be most abundant and these predictions were tested with directed fishing.

Impact of human activities

The vulnerability of the essential fish habitat to human activities including impacts from fishing gears, oil and gas exploration, development and production activities, as well as other activities with the potential to impact benthic habitats (e.g., marine mining, submarine cables and pipelines) was assessed. Observed impacts of mobile fishing gear on marine habitat and biological communities was used to predict potential impacts of fish stocks over large spatial scales. Recommendations were provided on the future management of the Haddock Nursery Area in order to meet management objectives for fisheries, habitat protection and the maintenance of biodiversity.

Historical and Contemporary Inventories of Finfish Species Richness (K. Frank) 40K

One of the most profound and important empirical observations in ecology is that species diversity is predictably related to the area of habitat in both continental and island faunas. This is widely known as the species-area relationship or SAR. Our recent research has established the existence of a highly significant positive relationship between the number of finfish species and bank area, with banks of similar size yielding similar species richness regardless of the distance between them. We have been exploring the ecological basis of this relationship by examining the relative influence of habitat diversity and area per se, as described in the equilibrium theory of island biogeography. This research is made possible by the availability of detailed annual research vessel surveys of the abundance and distribution of finfish fauna on these banks. We intend to test the generality of this relationship by expanding the geographic scale of the analysis.

Other aspects of this work include application of analytical techniques to address the question of what is a sufficient sample size for quantifying finfish diversity that may help to circumvent repeated, extensive sampling. For example, the order in which samples are used to construct a species accumulation curve determines the slope of that relationship. This and other alternatives have been proposed and we will examine them (Flather 1996, Colwell and Coddington 1994, Coleman 1981). We will also investigate how population dynamics and life history patterns influence the SARs. Initially, we will explore how SARs are influenced by species turnover and whether turnover is related to changes in environment or fishing intensity. Using the above information, population dynamics (growth and extinction), dispersal and migration will be modeled by using a metapopulation community model. Such models can illuminate the determinants that generate local and regional species richness (see vanWoesik 2000).

Invasion of Macroalgae on the Scotian Shelf Study (Scheibling, Kenchington-DFO Internal Contact)


Synergistic interactions between invasive species (an epiphytic bryozoan, Membranipora membranacea, and a green alga, Codium fragile ssp. tomentosoides) have resulted in large-scale replacement of kelps by Codium along the rocky coast of Atlantic Nova Scotia. Changes in species composition and abundance of invertebrates and fish associated with this alteration of biogenic habitat have important implications for management of coastal resources, including assessment of biodiversity and identification of species/habitats at risk. This project will provide the first assessment of the impact of invading species on the structure and function of a marine ecosystem in Canadian waters.


Codium fragile was, until recently, constrained to New England waters since it's introduction to North America through ballast water in 1952. The species was first reported in Canadian waters in the 1980s in Mahone Bay, Nova Scotia. Since then it has spread through Mahone Bay, St. Margaret's Bay and may have reached Cape Breton and the Bras D'Or on the Atlantic coast, and PEI in the Gulf. This prolific green seaweed occupies the upper subtidal zone, displacing kelp forests on rocky shores and can survive a broad range of environmental conditions, including tidal pools. As a siphonous alga it contains siphoneins and other chemicals which are highly unpalatable to all but specialized grazers. It is able to spread through both sexual and asexual (fragmentation) means and has altered our seaweed communities both structurally and functionally. This seaweed is also known as "Oyster Thief" as it commonly attaches itself to oyster shells, killing the oyster through shear weight. It will undoubtedly be a major problem for oyster and other shellfish growers in our region. The urchin fishery may also be compromised by the loss of the kelp beds (100% loss over large tracts of St. Margaret's and Mahone Bays).

Project Goals and Objectives

  • To assess the feasibility of using hyperspectral remote sensing as a means to detect, map and monitor invasive species in the coastal waters of Nova Scotia.
  • To determine the extent of the current invasion of the green alga Codium fragile and the bryozoan Membranipora membranacea along the southwest shore of Nova Scotia through the development of subtidal habitat classification maps.
  • To collect Local Ecological Knowledge (LEK) and examine its potential use as a means to map and monitor these species invasions.

General Method


  • A Compact Airborne Spectrographic Imager (CASI), operated by Hyperspectral Data International (HDI), was used to collect hyperspectral imagery of the subtidal zone in select areas of St. Margaret's Bay, Mahone Bay, and Lunenburg Bay.
  • The CASI survey was conducted during July and August 2001. Flights occurred on days when weather and ocean conditions were optimal for hyperspectral data collection.
  • SCUBA-based ground-truthing was conducted in conjunction with each aerial survey using a diver-operated underwater video camera. Data on percentage cover of the substratum by different vegetative habitat types were collected at depths of 2, 4, and 6 m (below MLLW) at 15 sites within the survey areas.
  • Reflective targets were placed at two sites in each survey area prior to the CASI flyover. These targets were used to examine spectral attenuation due to the water column over depths of 2-8 m.
  • The CASI imagery underwent preliminary processing by HDI, including atmospheric correction, geo-correction, and radiometric balancing.
  • Data on substratum cover was compared with similar data from a SCUBA survey conducted in 2000 (RE Scheibling and T Balch, unpublished data)


  • To solicit participants for a questionnaire survey, information on the natural history and spread of Codium and Membranipora in Nova Scotia was disseminated to SCUBA divers and fishermen via phone, email, and an article published in "Hook, Line and Thinker, the newsletter of the Fishermen and Scientist Research Society".
  • An invasive species website focusing on Codium and Membranipora was created to increase public awareness of these species and provide information on their origins, environmental impact, and keys to identification.
  • Quick reference identification cards for both species were designed for distribution at local dive shops and other organizations.



  • Preliminary analysis of CASI imagery from all each survey areas shows good resolution to at least 10 meters depth. The presence of various vegetated habitats within this depth range is clearly evident by visual examination.
  • Ground-truthing data show a decrease in percentage cover of Codium with increasing depth from 1-10 m, with maximum cover occurring at 2-4 m. The shallow distribution of the invasive alga is well within the limits of detection and fine-scale resolution by CASI.
  • Comparison of Codium cover data collected in 2000 and 2001 shows a strong positive correlation between years, indicating little change in cover at a local scale over a one-year period.


  • We received a poor response to requests for participants in the questionnaire survey. While most of the sport diving businesses and fisheries organizations that we contacted did offer to distribute our information and request for survey participants to clients, only four responses were received.

Ongoing Work/ Corrective Action


  • The imagery is currently undergoing further processing by HDI to normalize the data (to facilitate the merging of image strips into classification maps) and incorporate additional data on bathymetry (in a preliminary attempt to adjust for water column attenuation of the spectral signal). This requirement for additional processing was not anticipated at the start of the project and has significantly delayed the acquisition of images necessary for developing the classification maps.
  • Spectral information collected from the reflective targets is being used to develop a more accurate method of correcting for water column attenuation.
  • Imagery will be classified using a method based on 'Fuzzy Logic' developed by Kosko and Isaka (1993). Classification maps will indicate the current extent of Codium as well as other important vegetated habitats, such as kelp beds. We expect to have these maps completed by June 2001.


  • Due to poor response to our requests for questionnaire participants, and in light of the success of the CASI surveys, we have shifted our focus to concentrate on the production of classification maps from the CASI data.
  • The website will continue to be maintained and updated on a regular basis.

Capital Support for Genetic SAR Programs (O'Reilly, Bentzen, Kenchington) 220K


Genetic diversity and maintenance of within-species diversity are both elements of biodiversity. The CMB is involved with the Live Gene Bank facilities, currently operating for Atlantic Salmon and Whitefish, and in the CBS project examining genetic diversity of haddock, herring and lobster. In support of those programs and the DFO Chair, a capital investment in automated technology is proposed.

The COSEWIC criteria for establishing operational units below the level of species have not been finally resolved, however, a conceptual framework based upon the Evolutionarily Significant Unit has been advocated by the US and it is likely that Canada will eventually adopt similar guidelines. The Evolutionary Significant Unit is a powerful concept that should be embedded in any conservation policy which involves genetic considerations. It is based on information on the partitioning of genetic variance within a species combined with quality decisions on the value of the components with respect to evolutionary and ecological "legacy".


Genetic information is essential in establishing an ESU as the concept currently stands. Yet for most marine species, even those of commercial importance, genetic information is not available to address this issue. The Scientific Gaps associated with many SAR will be their genetic structure. In anticipation of this, DFO and Dalhousie have established a senior chair in Fisheries Resource Conservation Genetics. However, the critical mass of individuals with expertise in this area is still small.

Automated equipment is needed to reduce the technical costs associated with project proposals and to increase the through put enabling more projects to be completed. Additionally, the live gene bank facilities have been identified as an important priority in the Inner Bay of Fundy recovery process. Team members belong to the Atlantic Salmon Genetic Technical Advisory Committee. The demands of this species alone require the purchase of dedicated equipment to provide the information required on breeding plans in a timely manner.


Therefore, this project will link to all recovery plans in the Maritimes Region and directly to those for the Atlantic Salmon, Whitefish and Dwarf Smelt. This request is for a dedicated automatic sequencer to meet the data requirements of these species. Ongoing requests are for capital replacement and expansion of the current facilities to meet program needs. This project was given an E1 (Essential 1) priority by the SARA Working Group for Generic Proposals.

Facility for Remote Sensing on Benthic Biodiversity (Bruce Hatcher)


The :: Centre for Marine Biodiversity :: has recently provided funding to Dr. Bruce G. Hatcher (Biology and Marine Affairs) at Dalhousie University for the establishment of a facility for remote sensing of benthic biodiversity. The funding was used to purchase an educational license for the latest version of PCI Geomatica Fundamentals(tm) and Geomatica Prime(tm) remote sensing and GIS software. PCI is a Canadian company that produces leading edge software for the analysis of remotely sensed imagery. Further, a custom designed computer was assembled to allow full use of the analytical power and 3-D presentation capabilities of this software. This work was done by KPC Computers here in Halifax.


Research in the remote-sensing laboratory will be focused on the development of synoptic depictions of marine benthic biodiversity, and their quantitative analysis in the context of hypotheses derived from ecological theory. Three projects currently underway are the quantification of physical habitat texture in the Mesoamerican Barrier Reef ecosystem for calibration of 3-D numerical models of connectivity among individual reef units (BG Hatcher, J Sheng, B Ruddick, & S Andrefouet with students P Pantaloni and T Beech - NSERC funded); geospatial analysis of the growth response of coral reefs of Maldives to asymmetries in Monsoon forcing (Ph.D. student A Naseer supervised by BG Hatcher - Commonwealth & NASA funded); discrimination of the spatial patterns of invasion of subtidal marine habitat by the invasive green alga (Codium fragile) in SW Nova Scotia (M.Sc. student C. Therriault supervised by R Scheibling & B Hatcher - NSERC & HDI funding).

Ecology and Biodiversity of Commercially Unexploited Marine Fishes in the Northwest Atlantic (Dr. Jeff Hutchings)

Funding provided through the Contribution Agreement and an NSERC Research Grant has permitted the initiation of a new, long-term research programme on the life history and ecology of commercially unexploited fish species in the Northwest Atlantic. This work represents the first step towards achieving a comprehensive understanding of the basic biology, ecology, and life history of species about which exceedingly little is known. Such a research initiative is without precedent in Canada, despite the fact that the demand for the research, and its importance to society, has never been greater.

The ultimate goal of the research is to provide new knowledge to science of importance to the conservation and biology of marine fishes. Being one of the goals of the Centre of Marine Biodiversity, the project thus represents a tangible example of cooperation between many Department of Fisheries DFO and Oceans (DFO) members and Dalhousie University.

The primary objectives of the research are to: (a) obtain basic life history data on non-commercial fish; (b) to identify predator-prey relationships among species; (c) to identify the habitat favoured by these species; and (d) to use these data in a larger study to evaluate the resistance of these species to collapse and to assess their ability to recover therefrom. For most of the fish, the data on life history, diet, and ecology will be the first ever described for the species in question. As such, the data collected during the present research should provide data of importance in assisting the DFO achieve its objective of adopting an ecosystem-based approach to ocean management and conservation.

Please see the final report for the results.

Seagrass Decline in Northern Nova Scotia
Dr. David Garbary
Department of Biology, St. Francis Xavier University, Antigonish, N.S., B2G 2W5 (

Between October 2000 and October 2001 a decline of 95% of living biomass of roots and rhizomes of Zostera marina was noted in Antigonish Harbour. This eelgrass decline was correlated with a change in the distribution and abundance (50% decline) of migrating Canada Geese and Common Goldeneye (Seymour, Miller & Garbary. 2002. Helgol. Mar. Res., in press). Anecdotal evidence suggests that the eelgrass population has also collapsed in Pomquet Harbour. Potential explanations for the decline include: seagrass wasting disease, cultural eutrophication and impacts of green crab. Preliminary observations in Antigonish Harbour in May, 2002, show vastly reduced Zostera beds in Antigonish Harbour relative to historical levels, as well as a major difference (at least four fold) in biomass between a remaining bed in Antigonish Harbour and an apparently healthy bed at Caribou Harbour.

The objective of the current study is to examine abundance of Z. marina on a monthly basis from June to September in four estuaries: Pomquet, Antigonish, Merigomish and Caribou Harbours. These systems provide a gradient of abundance of Z. marina (low in Pomquet and Antigonish to high in Caribou), and a gradient of abundance of the invasive green crab, Carcinus maenus (abundant in Pomquet and Antigonish to low in Merigomish and Caribou). Caribou Harbour is the only site with the invasive seaweed, Codium fragile. This research will: 1) document the abundance of Z. marina at these sites, 2) identify differences in general community structure (including green crab abundance) among the sites, and 3) characterize the physical (e.g., sediment particle sizes) and chemical (e.g., nitrogen and phosphorus levels in the water) features of the sites.

By gathering these data, a much better picture of the status of Z. marina at these sites will be achieved. In addition, these data should allow the development of concrete hypotheses to explain the collapse of eelgrass in Antigonish and Pomquet and identify the major impacts of the collapse on biodiversity.

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