The evolution of host

associated microbiomes separated by the Isthmus of Panama

Funding: Gordon and Betty Moore Foundation, STRI


The closure of the Isthmus of Panama, approximately 3 million years ago, presents an unrivaled opportunity to study processes of diversification and adaptation in the sea. An ancient ocean was split up into the Pacific and the Caribbean Sea, two environments with strikingly different geophysical characteristics. Populations of animals, plants and their microbial symbionts got separated and followed separate evolutionary trajectories in response to new and contrasting environments: the Caribbean became warmer, saltier and nutrient poor, whereas the Tropical Eastern Pacific became more acidic with seasonal fluctuations in temperature and nutrients caused by upwelling of deep water when trade-winds blow.

Extensive studies have used this natural experiment to examine evolutionary processes relating to molecular divergence and speciation of shallow-water marine macro-organisms in the two oceans, using pairs of sister species, one in the Western Atlantic (WA) and one TEP. In contrast to the macrofauna and flora, nothing was known about how the isthmian divergence has shaped the evolution of the microbiomes of sister hosts.


We take advantage of the isthmian experiment, leveraging extensive studies on the marine biology of hosts and their environments, to address key questions relating to the evolutionary divergence of marine microbiomes in changing environments and their functional significance such as:

  • What is the contribution of host phylogenetic relatedness, host traits such as diet or behavior, and environmental factors in shaping the structure of marine microbiomes in sister hosts from two different oceans?
  • Which microbes co-evolve with their hosts across the isthmus, indicating a long-term association? What is the functional significance of these co-diverging microbes and their potential roles in host adaptation and ecological interactions?
  • How do host-associated microbes adapted to the distinct environmental conditions in the WA and TEP, and what are the potential mechanisms underlying their adaptation? Is there evidence for convergent evolution of microbiomes in response to similar environmental pressures in different geographic locations?
  • How do microbial symbionts influence hosts’ resistance and resilience to environmental changes? Do symbionts associating with hosts in one ocean provide greater resilience and adaptability to environmental fluctuations than symbionts in the other ocean? And what are the underlying mechanisms behind these differences?


Laetitia GE Wilkins

Max Planck Institute for Marine Microbiology, Germany 

Marine Host-Microbe Ecology and Evolution

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Jonathan A Eisen 

University of California Davis, USA

Ecology, Evolution and Function of Microbes and Microbial Communities

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Jarrod J Scott 

Smithsonian Tropical Research Institute, Panama 

Microbial Ecology 

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Friederike Clever 

Manchester Metropolitan University, UK 

Coral Reef Fish Ecology and Genetics


Kristin M Hultgren 

Seattle University, USA 

Ecology and Evolution of Marine Invertebrates 


Benedict Yuen 

Max Planck Institute for Marine Microbiology, Germany 

Marine Host-Microbe Ecology and Evolution


Carla Hurt 

Tennessee Tech University, USA 

Molecular Ecology 

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Maggie D Johnson 

King Abdullah Univ of Science and Technology, Saudi Arabia

Global Change Ecology 

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