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.

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

Ecology and Evolution. 7: 2846–2860. 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.

Gru ̈ss, 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.

Johnston, M.W and J. L. Akins. 2016. The non-native royal damsel (Neopomacentrus cyanomos) in the southern Gulf of Mexico: An invasion risk?.

Marine Biology. 163: 12

A diminutive, non-native damselfish (Neopomacentrus cyanomos) was recently discovered inhabiting coral reefs near Veracruz, Mexico—far removed from where it is native in the Red Sea and the Indo-Pacific. This publication, co-authored by REEF's Director of Special Projects, Lad Akins, evaluates the threat of establishment and spread in the invaded range.

The quantities found in the Gulf of Mexico (GOM) suggest that the fish has already established a self-sustaining population in this new ecosystem. There is understandable concern, therefore, that this new arrival may become invasive and spread, yet the invasion risk imposed by this fish has not been assessed. In this study, a computer model was employed to deliver a forecast of the potential range of incursion of the damselfish in the GOM spanning 5 years. The model incorporated oceanic water flow in the region, tolerances of this damselfish to the ocean environment, and their reproductive strategy in order to supply a temporal and spatial forecast of their spread. From this study, targeted early detection and removal of the fish can be directed if the fish is deemed a threat to native fauna. On the basis of this work, it is foreseeable that the reefs presently harboring Regal Damselfish will likely see increased abundance of this damsel. Immediate attempts to eliminate the fish, therefore, should be focused in nearshore shallow waters spanning Veracruz to Frontera, Mexico. Further, water flows in the southern GOM are not widely conducive to long-distance transport of marine organisms with pelagic larvae, reducing the risk of this damsel permeating the greater GOM over 5 years. Aside from Regal Damselfish, this study implicitly adds to mounting evidence supporting a biogeographic disconnect between the Veracruz reef complex and the greater GOM and the Caribbean.

REEF surveyors are on the lookout for Regal Damselfish in the Gulf of Mexico and western Caribbean.

Bernard, AM, KA Feldheim, R Nemeth, E Kadison, J Blondeau, BX Semmens, MS Shivji. 2016. The ups and downs of coral reef fishes: the genetic characteristics of a formerly severely overfished but currently recovering Nassau grouper fish spawning aggregation.

Coral Reefs. 35:273–284

Like many places throughout the Caribbean, Nassau Grouper spawning aggregations in the US Virgin Islands were overfished until their disappearance in the 1970s and 1980s. In the early 2000s, however, Nassau Grouper were found gathering at Grammanik Bank, USVI, a mesophotic coral reef adjacent to one of the extinct aggregation sites, and regulatory protective measures were implemented to protect this fledgling aggregation. The authors of this study addressed two objectives: 1) which factors (local vs. external recruitment) are important in shaping recovery of the USVI spawning aggregations, and 2) the impact of severe past overfishing on the genetic structure of the Gremmanik Bank aggregation. For this second objective, REEF Grouper Moon Project scientists provided genetic samples from individual Nassau Grouper taken from the Little Cayman spawning aggregation, a much larger and less impacted aggregation.

No population structure was detected between the USVI and Cayman spawning aggregations. Additionally, the USVI spawning population showed signs of a genetic bottleneck, typical of greatly reduced populations. These collective results suggest that external recruitment is an important driver of the USVI spawning aggregation recovery. These findings also provide a baseline for future genetic monitoring of the spawning aggregations.

Schultz​, JA, RN Cloutier, IM Côté. 2016. Evidence for a trophic cascade on rocky reefs following sea star mass mortality in British Columbia.

PeerJ. 4:e1980

The US Pacific Northwest and western Canada experienced a mass mortality of sea stars between 2013 and 2015. The sunflower star (Pycnopodia helianthoides), a previously abundant predator, began to show signs of a wasting syndrome in early September 2013, and dense aggregations disappeared from many sites in a matter of weeks. REEF surveyors certainly noticed, and the decline was reflected in the REEF database. The authors used the REEF database to document the decline regionally, along with a four-fold increase in the number of green sea urchins (Strongylocentrotus droebachiensis). The sea urchin increase also resulted in declines in kelp canopy coverage. This type of ecological change or trophic cascade, is where a change in one species impacts many others. Because of the long-term and wide-spread nature of the REEF survey program, our data have proven invaluable in documenting the impacts of the seastar wasting disease.

Luis Malpica-Cruza, L, LCT Chavesa, IM Côté. 2016. Managing marine invasive species through public participation: Lionfish derbies as a case study.

Marine Policy. 74 (December 2016): 158–164

The authors of this study examined drivers of public involvement and success at invasive removal in tournaments (derbies) to catch Indo-Pacific lionfish (Pterois volitans/miles) in the Western Atlantic. Information on 69 lionfish derbies held in the wider Caribbean region from 2010 to 2015 was compiled, including REEF Lionfish Derbies. The authors found that the number of lionfish caught increased with effort and with time since lionfish were established in an area. They also found that derby participation was best predicted by national wealth (GDP per capita) and number of local dive shops. These findings support that, from the point of view of public engagement, derbies should be held in areas where lionfish are well established, and where the pool of potential participants is large. However, alternative strategies may be more effective in areas where few lionfish are present.

Montecino-Latorre, D, ME Eisenlord, M Turner, R Yoshioka, CD Harvell, CV Pattengill-Semmens, JD Nichols, and JK Gaydos. 2016. Devastating Transboundary Impacts of Sea Star Wasting Disease on Subtidal Asteroids.

PLoS ONE. 11(10): e0163190. doi:10.1371/journal.pone.0163190

Sea star wasting disease has devastated sea star populations on the West coast from Mexico to Alaska. The disease broke out in 2013, causing massive death of several species of sea stars. Infected animals develop lesions that eat away tissue, with limbs dropping off as the animals die. The disease has been linked to a virus, although environmental factors may also be involved. This study presents an analysis of REEF survey data on several asteroid species collected by divers in the Salish Sea over the last 15 years.

The results showed that some species were hit hard, while others increased in number. Populations of sunflower sea star (Pycnopodia helianthoides), an important keystone predator in the region, dropped dramatically after the beginning of the epidemic. Several other sea star species, including the spiny pink star (Pisaster brevispinus) also declined. Numbers of the less-common leather star (Dermasterias imbricate) and two species of sea urchin, which are prey for sea stars, increased after 2013.

The virus outbreak continues, and will have lasting effects on the ecosystem. Sunflower sea stars have effectively disappeared from the Salish Sea, the study concludes. Likely as a result, numbers of urchins have increased, which in turn will lead to more browsing on kelp. As a result, study co-author, Dr. Joe Gaydos, and his colleagues are currently in discussions with the National Marine Fisheries Service to get the sunflower sea star listed as a “species of concern.”

Hixon, MA, SJ Green, MA Albins, JL Akins, and JA Morris Jr.. 2016. Lionfish: a major marine invasion.

Marine Ecology Progress Series. Vol. 558: 161–165, doi: 10.3354/meps11909

This paper is the introduction to a special issue of the journal, Marine Ecology Progress Series, titled "Invasion of Atlantic coastal ecosystems by Pacific lionfish". The issue is a compilation of papers presented at the 2015 special session of the Gulf and Caribbean Fisheries Institute meeting, which was co-organized by REEF and partner organizations. New findings include mechanisms that enhance the success of the invader, the extremely broad and variable diet of invasive lionfish, the ecological effects of the invader on native fish populations in various environmental contexts, and non-consumptive interactions between invasive lionfish and native predators. The entire issue is available online at

Serafy JE, GS Shideler, RJ Araújo, and I Nagelkerken. 2015. Mangroves Enhance Reef Fish Abundance at the Caribbean Regional Scale.

PLoS ONE. 10(11): e0142022

Several studies conducted at the scale of islands, or small sections of continental coastlines, have suggested that mangrove habitats serve to enhance fish abundances on coral reefs, mainly by providing nursery grounds for several species known to have different habitats as juveniles and adults. However, evidence of such enhancement at a regional scale has not been reported, and recently, some researchers have questioned the mangrove-reef subsidy effect. Authors of this paper used the REEF database to evaluate mangrove-reef connectivity at the Caribbean regional scale. They specifically asked: (1) Are reef fish abundances limited by mangrove forest area?; and (2) Are mean reef fish abundances proportional to mangrove forest area after taking human population density and latitude into account? They tested for Caribbean-wide mangrove forest area effects on the abundances of 12 reef fishes that have been previously characterized as “mangrove-dependent”. Results showed that average reef fish densities of at least six of the 12 focal fishes were directly proportional to mangrove forest area. This is the first scientific study to show that at a large regional scale (i.e., the Wider Caribbean), greater mangrove forest size generally functions to increase the densities on neighboring reefs of those fishes that use these shallow, vegetated habitats as nurseries.

This study is a great example of the power and impact that long-term, wide-spread citizen science programs such as the REEF Volunteer Fish Survey Project can have on addressing important ecological and management questions that would otherwise be near impossible to evaluate.

Design by Joanne Kidd, development by Ben Weintraub