The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution explores the evolution and interaction of genomes of diverse organisms that play significant roles in environmental biology and human health. This dynamic research program integrates the powerful tools of genome science, molecular phylogenetics, and molecular ecology to advance our understanding of how living organisms are related to each other, to provide the tools to quantify and assess biodiversity, and to identify genes and underlying mechanisms of biomedical importance. Projects span all evolutionary time scales, ranging from deep phylogenetic divergence of ancient eukaryotic and prokaryotic lineages, to ecological analyses of how members of diverse communities contribute and respond to environmental change.

Recent Submissions

  • Mobile genetic elements : in silico, in vitro, in vivo 

    Arkhipova, Irina R.; Rice, Phoebe A. (2015-11-30)
    Mobile genetic elements (MGEs), also called transposable elements (TEs), represent universal components of most genomes and are intimately involved in nearly all aspects of genome organization, function, and evolution. ...
  • The obese gut microbiome across the epidemiologic transition 

    Dugas, Lara R.; Fuller, Miles; Gilbert, Jack A.; Layden, Brian T. (BioMed Central, 2016-01-11)
    The obesity epidemic has emerged over the past few decades and is thought to be a result of both genetic and environmental factors. A newly identified factor, the gut microbiota, which is a bacterial ecosystem residing ...
  • Microbial diversity - exploration of natural ecosystems and microbiomes 

    Gibbons, Sean M.; Gilbert, Jack A. (2015-09-29)
    Microorganisms are the pillars of life on Earth. Over billions of years, they have evolved into every conceivable niche on the planet. Microbes reshaped the oceans and atmosphere and gave rise to conditions conducive to ...
  • A simple novel device for air sampling by electrokinetic capture 

    Gordon, Julian; Gandhi, Prasanthi; Shekhawat, Gajendra; Frazier, Angel; Hampton-Marcell, Jarrad T.; Gilbert, Jack A. (BioMed Central, 2015-12-27)
    A variety of different sampling devices are currently available to acquire air samples for the study of the microbiome of the air. All have a degree of technical complexity that limits deployment. Here, we evaluate the use ...
  • The biogeography of the Plastisphere : implications for policy 

    Amaral-Zettler, Linda A.; Zettler, Erik R.; Slikas, Beth; Boyd, Gregory D.; Melvin, Donald W.; Morrall, Clare E.; Proskurowski, Giora; Mincer, Tracy J. (Ecological Society of America, 2015-12)
    Microplastics (particles less than 5 mm) numerically dominate marine debris and occur from coastal waters to mid-ocean gyres, where surface circulation concentrates them. Given the prevalence of plastic marine debris (PMD) ...
  • Microbial gene abundance and expression patterns across a river to ocean salinity gradient 

    Fortunato, Caroline S.; Crump, Byron C. (Public Library of Science, 2015-11-04)
    Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. ...
  • Anvi’o : an advanced analysis and visualization platform for ‘omics data 

    Eren​, A. Murat; Esen, Ozcan C.; Quince, Christopher; Vineis, Joseph H.; Morrison, Hilary G.; Sogin, Mitchell L.; Delmont, Tom O. (PeerJ, 2015-10-08)
    Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively ...
  • Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica 

    Delmont, Tom O.; Eren, A. Murat; Vineis, Joseph H.; Post, Anton F. (Frontiers Media, 2015-10-26)
    Antarctica polynyas support intense phytoplankton blooms, impacting their environment by a substantial depletion of inorganic carbon and nutrients. These blooms are dominated by the colony-forming haptophyte Phaeocystis ...
  • Chemical dispersants can suppress the activity of natural oil-degrading microorganisms 

    Kleindienst, Sara; Seidel, Michael; Ziervogel, Kai; Grim, Sharon L.; Loftis, Kathy; Harrison, Sarah; Malkin, Sairah Y.; Perkins, Matthew J.; Field, Jennifer; Sogin, Mitchell L.; Dittmar, Thorsten; Passow, Uta; Medeiros, Patricia M.; Joye, Samantha B. (2015-09)
    During the Deepwater Horizon oil well blowout in the Gulf of Mexico, the application of 7 million liters of chemical dispersants aimed to stimulate microbial crude oil degradation by increasing the bioavailability of oil ...
  • Aquarium microbiome response to ninety-percent system water change : clues to microbiome management 

    Van Bonn, William; LaPointe, Allen; Gibbons, Sean M.; Frazier, Angel; Hampton-Marcell, Jarrad T.; Gilbert, Jack A. (2015-04)
    The bacterial community composition and structure of water from an established teleost fish system was examined before, during and after a major water change to explore the impact of such a water-change disturbance on the ...
  • Lifestyle evolution in cyanobacterial symbionts of sponges 

    Burgsdorf, Ilia; Slaby, Beate M.; Handley, Kim M.; Haber, Markus; Blom, Jochen; Marshall, Christopher W.; Gilbert, Jack A.; Hentschel, Ute; Steindler, Laura (American Society for Microbiology, 2015-06-02)
    The “Candidatus Synechococcus spongiarum” group includes different clades of cyanobacteria with high 16S rRNA sequence identity (~99%) and is the most abundant and widespread cyanobacterial symbiont of marine sponges. The ...
  • Divergent responses of Atlantic coastal and oceanic Synechococcus to iron limitation 

    Mackey, Katherine R. M.; Post, Anton F.; McIlvin, Matthew R.; Cutter, Gregory A.; John, Seth G.; Saito, Mak A. (2015-06-19)
    Marine Synechococcus are some of the most diverse and ubiquitous phytoplankton, and iron (Fe) is an essential micronutrient that limits productivity in many parts of the ocean. To investigate how coastal and oceanic Atlantic ...
  • The ocean sampling day consortium 

    Kopf, Anna; Bicak, Mesude; Kottmann, Renzo; Schnetzer, Julia; Kostadinov, Ivaylo; Lehmann, Katja; Fernandez-Guerra, Antonio; Jeanthon, Christian; Rahav, Eyal; Ullrich, Matthias; Wichels, Antje; Gerdts, Gunnar; Polymenakou, Paraskevi; Kotoulas, Giorgos; Siam, Rania; Abdallah, Rehab Z.; Sonnenschein, Eva C.; Cariou, Thierry; O’Gara, Fergal; Jackson, Stephen; Orlic, Sandi; Steinke, Michael; Busch, Julia; Duarte, Bernardo; Cacador, Isabel; Canning-Clode, Joao; Bobrova, Oleksandra; Marteinsson, Viggo; Reynisson, Eyjolfur; Loureiro, Clara Magalhaes; Luna, Gian Marco; Quero, Grazia Marina; Loscher, Carolin R.; Kremp, Anke; DeLorenzo, Marie E.; Øvreås, Lise; Tolman, Jennifer; LaRoche, Julie; Penna, Antonella; Frischer, Marc; Davis, Timothy; Katherine, Barker; Meyer, Christopher P.; Ramos, Sandra; Magalhaes, Catarina; Jude-Lemeilleur, Florence; Aguirre-Macedo, Ma Leopoldina; Wang, Shiao; Poulton, Nicole; Jones, Scott; Collin, Rachel; Fuhrman, Jed A.; Conan, Pascal; Alonso, Cecilia; Stambler, Noga; Goodwin, Kelly; Yakimov, Michael M.; Baltar, Federico; Bodrossy, Levente; Van De Kamp, Jodie; Frampton, Dion M. F.; Ostrowski, Martin; Van Ruth, Paul; Malthouse, Paul; Claus, Simon; Deneudt, Klaas; Mortelmans, Jonas; Pitois, Sophie; Wallom, David; Salter, Ian; Costa, Rodrigo; Schroeder, Declan C.; Kandil, Mahrous M.; Amaral, Valentina; Biancalana, Florencia; Santana, Rafael; Pedrotti, Maria Luiza; Yoshida, Takashi; Ogata, Hiroyuki; Ingleton, Tim; Munnik, Kate; Rodriguez-Ezpeleta, Naiara; Berteaux-Lecellier, Veronique; Wecker, Patricia; Cancio, Ibon; Vaulot, Daniel; Bienhold, Christina; Ghazal, Hassan; Chaouni, Bouchra; Essayeh, Soumya; Ettamimi, Sara; Zaid, El Houcine; Boukhatem, Noureddine; Bouali, Abderrahim; Chahboune, Rajaa; Barrijal, Said; Timinouni, Mohammed; El Otmani, Fatima; Bennani, Mohamed; Mea, Marianna; Todorova, Nadezhda; Karamfilov, Ventzislav; ten Hoopen, Petra; Cochrane, Guy; L’Haridon, Stephane; Bizsel, Kemal Can; Vezzi, Alessandro; Lauro, Federico M.; Martin, Patrick; Jensen, Rachelle M.; Hinks, Jamie; Gebbels, Susan; Rosselli, Riccardo; De Pascale, Fabio; Schiavon, Riccardo; dos Santos, Antonina; Villar, Emilie; Pesant, Stephane; Cataletto, Bruno; Malfatti, Francesca; Edirisinghe, Ranjith; Herrera Silveira, Jorge A.; Barbier, Michele; Turk, Valentina; Tinta, Tinkara; Fuller, Wayne J.; Salihoglu, Ilkay; Serakinci, Nedime; Ergoren, Mahmut Cerkez; Bresnan, Eileen; Iriberri, Juan; Fronth Nyhus, Paul Anders; Bente, Edvardsen; Karlsen, Hans Erik; Golyshin, Peter N.; Gasol, Josep M.; Moncheva, Snejana; Dzhembekova, Nina; Johnson, Zackary; Sinigalliano, Christopher David; Gidley, Maribeth Louise; Zingone, Adriana; Danovaro, Roberto; Tsiamis, George; Clark, Melody S.; Costa, Ana Cristina; El Bour, Monia; Martins, Ana M.; Collins, R. Eric; Ducluzeau, Anne-Lise; Martinez, Jonathan; Costello, Mark J.; Amaral-Zettler, Linda A.; Gilbert, Jack A.; Davies, Neil; Field, Dawn; Glockner, Frank Oliver (BioMed Central, 2015-06-19)
    Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. ...
  • Ecological functions of uncultured microorganisms in the cobalt-rich ferromanganese crust of a seamount in the central Pacific are elucidated by fosmid sequencing 

    Huo, Yingyi; Cheng, Hong; Post, Anton F.; Wang, Chunsheng; Jiang, Xiawei; Pan, Jie; Wu, Min; Xu, Xuewei (2014-07)
    Cobalt-rich ferromanganese is an important seafloor mineral and is abundantly present in the seamount crusts. Such crusts form potential hotspots for biogeochemical activity and microbial diversity, yet our understanding ...
  • Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics 

    Delmont, Tom O.; Eren, A. Murat; Maccario, Lorrie; Prestat, Emmanuel; Esen, Ozcan C.; Pelletier, Eric; Le Paslier, Denis; Simonet, Pascal; Vogel, Timothy M. (Frontiers Media, 2015-04-30)
    Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution ...
  • Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus) 

    Traeger, Lindsay L.; Volkening, Jeremy D.; Moffett, Howell; Gallant, Jason R.; Chen, Po-Hao; Novina, Carl D.; Phillips, George N.; Anand, Rene; Wells, Gregg B.; Pinch, Matthew; Guth, Robert; Unguez, Graciela A.; Albert, James S.; Zakon, Harold H.; Sussman, Michael R.; Samanta, Manoj P. (BioMed Central, 2015-03-26)
    With its unique ability to produce high-voltage electric discharges in excess of 600 volts, the South American strong voltage electric eel (Electrophorus electricus) has played an important role in the history of science. ...
  • Evaluation of pyrrolidine and pyrazolone derivatives as inhibitors of trypanosomal phosphodiesterase B1 (TbrPDEB1) 

    Amata, Emanuele; Bland, Nicholas D.; Campbell, Robert K.; Pollastri, Michael P. (2015-04-13)
    Human African trypanosomiasis (HAT) is a parasitic disease, caused by the protozoan pathogen Trypanosoma brucei, which affects thousands every year and which is in need of new therapeutics. Herein we report the synthesis ...
  • The gut microbiota of rural Papua New Guineans : composition, diversity patterns, and ecological processes 

    Martinez, Ines; Stegen, James C.; Maldonado-Gomez, Maria X.; Eren, A. Murat; Siba, Peter M.; Greenhill, Andrew R.; Walter, Jens (Cell Press, 2015-04-16)
    Although recent research revealed an impact of westernization on diversity and composition of the human gut microbiota, the exact consequences on metacommunity characteristics are insufficiently understood, and the underlying ...
  • Rotifers as experimental tools for investigating aging 

    Snell, Terry W.; Johnston, Rachel K.; Gribble, Kristin E.; Mark Welch, David B. (Taylor & Francis, 2014-06-12)
    Comparative biogerontology has much to contribute to the study of aging. A broad range of aging rates have evolved to meet environmental challenges, and understanding these adaptations can produce valuable insights into ...

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