Research Overview

Our work utilizes computational biological approaches (and occasional forays into the field and the lab) for understanding a variety of evolutionary questions, with a long-standing interest is the origin and evolution of metabolism and biological energy cycling. A brief outline of our major research themes, as well as links to relevant papers and more detailed reading (pdfs coming soon), can be found below:

Using comparative genomics to understand the distribution, diversity, and evolutionary history of metabolic processes such as photosynthesis, carbon fixation, nitrogen fixation and cycling, and aerobic/anaerobic respiration. These pathways have complex histories that each present a unique cross-section and important details of evolution in action and have shaped the history of our planet. Our work has included sequencing and analyzing the genomes and metagenomes of microbes and communities from extreme environments that are relevant to how we think about the limits of life on Earth and potentially on habitable worlds.

  • Raymond, J. and Alsop, E. (2015) Microbial evolution in extreme environments: microbial migration, genomic highways, and geochemical barriers in hydrothermal ecosystems, Environmental Systems Research, 4: 14, doi 10.1186/s40068-015-0038-x.
  • Bailey, A.C., Kellom, M., Poret-Peterson, A.T., Noonan, K., Hartnett, H.E., Raymond, J. (2014) Draft Genome of Massilia   consociata BSC265, Isolated from Biological Soil Crust of Moab, Utah. Genome Ann, 2(6), e01199-14.
  • Bailey, A.C., Kellom, M., Poret-Peterson, A.T., Noonan, K., Hartnett, H.E., Raymond, J. (2014) Draft Genome of Microvirgo sp. BSC39, Isolated from Biological Soil Crust of Moab, Utah. Genome Ann, 2(6), e01197-14.
  • Bailey, A.C., Kellom, M., Poret-Peterson, A.T., Noonan, K., Hartnett, H.E., Raymond, J. (2014) Draft Genome of Bacillus   subtilis BSC154, Isolated from Biological Soil Crust of Moab, Utah. Genome Ann, 2(6), e01198-14.
  • Alsop, E.B., Boyd, E.S., Raymond, J. (2014) Merging Metagenomics and Geochemistry Reveals Environmental Controls on Biological Diversity and Evolution. BMC Ecology, 14:16, doi:10.1186.
  • Dodsworth, J.A., Blainey, P.C., Murugapiran, S.K., Swingley, W.D., Ross, C.A., Glavina, T., Tringe, S.G., Raymond, J., Quake, S.R., and Hedlund, B.P. (2013) Single-cell genomics and metagenomics suggests a fermentative, saccharolytic lifestyle for members of the OP9 lineage. Nature Communications, 4:1854, doi: 10.1038/ncomms2884.
  • Swingley, W.D., Meyer-Dombard, D.R., Alsop, E.B., Falenski, H.D., Havig, J.R., Shock, E.L., Raymond, J. (2012) Coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem. PLoS One, 7(6):e38108.
  • Meyer-Dombard, D.R., Swingley, W., Raymond, J., Shock, E.L., Summons, R.E. (2011) Hydrothermal ecotones and streamer biofilm communities in the Lower Geyser Basin, Yellowstone National Park. Environmental Microbiology, 8:2216-31.
  • Havig, J.R., Raymond, J., Meyer-Dombard, D.R., Zolotova, N., Shock, E.L. (2011) Merging isotopes and community genomics in a siliceous sinter-depositing hot spring. Journal of Geophysical Research, 116:G01005.
  • Sattley, W.M., Madigan, M.T., Swingley, W.D., Cheung, P.C., Clocksin, K.M., Conrad, A.L., Dejesa, L.C., Honchak, B.M., Jung, D.O., Karbach, L.E., Kurgdoglu, A., Lahiri, S., Mastrian, S.D., Page, L.E., Taylor, H.L., Wang, Z.T., Raymond, J., Chen, M., Blankenship, R.E., Touchman, J.W. (2008) The genome of Heliobacterium modesticaldum, a phototrophic representative of the Firmicutes containing the simplest photosynthetic apparatus. Journal of Bacteriology, 190:4687-96.
  • Swingley W.D., Chen M., Cheung P.C., Conrad A.L., Dejesa L.C., Hao J., Honchak B.M., Karbach L.E., Kurdoglu A., Lahiri S, Mastrian S.D., Miyashita H., Page L.E., Ramakrishna P., Satoh S., Sattley W.M., Shimada Y., Taylor H.L., Tomo T., Tsuchiya T., Wang Z.T., Raymond J., Mimuro M., Blankenship R.E. and Touchman J.W. (2008) Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina. Proceedings of the National Academy of Sciences, 105: 2005-10.

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We’re also developing tools to infer metabolic networks from genomic data, then simulate how the architecture of these networks changes in response to perturbations. Recent work showed how the utilization of oxygen, which began about 2.2 billion years ago when oxygen first appeared in Earth’s atmosphere, profoundly changed not only the energetics, but also the types of compounds that organisms could synthesize.

  • Raymond, J. and Segré, D. (2006) The effect of oxygen on biochemical networks and the evolution of complex life. Science, 311, 1764-7.
  • Falkowski, P.G. (2006) Tracing Oxygen’s Imprint on Earth’s Metabolic Evolution. Science, 311, 1724-5.
  • Guarnieri V. “Così l’ossigeno creò Gaia” La Stampa December 6, 2006 (Neat article on Raymond/Segré, for the Italians out there).
  • Interesting coverage of the Science paper by M.L. Phillips in The Scientist Raymond, J. and Blankenship, R.E. (2004) Biosynthetic Pathways, Gene Replacement and the Antiquity of Life. Geobiology, 2, 1472-4.

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We’re using comparative genomics to help resolve the tree of life and the origin of metabolic processes within that tree, with a particular focus on microbial diversity. This requires developing rigorous evolutionary models that are able to account for thousands of genes worth of evolutionary information, and accurately identify horizontal gene transfer events. As our knowledge of microbial diversity continues to explode, this evolutionary framework becomes more and more critical and we are developing novel approaches that integrate phylogenetic information from hundreds – and potentially thousands – of genes conserved at different taxonomic levels, in order to reconstruct accurate evolutionary trees for completed genomes.

  • Raymond, J. (2009) The Role of Horizontal Gene Transfer in Photosynthesis, Oxygen Production, and Oxygen Tolerance. In: Horizontal Gene Transfer: Genomes in Flux, M.B. Gogarten, J.P. Gogarten, and L.C. Olendzenski eds., pp. 323-338.
  • Swingley, W.D., Blankenship, R.E., and Raymond, J. (2009) Evolutionary Relationships Among Purple Photosynthetic Bacteria and the Origin of Proteobacterial Photosynthetic Systems. In: The Purple Phototrophic Bacteria, C.N. Hunter, F. Daldal, M.C. Thurnauer and J.T. Beatty eds., pp. 17-29.
  • Raymond, J. (2008) Coloring in the tree of life. Trends in Microbiology, 16:41-43.
  • Swingley, W.D., Blankenship, R.E. and Raymond, J., (2008) Integrating Markov clustering and molecular phylogenetics to reconstruct the cyanobacterial species tree from conserved protein families. Molecular Biology and Evolution, 25:643-54.
  • Swingley, W.D., Blankenship, R.E., and Raymond, J. (2008) Insights into cyanobacterial evolution from comparative genomics. In: The Cyanobacteria: Molecular Biology, Genomics and Evolution, A. Herrero and E. Flores eds., pp. 21-44.
  • Blankenship, R.E., Raymond, J., Staples, C., and Mukhopadhyay, B. (2007) Evolution of functional diversity in nitrogenase homologs. Biological Nitrogen Fixation: Towards Poverty Alleviation through Sustainable Agriculture, 42: 305-306.
  • Raymond, J. (2005) The Evolution of Biological Carbon and Nitrogen Cycling—a Genomic Perspective. Reviews in Mineralogy & Geochemistry, 59, 211-31.
  • Raymond, J. and Blankenship, R.E. (2004) Biosynthetic Pathways, Gene Replacement and the Antiquity of Life. Geobiology, 2, 1472-4.
  • Raymond, J., Siefert, J.L., Staples, C.R., and Blankenship, R.E. (2004) The Natural History of Nitrogen Fixation. Molecular Biology and Evolution, 21, 541-54. (Selected for Faculty of 1000)
  • Zhaxybayeva, O., Hamel, L., Raymond, J., and Gogarten, J.P. (2004) Visualization of Phylogenetic Content of Five Genomes with Dekapentagonal Maps. Genome Biology, 5(3):R20.
  • Raymond, J., Zhaxybayeva, O., Gogarten, J.P., and Blankenship, R.E. (2003) Evolution of photosynthetic prokaryotes: a maximum likelihood mapping approach. Philosophical Transactions of the Royal Society of London B, 358, 223-230. (Selected for Faculty of 1000)
  • Raymond, J., Zhaxybayeva, O., Gogarten, J.P., and Blankenship, R.E. (2002) Whole genome analysis of photosynthetic prokaryotes, Science, 298, 1616-1620. Science “News of the Week” article on the above paper

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Finally, we’ve been involved with developing novel approaches for understanding how protein structures evolve, and for detecting structural homology between distantly related proteins. This has included using so-called point-registration algorithms to detect regions of conserved atomic structure in and around the active sites of proteins (Raymond & Blankenship 2008) , making comparisons of protein 3D structures (Sadekar et al. 2006) as well as detecting positive and purifying selection in protein sequences and mapping these on to protein structures (Raymond & Blankenship 2004; Olson and Raymond 2003). These methods are providing new insights into how the molecular machinery that carries out photosynthesis may have originated and evolved.

  • Raymond, J. and Blankenship, R.E. (2008) The Origin of the Oxygen Evolving Complex. Coordination Chemistry Reviews, in press.
  • Blankenship, R.E., Sadekar, S., and Raymond, J. (2007) The Evolutionary Transition from Anoxygenic to Oxygenic Photosynthesis. In: Falkowski, P.G. and Knoll, A.H. (Eds.) Evolution of Primary Producers in the Sea, Elsevier, Amsterdam, pp. 22-37.
  • Sadekar, S., Raymond, J., and Blankenship, R.E. (2006) Conservation of Distantly Related Membrane Proteins: Photosynthetic Reaction Centers Share a Common Structural Core. Molecular Biology and Evolution, 23, 2001-7.
  • Raymond J., and Blankenship, R.E. (2004) The evolutionary development of the protein complement of Photosystem II. Biochimica et Biophysica Acta, 1655, 133-9.
    Olson, J.M. and Raymond, J. (2003) The FMO-protein is related to PscA in the reaction center of green sulfur bacteria. Photosynthesis Research, 75, 277-285.

Conference on Complex Systems 2015 at ASU

The international Conference on Complex Systems (#CCS15) was hosted by ASU this year, and featured some incredibly varied talks and symposia.  Click below to download Prof. Raymond[...]

Prof. Jason Raymond

Prof. Raymond studies the origin and co-evolution of life and our planet, as well as the metabolic systems upon which life is built.  His research ranges from using evolutionary genomics to understand key evolutionary transitions on the ancient Earth, and molecular genetic approaches for investigating the function and diversity of microbial life in extreme environments. <email><curriculum Vitae>

Matt Kellom

Presently a Ph.D. candidate in the Raymond lab, using systems biology to investigate how microbial communities adapt and evolve in some of the most extreme environments on the planet.

Alexis Bailey

An undergrad at William Woods University, Alexis has worked as a summer undergraduate research fellow with us since 2014, analyzing the genomes of microbes isolated from the extremely arid desert crusts of Moab, Utah, and developing phylogenomic tools to analyze the evolution and diversity of key metabolic pathways, such as carbon fixation, that have shaped Earth's history.

Dr. Eric Alsop

Eric completed his Ph.D. with Prof. Raymond in 2014, and is now a Joint Genome Institute postdoc with Nikos Kyrpides, working with Shell on metagenomic and geochemical analyses of petroleum deposits.

Prof. Wesley Swingley

Former NASA Exobiology postdoc with Prof. Raymond, now running his own research group at Northern Illinois University.

Jordan Okie

Now an Assistant Research Professor at ASU, Jordan worked with Prof. Raymond as a SESE Exploration Fellow in 2011-2012.  His research focuses on developing multiscale approaches for understanding how energy flow and metabolism shapes ecosystems.

Supplementary Data

Supplementary data from previous and upcoming papers.

Contact us

We’re actively recruiting motivated graduate and undergraduate students interested in research at the interface of evolutionary biology, biogeochemistry, microbial genomics, and network theory, as well as collaborators in these areas.  Note to potential graduate students that Prof. Raymond is a Faculty Affiliate in the School of Life Sciences and the Department of Chemistry and Biochemistry, and students in programs from those schools can pursue their graduate degrees working with him.

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