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Nicholas Putnam
Assistant Professor
Assistant Professor of Ecology and Evolutionary
Biology
e-mail:[email protected]
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Sc. B. Physics (1996) Brown University, Providence, RI
Ph.D. Physics, with Designated Emphasis in Genomic
and Computational Biology (2004) University of
California, Berkeley, Berkeley, California
Department Affiliations
 Institute of Biosciences and Bioengineering
Websites
Lab Website
Research Areas
Evolutionary Biology, Bioinformatics, Comparative Genomics
Evolution of Genome Organization
Research Vision After five hundred million years of independent evolution since their
divergence in the Pre-Cambrian, metazoan genomes still retain recognizable similarities that
allow the partial reconstruction not only of their common ancestors’ protein coding genes, but
of its genomic organization (intron-exon structures, organization into chromosomes, and cisregulatory elements). Also, there is new evidence for very ancient conservation of elements of
the gene networks controlling body plan and neural patterning. These recent developments,
and the dramatic increase in metazoan diversity spanned by genomic data sets, make
comparative genomics a promising approach to some of evolution and development's most
important questions: How do novelty and complexity arise in evolution? What impact does
evolutionary history have on the architecture, function, and future evolution of biological
systems? Our research approaches these questions by coupling the development of novel
computational analyses with genomic experiments designed to leverage them. Our goal is to
reconstruct ancestral genomes, pathways, and regulatory networks, and use these
reconstructions to test the predictions of models of evolution, and functional hypotheses.
Projects: Evolution of Genome Organization It has recently been shown that the organization
of animal genomes at the chromosomal scale is preserved in the human genome and in the
genomes of very distantly-related animals in other phyla (sea anemones, mollusks, and
others; but not in insects or nematodes), and is therefore a relic of, and allows us to
reconstruct, the genome organization of ancient animal ancestors going back at least to the
last common ancestor of all “eumetazoans” — all animals excluding sponges — and perhaps
further. The biological explanation for this conservation is unknown, but there are two broad
possibilities: either this organization is conserved because it has a role in an unknown
mechanism for regulating the genome, or it has no functional importance to the animal, but
changes much more slowly than was suggested by previously-available data. This project aims
to answer this question, and investigate the mechanisms and dynamics of genome evolution.
The primary method we employ is computational comparative genomics: we are building on
methods developed by Dr. Putnam as a post-doc in Dan Rokhsar’s lab, comparing the largescale organization of sequenced genomes (and other genomic data sets) to theoretical models
of genome evolution. Genome Structure Variation in a Natural Population The recentlypublished genome of the Florida lancelet, also commonly called amphioxus (Branchiostoma
floridae) showed a very high degree of variation between the two copies of the genome
sequenced (polymorphism). The source DNA for the project was taking from a single wildcaught animal, and therefore contained two copies of the genome: one inherited from each
parent of that individual. The assembly of the genome was able to reconstruct both of these
copies independently for many regions of the genome, providing a large data set in which to
examine variations between the two sampled genotypes, including insertions (or deletions) in
one relative to the other, and inversions. The distribution of sequence differences between the
two genotypes is consistent with a very large population size, which has been free of dramatic
bottlenecks for a long time, making it a potentially useful natural laboratory for studying the
rates of various mutational processes, including those that produce structural variation. We
are using this resource to identify structural variants in the data, which serve as the starting
point for sampling from the B. floridae population in the Gulf of Mexico.
Teaching Areas
Bioinformatics, Phylogenetics, Evolutionary Biology, Computational Biology
Selected Publications
Refereed articles
Sucgang, R., Kuo, A., Tian, X., Salerno, W., Parikh, A., Feasley, C., Dalin, E., Tu, H., Huang,
E., Barry, K., Lindquist, E., Shapiro, H., Bruce, D., Schmutz, J., Salamov, A., Fey, P., Gaudet,
P., Anjard, A., Babu, M., Basu, S., Bushmanova, Y., van der Wel, H., Katoh-Kurasawa, M.,
Dinh, C., Coutinho, P., Saito, S., Elias, M., Schaap, P., Kay, R., Henrissat, B., Eichinger, L.,
Rivero, F., Putnam, N., West, C., Loomis, W., Chisholm, R., Shaulsky, G., Strassmann, J.,
Queller, D., Kuspa, A., and Grigoriev, I. 2011. Comparative genomics of the social amoebae
Dictyostelium discoideum and Dictyostelium purpureum. Genome Biology 12:R20
Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T,
Balasubramanian PG, Borman J, Busam D, Disbennett K, Pfannkoch C, Sumin N, Sutton GG,
Viswanathan LD, Walenz B, Goodstein DM, Hellsten U, Kawashima T, Prochnik SE, Putnam NH,
Shu S, Blumberg B, Dana CE, Gee L, Kibler DF, Law L, Lindgens D, Martinez DE, Peng J,
Wigge PA, Bertulat B, Guder C, Nakamura Y, Ozbek S, Watanabe H, Khalturin K, Hemmrich G,
Franke A, Augustin R, Fraune S, Hayakawa E, Hayakawa S, Hirose M, Hwang JS, Ikeo K,
Nishimiya-Fujisawa C, Ogura A, Takahashi T, Steinmetz PR, Zhang X, Aufschnaiter R, Eder
MK, Gorny AK, Salvenmoser W, Heimberg AM, Wheeler BM, Peterson KJ, Böttger A, Tischler P,
Wolf A, Gojobori T, Remington KA, Strausberg RL, Venter JC, Technau U, Hobmayer B, Bosch
TC, Holstein TW, Fujisawa T, Bode HR, David CN, Rokhsar DS, Steele RE. "The dynamic
genome of Hydra." Nature, 464 (2010) : 592-6.
Articles
David M Goodstein, Shengqiang Shu, Russell Howson, Rochak Neupane, Richard D Hayes, Joni
Fazo, Therese Mitros, William Dirks, Uffe Hellsten, Nicholas Putnam, Daniel S Rokhsar
"Phytozome: a comparative platform for green plant genomics." Nucleic acids research
(2012/1/1)
Oleg Simakov, Ferdinand Marletaz, Sung-Jin Cho, Eric Edsinger-Gonzales, Paul Havlak, Uffe
Hellsten, Dian-Han Kuo, Tomas Larsson, Jie Lv, Detlev Arendt, Robert Savage, Kazutoyo
Osoegawa, Pieter de Jong, Jane Grimwood, Jarrod A Chapman, Harris Shapiro, Andrea Aerts,
Robert P Otillar, Astrid Y Terry, Jeffrey L Boore, Igor V Grigoriev, David R Lindberg, Elaine C
Seaver, David A Weisblat, Nicholas H Putnam, Daniel S Rokhsar "Insights into bilaterian
evolution from three spiralian genomes." Nature (2012/12/19)
Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam
NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC,
Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T,
Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J,
Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK,
Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS.
"The genome of the Western clawed frog Xenopus tropicalis.." Science, 328 (2010) : 633-6.
Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, Mitros T, Richards GS, Conaco
C, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, Degnan SM,
Oakley TH, Plachetzki DC, Zhai Y, Adamski M, Calcino A, Cummins SF, Goodstein DM, Harris
C, Jackson DJ, Leys SP, Shu S, Woodcroft BJ, Vervoort M, Kosik KS, Manning G, Degnan BM,
Rokhsar DS. "The Amphimedon queenslandica genome and the evolution of animal
complexity.." Nature, 466 (2010) : 720-6.
Takeshi Kawashima, Shuichi Kawashima, Chisaki Tanaka, Miho Murai, Masahiko Yoneda,
Nicholas H. Putnam, Daniel S. Rokhsar, Minoru Kanehisa, Nori Satoh and Hiroshi Wada
"Domain shuffling and the evolution of vertebrates." Genome Research, 19 (2009) : 13931403.
Martinez et al. Genome sequencing and analysis of the biomass-degrading fungus
Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol (2008) vol. 26 (5) pp. 553-60
Holland et al. The amphioxus genome illuminates vertebrate origins and cephalochordate
biology. Genome Res (2008) vol. 18 (7) pp. 1100-11
Srivastava et al. The Trichoplax genome and the nature of placozoans. Nature (2008) vol. 454
(7207) pp. 955-60
Putnam et al. The amphioxus genome and the evolution of the chordate karyotype. Nature
(2008) vol. 453 (7198) pp. 1064-71
King et al. The genome of the choanoflagellate Monosiga brevicollis and the origin of
metazoans. Nature (2008) vol. 451 (7180) pp. 783-8
Conference papers
Lv, J, Havlak, P, and Putnam, N. 2011. Constraints on genes shape long-term conservation of
macro-synteny in metazoan genomes. BMC Bioinformatics 12:S11
Presentations
Invited Talks
"Reconstructing ancient transitions in metazoan genome organization." Developmental Biology
of the Sea Urchin XVIII, Woods Hole, MA. (April 24 2008)
Keynote Speaker
"Long time scale evolution of metazoan genome organization. ." Eighth Annual
RECOMB Satellite Workshop on Comparative Genomics, Ottawa, Canada. (October 11, 2010)
Posters
"Testing for the action of selection on genome rearrangement dynamics deep in the metazoan
tree. ." Society for Integrative and Comparative Biology, Seattle, Washington. (1/4/2010)
Seminar Speaker
Lv, J., Havlak, P, and Putnam, N. 2011. Constraints on genes shape long-term conservation
of macro-synteny in metazoan genomes. Ninth Annual RECOMB Conference on Comparative
Genomics. Oct. 7-10, 2011. Galway, Ireland.
Putnam, N. 2011. Selective constraints on the evolution of metazoan genome
organization. Society for Molecular Biology and Evolution (SMBE) conference. July 26-30,
2011. Kyoto, Japan
"Reconstructing ancient transitions in metazoan genome evolution.." Okinawa Institute of
Science and Technology, Okinawa, Japan. (3/19/09)
"Reconstructing ancient transitions in metazoan genome evolution.." University of Houston,
Department of Biology, Houston, TX. (10/7/09)
"Reconstructing ancient transitions in metazoan genome evolution.." Rice University Institute
of Biosciences and Bioengineering Symposium, Houston, TX. (7/15/09)
"Reconstructing ancient transitions in metazoan genome evolution.." University of Pittsburgh,
Department of Biology, Pittsburgh, PA. (11/23/09)
"Reconstructing ancient transitions in metazoan genome evolution.." Dept. Marine Biology and
Oceanography, Texas A&M University, Galveston, TX. (2/3/09)
Supervised Theses & Dissertations
Xiaoyun "Sean" Liao, PhD Evolution of Altruism and Eusociality: Fitness Cost and Benefit,
Genetic Relatedness. (2012) (Committee Member)
Shuwei Li, PhD Network-guided population genomics of warfarin resistant rats (Rattus
norvegicus) . (2015) (Committee Member)
Ching-Hua Shih, PhD Exploration of some effects genetic interactions have on polyphorism
and divergence. (2015) (Committee Member)
Jie Lv, PhD Functional constraints on genes shape long-term conservation of synteny in
metazoan genomes. (2017) (Thesis or Dissertation Director)
Juan Diaz, PhD Testing models of adaptive trait evolution: Studies of convergent evolution,
ancestral standing variation and de novo mutation in candidate genes underlying rodenticide
resistance and coat color variation in rats. (2018) (Committee Member)
Jiaxing Yue, PhD Population Genomics of Amphioxus. (2018) (Thesis or Dissertation Director)
Kimberly Vincent, PhD The role of chromosomal inversions in the adaptation of an invasive
species, Aedes albopictus. (Thesis or Dissertation Director)
Kimberly Y Vincent, Ph.D. The role of CCAT2 in miRNA expression and processing. (Thesis or
Dissertation Director)
Jie Lv, Ph.D. TBD. (Thesis or Dissertation Director)
Shuwei Li, Ph.D. Detecting selection on genetic network components using population genetic
statistics. (Committee Member)
Ching-Hua Shih, Ph.D. The speciation and comparative genomics of genetic barriers to gene
flow. (Committee Member)
Chandra Jack, Ph.D. Kin discrimination in Dictyostelium. (Committee Member)
Awards, Prizes, & Fellowships
Kavli Fellow, National Academy of Science (2011)
Beckman Young Investigator Award, Arnold and Mabel Beckman Foundation (August 2009)