Staff scientists

Matthieu Leray

Language English

Biodiversity Microbial Ecology Evolutionary Biology

The astonishing diversity of animals, algae and plants that live in the world’s oceans today would either not exist, or would exist in a very different form, if organisms had not interacted with microbial partners for millions of years. If we truly want to understand how biological diversity originated, how species coexist and how organisms cope with global changes, we must study the functional role of microbial partners and how microbes co-evolve with hosts.

Visit our lab

In our lab, we conduct basic and applied research on (1) the mechanisms of coral reef resilience with the ultimate goal of finding ways to boost coral reef resilience; (2) the ecology of evolution of host-microbe interactions by leveraging the many sister species of fish, crustacean and mollusks that emerged after the closure of the Isthmus of Panama; (3) the population dynamics of endangered sharks and rays in the Tropical Eastern Pacific using non-invasive environmental genomics.

How do microbes support marine animal host acclimatization and adaptation to environmental changes?

The dynamic nature of microbes may provide a unique source of ecological and evolutionary novelty to support host responses to local (deoxygenation, pollution) and global environmental stressors (warming, acidification). The composition of microbiomes can shift rapidly through the loss, gain, or replacement of taxa. In addition, high rates of mutation and exchange of genetic material generate new genetic variants that may be better suited to novel conditions. We study how microbes influence host traits and how they are influenced by host traits over ecological and evolutionary time scales. We address these questions in a range of taxonomic groups, including corals, fish, crustaceans and mollusks.

How does ecological niche versatility contribute to the persistence of populations, species and communities on coral reefs of the Anthropocene?

The classical explanation for how many species can co-exist in species rich communities, such as coral reefs, is fine-scale niche partitioning of resources. High levels of morphological, behavioral and/or physiological specializations provide a refuge for species during periods of intense competition such as when ecosystems are in healthy states. Alternatively, specializations can make species vulnerable when resources become scarce. We study how coral reef associated fish and invertebrates with apparent specializations can switch to alternative resources as a mechanism to cope with changing environmental conditions. We investigate the consequences of niche versatility for the persistence of populations and the functional role of organisms on coral reefs of the Anthropocene.

Do marine animals and their associated microbes evolve in predictable ways?

Natural experiments, such as time-calibrated geological events with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to understand how hosts and microbes have coevolved. Organisms on opposing sides of dispersal barriers follow separate evolutionary trajectories under the influence of local environmental conditions. We are leveraging a natural experiment, the formation of the Isthmus of Panama, to investigate how similar features arise in different organisms in response to experiencing similar selective pressures.

How do human activities affect the distribution, life history strategies and the functional roles of sharks and rays in the Tropical Eastern Pacific?

Many vulnerable shark and ray species, use mangrove-fringed bays and estuaries of the Tropical Eastern Pacific (TEP) as nurseries and feeding grounds. However, the persistence of these populations is threatened due to habitat loss, unregulated fishing pressure and pollution that impact them directly as well as their food source. The implementation of effective management strategies requires high frequency time series data (such as monthly or seasonal population size estimates) that traditional methods such as mark-recapture, acoustic and satellite tagging cannot provide effectively because they are time-consuming, expensive, and often invasive. We develop and apply non-invasive environmental DNA (eDNA) genomic techniques to scale up our understanding of shark and ray population dynamics for conservation.

M.Sc. University Pierre and Marie Curie, Paris 6, France, 2008

Ph.D., University Pierre and Marie Curie, Paris 6, France, 2012.

** shared first authorship

Clever F, Sourisse JM, Preziosi RF, Eisen JA, Rodriguez Guerra EC, Scott JJ, Wilkins LGE, Altieri AH, McMillan WO, Leray M. 2022. The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs. Communications Biology In Press

Leray M, Knowlton N, Machida R. 2022. MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences. Environmental DNA. 0, 1-14

Leray M**, Wilkins LGE**, Apprill A, Bik HM, Clever F, Connolly SR, De León ME, Duffy EJ, Ezzat L, Gignoux-Wolfsohn S, Herre EA, Kaye JZ, Kline DI, Kueneman JG, McCormick MK, McMillan OW, O’Dea A, Pereira TJ, Petersen JM, Petticord DJ, Torchin ME, Vega Thurber R, Videvall E, Wcislo WT, Yuen B, Eisen JA. 2021. Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution. PLoS Biology. 19, e3001322

Johnson MD**, Scott JJ**, Leray M**, Lucey N**, Bravo LMR, Wied WL, Altieri AH. 2021. Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef. Nature Communications. 12, 1-12

Leray M, Knowlton N, Ho S, Nguyen BN, Machida R. 2019. GenBank is a reliable resource for 21st century biodiversity research. Proceedings of the National Academy of Sciences of the United States of America. 116, 22651-22656

Wilkins LGE**, Leray M**, Yuen B, Peixoto R, Pereira TJ, Bik HM, Coil DA, Duffy JE, Herre EA, Lessios H, Lucey N, Mejia LC, O'dea A, Rasher DB, Sharp K, Sogin EM, Thacker RW, Vega Thurber R, Wcislo WT, Wilbanks EG, Eisen JA. 2019. Host-associated microbiomes drive structure and function of marine ecosystems. PLoS Biology 17, e3000533

Leray M, Alldredge AL, Yang JY, Meyer CP, Holbrook SJ, Schmitt RJ, Knowlton N, Brooks AJ. 2019. Dietary partitioning promotes the coexistence of planktivorous species on coral reefs. Molecular ecology 28, 2694-2710

Leray M, Ho S-L, Lin J, Machida R. 2018. MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database. Bioinformatics bty454

Leray M, Knowlton N. 2016. Censusing marine eukaryotic diversity in the twenty-first century. Philosophical Transactions of the Royal Society B 371,20150331

Leray M, Meyer CP, Mills SC. 2015. Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet. PeerJ 3,e1047

Leray M, Knowlton N. 2015. DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proceediengs of the National Academy of Sciences of the United States of America. 112,2076-2081

Leray M, Yang JY, Meyer CP, Mills SC, Agudelo N*, Ranwez V, Boehm JT, Machida RJ. 2013. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity, application for characterizing coral reef fish gut contents. Frontiers in Zoology 10,34

leraym [at] si.edu

202-633-1752

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Name

Matthieu

Last name

Leray

Position

Staff Scientist

External CV:

Download CV

Department:

Staff scientists

Erin Spear

Language English

Microbial Ecology Disease Ecology Forest Ecology

To understand the awe-inspiring diversity of tropical forests, we must pay as much attention to the biology of fungi, bacteria and other microbes, as that paid to rainforest trees during the last 100 years. New tools revealing relationships between plants and their associated organisms make this the Century of Microbial Ecology.

DEATH Lab

Research in our lab integrates disease ecology, mycology, and community ecology. We explore the nature and outcomes of plant-microbe interactions, as well as the ecology and epidemiology of fungal pathogens of tropical trees, using a combination of surveys and experiments in the forest, greenhouse, and lab.

How do species intensely competing for the same resources coexist in diverse communities?

Disease carries negative connotations. In agriculture, disease can mean the loss of food and revenue. However, in species-rich forests, pathogens can promote the overall health of the forest by preventing any single tree species from monopolizing limited resources and becoming overly abundant, leading to the loss of other tree species with key ecosystem roles. Importantly, in this self-reinforcing system, the spread of disease is limited, and epidemics are avoided by the very plant diversity pathogens are maintaining. Currently, we have an incomplete understanding of fungal pathogens in tropical forests and their interactions with plants, despite their ubiquity and ecological and economical importance. This hinders our ability to detect and predict the impacts of exotic fungi, reductions in tree diversity in human-modified landscapes, and plant-microbe responses to a changing climate.

What is the role of multi-host pathogens in the maintenance of tropical forest diversity?

Pathogens exhibit a continuum of specificities. Some infect across host families and orders (generalists), others are limited to specific host species or genotypes (specialists). For free-living, dispersal-limited pathogens inhabiting species-rich host communities, selection should favor an ability to infect a variety of unrelated hosts. Indeed, many seedling pathogens in Panama’s diverse lowland forests exhibit host generalism. Yet, on local scales, analyses of spatial and temporal patterns suggest host-specific pathogens are limiting the abundance of a given species. How do we reconcile these findings? We are exploring non-mutually exclusive mechanisms by which multi-host pathogens could produce the patterns attributed to host-specific pathogens. Our lab is also interested in the factors dictating the host range of plant-associated pathogens in hyperdiverse tropical forests.

What factors exclude certain species from otherwise suitable habitats?

Disease varies across environmental gradients that impact pathogen and plant fitness. Tree species adapted to environments with elevated disease pressure are under selection to invest in disease-resistance and tolerance traits, despite the costs of those traits. Conversely, the fitness costs of defenses outweigh the benefits for tree species adapted to environments with reduced disease pressure. Consequently, poorly defended, disease-sensitive tree species can be excluded from disease-prone areas while well-defended, disease-tolerant species can persist. We are exploring disease gradients and interspecific variability in disease susceptibility to evaluate the role of microorganisms in the spatial turnover of tree species and, thereby, the maintenance of local and regional forest diversity.

How are microorganisms distributed across space and time, and what are the constraints?

We are testing five interlinked hypotheses: (1) fungal pathogen communities are diverse and differences in diversity across geographic space are driven by abiotic factors, and are largely independent of plant community diversity. The majority of pathogens are (2) host generalized and (3) relatively geographically widespread, spanning the Isthmus of Panama and associated abiotic and floristic gradients, but (4) their relative abundances are spatially and temporally variable. (5) A given pathogen’s spatial distribution and abundance are decoupled from the presence of a single host species. To do this, we use a combination of culturing, metabarcoding, and other molecular diagnostic techniques to identify plant-associated fungi, particularly pathogens, and to describe their spatial and temporal distributions, and host associations.

What makes a pathogen a pathogen?

Symbiotic relationships are omnipresent. Yet, we are just beginning to understand and characterize the nuanced nature of these relationships, particularly in tropical forests. Symbioses represent a continuum, from beneficial to detrimental for the host. Moreover, these relationships are not fixed in time and space, they are highly context dependent. A commensal microbe can become pathogenic when a plant’s health or nutritional status changes and plant-microbe mutualisms can fracture when a partner cheats. Moreover, a pathogen can actually benefit a host plant if the pathogen does more harm to the host plant’s neighbors who are competing for the same resources (sensu the enemy of my enemy is my friend).

Ph.D., University of Utah (2015)

B.S. Biology (Honors), minor Environmental Studies (2005)

Spear, E. R. and K. D. Broders. 2021. Host-generalist fungal pathogens of seedlings may maintain forest diversity via host-specific impacts and differential susceptibility among tree species. New Phytologist 231: 460–474.

Spear, E. R. and E. A. Mordecai. 2018. Foliar pathogens are unlikely to stabilize coexistence of competing species in a California grassland. Ecology 99: 2250-2259.

Spear, E. R. 2017. Phylogenetic relationships and spatial distributions of putative fungal pathogens of seedlings across a rainfall gradient in Panama. Fungal Ecology 26: 65–73.

Spear, E. R., P. D. Coley, and T. A. Kursar. 2015. Do pathogens limit the distributions of tropical trees across a rainfall gradient? Journal of Ecology 103: 165–174.

SpearER [at] si.edu

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Name

Erin

Last name

Spear

Position

Staff Scientist

Department:

Staff scientists

Sean Connolly

Language English

Biodiversity Marine Biology Global Change

I am intrigued by the dynamics of biological turnover at all scales – from the turnover of energy and nutrients at the scale of individual organisms, to global gradients in biodiversity and macroevolutionary turnover in species over tens of millions of years. My recent work focuses on two areas: the maintenance of biodiversity in species-rich systems, especially coral reefs; and the effects of human impacts on the structure and dynamics of populations and communities in coral reef ecosystems.

Connolly Lab

Research in my lab combines empirical work with mathematical and statistical modelling to study patterns, dynamics, causes and consequences of biodiversity at scales ranging from local coexistence of species with similar resource requirements, to species interactions and coexistence at the seascape scale, to global-scale dynamics of origination and extinction that play out over tens of millions of years. In nearshore marine ecosystems like coral reefs, human activity ranging from coastal development and fishing to global climate change profoundly affects biodiversity, making human impacts one focus of our work.

I moved to STRI in late 2019, after approximately 20 years focusing on the coral reefs of the Central Indo-Pacific. I am excited to launch a new phase of my research program, focused on the coral reefs of the Tropical East Pacific and the Caribbean, as well as other high-diversity ecosystems in and around the Isthmus of Panama

What mechanisms and processes underpin the high biodiversity of coral reefs?

How do large numbers of species coexist when they utilize the same, or very similar, resources? This has been one of the central motivating questions of ecology, particularly tropical ecology, for more than a century. I investigate mechanisms of coexistence, from tradeoffs between specialization and competitive dominance, to cryptic resource partitioning, to the role of different types of environmental fluctuations. This work involves formulation, empirical calibration, and analysis of ecological models at multiple scales: from individual physiology and energetics to species interactions, demography and connectivity.

What determines the commonness or rarity of different species in high-diversity ecosystems like coral reefs?

What makes some species common and others rare? Why do different species’ abundances vary from place to place to such different degrees? Modern biodiversity theories often make competing predictions about the degree to which coexisting species’ abundances vary, and about the spatial and temporal dynamics of those abundances. We apply contemporary biodiversity models to gain insights into the relative importance of factors such as environmental fluctuations and differences in species’ ecological traits in driving these patterns of commonness and rarity. Two dramatically different reef bioregions on either side of the Isthmus make Panama ideal comparative natural laboratory for such work: in the Tropical East Pacific, one group of corals overwhelmingly dominates in the marginal reef conditions there, while in the Caribbean, former community dominants have collapsed to a tiny fraction of their historical abundances.

How do fishing and management tools, such as marine reserves, impact exploited species and the broader functioning of reef ecosystems?

Fishing directly and profoundly impacts the abundances of the species that fishers target, but what impact does it have on the rest of the ecosystem, and how do contemporary management tools like no-take marine reserves mediate these impacts? Our group tackles a range of research problems related to these core questions, including how marine reserve networks influence the recovery of fished populations and fisheries yields, to identifying benchmarks for the sustainability of non-selective, multi-species fisheries, to understanding how levels of critical ecosystem functions depend on the extent and trophic structure of fishing.

How do reef ecosystems respond to climate change?

Today’s coral reefs respond to a very different environment than those to which modern coral reefs have been exposed for hundreds of thousands, and probably millions, of years. These dramatic changes in the physical and chemical environment have impacts that range from higher mortality and reduced growth and reproduction of organisms, to changes in the biogeochemical rates that determine whether reef structures grow or dissolve. This has profound implications for how reef organisms interact with each other, and how they will evolve in the coming decades and centuries. In addition to studying the ongoing changes experienced by today’s reefs, I am interested in using the fossil record to understand how profound environmental upheavals in the past led to reorganizations in the structure and functioning of marine ecosystems.

B.A. Earlham College, 1994

Ph.D., Stanford University, 1999.

Hughes, T.P., J. T. Kerry, S.R. Connolly, J. G. Álvarez-Romero, C.M. Eakin, S.F. Heron, J. Moneghetti, M.A. Gonzalez. 2021. Emergent properties in the responses of tropical corals to recurrent climate extremes. Current Biology 31: 5393-5399. https://doi.org/10.1016/j.cub.2021.10.046

Bairos-Novak, K.R., M.O Hoogenboom, M.J.H. van Oppen, and S.R. Connolly. 2021. Coral adaptation to climate change: meta-analysis reveals high heritability across multiple traits. Global Change Biology 27: 5594-5710. DOI 10.1111/gcb.15829.

Thibaut, L.M., and S.R. Connolly. 2020. Hierarchical modelling strengthens evidence for density-dependence in observational time series of population dynamics. Ecology 101:e02893. DOI 10.1002/ecy.2893.

Moneghetti, J., J. Figueiredo, A.H. Baird, and S.R. Connolly. 2019. High-frequency sampling and piecewise models reshape dispersal kernels of a common reef coral. Ecology 100: e02730. DOI: 10.1002/ecy.2730

Hopf, J. G.P. Jones, D.H. Williamson, and S.R. Connolly. 2019. Marine reserves stabilize fish populations and fisheries yields in disturbed coral reef systems. Ecological Applications 29: e01905. DOI: 10.1002/eap.1905.

Hughes, T.P., K.D. Anderson, S.R. Connolly, S.F. Heron, J.T. Kerry, J.M. Lough, A.H. Baird, J.K. Baum, M.L. Berumen, T.C. Bridge, D.C. Claar, C.M. Eakin, J.P. Gimour, N.A.J. Graham, H. Harrison, J.-P.A. Hobbs, A.S. Hoey, M. Hoogenboom, R.J. Lowe, M.T. McCullough, J.M. Pandolfi, M. Pratchett, V. Schoepf, G. Torda, S.K. Wilson. 2018. Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science 359: 80-83.

Connolly, S.R., S.A. Keith, R.K. Colwell, and C. Rahbek. 2017. Process, mechanism, and modelling in macroecology. Trends in Ecology and Evolution 32: 835-844.

Connolly, S.R., T.P. Hughes, and D.R. Bellwood. 2017. A unified model explains commonness and rarity on coral reefs. Ecology Letters 20: 477-486.

Hopf, J.K., G.P. Jones, D.H.Williamson, and S.R. Connolly. 2016. Synergistic effects of marine reserves and harvest controls on the abundance and catch dynamics of a coral reef fishery. Current Biology 26: 1543-1548.

Connolly, S.R., M.A. MacNeil, M.J. Caley, N. Knowlton, E. Cripps, M. Hisano, L.M. Thibaut, B.D. Bhattacharya, L. Benedetti-Cecchi, R. E. Brainard, A. Brandt, F. Bulleri, K.E. Ellingsen, S. Kaiser, I. Kröncke, K. Linse, E. Maggi, T. O’Hara, L. Plaisance, G.C.B. Poore, S.K. Sarkar, K.K. Satpathy, U. Schückel, A. Williams, R.S. Wilson. 2014. Commonness and rarity in the marine biosphere. Proceedings of the National Academy of Sciences, USA 111: 8524-8529.

Figueiredo, J., A.H. Baird, S. Harii, and S.R. Connolly. 2014. Increased local retention of reef coral larvae as a result of ocean warming. Nature Climate Change 4: 498-502.

Ban, S.S., N.A.J. Graham, and S.R. Connolly. 2014 Evidence for multiple stressor interactions and effects on coral reefs. Global Change Biology 20: 681-697.

Thibaut, L.M.*, and S.R. Connolly*. 2013. Understanding diversity-stability relationships: toward a unified model of portfolio effects. Ecology Letters 16: 140-150.

Madin, J. S. and S. R. Connolly. 2006. Ecological consequences of major hydrodynamic disturbances on coral reefs. Nature 444: 477-480.

Dornelas, M.., S. R. Connolly, and T. P. Hughes. 2006. Coral reef diversity refutes the neutral theory of biodiversity. Nature 440: 80-82.

ConnollyS [at] si.edu

+507 212 0757

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Name

Sean

Last name

Connolly

Position

Staff Scientist

Department:

Staff scientists

Martijn Slot

Language English

Forest Ecology Global Change Plant Physiology

It’s fascinating that Panama’s spectacular tropical forests are ultimately the result of plants harnessing the sun’s energy and using it to fuel growth. But as powerful as this foundation for plant growth is, tropical forests are not invulnerable. Small changes in our climate could dramatically impact growth, survival, and carbon storage capacity of these forests to take up and store carbon, and could upset the delicate balance of species coexistence.

Forest Biology

In my lab we try to understand how climate change affects tropical forests by studying how environmental factors influence the physiology and ecology of tropical trees and lianas. We are interested in identifying threshold temperatures for various aspects of plant performance, including carbon fixation in photosynthesis, growth, survival of leaves, and sexual reproduction.

What limits the rate of photosynthetic carbon fixation in tropical trees?

Photosynthesis is a complex process for capturing carbon from the atmosphere. Multiple steps in this process can control the maximum rate of carbon capture. We use a combination of manipulative experiments and field observations to understand the rate-limiting steps for photosynthesis in different tropical tree species. We also study how environmental conditions and plant ontogeny might influence which step is rate-limiting.

How do species differ in their risk of overheating?

Species may differ in their heat tolerance but they also differ in the extent to which they experience heat, based on their architecture, morphology, and physiology. New technologies enable us to monitor temperatures of leaves in the canopy at a larger scale than traditional methods that involved attaching thermocouple wires to leaves. Monitoring canopy temperatures in diverse forest plots allows us to identify the species that experience the highest temperature extremes. We study these species in more detail to evaluate their physiological capacity to withstand high temperatures, and analyze the relative importance of architecture, morphology, and physiology as predictors of “overheating” of plants.

Does global warming threaten plant fertility in tropical forests?

Little is known about high-temperature thresholds for reproduction in wild plants, but studies on crops suggest that reproduction may fail at 30–39°C. If thresholds for reproduction are universal, tropical species are close to exceeding them, as temperatures there already routinely exceed 30°C. As temperatures continue to rise, seed production may drastically change in tropical forests, with consequences for species composition and community dynamics. Through experiments and field observations, we are studying tropical tree species’ vulnerability to heat-induced sterility, with the ultimate goal of understanding how rising temperatures may change forest community composition.

M.Sc. Wageningen University, 2003

M.Res. University of York, 2004

Ph.D. University of Florida, 2013.

Slot M, Krause GH, Krause B, Hernández GG, Winter K (2019) Photosynthetic heat tolerance of shade and sun leaves of three tropical tree species. Photosynthesis Research 141, 119–130.

Slot M, Winter K (2018) High tolerance of tropical sapling growth and gas exchange to moderate warming. Functional Ecology 32, 599–611.

Slot M, Winter K (2017) Photosynthetic acclimation to warming in tropical forest tree seedlings. Journal of Experimental Botany 68, 2275–2284.

Slot M, Winter K (2017) In situ temperature response of photosynthesis of 42 tree and liana species in the canopy of two Panamanian lowland tropical forests with contrasting rainfall regime. New Phytologist 214, 1103–1117.

Rey-Sánchez C, Slot M, Posada JM, Kitajima K (2016) Spatial and seasonal variation of leaf temperature within the canopy of a tropical forest. Climate Research 71, 75–89.

Slot M, Kitajima K (2015) General patterns of acclimation of leaf respiration to elevated temperatures across biomes and plant types. Oecologia 177, 885–900.

Slot M, Rey-Sánchez C, Gerber S, Lichstein JW, Winter K, Kitajima K (2014) Thermal acclimation of leaf respiration of tropical trees and lianas: response to experimental canopy warming, and consequences for tropical forest carbon balance. Global Change Biology 20, 2915–2926.

Slot M, Poorter L (2007) Diversity of tropical tree seedling responses to drought. Biotropica 39, 683–690.

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Name

Martijn

Last name

Slot

Position

Staff Scientist

Department:

Staff scientists

Jeremy Jackson

Language English

Paleontology and Paleobiology Conservation Biology

“There are no important questions today for understanding how the Earth works - ecologically, evolutionary, geochemically, oceanographically, meteorologically - that can be answered by a single person, or by a single discipline. All of the great questions are interdisciplinary. All of them require multiple kinds of expertise and all of them require teamwork and interaction.”

My research interests have evolved from a strict focus on the ecology of coral reefs to paleontological investigations of the evolution of Caribbean marine ecosystems in response to environmental change and finally towards elucidating the causes and consequences of past and ongoing human activities on the health of ocean ecosystems. I co-founded with Tony Coates a multidisciplinary international research team to document the ecological responses of Caribbean marine ecosystems to changes in oceanography due to the gradual isolation of the Caribbean by the rise of the Central American Isthmus and am continuing research on the underlying factors responsible for evolutionary change in select lineages and the mass extinction that occurred at the beginning of the Pleistocene. My other current focus is on historical ecology, more specifically in demonstrating the trajectory and ecological consequences of different human activities on the structure and function of ocean ecosystems over the past few thousand years.

How do different factors interact to cause a mass extinction?

Paleontologists traditionally look for prominent environmental events to explain pulses of speciation and extinction in the fossil record. But ecological insight suggests that a more complex series of cascading events stretching over a million years or more are most likely responsible, including not only environmental change but also biological interactions and the phenomenon of ‘extinction debt’ developed for conservation biology. I am examining changes in functional biology and life history patterns to better understand the chronology of Caribbean extinctions over the past 5 million years.

Why does the Indo-West Pacific have so many more species than the Caribbean?

Our recent work on bryozoans demonstrates that species richness was similar in both regions 5 million years ago, and the same was apparently true for reef corals. Ongoing work suggests that the Mediterranean host similar species diversity before it dried up at about the same time. The obvious implication is that the great differences in species diversity today between the Caribbean and Mediterranean versus the Indo-West Pacific is due mass extinction in the Caribbean and Mediterranean rather than, has long been speculated, higher speciation rates in the Pacific.

How and when has the trajectory of human activities on the oceans transitioned from predominantly local to global impacts and what is their relative importance today?

We have long known that fishing intensified sufficiently by the time of the Roman Empire to drastically deplete Mediterranean fish stocks but have only recently documented the deep historical roots of overfishing worldwide. My group is working to untangle the history of human disturbance and the comparative consequences, of fishing, land use, habitat destruction, pollution, and climate change on Caribbean coral reef ecosystems. The central question is to what extent local management to regulate and diminish fishing, habitat destruction, and pollution on coral reefs can increase their resilience to coral bleaching, disease, and acidification due to the anthropogenic rise in CO2?

How distinct is the Caribbean marine biota from other tropical seas?

The Caribbean is a Mediterranean sea landlocked to the north, west, and south, and isolated from all other tropical oceans for 5 to 3 million years. Biotas in many groups are also deeply divergent as demonstrated especially for reef corals, but also for other groups such as bryozoans. I am interested in the extent to which this isolation has affected the ability of Caribbean biotas to cope with human disturbance. For example, the recent supposedly global extreme coral bleaching events did not occur in the Caribbean, whereas disease outbreaks appear to be more pervasive and fatal to Caribbean invertebrates such as corals and sea urchins than elsewhere in the tropics.

B. A. The George Washington University, 1965

M. A. The George Washington University, 1968

M. Phil. Yale University, 1970

Ph. D. Yale University, 1971

DiMartino E, Jackson JBC, Taylor PD, Johnson KG (2018) Differences in extinction rates drove modern geographic patters of tropical marine biodiversity. Science Advances 4, eaaq150

Jackson JBC, Chapple S. (2018) Breakpoint: Reckoning with America’s Environmental Crises. Yale University Press

McClenachan L, O’Connor G, Neal BP, Pandolfi JM, Jackson JBC (2017) Ghost reefs: Nautical Charts document large spatial scale reef loss over 240 years. Science Advances 3: e1603155.

Simpson C, Jackson JBC, Hererra-Cubilla (2017) Evolutionary determinants of morphological polymorphism in colonial animals. The American Naturalist 190:

Jackson JBC, Donovan M, Cramer K, Lam V (eds) (2014) Status and trends of Caribbean coral reefs: 1970-2012. International Union for the Conservation of Nature, Gland, Switzerland.

O’Dea A, Lessios, Coates AG, Eytan RI, et al. and Jackson JBC (2016) Formation of the Isthmus of Panama. Science Advances 2:e1600883:12 pp

Cramer K, Jackson JBC, Angioletti C, Leonard-Pingell J & Guilderson T (2012) Anthropogenic mortality on coral reefs in Caribbean Panama predates coral disease and bleaching. Ecology Letters doi: 10.1111/j.1461-0248.2012.01768.x

Jackson JBC & Jacquet J (2011) The shifting baselines syndrome: perception, deception, and the future of our oceans. Pp. 128-141 in Ecosystem Approaches to Fisheries: A Global Perspective, V Christensen & J Maclean (eds) Cambridge University Press

Jackson JBC, Alexander K, Sala E (eds.) (2011) Shifting Baselines in Fisheries: Using the Past to Manage the Future. Island Press, Washington DC

Smith JT & Jackson JBC (2009) Ecology of extreme faunal turnover of tropical American scallops. Paleobiology 35:77-93

Johnson KG, Jackson JBC, & Budd AF (2008) Caribbean reef development was independent of coral diversity over 28 million years. Science 319:1521-1523

Jackson JBC (2008) Evolution and extinction in the brave new ocean. Proceedings of the National Academy of Sciences USA 105 (Suppl. 1):11458-11465

Lotze HK, Lenihan HS, Bourque BJ, Bradbury RH, Cooke RG, Kay MC, Kidwell SM, Kirby MX, Peterson CH & Jackson JBC (2006) Depletion, degradation, and recovery potential of estuaries and coastal seas. Science 312:1806-1809

Jackson JBC and 17 others (2001) Historical overfishing and the recent collapse of coastal ecosystems. Science 293:629-638

jjackson [at] amnh.org

+1 (858) 518-7613

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Scientist Type:

Emeritus

Name

Jeremy

Last name

Jackson

Department:

Staff scientists

Sabrina Amador

Language English

Animal Behavior Evolutionary Biology Natural History

Ecological and social interactions affect the behavioral responses of organisms. Ant societies in obligate mutualisms with plants are a fascinating pairing for studying coevolution. The plant and the needs it creates on the ant society shapes the behavior and morphology of society members.

ResearchGate

Tropical Behavioral Ecology Lab

Research projects in our lab combine approaches from behavioral ecology, functional morphology, ethology and evolution of behavior. Our work focuses mostly on the ultimate and proximate causes of behavior in an ecological and social context, with an emphasis on how ecological or social interactions shape behavioral and morphological traits. We are inspired by field observations and combining theory and natural history to understand natural phenomena, and we welcome collaborators who study behavior in a broad range of tropical organisms.

What is the role of ecological associations on behavioral and morphological trait evolution?

Obligatory associations between different organisms have consequences for the evolution of traits in the interacting species. We focus our research on the effects of obligatory plant parasitism or mutualisms on the behavior and morphology of acacia ants. Specifically, we study navigation, memory and learning in ants with different types of ecological associations. We are also interested in how the behaviors associated with the mutualistic or parasitic association may shape the morphology of ants.

How do individual decisions add up to achieve common goals in insect societies?

We study how insect societies work to achieve common goals without central control. Focusing on acacia ants, we addressed how workers that are similar in shape and morphology are able to cover the whole variety of tasks that must be performed in the colony. We assess how society shapes the behavior and brain of individual ants. We are interested in understanding how experiences can affect the specialization, performance and range of tasks that workers execute.

How do organism make decisions, and what is the role of memory and learning on decision-making?

We are broadly interested in how organisms modulate a response based on previous experiences, that is, how organism learn. Hence, we are researching plant decision making, aiming at understanding habituation-like responses in the sensitive plant Mimosa pudica. Also, we study memory, learning and orientation in ants.

Ph.D. Ecology, Evolution and Behavior. University of Texas at Austin, 2014. Dissertation: Brain and behavioral traits of acacia ants.

M.Sc. in Biology with honors. Universidad de Costa Rica, 2009. Dissertation: Division of labor and pruning behavior of acacia ants

B.S. in Biology. Universidad de Costa Rica, 2005.

Amador-Vargas S., Wcislo W.T. 2021. Nestmate interference in acacia ants vary with colony size and task-specialization. Animal Behavior 181: 151–163.

Gijsman, F., Gonzalez Y., Guevara M. & Amador-Vargas S. 2021. Short-term plasticity and variation in acacia ant-rewards under different conditions of ant occupancy and herbivory. The Science of Nature. 108(4):31. doi: 10.1007/s00114-021-01738-w.

Farji-Brener A.G.& Amador-Vargas, S. 2020. Plasticity in extended phenotypes: how the antlion Myrmeleon crudelis adjusts the pit traps depending on biotic and abiotic conditions. Israel Journal of Ecology and Evolution 66: 41–47.

Amador-Vargas, S., Dyer J., Arnold N., Cavanaugh L. & Sánchez E. 2019. Acacia trees with parasitic ants have fewer and less spacious spines than trees with mutualistic ants. Naturwissenschaften 107:3.

Amador-Vargas, S. & Mueller, U.G. 2017. Ability to reorient is weakly correlated with central-place versus non-central-place foraging in acacia ants. Behavioral Ecology and Sociobiology 71: 43.

Amador-Vargas, S., W. Gronenberg, W. Wcislo, U. G. Mueller. 2015. Specialization and group size: brain and behavioural correlates of colony size in ants lacking morphological castes. Proceedings of the Royal Society B. 282: 2014-2502.

Kardish, M.R., Mueller, U.G., Amador-Vargas, S., Dietrich, E.I., Ma, R., Barrett, B., Fang, C.-C., 2015. Blind trust in unblinded observation in Ecology, Evolution, and Behavior. Frontiers in Ecology and Evolution 3: 51.

Amador-Vargas, S., M. Dominguez, G. León, B. Maldonado, J. Murillo, and G. L. Vides. 2014. Leaf-folding response of a sensitive plant shows context-dependent behavioral plasticity. Plant Ecology 215: 1445–1454.

Amador-Vargas S. 2012c. Run, robber, run: parasitic acacia ants use speed and evasion to steal food from ant-defended trees. Physiological Entomology 37: 323-329.

Amador-Vargas S. 2012b. Behavioral responses of acacia ants correlate with age and location on the host plant. Insectes Sociaux. 59: 341- 350.

Amador-Vargas S. 2012a. Plant killing by acacia ants (Pseudomyrmex spinicola) increases the density of host species seedlings in the dry forest of Costa Rica. Psyche. Special Issue: Advances in Neotropical Myrmecology 2012: 1-6.

amadors [at] si.edu

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Sabrina Amador

Name

Sabrina

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Amador

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Yves Basset

Language English

Entomology Biodiversity

We urgently need to implement monitoring schemes to evaluate the effects of anthropogenic change on the spatio-temporal distribution of arthropods in the tropics. Or else we may grossly underestimate arthropod extinction risks in tropical rainforests.

Higher predation risk for insect prey at low latitudes and elevations, 2017

Contrasting the distribution of butterflies and termites in plantations and tropical

forests, 2017

Yves Basset Lab

ForestGEO Arthropod monitoring

Insect Conservation and Diversity

Media coverage - Science, 2012

Toward a world that values insects – Science 2019

My colleagues and I are interested to understand the main factors that affect the maintenance of local arthropod biodiversity in tropical rainforests. Our research program has several components. We have studied insect-plant interactions, the host-specificity of insect herbivores and interaction networks in tropical rainforests. However, we are now increasingly focusing on the threats to tropical insects induced by global climate change. To this end, we have build a small network of sites recruiting from the Smithsonian ForestGEO network (notably in Panama, Thailand and Papua New Guinea), where we monitor in the long-term various insect taxa, from butterflies to termites. We apply new analytical and molecular methods to forecast how climate change may alter functional groups represented by insect taxa with diverse life-histories.

Are arthropod species/assemblages functionally replaced among rainforest locations?

We are broadly interested in estimating the relative influence of biogeography, rainfall seasonality, productivity and local woody plant richness on the diversity and composition of arthropod assemblages in tropical rainforests. To achieve this, comparison of arthropod community variables among ForestGEO sites located in different biogeographic regions is essential. We are also interested to evaluate what is the relative importance of plant phylogeny and functional traits in shaping the abundance and diversity of herbivore and detritivore communities. Further, predicting and mitigating the loss of biodiversity remains essential. We seek to identify species traits that may increase the likelihood of species extinction for a wide variety of arthropod groups.

How consistent is the structure of interaction networks based on insects across rainforests?

Trophic interactions have been described as the glue that holds together ecological communities and several authors have called for the conservation of interactions (rather than individual species) as a goal for conservationists. Networks of feeding interactions among insect herbivores, their hosts and natural enemies such as parasitoids, describe the structure of these assemblages and may be critically linked to their dynamics and stability. We are interested to understand how is variability in food web structure (“connectivity” and other measures of insect interaction structure and relative insect abundance, including host-specificity) affected by the phylogenetic structure of plant communities (formed from different regional species pools), rainfall and productivity.

How can we efficiently monitor insect populations in the long-term with new molecular techniques?

In the tropics, where both insect diversity and taxonomic impediment are high, we routinely use DNA barcoding and Barcode Index Numbers to identify or distinguish focal species. We are currently exploring how we can develop protocols to apply metabarcoding to derive annual population indices relevant to a large fraction of local arthropod assemblages, and not to just a few focal groups. This represents a formidable challenge as we have shown that small areas of tropical rainforests can easily support 25,000 arthropod species or more.

M.Sc., University of Neuchâtel, Switzerland, 1985

Ph.D., Griffith University, Australia, 1990

Bonadies, E., Lamarre, G.P.A., Souto-Vilarós, D., Pardikes, N.A., Ramírez Silva, J.A., Perez, F., Bobadilla, R., Lopez, Y. & Basset, Y. 2024. Population trends of insect pollinators in a species-rich tropical rainforest: stable trends but contrasting patterns across taxa. Biology Letters, in press.

Tsang, T.P.N., De Santis, A.A.A., Armas-Quiñonez, G., Ascher, J.S., Ávila-Gómez, E.S., Báldi, A., Ballare, K.M., Balzan, M.V., Banaszak-Cibicka, W., Bänsch, S., Basset, Y., …, & Bonebrake, T.C. 2024. Land use change consistently reduces α but not β and γ diversity of bees. Global Change Biology, in press.

Leponce, M., Basset, Y., Aristizábal-Botero, Á., Baïben, N., Barbut, J., Buyck, B., Butterill, P., Calders, K., Cárdenas, G., Carrias, J.-F., Catchpole, D., D’hont, B., Delabie, J., Drescher, J., Ertz, D., Heughebaert, A., Hofstetter, V., Leroy, C., Melki, F., Michaux, J., Neita-Moreno, J.C., Poirier, E., Rougerie, R., Rouhan, G., Rufray, V., Scheu, S., Schmidl, J., Vanderpoorten, A., Villemant, C., Youdjou, N. & Pascal, O. 2024. Unveiling the above-ground eukaryotic diversity supported by individual large old trees: the “Life on Trees” integrative protocol. Frontiers in Forests and Global Change, 7, 1425492.

Jain, A., Cunha, F., Bunsen, M.J., Cañas, J.S., Pasi, L., Pinoy, N., Helsing, F., Russo, J., Botham, M., Sabourin, M., Fréchette, J., Anctil, A., Lopez, Y., Navarro, E., Perez Pimentel, F., Zamora, A.C., Ramirez Silva, J.A., Gagnon, J., August, T., Bjerge, K., Gomez Segura, A., Bélisle, M., Basset, Y., McFarland, K.P., Roy, D., Høye, T.T., Larrivée, M., Rolnick, D. 2024. Insect identification in the wild: The AMI dataset. Proceedings of the European Conference on Computer Vision, Milano, 2024, in press.

Souto-Vilarós, D., Basset, Y., Blažek, P., Laird-Hopkins, B., Segar, S.T., Navarro-Valencia, E., Cecilia Zamora, A., Campusano, Y., Čtvrtečka, R., Savage, A.F., Perez, F., Lopez, Y., Bobadilla, R., Ramírez Silva, J.A. & Lamarre, G.P.A. 2024. Illuminating arthropod diversity in a tropical forest: Assessing biodiversity by automatic light trapping and DNA metabarcoding. Environmental DNA, DOI: 10.1002/edn3.540

Segar, S.T., Re Jorge, L., Nicholls, L., Basset, Y., Rota, J., Kaman, O., Sisol, M., Gewa, B., Dahl, C., Butterill, P., Mezzomo, P., Miller, S.E., Weiblen, G., Salminen, J.-P., Novotny, V. & Volf, M. 2024. Species swarms and their caterpillar colonisers: phylogeny and polyphenols determine host plant specificity in New Guinean Lepidoptera. Frontiers in Ecology and Evolution, 11, 1308608.

August, T., Basset, Y., Boislard, T., Gomez-Segura, A., Høye, T. T., … & Roy, D. B. 2023. Automated monitoring of biodiversity in the tropics: A pilot study at Barro Colorado Island (1.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7598393

Ashe-Jepson, E., Arizala Cobo, S., Basset, Y., Bladon, A.J., Kleckova, I., Laird-Hopkins, B.C., Mcfarlane, A., Sam, K., Savage, A.F., Zamora, A.C., Turner, E.C. & Lamarre, G.P.A. 2023. Tropical butterflies use thermal buffering and thermal tolerance as alternative strategies to cope with temperature increase. Journal of Animal Ecology, doi.org/10.1111/1365-2656.13970.

Laird-Hopkins, B. C, Ashe-Jepson, E., Basset, Y., Cobo, S. A., Eberhardt, L., Freiberga, I., Hellon, J., Hitchcock, G.W., Kleckova, I., Linke, D., Lamarre, G.P.A., McFarlane, A., Savage, A.F., Turner, E.C., Zamora, A.C., Sam, K. & Bladon, A. J. 2023. Thermoregulatory ability and mechanism do not differ consistently between neotropical and temperate butterflies. Global Change Biology, 29, 4180-4192.

Basset, Y., Butterill, P.T., Donoso, D.A., Lamarre, G.P.A., Souto-Vilaros, D., Perez, F., Bobadilla, R., Lopez, Y., Ramírez Silva, J.A. & Barrios, H. 2023. Abundance, occurrence and time series: long-term monitoring of social insects in a tropical rainforest. Ecological Indicators, 150, 110243.

Harvey, J.A., Tougeron, K., Gols, R., …, Basset, Y., … & Chown, S.L. 2022. Scientists’ warning on climate change and insects. Ecological Monographs, in press.

Basset, Y., Blažek, P., Souto-Vilarós, D., Vargas, G., Ramírez Silva, J.A., Barrios, H., Perez, F., Bobadilla, R., Lopez, Y., Ctvrtecka, R., Šípek, P., Solís, A., Segar, S.T. & Lamarre, G.P.A. 2022. Towards a functional classification of poorly known tropical insects: The case of rhinoceros beetles (Coleoptera, Dynastinae) in Panama. Insect Conservation and Diversity, in press.

Basset, Y., Hajibabaei, M., Wright, M.T.G., Castillo, A.M., Donoso, D.A., Segar, S.T., Souto‑Vilarós, D. Soliman, D.Y., Roslin, T., Smith, M.A., Lamarre, G.P.A., De León, L.F., Decaëns, T., Palacios‑Vargas, J.G., Castaño‑Meneses, G., Scheffrahn, R.H., Rivera, M., Perez, F., Bobadilla, R., Lopez, Y., Ramirez Silva, J.A., Montejo Cruz, M., Arango Galván, A. & Barrios, H. (2022). Comparison of traditional and DNA metabarcoding samples for monitoring tropical soil arthropods (Formicidae, Collembola and Isoptera). Scientific Reports, 12, 10762. https://doi.org/10.1038/s41598-022-14915-2

Donoso, D.A., Basset, Y., Shik, J.Z., Forrister, D.L., Uquillas, A., Salazar Méndez , Y., Arizala, S., Polanco, P., Beckett, S., Dominguez G., D. & Barrios, H. 2022. Male ant reproductive investment in a seasonal wet tropical forest: consequences of future climate change. PLOs One, 17, e0266222.

Lamarre, G.P.A., Pardikes, N.A., Segar, S., Hackforth, C.N., Laguerre, M., Vincent, B., Lopez, Y., Perez, F., Bobadilla, R., Ramírez Silva, J.A., Basset, Y. 2022. More winners than losers over 12 years of monitoring tiger moths (Erebidae: Arctiinae) on Barro Colorado Island, Panama. Biology Letters, 18, 20210519.

Roubik, D.W., Basset, Y., Lopez, Y., Bobadilla, R., Perez, F. & Ramírez Silva, J.A. 2021. Long-term (1979-2019) dynamics of protected orchid bees in Panama. Conservation Science and Practice, 3, e543.

Basset, Y., Miller, S.E., Gripenberg, S., Ctvrtecka, R., Dahl, C., Leather, S.R. & Didham, R.K. 2019. An entomocentric view of the Janzen-Connell hypothesis. Insect Conservation and Diversity, 12, 1-8.

Basset, Y., Dahl, C., Ctvrtecka, R., Gripenberg, S., Lewis, O.T., Segar, S.T., Klimes, P., Barrios, H., Brown, J.W., Bunyavejchewin, S., Butcher, B.A., Cognato, A.I., Davies, S.J., Kaman, O., Knizek, M., Miller, S.E., Morse, G.E., Novotny, V., Pongpattananurak, N., Pramual, P., Quicke, D.L.J., Robbins, R.K., Sakchoowong, W., Schutze, M., Vesterinen, E.J., Wang, W.-z., Wang, Y.-y., Weiblen, G. & Wright, S.J. 2018. A cross-continental comparison of assemblages of seed- and fruit-feeding insects in tropical rainforests: faunal composition and rates of attack. Journal of Biogeography, 45, 1395-1407.

Didham, R.K., Leather, S.R. Basset, Y. 2017. Don’t be a zero-sum reviewer. Insect Conservation and Diversity, 10, 1-4.

Lucas, M., Forero, D. & Basset, Y. 2016. Diversity and recent population trends of assassin bugs (Hemiptera: Reduviidae) on Barro Colorado Island, Panama. Insect Conservation and Diversity, 9, 546-558.

Basset, Y., Cizek, L., Cuénoud, P., Didham, R.K., Novotny, V., Ødegaard, F., Roslin, T., Tishechkin, A.K., Schmidl, J., Winchester, N.N., Roubik, D.W., Aberlenc, H.-P., Bail, J., Barrios, H., Bridle, J.R., Castaño-Meneses, G., Corbara, B., Curletti, G., da Rocha, W.D., De Bakker, D., Delabie, J.H.C., Dejean, A., Fagan, L.L., Floren, A., Kitching, R.L., Medianero, E., de Oliveira; E.G., Orivel, J., Pollet, M., Rapp, M., Ribeiro, S.P., Roisin, Y., Schmidt, J.B., Sørensen, L., Lewinsohn, T.M., Leponce, M. 2015. Arthropod distribution in a tropical rainforest: tackling a four dimensional puzzle. PLoS ONE 10(12): e0144110. doi:10.1371/journal.pone.0144110

Basset, Y., Barrios, H., Segar, S., Srygley, R.B., Aiello, A., Warren, A.D., Delgado, F., Coronado, J., Lezcano, J., Arizala, S., Rivera, M., Perez, F., Bobadilla, R., Lopez, Y. & Ramirez, J.A. 2015. The butterflies of Barro Colorado Island, Panama: local extinction since the 1930s. PLoS ONE, 10, e0136623. doi:10.1371/journal.pone.0136623

Fayle, T.M., Turner, E.C., Basset, Y., Ewers, R.M., Reynolds, G. & Novotny, V. 2015. Whole-ecosystem experimental manipulations of tropical forests. Trends in Ecology and Evolution, 30, 334-346.

Basset, Y., Eastwood, R., Sam, L., Lohman, D.J., Novotny, V., Treuer, T., Miller, S.E., Weiblen, G.D., Pierce, N.E., Bunyavejchewin, S., Sakchoowong, W., Kongnoo, P. & Osorio-Arenas, M.A. 2013. Cross-continental comparisons of butterfly assemblages in rainforests: implications for biological monitoring. Insect Conservation and Diversity, 6, 223-233.

Basset, Y., Cizek, L., Cuénoud, P., Didham, R.K., Guilhaumon, F., Missa, O., Novotny, V., Ødegaard, F., Roslin, T., Schmidl, J., Tishechkin, A.K., Winchester, N.N., Roubik,D.W., Aberlenc, H.-P., Bail, J., Barrios, H., Bridle, J.R., Castaño-Meneses, G., Corbara, B., Curletti, G., Duarte da Rocha, W., De Bakker,D., Delabie, J.H.C., Dejean, A., Fagan, L.L., Floren, A., Kitching, R.L., Medianero, E., Miller, S.E., de Oliveira, E.G., Orivel, J., Pollet, M., Rapp, M., Ribeiro, S.P., Roisin, Y., Schmidt, J.B., Sørensen, L., & Leponce, M. 2012. Arthropod diversity in a tropical forest. Science, 338, 1481-1484.

Basset, Y., Missa, O., Alonso A., Miller, S.E., Curletti, G., De Meyer, M., Eardley, C., Lewis, O.T., Mansell, M.W., Novotny, V. & Wagner, T. 2008. Changes in arthropod assemblages along a wide gradient of disturbance in Gabon. Conservation Biology, 22, 1552-1563.

Basset, Y., Novotny, V., Miller, S.E. & Kitching, R.L. (eds) 2003. Arthropods of Tropical Forests. Spatio-temporal Dynamics and Resource Use in the Canopy. Cambridge University Press, xvi + 474 pp.

Novotny, V., Basset, Y., Miller, S.E., Weiblen, G.D., Bremer, B., Cizek, L. & Drozd, P. 2002. Low host specificity of herbivorous insects in a tropical forest. Nature 416, 841-844.

Basset, Y., Miller, S.E., Gripenberg, S., Ctvrtecka, R., Dahl, C., Leather, S.R. & Didham, R.K. 2019. An entomocentric view of the Janzen-Connell hypothesis. Insect Conservation and Diversity, 12, 1-8.

Basset, Y., Dahl, C., Ctvrtecka, R., Gripenberg, S., Lewis, O.T., Segar, S.T., Klimes, P., Barrios, H., Brown, J.W., Bunyavejchewin, S., Butcher, B.A., Cognato, A.I., Davies, S.J., Kaman, O., Knizek, M., Miller, S.E., Morse, G.E., Novotny, V., Pongpattananurak, N., Pramual, P., Quicke, D.L.J., Robbins, R.K., Sakchoowong, W., Schutze, M., Vesterinen, E.J., Wang, W.-z., Wang, Y.-y., Weiblen, G. & Wright, S.J. 2018. A cross-continental comparison of assemblages of seed- and fruit-feeding insects in tropical rainforests: faunal composition and rates of attack. Journal of Biogeography, 45, 1395-1407.

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Yves Basset

Name

Yves

Last name

Basset

Position

Staff Scientist

Discipline (Private):

External CV:

Department:

Ashley Sharpe

Language English

Archaeology Zooarchaeology

Humans have held a precarious position on this planet, intentionally and unintentionally modifying it for millennia. To understand the world today we must look back in time and trace our role in the ongoing process of environmental change on local and global scales.

Mobility and lead isotopes, 2017

Contemporary Challenges in Zooarchaeological Specimen Identification, 2017

Archaeology Lab

Publications

Research in my lab examines the long and complex history of peoples and cultures in the Americas, and how these ancient societies developed both by changing, and being transformed by, their surrounding environment. My lab uses zooarchaeology, or the identification of animal bones, shells, and other faunal materials from archaeological excavations, in combination with stable isotope analysis to address the many questions concerning how humans made use of animals in the past, such as for food and as craft items, for fostering and maintaining status distinctions, for exchange and tribute relations, and for ritual performances and as symbols.

What effect have humans had on tropical environments over the last several thousand years?

We often take for granted how unnatural our present-day landscape actually is. The Neotropics are no exception, having been occupied by untold numbers of humans for thousands of years. These societies permanently altered plant and animal populations through hunting and harvesting, by domesticating new species, moving and introducing species into new areas, and by occasionally harming or exterminating certain taxa, especially in recent years. To understand the tropical landscape today and what is “natural,” we need to examine and be able to recognize where and how humans have influenced the environment in the past.

How were animals integral to the rise of ancient communities and early states?

Animals and their resources were used for much more than just food in ancient societies, just as they are today. Hunting, fishing, raising and exchanging animals has happened for centuries, profoundly changing both the course of human societies as well as the spread and evolution of animal species on the landscape. As human populations grew over time, people made increasing efforts to control and selectively distribute certain animals and their products, which helped develop and maintain complex political and economic state systems.

How did ancient pre-Columbian societies manage and move animal resources?

Ancient peoples in the Americas were often on the move, and so were their animals. Dogs, turkeys, macaws, fish, and shellfish are only a few of the animals we know that were moving frequently throughout Central America as part of an extensive trade network. Moving and raising animals necessitated specialized experience and knowledge of how to acquire, maintain, and breed particular species. Using zooarchaeological analysis in combination with stable isotope geochemistry, we can study how animals were hunted or bred (often resulting in dramatic changes to their skeletal development), were raised in captivity and fed a human-mandated diet, and were exchanged long distances from one area to another.

2016 Ph.D., Anthropology, University of Florida. Dissertation: A Zooarchaeological Perspective on the Formation of Maya States.

2011 M.A., Anthropology, University of Florida Master’s Thesis: Beyond Capitals and Kings: A Comparison of Animal Resource Use among Ten Late Classic Maya Sites.

2009 B.A., Archaeology, Minor in Biology, Magna cum Laude, Boston University Senior Honors Thesis: From Ritual to Rubbish: The Maya Zooarchaeological Record from San Bartolo, El Petén, Guatemala.

Sharpe, Ashley E., Juan Manuel Palomo, Takeshi Inomata, Daniela Triadan, Flory Pinzón, Jason Curtis, Kitty Emery, George Kamenov, John Krigbaum, Jessica MacLellan, and María Paula Weihmüller. 2024. An isotopic examination of Maya Preclassic and Classic animal and human diets at Ceibal, Guatemala. Journal of Archaeological Science: Reports 55:104522. https://doi.org/10.1016/j.jasrep.2024.104522

Sharpe, Ashley E. and John Krigbaum, editors. 2022. Isotope Research in Zooarchaeology: Methods, Applications, and Advances. University Press of Florida, Gainesville. ISBN 13: 9780813069418.

Sharpe, Ashley E., Bárbara Arroyo, Lori E. Wright, Gloria Ajú, Javier Estrada, George D. Kamenov, Emanuel Serech, and Emily Zavodny. 2022. Comparison of human and faunal enamel isotopes reveals diverse paleodiet and exchange patterns at the highland Maya Site of Kaminaljuyu, Guatemala. Archaeological and Anthropological Sciences 14(1):1-17. https://doi.org/10.1007/s12520-021-01498-8

Sharpe, Ashley E., Nicole Smith-Guzmán, Jason Curtis, Ilean Isaza-Aizpurúa, George D. Kamenov, Thomas A. Wake, and Richard G. Cooke. 2021. A Preliminary Multi-isotope Assessment of Human Mobility and Diet in Pre-Columbian Panama. Journal of Archaeological Science: Reports 36:102876. https://doi.org/10.1016/j.jasrep.2021.102876

Sharpe, Ashley E., Takeshi Inomata, Daniela Triadan, Melissa Burham, Jessica MacLellan, Jessica Munson, and Flory Pinzón. 2020. The Maya Preclassic to Classic Transition Observed through Faunal Trends from Ceibal, Guatemala. PLOS ONE 15(4):e0230892. https://doi.org/10.1371/journal.pone.0230892

Sharpe, Ashley E., Kitty F. Emery, Takeshi Inomata, Daniela Triadan, George D. Kamenov, and John Krigbaum. 2018. Earliest Isotopic Evidence in the Maya Region for Animal Management and Long-Distance Trade at the Site of Ceibal, Guatemala. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1713880115

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Mark Torchin

Language English

Marine Ecology Invasion Biology Disease Ecology

The tropics are believed to be more resistant to invasive species compared to temperate regions. More native biodiversity results in increased competition, predation and parasitism, which leave fewer opportunities to invade. Is that really the case?

Protistan Biogeography: A Snapshot Across a Major Shipping Corridor Spanning Two Oceans, 2017

Tropical fish community does not recover 45 years after predator introduction, 2017

Pan-NEMO Database

My lab’s research focuses on coastal marine ecology with an emphasis on host-parasite and consumer interactions, infectious diseases and biological invasions. I focus on how trophic interactions such as parasitism and predation alter populations, community structure and ecosystems. Parasites are common in many systems, yet their interactions with free-living communities are often poorly understood. This is particularly true in marine and estuarine environments. The land-sea interface is a region of high productivity and biological diversity, but it is changing at an accelerated pace due to increasing human pressures including biological invasions. This provides both research opportunities as well as urgency for understanding how to manage these ecosystems. My lab is working on biological invasions across tropical and temperate systems developing a global perspective on factors driving invasions. With collaborators around the world, we are developing a latitudinal framework approach to examine factors (a) influencing patterns of marine diversity, (b) driving invasions and (c) facilitating parasite/ disease transmission in coastal regions. My research is at the intersection of biological invasions and parasite/ disease ecology.

What would the world look like without parasites?

Parasites are often considered 'bad' but actually they are a natural part of ecosystems and biological diversity. Parasites control host populations, which prevents hosts from becoming excessively abundant. Parasitism is the most common lifestyle on Earth and it may even promote species coexistence and stabilize ecosystems.

Are the tropics more resistant to marine invaders than the temperate zones?

The idea is that tropical regions and their native biodiversity are better at resisting invasive species than temperate regions due to high biodiversity and strong biotic interactions like predation, parasitism and competition. We are testing this hypothesis by using the same experiments across a latitudinal framework that has not been applied in marine systems. The fundamental goal is to learn how biotic interactions shape invasions and shape the biodiversity of marine communities in general.

What happens when you remove parasites from an ecosystem?

Most people think of parasites and diseases as being detrimental to the overall health of an ecosystem. But researchers are now realizing that parasites and pathogens are consumers that have important roles in ecosystems. When we discuss disease ecology, people tend to focus on emerging diseases or outbreaks in a particular place, not necessarily the underlying infectious processes that connect communities and that might be keeping ecosystems healthy. Parasites and pathogens are normal components of ecosystems and contribute to biodiversity. We are now beginning to ask if it is possible to use parasites to understand fundamental principles in patterns of biodiversity.

Some other research questions

Do native predators and parasites control marine invaders? How do consumer interactions, shape the diversity you see on the rocks in the intertidal zone or on tropical or temperate reefs? Are predators and parasites more important in limiting invasions in the tropics compared to higher latitudes? In other words, are you more likely to get eaten in the tropics than in the temperate zone — whether it’s a by parasite, a predator or something that is taking a little bite like a mosquito or a browser like a deer?

Ph.D., University of California, Santa Barbara, 2002

M.S., University of Oregon, 1994

B.A., University of California, Santa Barbara, 1991

Miura, O., M.E. Torchin, E. Bermingham, D.K. Jacobs, R.F. Hechinger (2012). Flying shells: historical dispersal of marine snails across Central America. Proceedings of the Royal Society of London 279:1061-1067. doi: 10.1098/rspb.2011.1599

Freestone, A.L, R.W. Osman, G.M. Ruiz, M.E. Torchin (2011). Stronger predation in tropics shapes species richness patterns in marine communities. Ecology 92: 983-993.

Roche, D.G., B. Leung, E.F. Mendoza Franco, M.E. Torchin (2010). Higher parasite richness, abundance, and impact in native versus introduced cichlid fishes. International Journal of Parasitology 40:1525–1530

Torchin, M.E. and C.E. Mitchell (2004). Parasites, pathogens and invasions by plants and animals. Frontiers in Ecology and the Environment 2: 183-190.

Torchin, M.E., K.D. Lafferty, A.P. Dobson, V.J. McKenzie, A.M. Kuris (2003). Introduced species and their missing parasites. Nature 421: 628-630.

torchinm [at] si.edu

+507 212-8713

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Mark E. Torchin

Name

Mark

Last name

Torchin

Position

Staff Scientist

Discipline (Private):

External CV:

Department:

Ira Rubinoff

Language English

Marine Biology

Understanding the biodiversity of Planet Earth is the most interesting of human endeavors. Where better to pursue this interest than in the tropics?

A century of the Smithsonian Institution on the Isthmus of Panama, 2013

Smithsonian Institution Global Earth Observatories, 2007

As STRI director for 34 years, a lot of innovative things were enabled under my watch. One of the most important was the addition of the five peninsulas to the Barro Colorado Nature Monument, which created a buffer zone around Barro Colorado Island and added research areas that allow for manipulative experiments. Some of the big research accomplishments included the establishment of the 50-hectare forest dynamics plot on Barro Colorado, which led to the Center for Tropical Forest Science and today’s ForestGEO network that has more than 60 plots around the globe. We innovated the use of construction cranes to gain access to the forest canopy for the study of canopy biodiversity and gas exchange between the biosphere and the atmosphere. We also probably opened one of the first, if not the first, molecular lab in the tropics, established a telemetry system to monitor moving organisms in the forest around the clock, and we developed two ocean marine laboratories.

Please note: I no longer advise students. Prospective interns, fellows and postdoctoral researchers should contact STRI’s academic programs office.

Have marine fishes separated by the Isthmus of Panama formed new species?

To answer the question, we examine four species of the fish genus Bathygobius, two species of which are found on the Atlantic coast and two on the Pacific. The differences allopatric species had presumably arisen due to separation of the original common gene pool by the closure of the Isthmus of Panama. By using artificial hybridization experiments and laboratory breeding tests we were able to show that the species on the same side of the Isthmus are completely reproductively separated by pre-mating behavioral isolating mechanisms. The allopatric (transisthmian) species, although now morphologically different, have still not, after 3 million years, evolved complete reproductive isolation, and hybridization in aquaria occurs regularly when presented with no choice of mates or with unbalanced sex ratios of allopatric species.

Could we establish a graduate university at STRI?

I’m currently exploring the possibility of establishing a graduate-level university at STRI that would train students from around the world and allow them to spend their full graduate careers doing research in the tropics. Hundreds of students have completed Ph.D. research at STRI but they are generally required to return to their home institutions for at least a year to complete their doctoral degrees. Establishing a graduate-level university based in the tropics would, in a significant way, help address the global imbalance between the world’s best universities, 94 percent of which are in the temperate zone, and Earth’s biodiversity, 80 percent of which is found in the tropics.

1963 Ph.D., Harvard University, Cambridge, Massachusetts

1961 M.A., Harvard University, Cambridge, Massachusetts

1959 B.S., Queens College, Queens, New York

Rubinoff, Ira. 2013. A Century of the Smithsonian Institution on the Isthmus of Panama. ReVista: Harvard Review of Latin America, 12(3): 62-66.

Rubinoff, Ira; Bermingham, Eldredge; Lydeard, Charles; Davies, Stuart James. 2007. Smithsonian Institution Global Earth Observatories. In: The Full Picture. Geneva: Tudor Rose on Behalf of Group on Earth Observations, pp.82-84.

Rubinoff, Ira; Leigh, Egbert Giles, Jr. 1990. Dealing with Diversity: The Smithsonian Tropical Research Institute and Tropical Biology. Trends in Ecology and Evolution, 5(4): 115-118.

Rubinoff, Ira; Graham, Jeffrey B.; Motta, Jorge. 1986. Diving of the Sea Snake Pelamis platurus in the Gulf of Panamá. I. Dive Depth and Duration. Marine Biology, 91(2): 181-191.

Rubinoff, Ira. 1983. A strategy for preserving tropical forests. In: Sutton, S. L., Tropical Rain Forest: Ecology and Management. Oxford: The British Ecological Society, pp.465-476.

rubinoff [at] si.edu

+507 212.8150

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