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

  • 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 ...
  • Sewage reflects the microbiomes of human populations 

    Newton, Ryan J.; McLellan, Sandra L.; Dila, Deborah K.; Vineis, Joseph H.; Morrison, Hilary G.; Eren, A. Murat; Sogin, Mitchell L. (American Society for Microbiology, 2015-02-24)
    Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker ...
  • Minimum entropy decomposition : unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences 

    Eren, A. Murat; Morrison, Hilary G.; Lescault, Pamela J.; Reveillaud, Julie; Vineis, Joseph H.; Sogin, Mitchell L. (Nature Publishing Group, 2014-10-17)
    Molecular microbial ecology investigations often employ large marker gene datasets, for example, ribosomal RNAs, to represent the occurrence of single-cell genomes in microbial communities. Massively parallel DNA sequencing ...
  • Satellite remote sensing data can be used to model marine microbial metabolite turnover 

    Larsen, Peter E.; Scott, Nicole; Post, Anton F.; Field, Dawn; Knight, Rob; Hamada, Yuki; Gilbert, Jack A. (Nature Publishing Group, 2014-07-29)
    Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial ...
  • A single genus in the gut microbiome reflects host preference and specificity 

    Eren, A. Murat; Sogin, Mitchell L.; Morrison, Hilary G.; Vineis, Joseph H.; Fisher, Jenny C.; Newton, Ryan J.; McLellan, Sandra L. (Nature Publishing Group, 2014-06-17)
    Delineating differences in gut microbiomes of human and animal hosts contributes towards understanding human health and enables new strategies for detecting reservoirs of waterborne human pathogens. We focused upon Blautia, ...
  • Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents 

    Anderson, Rika E.; Sogin, Mitchell L.; Baross, John A. (2014-11)
    Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in ...
  • Phaeocystis antarctica blooms strongly influence bacterial community structures in the Amundsen Sea polynya 

    Delmont, Tom O.; Hammar, Katherine M.; Ducklow, Hugh W.; Yager, Patricia L.; Post, Anton F. (Frontiers Media, 2014-12-19)
    Rising temperatures and changing winds drive the expansion of the highly productive polynyas (open water areas surrounded by sea ice) abutting the Antarctic continent. Phytoplankton blooms in polynyas are often dominated ...
  • Oligotyping reveals community level habitat selection within the genus Vibrio 

    Schmidt, Victor T.; Reveillaud, Julie; Zettler, Erik R.; Mincer, Tracy J.; Murphy, Leslie G.; Amaral-Zettler, Linda A. (Frontiers Media, 2014-11-13)
    The genus Vibrio is a metabolically diverse group of facultative anaerobic bacteria, common in aquatic environments and marine hosts. The genus contains several species of importance to human health and aquaculture, including ...
  • Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping 

    Mark Welch, Jessica L.; Utter, Daniel R.; Rossetti, Blair J.; Mark Welch, David B.; Eren, A. Murat; Borisy, Gary G. (Frontiers Media, 2014-11-07)
    The human mouth is an excellent system to study the dynamics of microbial communities and their interactions with their host. We employed oligotyping to analyze, with single-nucleotide resolution, oral microbial 16S ribosomal ...
  • The transcriptional response to oxidative stress during vertebrate development : effects of tert-butylhydroquinone and 2,3,7,8-tetrachlorodibenzo-p-dioxin 

    Hahn, Mark E.; McArthur, Andrew G.; Karchner, Sibel I.; Franks, Diana G.; Jenny, Matthew J.; Timme-Laragy, Alicia R.; Stegeman, John J.; Woodin, Bruce R.; Cipriano, Michael J.; Linney, Elwood A. (Public Library of Science, 2014-11-17)
    Oxidative stress is an important mechanism of chemical toxicity, contributing to teratogenesis and to cardiovascular and neurodegenerative diseases. Developing animals may be especially sensitive to chemicals causing ...
  • Phytoplankton responses to atmospheric metal deposition in the coastal and open-ocean Sargasso Sea 

    Mackey, Katherine R. M.; Buck, Kristen N.; Casey, John R.; Cid, Abigail; Lomas, Michael W.; Sohrin, Yoshiki; Paytan, Adina (Frontiers Media, 2012-10-12)
    This study investigated the impact of atmospheric metal deposition on natural phytoplankton communities at open-ocean and coastal sites in the Sargasso Sea during the spring bloom. Locally collected aerosols with different ...
  • Marine bacterial, archaeal and eukaryotic diversity and community structure on the continental shelf of the western Antarctic Peninsula 

    Luria, Catherine M.; Ducklow, Hugh W.; Amaral-Zettler, Linda A. (Inter-Research, 2014-10-02)
    The classic view of polar ocean foodwebs emphasizes large predators sustained by energy and material flow through short, efficient diatom-krill-predator food chains. Bacterial activity is generally low in cold polar waters ...

View more submissions >