Scientific Papers and Reports

This is an annotated list of the published papers and reports that have included REEF data. The list is in chronological order. Papers that are available for viewing in .pdf format are noted.

Also see the Projects page for links to additional reports.

Thorson, JT, MD Scheuerell, BX Semmens, and CV Pattengill-Semmens. 2014. Demographic Modeling of Citizen Science Data Informs Habitat Preferences and Population Dynamics of Recovering Fishes.


Managing natural populations and communities requires detailed information regarding demographic processes (or status of a population) at large spatial and temporal scales. This combination is challenging for both traditional scientific surveys, which often operate at localized scales, and citizen science designs, which often provide data with few auxiliary information (i.e. no information about individual age or condition). The authors of this study combine citizen science data collected at large scales (REEF Volunteer Fish Survey Project data) with recently developed statistical demographic modeling techniques. The model analysis included two managed reef fishes in the Gulf of Mexico to estimate demographic trends, habitat associations, and interannual variability in recruitment of Goliath Grouper and Mutton Snapper. The results identify strong preferences for artificial structure for the recovering Goliath Grouper, while revealing little evidence of either habitat associations or trends in abundance for Mutton Snapper. Results are also contrasted with a typical modeling approach to demonstrate the importance of accounting for the statistical complexities implied by spatially structured citizen science data. Results also highlight the utility and management benefits of combining demographic models and citizen science data.

Akins, JL, JA Morris Jr, and SJ Green. 2014. In Situ Tagging Technique for Fishes Provides Insight Into Growth and Movement of Invasive Lionfish.

Ecology and Evolution. 10.1002/ece3.1171

Information on fish movement and growth is primarily obtained through the marking and tracking of individuals with external tags, which are usually affixed to anesthetized individuals at the surface. However, the quantity and quality of data obtained by this method is often limited by small sample sizes owing to the time associated with the tagging process, high rates of tagging-related mortality, and displacement of tagged individuals from the initial capture location. To address these issues, we describe a technique for applying external streamer and dart tags in situ, which uses SCUBA divers to capture and tag individual fish on the sea floor without the use of anesthetic. We demonstrate this method for Indo-Pacific lionfish (Pterois volitans/P. miles), species which are particularly vulnerable to barotrauma when transported to and handled at the surface. To test our method, we tagged 161 individuals inhabiting 26 coral reef locations in the Bahamas over a period of 3 years. Our method resulted in no instances of barotrauma, reduced handling and recovery time, and minimal post-tagging release displacement compared with conventional ex situ tag application. Opportunistic resighting and recapture of tagged individuals reveals that lionfish exhibit highly variable site fidelity, movement patterns, and growth rates on invaded coral reef habitats. In total, 24% of lionfish were resighted between 29 and 188 days after tagging. Of these, 90% were located at the site of capture, while the remaining individuals were resighted between 200 m and 1.1 km from initial site of capture over 29 days later. In situ growth rates ranged between 0.1 and 0.6 mm/day. While individuals tagged with streamer tags posted slower growth rates with increasing size, as expected, there was no relationship between growth rate and fish size for individuals marked with dart tags, potentially because of large effects of tag presence on the activities of small bodied lionfish (i.e., <150 mm), where the tag was up to 7.6% of the lionfish's mass. Our study offers a novel in situ tagging technique that can be used to provide critical information on fish site fidelity, movement patterns, and growth in cases where ex situ tagging is not feasible.

Côté, IM, SJ Green, JA Morris Jr, JL Akins, D Steinke. 2013. Diet richness of invasive Indo-Pacific lionfish revealed by DNA barcoding.

Marine Ecology Progress Series. 72: 249–256

Invasive lionfish in the western Atlantic are known to be voracious predators. Their unusual hunting behavior suggests that they could prey on most fish species within their gape size limits. Significant research by REEF researchers and others has been conducted looking at stomach contents of lionfish to identify prey. However, relatively few prey species have been identified because of the challenge of identifying partly digested prey. It is also difficult to know how well the identifiable diet reflects the unidentified portion. The authors of this study addressed this issue by DNA-barcoding unidentifiable fish items from the stomachs of 130 lionfish. They identified 37 prey species, half of which had previously not been recorded. The visually identifiable species only accounted for 25% of the total prey items, making it clear that extrapolating total prey from the identifiable portion is not accurate. The barcoding technique used can increase the ability to predict the impacts of invasive predators on recipient communities.

Holt, BG, R Rioja-Nieto, MA MacNeil, J Lupton, and C Rahbek. 2013. Comparing Diversity Data Collected Using a Protocol Designed for Volunteers with Results from a Professional Alternative.

Methods in Ecology and Evolution. doi: 10.1111/2041-210X.12031

Research conducted by Dr. Ben Holt from University of East Angila in the UK shows that methods to record marine diversity used by REEF surveyors returned results consistent with techniques favoured by peer-reviewed science. The findings give weight to the growing phenomenon of citizen science programs such as REEF's Volunteer Survey Project. The field study compared methods used by REEF volunteer SCUBA divers with those used by professional scientists to measure the variety of fish species in three Caribbean sites in the Turks and Caicos. The divers surveyed the sites using two methods – the 'belt transect', used in peer reviewed fish diversity studies, and the 'roving diver technique', used by REEF volunteers. Two teams of 12 divers made 144 separate underwater surveys across the sites over four weeks. While the traditional scientific survey revealed sightings of 106 different types of fish, the volunteer technique detected greater marine diversity with a total of 137 in the same waters. Dr Holt led the research in partnership with the Centre for Marine Resource Studies in the Caribbean and the University of Copenhagen, Denmark. He said: "The results of this study are important for the future of citizen science and the use of data collected by these programs. Allowing volunteers to use flexible and less standardised methods has important consequences for the long term success of citizen science programs. Amateur enthusiasts typically do not have the resources or training to use professional methodology. Our study demonstrates the quality of data collected using a volunteer method can match, and in some respects exceed, protocols used by professional scientists."

Wolfe, JR and CV Pattengill-Semmens. 2013. Estimating Fish Populations From REEF Citizen Science Volunteer Diver Order-of-Magnitude Surveys.

CalCOFI Reports. 54 (2013)

This paper describes several models to convert order-of-magnitude count data that are collected during REEF Roving Diver Technique (RDT) surveys to a numeric mean, and demonstrate that with a sufficient number of surveys, estimates of the mean with a reasonably small confidence interval can be attained. For each model, parameter estimates and associated confidence intervals were derived from 292 RDT surveys where precise counts were also made. Models were compared using the small sample Akaike Information Criteria (AICc). The best-fitting model uses disaggregated bin-count data and considers the relative proportion of counts in adjacent bins. A companion paper was published in the same CalCOFI issue that uses the model to evaluate population trends in rocky reef fish species along the Monterey Peninsula region in central California.

Wolfe, JR and CV Pattengill-Semmens. 2013. Fish Population Fluctuation Estimates Based on Fifteen Years of REEF Volunteer Diver Data For the Monterey Peninsula, California.

CalCOFI Reports. 54 (2013): 127-140

A database of fish surveys conducted by volunteer recreational divers trained by REEF was used to examine fish populations in Monterey Peninsula, California, between 1997 and 2011. Over 3,000 surveys were conducted as part of this ongoing citizen science effort. The analysis was conducted using a numerical conversion method to calculate population estimates from REEF log-scale data (this method was described in a companion paper published in the same CalCOFI Reports issue). Variations in relative density over time are reported for 18 fish species, including several fisheries-targeted species. Two recruitment pulses of young-of-the-year rockfish (Sebastes spp.) were observed over the study period, with subsequent increases in older rockfish. Several predator species increased and subsequently declined, peaking two years after prey populations. Strong concordance was found between REEF data and those collected by Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO), a consortium of academic institutions. Results show that data collected by REEF has great potential to augment and strengthen professional research data and serve as a valuable baseline to evaluate marine reserves.

Ward-Paige CA, B Davis, and B Worm. 2013. Global Population Trends and Human Use Patterns of Manta and Mobula Rays.

PLoS ONE. 8(9): e74835. doi:10.1371/journal.pone.0074835

Despite being the world’s largest rays and providing significant revenue through dive tourism, little is known about the population status, exploitation, and trade volume of the Mobulidae (mobulids; Manta and Mobula spp.). There is anecdotal evidence, however, that mobulid populations are declining, largely due to the recent emergence of a widespread trade for their gill rakers. Researchers from Dalhousie University and used expert divers’ observations from two citizen science programs, REEF's Volunteer Fish Survey Project and, to describe global manta and devil ray abundance trends and human use patterns. The study highlights the relative rarity of aggregation sites on a global scale and reveals that many populations appear to be declining. The authors warn that newly emerging fisheries for the rays gill-­‐rakers likely exceed their ability to recover. The study also demonstrates the deficiency of official catch reports, as only four countries have ever reported landing manta or devil rays– Indonesia, Liberia, Spain and Ecuador. However, numerous diver reports compiled in the paper illustrate that many other countries are regularly landing and selling these rays without reporting.

Auster PJ, L Kracker, V Price, E Heupel, G McFall, and D Grenda. 2013. Behavior Webs of Piscivores at Subtropical Live-Bottom Reefs.

Bulletin of Marine Science. 89(1):377–396

The authors describe the behavioral interactions of piscivorous mid-water and demersal fishes at subtropical live-bottom reefs off the coast of Georgia and off the west coast of Florida in the northeast Gulf of Mexico. The observations are used to construct a topological behavior web of the interactions of mid-water and demersal piscivores, their prey, and those associated species that modify predator-prey interactions. Results show that inter-specific behavioral interactions are common attributes of piscivores in these reef fish communities. The authors propose a framework for assessing the demographic consequences of such interactions. Data for this study were collected using a modified Roving Diver Technique, the method employed by REEF surveyors. One of the co-authors, Dave Grenda, is a member of REEF's Advanced Assessment Team.

Francisco-Ramos V, Arias-González JE . 2013. Additive Partitioning of Coral Reef Fish Diversity Across Hierarchical Spatial Scales Throughout the Caribbean.

PLoS ONE. 8(10): e78761. doi:10.1371/journal.pone.0078761

There is an increasing need to examine regional patterns of diversity in coral-reef systems because their biodiversity is declining globally. The authors used REEF data from 80 sites from 6 eco-regions throughout the Caribbean to evaluate patterns of biodiversity. Specifically, they used "additive partitioning", which quantifies the contribution of different types of diversity (alpha and beta; comparing diversity between sites within a region and between regions) to total diversity across different spatial scales. The primary objective was to identify patterns of reef-fish diversity across multiple spatial scales under different scenarios, examining factors such as fisheries and demographic connectivity. Total diversity at the Caribbean scale was attributed to β-diversity (nearly 62% of the species), with the highest β-diversity at the site scale. α⎯⎯-diversity was higher than expected by chance in all scenarios and at all studied scales.

This suggests that fish assemblages are more homogenous than expected, particularly at the ecoregion scale. Within each ecoregion, diversity was mainly attributed to alpha, except for the Southern ecoregion where there was a greater difference in species among sites. β-components were lower than expected in all ecoregions, indicating that fishes within each ecoregion are a subsample of the same species pool. The scenario involving the effects of fisheries showed a shift in dominance for β-diversity from regions to subregions, with no major changes to the diversity patterns. In contrast, demographic connectivity partially explained the diversity pattern. β-components were low within connectivity regions and higher than expected by chance when comparing between them. The author's results highlight the importance of ecoregions as a spatial scale to conserve local and regional coral reef-fish diversity.

Haggarty, D. 2013. Rockfish Conservation Areas in BC: Our current state of knowledge.

Report by the David Suzuki Foundation. 84 pp

In response to conservation concerns for inshore rockfish, Fisheries and Oceans Canada implemented a system of 164 rockfish conservation areas (RCAs) in British Columbia as part of the Rockfish Conservation Strategy. RCAs were established between 2004 and 2007. RCAs are not marine protected areas (MPAs) because they were not designated though any MPA legislative tool such as Canada’s Ocean Act, but rather through a fishery closure using the Fisheries Act. They can, however, be considered harvest refugia. Evaluations of the performance of RCAs have recently been undertaken by government agencies, academics, non- governmental organizations (NGOs) and First Nations. This report describes the most recent scientific research on RCAs. Research has been done using remotely operated vehicles (ROVs), scuba surveys, hook-and-line fishing surveys, genetic analysis and compliance monitoring. Although some empirical research shows some RCAs are demonstrating an effect, most have not shown statistical differences in rockfish density among RCAs and non-RCA sites. One reason for this might be that RCAs are still considered to be “new” or “young” and it is thought that rockfish will take numerous years to respond to protection. REEF survey data for inshore rockfish and greenling species from Whytecliff Park between 1998 and 2013 were included in this report. Whytecliff Park is in West Vancouver, and was made the West Vancouver RCA in 2006.

Design by Joanne Kidd, development by Ben Weintraub