U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2012–3016

Februrary 2012

Prepared in cooperation with the University of Florida and Arkansas State University

Connectivity of Tropical Marine Ecosystems: An Overview 

of Interdisciplinary Research to Understand Biodiversity and 

Trophic Relationships in the Virgin Islands and Puerto Rico 

Printed on recycled paper

Tropical Marine Reserves and 

Protected Areas

The Virgin Islands and Puerto Rico 

contain marine reserves and protected 

areas that encompass a variety of 

tropical ecosystems, including coral 

reefs, mangroves, and seagrass beds 

(fig. 1). Reserves and protected areas 

are established for a variety of reasons, 

such as preserving nursery habitats and 

biodiversity, or reducing anthropogenic 

effects associated with pollution and 

land use. Questions remain regarding 

the effectiveness of these designated 

areas in preserving and protecting 

spatially connected habitats and 

associated fishes and invertebrates. 

Scientists from the U.S. Geological 

Survey (USGS), University of Florida, 

and Arkansas State University are 

collaborating on interdisciplinary 

research in the Virgin Islands and 

Puerto Rico to examine the biodiversity and trophic dynamics of fishes and 

invertebrates residing in connected 

mangroves, seagrasses, and coral reefs 

to discern the effectiveness of current 

marine reserves and protected areas for 

conserving reef resources.

Trophic Relationships

Energy transfer within and among 

tropical marine ecosystems involves 

communities associated with reefs, 

mangroves, and seagrass beds. Little 

is known about the influence of fish 

habitat utilization, prey preferences, 

and movement patterns, on the flow of 

energy occurring between trophic levels 

(that is, from a prey to its predator). 

Figure 1. Examples of A, coral reefs, B, mangroves, and C, seagrass beds sampled 

during this interdisciplinary research of tropical marine ecosystems. Photographs by 

Amanda Demopoulos, USGS.

A B

C

Collaborative research efforts are using 

telemetry and stable isotope analyses 

(SIA) to track fish movement patterns 

(for example, schoolmaster snapper, 

Lutjanus apodus) in and out of 

connected habitats, marine reserves 

and protected areas, and identifying 

invertebrates found within fish foraging 

habitats (fig. 2). Additionally, researchers are characterizing trophic relationships between fishes and their prey by 

examining fish stomach contents and 

conducting SIA of fishes and invertebrates. These efforts could identify 

critical habitats used by fishes (both 

within and outside the reserves and 

protected areas) and quantify these 

habitats as foraging sites. Findings 

from this research may assist government officials in designating appropriate 

areas for protection.
descriptions for the majority of invertebrate taxa and incomplete taxonomic 

keys make it difficult to assess invertebrate diversity and species composition. 

DNA barcoding is a molecular technique 

that can assist with species discoveries, identify unknown or poorly defined 

taxonomic groups and cryptic species, 

and improve the quality and quantity 

of data available for conservation 

efforts (Neigel and others, 2007). USGS 

is developing markers for a DNA barcoding technique to complement 

traditional morphology-based identification with the goal of improving identification and understanding of the diversity 

within habitats. DNA barcoding will 

also help to identify marine organisms 

in fish stomachs, thus providing data 

on prey consumed by reef fishes. This 

information, coupled with the invertebrate surveys described above, will 

enhance scientific understanding of the 

invertebrate resources available in fish 

foraging areas. 

Connectivity of Tropical 

Ecosystems

Many of the organisms examined 

for these studies are important prey 

to higher trophic levels. For example, 

French grunt (Haemulon flavolineatum) 

habitat requirements and movements 

likely influence other ecologically and 

economically important species, such 

as red hind (Epinephelus guttatus). 

The interdisciplinary research described 

here will enhance our understanding 

of the complex biological and ecological 

interactions among resident and 

transient reef organisms. This knowledge is a critical component for evaluating the effectiveness of marine reserves 

Figure 2. A, A USGS 

employee records marine 

organisms present in a 

0.5 m2 quadrat in a coral 

reef. B, Push cores sampled 

benthic invertebrates in 

seagrass beds. Both types 

of sampling occurred in all 

habitat types. Photographs 

by Amanda Demopoulos, 

USGS.

The Role of Parasitism

Parasitism is an important 

ecological interaction that affects 

community and trophic structure 

of coral reefs and connected habitats. 

However, the influence of parasites 

on food webs has been largely 

ignored (Lafferty and others, 2008). 

Parasites attached to the outside of 

reef fishes—known as ectoparasites

—can be transferred between habitats by their hosts (Grutter, 1998). 

Ectoparasites can be consumed by 

cleaner organisms, such as shrimp, 

or become dislodged and return to 

the benthos; both circumstances are 

potential mechanisms for transferring energy among habitats (fig. 3).

Through the use of SIA and 

parasite feeding experiments, this 

research will advance understanding 

of host-parasite and parasite consumer trophic relationships and their 

influence on coral reef food-web 

dynamics. Additionally, this research 

is addressing how human activities, 

such as pollution and land use that 

can cause increased sedimentation 

and eutrophication, may affect reef 

habitats and associated parasite-host 

interactions.

and protected areas and determining 

whether designated areas may need to 

incorporate additional habitat types. 

References Cited

Grutter, A., 1998, Habitat-related 

differences in the abundance of 

parasites from a coral reef fish: An 

indication of the movement patterns of 

Hemigymnus melapterus (Bloch, 1791) 

(Labridae), Journal of Fish Biology, 

v. 53, p. 49–57.

Lafferty, K.D., Allesina, S., Armi, M., 

Briggs, C.J., De Leo, G., Dobson, A.P., 

Dunne, J.A., Johnson, P.T.J., Kuris, 

A.M., Marcogliese, D.J., Martinez, 

N.D., Memmott, J., Marquet, P.A., 

McLaughlin, J.P., Mordecai, E.A., 

Pascual, M., Poulin, R., and Thieltges, 

D.W., 2008, Parasites in food webs: 

The ultimate missing links: Ecology 

Letters, v. 11, p. 533–546.

Neigel, J., Domingo, A., and Stake, J., 

2007, DNA barcoding as a tool for coral 

reef conservation: Coral Reefs, v. 26, 

p. 487–499.

By Jennifer McClain-Counts and 

Amanda Demopoulos

For additional information, contact:

Amanda Demopoulos 

USGS Southeast Ecological Science Center

7920 NW 71st Street

Gainesville, Florida 32653

352-264-3490 

ademopoulos@usgs.gov

http://pubs.usgs.gov/fs/2012/3016

Publishing support provided by the USGS Science 

Publishing Network, Raleigh Publishing Service 

Center

Figure 3. An ectoparasite (Anilocra 

sp.) on a blackbar soldierfish (Myripristis 

jacobus). Photograph by Philip Hodgens.

Biodiversity and Species 

Identification

Conservation efforts in the Virgin 

Islands and Puerto Rico are dependent 

on good documentation of species 

present within the mangroves, seagrass 

beds, and coral reefs. Benthic invertebrates are an integral part of these 

habitats, but the scarcity of species 

A B