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.

Heery, EC, AY Olsen, BE Feist, and KP Sebens. 2018. Urbanization-related distribution patterns and habitat-use by the marine mesopredator, Giant Pacific Octopus (Enteroctopus dofleini).

Urban Ecosystems. https://doi.org/10.1007/s11252-018-0742-1

The authors, Eliza Heery and colleagues at the Seattle Aquarium, NOAA, and the University of Washington, used REEF sightings data on Giant Pacific Octopus (Enteroctopus dofleini) in Washington State to evaluate patterns of occurrence with urbanization. The species is the largest known octopus in the world, and they can reach over 20 feet in length from one tentacle tip to the other. The study objectives were to determine whether the distribution and habitat-use patterns of Giant Pacific Octopus were correlated with urbanization intensity on nearby shorelines in Puget Sound. REEF was instrumental in the study, providing data for a much larger spatial area and longer time period than would otherwise have been available. Heery et al. used REEF data in a series of statistical models and found that urban effects varied with depth. On deeper dives (> 24 m), REEF divers had a higher probability of encountering octopus in more urban locations.

Why might this be? The study's authors conducted additional field surveys to explore two potential explanations. To determine whether food resources played a role, Heery et al. collected middens – piles of shells leftover from past meals of octopus – from octopus dens throughout Puget Sound. Midden piles indicated there were no differences in the diets of urban octopus and rural octopus, suggesting that food resources were not the driver of urban-related distribution patterns. Secondly, they conducted a series of video surveys in sets of adjacent sites where there was a lot versus very little anthropogenic debris (junk). As many recreational divers might have predicted, they found more octopus in locations where there was a lot of junk.

How is this important for science? Past studies in urban ecology have suggested that mesopredators (mid-sized consumers) benefit from urbanization because of the food and shelter resources city environments provide, but those studies have focused exclusively on terrestrial mesopredators (like racoons and coyotes). This is the first study to examine whether marine mesopredators exhibit comparable patterns. It concludes that within certain habitats (deeper zones), octopus are indeed positively correlated with urbanization. Yet it is likely that shelter resources (from junk) rather than food are the driver.

Gruss, A, et al. 2018. Monitoring Programs of the U.S. Gulf of Mexico: Inventory, development and use of a large monitoring database to map fish and invertebrate spatial distributions.

Reviews in Fish Biology and Fisheries. 28 June 2018

This paper is an inventory of fish and invertebrate monitoring programs in the US Gulf of Mexico, including the REEF Volunteer Fish Survey Project, which has been active in the region since 1994. The authors conducted a gap analysis of the programs, and provided recommendations for improving current monitoring programs and designing new programs, and guidance for more comprehensive use and sharing of monitoring data. They also compiled a large monitoring database encompassing much of the monitoring data collected in the region using random sampling schemes and employed this database to fit statistical models to then map the spatial distributions of 61 fish and invertebrate functional groups, species and life stages. The study included 73 monitoring programs in the region. This study was funded by the National Oceanic and Atmospheric Administration (NOAA) RESTORE Act Science Program.

Gruss, A, DD Chagaris, EA Babcock, and JH Tarnecki. 2018. Assisting Ecosystem‐Based Fisheries Management Efforts Using a Comprehensive Survey Database, a Large Environmental Database, and Generalized Additive Models.

Marine and Coastal Fisheries. 10(1): 40-70

Statistical habitat models, such as generalized linear models (GLMs) and generalized additive models (GAMs), are key tools for assisting Ecosystem-based Fisheries Management (EBFM) efforts. These models can be used to map species distributions and assist in marine protected area (MPA) planning. In this study, the authors applied a statistical methodology to produce preference functions for fish and invertebrates along the West Florida Shelf, and then mapped the hotspots of juveniles and adults of three economically important species (Red Snapper, Gag, and Red Grouper) for informing future MPA planning. The analysis used a comprehensive survey database that included all encounter and nonencounter data of the study ecosystem collected by fisheries‐independent and fisheries‐dependent surveys. The REEF Volunteer Fish Survey Project dataset was one of 37 used in the analysis.

Tolimieri, N, EE Holmes, GD Williams, R Pacunski, and D Lowry. 2017. Population assessment using multivariate time-series analysis: A case study of rockfishes in Puget Sound.

Ecology and Evolution. 7: 2846–2860. https://doi.org/10.1002/ ece3.2901

Estimating a population’s growth rate and year-to-year variance is a key component of population viability analysis (PVA). However, standard PVA methods require time series of counts obtained using consistent survey methods over many years. The authors of this study used REEF data along with two other fisheries datasets to evaluate the long-term trends of rockfish in Puget Sound, Washington State. The time-series analysis was performed with a multivariate autoregressive state-space (MARSS) model. The authors show that using a MARSS modeling approach can provide a rigorous statistical framework for solving some of the challenges associated with using multiple, sometimes inconsistent datasets, and can reduce the proportion of fisheries assessment cases that are assigned a designation of “data deficient.”

The analysis of the paper was part of the 5-year review of the Endangered Species Act (ESA) listing of Puget Sound populations of three rockfish species (Bocaccio, Canary Rockfish, and Yelloweye Rockfish), and was conducted by scientists at the National Marine Fisheries Service and Washington Department of Fish and Wildlife. The three sources of data included in the study were: (1) recreational catch data, (2) scuba surveys conducted by REEF surveyors, and (3) a fishery-independent trawl survey. Because there were too few observations of the three species of rockfish in the data sources to analyze these species directly, the MARSS analysis estimated the abundance of all rockfish. Because Bocaccio, Canary, and Yelloweye are deep water species, they are not often seen by REEF surveyors. The other two data sets showed that these rockfishes declined as a proportion of recreational catch between the 1970s and 2010s. The REEF data suggest that other species like Copper and Quillback rockfish have experienced population growth in shallower depths.

Clauson-Kaas, S, K Richardson, C Rahbek, and BG Holt. 2017. Species-specific environmental preferences associated with a hump shaped diversity/temperature relationship across tropical marine fish assemblages.

Journal of Biogeography. 2017(00): 1–11

The study used REEF's Volunteer Fish Survey Project database to produce a new map of marine fish biodiversity across the Caribbean and tropical western Atlantic. The work, performed by scientists from the Center for Macroecology, Evolution & Climate in Denmark and the Marine Biological Association, studied REEF’s extensive data base collected by our volunteer surveyors to produce the map and find that fish biodiversity is strongly linked to sea temperatures. However, results also show that while fish biodiversity is higher in warmer waters, the very hottest sites in fact have fewer species than sites with intermediate temperatures, something not shown before in previous studies. These results will be of concern given the rising water temperatures in the region. For more details, see this REEF enews article.

Gruss, A., JT Thorson, EA Babcock, and JH Tarnecki. 2017. Producing distribution maps for informing ecosystem-based fisheries management using a comprehensive survey database and spatio-temporal models.

ICES Journal of Marine Science. doi:10.1093/icesjms/fsx120

In this paper, authors use data regarding where REEF divers did or did not encounter three species of fisheries importance: red snapper, red grouper, and gag grouper. They then combined these data with 36 other data sets, each sampling different areas of the Gulf of Mexico, and created distribution maps for use in ecosystem models of the Gulf of Mexico. These distribution maps picked up fish hotspots that are not identifiable by any individual data set, highlighting the complementary nature of the REEF data.

Starck, WA, Estapé CJ & Morgan Estapé, A. 2017. The Fishes of Alligator Reef and Environs in the Florida Keys: a half-century update.

Journal of the Ocean Science Foundation. 27

From 1958-67, Walter A. Starck II conducted marine biological studies in the area of Alligator Reef, off of Islamorada in the Florida Keys, these included extensive fish collecting. In 1968, he published A list of fishes of Alligator Reef.

Over the half-century since the original Alligator Reef survey, there have been great advances in the taxonomy of Greater Caribbean reef fishes, with numerous changes in scientific names and classification. As part of the update these changes are addressed so as to bring the list to current status.

In 2013 the junior authors (REEF Advanced Assessment Team members) undertook a four-year census of the fishes of the area with a goal to photo-document as many of their sightings as possible. This effort has subsequently entailed 1039 combined dives devoted to fish counts, photographic documentation, or both. During these surveys, they have photographed 278 of the species reported by Starck (1968) plus 35 additional and/or newly described or reclassified species not recorded in the earlier study.

An update of the checklist of fishes of Alligator Reef and environs some fifty years later provides an unparalleled opportunity to evaluate the species richness for a limited reef area, as well as a unique opportunity to explore changes in diversity over a half-century time scale. In the updated study the authors added 107 species and subtracted 5 from the original total of 516 species: thus the checklist now totals 618 species, of 122 families, the most recorded for any similarly sized area in the New World. The additional species records are made up from a number of subsequent collections as well as from a comprehensive effort by the junior authors.

Among the other databases of relevance to the study area used for comparison, the Smithsonian Tropical Research Institute (STRI) Shorefishes of the Greater Caribbean by D.R. Robertson & J. Van Tassell and that of the Reef Environmental Education Foundation (REEF).

REEF maintains an online database of worldwide visual fish-count surveys conducted by volunteer researchers and fish-count enthusiasts. While such surveys are biased towards easily observed species, they are indicative for a large portion of the reef fish fauna and comprise a valuable source of comparative information (Schmitt & Sullivan 1996, Pattengill-Semmens & Semmens 2003, Holt et al. 2013). The local REEF data includes that of the Estapés, who have conducted 185 roving-diver REEF surveys on Alligator Reef. An additional 1807 surveys at 94 sites in the study area have also been conducted by other REEF volunteers (as of July, 3, 2016).

Egerton, JP, AF Johnson, L Le Vay, CM McCoy, BX Semmens, SA Heppell, and JR Turner. 2017. Hydroacoustics for the discovery and quantification of Nassau grouper (Epinephelus striatus) spawning aggregations.

Coral Reefs. 36 (2): 589-600

The Grouper Moon Project is always looking for new and/or better ways of accurately estimating the number of spawning Nassau Grouper at the aggregation sites being monitored. In 2014, we tested the use of a split-beam echosounder as a tool for surveying the abundance and size of fish at the aggregation site; the results of the study are detailed in this peer-reviewed paper. We found that the echosounder performs fairly well at providing an index of abundance, although the absolute accuracy of the method was not sufficient to replace other survey methods (e.g. mark and recapture monitoring). After calibrating the method with diver-based fish length surveys, the tool was able to accurately capture estimates of aggregating fish sizes. Surveys on all 3 islands (Little Cayman, Cayman Brac, and Grand Cayman) showed that the average size of Nassau Grouper on Little Cayman was significantly larger than on both Brac and Grand. On the other hand, the sizes of Nassau Grouper on Brac and Grand were not significantly different. Based on this study, the echosounder is a potentially useful tool for surveying aggregations, but is likely best use to complement more intensive diver-based survey methods. 

Roberts M, N Hanley, S Williams, and W Cresswell. 2017. Terrestrial degradation impacts on coral reef health: Evidence from the Caribbean.

Ocean & Coastal Management. 149 (5): 52-68

REEF fish survey data collected from Bonaire in 2015 were used to help evaluate the impact of terrestrial degradation on nearby coral reefs, specifically investigating the link between vegetation ground cover and tree biomass index to coral cover, fish communities and visibility. The authors found a positive relationship between ground cover and coral cover below 10 m depth, and a negative relationship between tree biomass index and coral cover below 10 m. Greater ground cover is associated to sediment anchored through root systems, and higher surface complexity, slowing water flow, which would otherwise transport sediment. The negative relationship between tree biomass index and coral cover is unexpected, and may be a result of the deep roots associated with dry-forest trees, due to limited availability of water, which therefore do not anchor surface sediment, or contribute to surface complexity. The analysis provides evidence that coral reef managers could improve reef health through engaging in terrestrial ecosystem protection, for example by taking steps to reduce grazing pressures, or in restoring degraded forest ecosystems.

Green, SJ, E Underwood, and JL Akins. 2017. Mobilizing volunteers to sustain local suppression of a global marine invasion.

Conservation Letters. DOI: 10.1111/conl.12426

Lionfish derbies and tournaments were first implemented in 2009 with the intent of increasing public awareness about the lionfish invasion in the western Atlantic, gathering specimens for research, and training volunteers to safely and effectively collect the venomous species. Since then, REEF has coordinated a series of derbies each year and assisted other organizations and groups in organizing and running their own derbies, resulting in the removal of tens of thousands of invasive lionfish.

The increasing number of derbies held across the region presents an excellent opportunity to investigate the extent to which volunteer removal activities during such derbies can be an effective means of population suppression. Using REEF lionfish derbies as a test case, REEF staff, affiliated scientists, and volunteers worked together to address six key questions: 1) What is the total area over which removal can be affected during a derby event? 2) Is capture during derbies size-selective? 3) To what extent are local invader populations suppressed by derby activities? 4) At what rate do lionfish re-colonize following derby events? 5) Is removal sufficient to reduce and sustain densities below those predicted to cause predation-mediated declines in native species? and 6) Is the magnitude of invader removal related to catch per unit effort (CPUE)? To answer these questions, the authors collected data on landings and participant effort over three years of lionfish derbies in both Key Largo, Florida and Green Turtle Cay, Bahamas.

The study documented that from 2012-2014, single day derbies reduced lionfish densities by 52% across an area of 192 km2 on average each year. Differences in recolonization and productivity between regions meant that annual events were sufficient to suppress the invasion below levels predicted to cause declines in native species in one region, but not the other. Population reduction was not related to CPUE, confirming the importance of in situ monitoring to gauge control effectiveness. Future work to assess rates of recolonization in relation to derby frequency will help guide management and control decisions.

Design by Joanne Kidd, development by Ben Weintraub