Molecular phylogenetics reveals first record and invasion of Saccostrea species in the Caribbean

Our ability to track invasive species is complicated by the fact that many organisms superficially resemble each other, even though they may in fact be quite different from one another. This is particularly true of oysters, whose physical similarities are particularly problematic for identification. By using advanced genetic techniques, we can not only identify these ‘cryptic’ species, but can also draw conclusions regarding their distribution across the landscape, their role as invaders, and their interactions with the surrounding environment. In this study, 10 oyster species were identified on the Pacific and Caribbean coasts of Panama using unique genetic markers.  Among them was the Eastern Oyster, which was found in the Panamanian Caribbean for the first time. In addition, a Rock Oyster native to the Pacific was also found to be widespread on the Caribbean side of the Panama canal, though it does not appear to be interbreeding with any other oyster species in the region. It is likely that Rock Oysters were introduced to the Caribbean by recreational or commercial fishing vessels, though it’s difficult to say when exactly this first occurred.

Katrina M. Pagenkopp Lohan, Kristina M. Hill-Spanik, Mark E. Torchin, Ellen E. Strong, Robert C. Fleischer, Gregory M. Ruiz (2015) Molecular phylogenetics reveals first record and invasion of Saccostrea species in the Caribbean,Marine Biology DOI 10.1007/s00227-015-2637-5

March 2015 | download pdf

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

Leray M and Knowlton N (2015) DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity, Proc Natl Acad Sci USA

February 2015 | download pdf


Smithsonian Ocean Portal


TMON MarineGEO Research Plan

April 2014 | download pdf

Smithsonian Marine Research Scientists

The Smithsonian has more than 70 marine scientists conducting research around the world.  

View a directory of marine scientists.

News & Media

DNA Barcoding Reveals Enormous Biodiversity in Oyster Reefs

MarineGEO scientists Matthieu Leray and Nancy Knowlton use standardized sampling with DNA barcoding and metabarcoding to uncover patterns of oyster reef biodiversity in MarineGEO's first-ever scientific publication. The paper was featured in a story by The Washington Post.
February 2015 | download pdf 

Sustaining Coastal Resilience

The ambitious new Tennenbaum Marine Observatories Network focuses on biodiversity as the key to maintaining resilient coastal ecosystems worldwide.
September 2014 | download pdf

Taking the Ocean’s Pulse

Marine biologists Drs. Emmett Duffy and Nancy Knowlton discuss their efforts to help quantify global marine biodiversity.
June 2014 | download pdf

Emmett Duffy Named Director of Smithsonian’s Tennenbaum Marine

Observatories Network
June 2013 | press release 

Smithsonian Launches Global Marine Biodiversity Project with $10 Million

October 2012 | press release

Postdoctoral Fellowships


The Tennenbaum Marine Observatories Network is the first global network of marine observatories focused on long-term study of coastal biodiversity and ecosystems using standardized approaches. The network is a developing partnership of diverse organizations facilitating long-term interdisciplinary, comparative research.

TMON invites research proposals for a postdoctoral fellowship that will complement our developing comparative research program.

More Information

Post Doctoral Fellowship Awards 2014

Dr. Brian S. Cheng


Project Title:  Species invasions across latitude: a comparative approach to understanding biotic resistance and propagule pressure in driving biogeographic patterns of invasion

Advisors:  Greg Ruiz, Mark Torchin, Andrew Altieri

Invasive species have resulted in substantial ecological and economic damage in terrestrial and marine ecosystems. A global pattern of marine invasion is emerging, suggesting high densities of invaders at mid-latitudes with declines towards the tropics and polar regions. It has been proposed that high biotic resistance (ability of native communities to suppress invasion) may be driving this pattern in the tropics as a result of high species diversity. However, propagule pressure (number and rate of recruit arrival) is also known to be a major determinant of invader establishment and available evidence suggests that this also varies along a latitudinal gradient. Therefore, it is unclear if this global pattern of invasion is the result of biotic resistance, propagule pressure, or their interaction. I propose to experimentally alter propagule pressure and biotic resistance at field sites within the Tennenbaum Marine Observatory Network in order to clarify the roles of both of these ecological processes in shaping biogeographic patterns of invasion. I will use the comparative-experimental approach, establishing identical replicated experimental assemblages of focal invaders (solitary and compound tunicates) among three regions of the observatory network (SERC, SMSFP, STRI) that span 29° of latitude.

This proposed research incorporates classic ecological concepts (latitudinal gradient in species richness, biotic interactions hypothesis, supply-side ecology) with applied problems (invasions) to advance our understanding of the relationship between marine biodiversity and anthropogenic processes. Furthermore, this work is of management importance because invasive species can incur significant economic costs and are a threat to native biodiversity.

Post Doctoral Fellowship Awards 2014

Dr. Lisa M. Schile


Project Title:  Carbon sequestration and decomposition in coastal vegetated ecosystems: comparison of rates and methodologies across latitudinal gradients

Advisors:  Patrick Megonigal, Andrew Altieri

Recognition that vegetated coastal ecosystems such as mangroves, seagrasses and marshes sequester significant amounts of carbon has garnered strong global interest, yet many gaps in understanding carbon sequestration remain, particularly in variation across habitat types and latitudes. These ecosystems can exceed tropical and temperate forest carbon storage, and considerable anthropogenic and climate change related pressures could convert them to large carbon sources if they are degraded and destroyed. Furthermore, we know far less about how decomposition of plant material, a major biotic process that governs soil carbon, varies in space and time. The primary objective of this research is to measure carbon stocks and decomposition across herbaceous marshes, mangroves, and seagrasses and compare rates among intertidal and subtidal habitats in the Chesapeake Bay, San Francisco Bay, southern Florida, and Panama. Additionally, the sites selected will vary in proximity to anthropogenic disturbance. Two standardized methods for measuring both carbon stocks and decomposition rates will be employed to examine utility and effort and could aid in decision-making about implementing sampling protocols across the Tennenbaum Marine Observatories Network. Understanding differences in processes and rates governing carbon in coastal ecosystems is key to predicting how anthropogenic disturbance could impact carbon cycling.

Post Doctoral Fellowship Awards 2012

Dr. Katie L. Cramer


Project Title: Changes in Caribbean coral reef environments and fish communities over the last millennium

Advisors:  Torben Rick, Aaron O’Dea

Caribbean reef corals have declined precipitously since the 1980s from coral bleaching and disease outbreaks related to climate change, and algal overgrowth related to overfishing. Paleoecological data collected in Bocas del Toro, Panama for my dissertation work revealed that declines in coral and molluscan communities occurred at least decades before coral bleaching and disease, implicating pre-historical/historical land clearing and fishing. However, the extent of earlier degradation from these local anthropogenic stressors is unresolved due to a lack of a quantitative ecological baseline of reef environments and fish communities.

To resolve this issue, I will implement a retrospective monitoring program for Caribbean coral reefs, utilizing the fossil record to document ecological change over large temporal and geographic scales. A millennial-scale quantitative record of reef environments and fish communities in Bocas del Toro and southern Belize will be obtained from sediment cores collected from up to 5m below modern lagoonal reefs. This work will launch a new interdisciplinary collaboration among collaborators Dr. Torben Rick at NMNH, Aaron O’Dea at STRI, and Dr. Richard Norris at Scripps Institution of Oceanography. 

Trends in land-based sediments and pollution will be assessed from sediment elemental composition, grain size distribution, and percent carbonate/organic material, whereas trends in reef fish abundance, taxonomic composition, and trophic structure will be assessed from fish teeth. Results will be compared with historical trends in coral communities previously documented in my dissertation work and a coring study in Belize to assess the role of past land clearing and fishing in more recent reef decline. This study will provide a more complete understanding of the full extent of long-term anthropogenic and natural change in the structure and function of coral reefs and will directly address several fundamental questions posed by MarineGEO.

Post Doctoral Fellowship Awards 2012

Dr. Christopher J. Freeman


Project Title:  Establishing Baselines for Symbiotic Interactions in Marine Sponges Across Naturally Occurring and Anthropogenic Gradients

Advisors:  Valerie Paul, Rachel Collin, Co-Advisor: Nancy Knowlton

In the marine environment, symbiotic interactions are exemplified by the mutualisms between benthic invertebrates and microbial and algal symbionts that allow these organisms to survive and compete for space in nutrient-poor waters. Although these symbioses are crucial for the maintenance of functional diversity in productive and diverse reef systems, our understanding of these interactions and factors structuring them or leading to their disruption is largely restricted to reef-building corals. By forming an ancient symbiosis with diverse and productive microbial communities, marine sponges represent a significant portion of the biomass on reef, seagrass, and hardbottom habitats throughout the world. Moreover, their nutritional diversity and flexibility makes them crucial to biogeochemical cycles and productivity in these distinct systems. However, as disease outbreaks and bleaching events increasingly lead to mass mortality of sponges, it becomes clear that there is a substantial gap in our knowledge of how sponges interact with their environment and how these interactions vary across large geographic regions and local habitats.

This proposal aims to 1) provide an initial evaluation of how these interactions vary across naturally occurring and anthropogenic gradients and 2) conduct experiments to assess whether land-based anthropogenic inputs impact holobiont productivity and the efficiency of nutrient assimilation and transfer to the host.

Post Doctoral Fellowship Awards 2012

Dr. Matthieu Leray


Project Title:  The role of competition during succession across a latitudinal gradient

Advisors:  Nancy Knowlton, Rick Osman, Co-Advisor: Chris Meyer

Introduction. Numerous hypotheses have been proposed to explain the latitudinal gradients in species diversity on Earth. One of them suggests that these patterns are the result of an increased gradient in the strength of biotic interactions from the poles to the tropics. Yet there is still limited support for a gradient in the strength of competitive interactions at the community level. This is partly due to the difficulty of quantifying diffuse competitive interactions. Furthermore, the relative influence of intensity of competition and productivity on the rate of ecological succession across latitude is currently unknown despite significant implications for management and conservation strategies.

Objectives. Here, I propose to use a large-scale experimental approach to investigate latitudinal patterns in the role of competition at structuring local assemblages of marine invertebrates in these reef communities during the course of ecological succession.

Methods. I will employ Autonomous Reef Monitoring Structures (ARMS) as a standardized sampling method. ARMS will be deployed on oyster reefs in Maryland and Florida, and on coral reefs in Belize and Panama [total of 4 sites x 4 settlement durations (see below) x 6 replicates or 96 ARMS in total]. Sampling will be conducted after 3 months (November 2012), 6 months (February 2013), 12 months (September 2013), and 18 months (February 2014). I will use novel metrics of phylogenetic composition to determine the relative influence of competition at structuring assemblages across locations and through time.

Significance/relevance. The proposed work would address major goals of the Smithsonian Marine Science Network program by (1) investigating macroecological patterns that can be explored across all MSN sites, (2) developing standardized sampling approaches that could be used in future MarineGEO studies, (3) using novel community phylogenetic tools, and (4) complementing previous research conducted as part of the MSN network by Amy L. Freestone on local interactions and predation across the same spatial scale. Moreover, I will be able to provide the first experimental data on the dynamics of community recovery across a large spatial scale. This is particularly important as human-induced perturbations increase in intensity and frequency worldwide.

Post Doctoral Fellowship Awards 2012

Dr. Katrina M. Pagenkopp Lohan


Project Title: A metagenomics approach to assessing latitudinal gradients in bivalve
parasites and other planktonic microorganisms

Advisors:  Greg Ruiz, Rob Fleischer

​Though parasites can have important roles in host population dynamics and ecosystem function, we currently know little about the distribution of marine parasites and other microorganisms in the ocean. Given the current changes occurring in marine ecosystems such as warming ocean temperatures and the anthropogenic movement of organisms through shipping and trade, knowing the diversity and distribution of marine parasites as well as other pathogenic or toxic microorganisms is essential to continued monitoring of the spread or range shifts of these organisms.

I propose using next generation sequencing technology, specifically multi-tag amplicon pyrosequencing, to examine the diversity and distribution of microorganisms associated with oysters and in the surface waters of the temperate and tropical waters of the USA. My first objective is to compare the diversity of eukaryotic and prokaryotic microorganisms associated with oysters to those found in environmental water samples. By comparing these two sampling methods, I will be able to determine what types of sampling future projects should include. In addition, monitoring bivalve parasites is of particular importance given the many economic and ecological aspects of bivalves and their ability to filter and concentrate not only marine parasites, but also human pathogens and toxic microorganisms.

My second objective is to determine and compare the eukaryotic and prokaryotic microorganisms associated with oysters and environmental water samples from tropical waters to those collected in temperate waters. The data generated will provide the current prevalence and distribution of bivalve parasites associated with the oysters sampled, which can be used to assess the risks of unintentional introductions of bivalve parasites to other areas and to develop informed management strategies to minimize introduction risk.

Lastly, I will highlight the toxic and pathogenic organisms present in the tropical waters of the USA that may be capable of expanding their range northward under the appropriate conditions.