The Great
TransIsthmian
Experiment

A bridge on land, a barrier in the sea

Click here and here for presentations on the
rise of the Isthmus & how it changed the world.
.

For more information about the Istmobiome Project please see the
About page.

Some three million years ago, a spectacular natural experiment began when the Isthmus of Panama finally closed, a process that began several million years earlier.

For terrestrial organisms, the formation of the Isthmus created a land bridge that connected North & South America, allowing for massive migrations of plants & animals.

For marine organisms, the story unfolded quite differently. Where once a single tropical ocean flowed, the land bridge became a marine barrier, altering ocean currents & causing different physicochemical environments to emerge.

These radically different conditions are reflected in the resident benthic communities. Many species went locally extinct after the Isthmus closed (e.g., coral, fish, bivalves) and gene flow ceased.

Yet pairs of closely related sister species (geminates) thrive on either side today. Some of these species pairs are so similar that morphology alone is not enough to tell them apart.

How did the close of the Isthmus affect the evolution of microorganisms, the structure of microbial communities, and the function of host-associated microbiomes?

In this project, we make use of contrasting (a) geographic regions, (b) benthic habitats, (c) environmental gradients, and (d) host biology, to understand the evolutionary divergence of marine microbiomes in changing environments & their functional significance in different systems.

We also look more generally at microbial communities from a variety of habitats and envrionments around Panama and beyond.

There are many great reviews about the effects the rise of the Isthmus of Panama had on the evolution of terrestrial and marine organisms, including Lessios (2008), Leigh et. al. (2013), and O’Dea et al. (2016).

Geminate Species

Each card contains a geminate pair; top panels (peach) are Western Atlantic species and bottom panels (royal blue) are Eastern Pacific species.

Click here to see a gallery of all geminates.

Project Portal

Use the cards to access individual project pages or Click here to see a list of projects. On each project page you will find links to the project site, raw data and data products, code, & associated publications

Hypocolypse

Hypocolypse

Field surveys, physiological analyses, & microbial communities during a marine hypoxic event.

BocasBiome

BocasBiome

Intestinal microbiomes from butterflyfish on degraded reefs in Bocas del Toro.

ProjectDIGEST

ProjectDIGEST

Intestinal microbiomes of herbivorous fish from a Florida reef.

Transisthmian Water Microbiomes

Transisthmian Water Microbiomes

Assembly-based metagenomics of coral reef & mangrove water samples from both sides of the Isthmus of Panama.

Interactive fish phylogeny

Interactive fish phylogeny

Betancur-R fish phylogeny, anvi’o, and rvest webscraping

Publications

By people involved in the Istmobiome Project

Quickly discover relevant content by filtering publications.

Workshops

During this project we created, organized, & hosted two marine microbiome workshops in Panama. The objective was to bring experts from various fields together to discuss the evolutionary ecology and function of host-microbiomes, to synthesize discussions into whitepapers, & to build cross-disciplinary collaborations.

Learn More

Eucidaris tribuloides (Slate-pencil Urchin) by Nick Hobgood retrieved from Wikimedia Commons (original) licensed under CC BY-SA 3.0.

Workshops

Field Guides

Fishes & Invertebrates from Panama’s Caribbean & Pacific Coasts

Field guide to fishes of the Eastern Pacific coast of Panama
Includes species reported on coral reefs and on shallow rocky shores in the Coiba National Park and the Pearl Islands.
Field guide to fishes of the Eastern Pacific coast of Panama
Field guide to corals & other macro-invertebrates of the Eastern Pacific coast of Panama
Includes species reported on coral reefs in the Coiba National Park and the Pearl Islands.
Field guide to corals & other macro-invertebrates of the Eastern Pacific coast of Panama
Field guide to fishes of the Caribbean coast of Panama
Includes species reported on coral reefs, mangroves and seagrass beds inside and outside the Bay of Almirante (Bocas del Toro), and around Isla Grande.
Field guide to fishes of the Caribbean coast of Panama
Field guide to cryptobenthic invertebrates of the Caribbean coast of Panama
Photographs of small invertebrates collected in the reef structure created by dead corals in the Bahia Almirante, Bocas del Toro.
Field guide to cryptobenthic invertebrates of the Caribbean coast of Panama

Presentations

A gallery of talks & presentations created by members of the Istmobiome Project

Press Coverage

Stories about our science.

Caribbean asphyxiation

Caribbean asphyxiation

Desperate brittlestars, suffocating corals and resilient microbes. A story by Beth King from STRI about our Bocas del Toro hypoxia study featuring Jarrod Scott & Matt Leray. Photo by Maggie Johnson.

What happens to marine life when oxygen is scarce?

What happens to marine life when oxygen is scarce?

A story by Kylee Denesha from Woods Hole Oceanographic Institution about our Bocas del Toro hypoxia study featuring Jarrod Scott. Photo by Maggie Johnson.

Picture the Unseen

Picture the Unseen

A story about visualizing microbial communities featuring Jarrod Scott. Design by Jorge Alemán.

Seafood Stew

Seafood Stew

A story about a new shrimp species from Panama’s Coiba National Park featuring Matt Leray. Photo by Arthur Anker.

The future of Coiba coral reefs

The future of Coiba coral reefs

An interview with Matt Leray. Photo by Sean Mattson.

Reef Fish & their Microbes

Reef Fish & their Microbes

Study finds fish have diverse, distinct gut microbiomes. Photo by José Alejandro Alvarez.

Tropical Microbiomes

Tropical Microbiomes

STRI hosts 2019 marine microbiome workshop.

Coiba: From Prison to Biodiversity Sanctuary

Coiba: From Prison to Biodiversity Sanctuary

A short documentary piece about Isla Coiba by one of our students. Photo by Toa Heftiba.

Eastern Tropical Pacific

Eastern Tropical Pacific

A story about our first expedition to Panama’s Coiba National Park. Photo by Sean Mattson.

Meet the Istmobiome Team

Researchers

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Jarrod J Scott

Postdoctoral Fellow

Complex systems, Microbiomes, Coral reefs, Ants, Panama, Hydrothermal vents, Archaeology, Knots

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Laetitia GE Wilkins

Postdoctoral Fellow

Host-microbe interactions, Host-microbe evolution, Host-microbes in ecosystem function & stability

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Matthieu Leray

Postdoctoral Fellow

Biodiversity, Symbiosis, Shrimp, Trophic ecology, Microbes, Coral reefs, Tropical fish, Mangroves

Principal Investigators

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William T Wcislo

Staff Scientist

Project Scientists

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David Coil

Project Scientist

Microbiology, Bacteriology, Next-generation sequencing, Bacterial genomics, Genome assembly