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2012 Annual Science Report

Massachusetts Institute of Technology Reporting  |  SEP 2011 – AUG 2012

Executive Summary

The Neoproterozoic Environment
Tanja Bosak and her collaborators investigated 1) how microbial processes shape some sedimentary rocks, 2) how microbial processes influence the isotopic composition of sulfur-rich minerals that are used to understand the evolution of oxygen and the cycling of carbon in the past, 3) searched for fossils of organisms that lived between 716 and 635 million years ago, surviving times when ice covered entire oceans, even at the equator and 4) used these fossils, recovered from limestone rocks, to understand the cycling of carbon during this unusual time.

In their investigations of the dynamics of the rise of oxygen during the Neoproterozoic Rothman and Bosak have been testing the predictions of the “anti-priming” hypothesis: if more easily degradable organic matter was degraded in oxic environments, this may have slowed down the degradation of organic matter in anaerobic environments and the overall degradation of organic matter, increasing the concentration of oxygen in the atmosphere and the surface ocean.

To complement work in the Neoproterozoic oxygenation of the Earth, Pearson, Ono and Bosak worked on studies of metabolims that are characteristic of anoxic worlds. At MIT, Ono and Bosak calibrated microbial sulfur isotope effects to infer the redox level of paleoenvironments in geologic past. At Harvard, the Pearson lab studied bacterial vs. eukaryotic signatures of primary production as expressed in nitrogen isotope ratios and began new work on the diversity of microbial community metabolism in anoxic, sulfur-rich environments. The Pearson lab also continued their research aimed at understanding the role and distribution of hopanoid biosynthesis in bacteria. Complementary studies at MIT conducted by Welander and Summons, examined key biosynthetic genes responsible for hopanoid production in aerobic bacteria. Such studies inform us about the evolution of aerobic environments in the early Earth, a key process that set the stage for animal evolution.

Kristen Bergmann and Magdelena Osburn, graduate students working with John Grotzinger at Caltech studied the geology and geochemistry of the Neoproterozoic Khufai and Shuram Formation in South Oman. They found no evidence that the extreme carbon isotopic excursion in that begins in the Khufai and reaches a nadir of -12‰ VPDB in the Shuram Formation, is a consequence of diagenetic alteration processes.

David Johnston, Francis Macdonald, Phoebe Cohen, Tanja Bosak, Andy Knoll and Ross Anderson are working to understand what the world looked like just before and just after the evolution of animals. This encompasses extensive field geology (identifying and collecting rocks of that age), chemical analysis of those rocks, and close examination of the small, enigmatic fossilized forms within those same geologic units. To synthesize these interdisciplinary approaches, our team also works to contribute overview/review papers that speak to the contribution from each field.

Evolution and Development of Complex Life
Our comprehensive analysis of the Ediacaran-Cambrian diversification of animals, using a new database of first occurrences combined with new molecular clock results (in collaboration with Peterson’s group), was published last year in Science. Erwin and Valentine completed the first comprehensive book on the Cambrian explosion, which is in production and due for release in early 2013.

Nicole King and collaborators found that cadherins, cell surface proteins that are essential for the advent of animal life, predate the split between choanoflagellates, which are the metazoans nearest single-celled relatives, and the metazoa.

Since the beginning of 2011, the Peterson Lab has published 12 peer-reviewed papers centered on three themes. They have pioneered the use of microRNAs (miRNAs) – small 22 nucleotide non-coding RNAs – as phylogenetic characters, and have recently gained new insights into the relationships of vertebrates, arthropods, brachiopods, and flies. They have also noted that the number of miRNAs an organism possesses seems related to their relative morphological complexity such that more complex animals have many more miRNAs than simple animals. They have also observed that bilaterians have a fairly extensive cryptic Precambrian history, which when coupled with our miRNA work makes this missing record even more enigmatic, and the resolution of this paradox is the focus of our continuing NASA-sponsored work.

Animals interact with the world through complex sensory structures (eyes, ears, antennas, etc.), which are coordinated by collections of neurons. While the nervous and sensory systems of animals are incredibly diverse, a growing body of evidence suggests that many of these systems are controlled by similar sets of genes. David Jacobs and his students at UCLA have been looking at early branching and understudied lineages of the animal family tree (the jellyfish Aurelia and the worm Neanthes) to see if these animals use similar genes during neurosensory development as the better-studied fruit fly and mouse. This research is critical for determining which structures are shared between animals because of common ancestry (known as homologous structures) and those that evolved independently in different lineages. Ultimately, such research informs how morphologically and behaviorally complex animals evolve.

Development of Metabolic Networks
Members of the Segré group use systems biology approaches to study the complex network of metabolic reactions that allow microbial cells to survive and reproduce under varying environmental conditions. The resource allocation problem that underlies these fundamental processes changes dramatically when multiple cells can compete or cooperate with each other, for example through metabolic cross-feeding. Through mathematical models of microbial ecosystems and computer simulations of spatially structured cell populations, the Segre’ team contributes to improved understanding of the environmental conditions and evolutionary processes that favor the emergence of multicellular organization. Over the past year, has developed a cost-benefit model to explain how genetic interaction and hierarchical modules contribute to the evolution of biological complexity. They have also studied and elucidated aspects of the regulatory and environmental control of respiration.

The Fossil Record
Erwin and colleagues have also been studying the putative Ediacaran-Cambrian mass extinction. A comprehensive database of first and last occurrences and biogeographic distributions of all Ediacaran species, combined with paleoecological evaluations of diverse Ediacaran communities, was compiled by NAI funded postdoctoral fellow Marc Laflamme. Our study does not support an environmentally-driven mass extinction akin to the Phanerozoic “big five”, but instead supports a drastic ecosystem restructuring across the Ediacaran-Cambrian boundary driven by metazoan ecosystem engineers. This paper was invited and is presently in review at Gondwana Research.

Andrew Knoll and his colleagues completed several paleontological projects on the early evolution of eukaryotic organisms. Cohen and Knoll (2012) published a monographic on scale microfossils in the ca. 800 million year old Fifteen Mile group, northwestern Canada. These fossils, which document defenses against protistan predation, constitute the most diverse eukaryotic fossils known from pre-Ediacaran rocks. Justin Strauss discovered a rich new assemblage of testate microfossils in Neoproterozoic strata from northwestern Canada (Strauss et al., 2012), and undergraduate student Ross Anderson completed a senior thesis on probable testate protists in metamorphosed shales from the Neoproterozoic Dalradian succession in Scotland (Anderson et al., 2012). Graduate student Jessica Creveling completed her Ph.D. thesis on Cambrian phosphorite deposition, providing detailed sedimentological, geochemical and paleobiological analyses of phosphatic limestones in Australia that shed welcome light on the environmental circumstance favoring Ediacaran-Cambrian phosphate deposition and the consequences of these processes for fossil preservation.

Completing some earlier projects on the Permian mass extinctions led to a review article in Science (Shen et al.) providing new high-resolution radiometric dates for a suite of localities across South China, showing that the extinction happened in less than 300 k.y, and probably less than 90 k.y. A paper to Geology provides the first geochronologic framework for the terrestrial Permo-Triassic sequence in the Karoo of South Africa, finding little evidence for a terrestrial correlate to the marine end-Guadalupian mass extinction.

As well as providing precise temporal constraints on major events in the history, members of the Bowring lab, collaborating with Rothman, Alm, Fournier, Summons, French and Boyle, used a combination of trace element geochemistry and Sr isotopes to understand the chemical signals of seawater during the end-Permian extinction. Central to this work is the evaluation of whether Large Igneous Provinces (LIPS) have played a role in the extinctions.

Mars Exploration
MIT Team member John Grotzinger is the Project Scientist of the MSL mission currently underway at Gale Crater on Mars. John, and his team at Caltech, led a major study of potential landing sites which resulted in the selection of Gale Crater and were involved in the Gale Imaging Working Group, which has been identifying key HiRISE and CRISM data products, to enhance the science mission. Several members of the Grotzinger group have also been involved in creating a geologic map of the landing site and, since the landing, compiling a regional map to understanding the details of the units and geological relationships in the immediate vicinity of Curiosity. Grotzinger and Knoll continue to be active in the operation of the MER rover opportunity.

Extrasolar Planets
The past year brought us, finally, a confirmed transiting small-size planet in the classical Habitable Zone of a Sun-like star – Kepler-22b of 2.4 Earth radius. Kaltenegger and Sasselov contributed the analysis of this planet in terms of its habitability characteristics and location within the habitable zone to the
discovery paper by the Kepler team.

Research by NPP Fellows Fournier and Welander
The genetic code is one of the most ancient and universal aspects of biology on Earth, and determines how specific DNA sequences get interpreted as peptide sequences, which then fold into all the proteins necessary for the growth and function of living cells. To a large extent, this code is determined by a class of proteins that specify which RNA adaptor molecules (tRNA) become attached to which amino acids, aminoacyl-tRNA synthetases. Therefore, Greg Founier, working with Eric Alm, has been reconstructing the amino acid sequences of the ancestors of aminoacyl-tRNA synthetases, existing ~4 billion years ago, to help identify the mechanisms by which the genetic code arose, and how it evolved to the modern form inherited by all known living organisms.

Paula Welander discovered the gene responsible for production of 3-methylhopanoids in Methylococcus capsulatus, a microphilic methane oxidising bacterium. Deletion of the gene resulted in a mutant bacterium that could no longer make these molecules the cores of which can be found in rocks as old a 2700 myr. The mutant bacterium also had compromised internal membranes and drastically reduced survival in stationary phase.

Education, Public Outreach and Training Success
Phoebe Cohen organised a wide range of activities of the past year. These include: Down to Earth Outer Space @ the MIT Museum as a part of the 2012 Cambridge Science Festival. In collaboration with the MIT Youth Astronomy Apprenticeship program, we created and displayed a temporary museum exhibit on Astrobiology called Worlds Beyond: The Search for Life in the Universe. Also, as a part of the Cambridge Science Festival in April 2012, we displayed our popular to-scale Geological Timeline walk signs along the Charles River for 9 days. Each sign on the walk provides information on an event in earth or life history and the signs are spaces out to scale to give the public a better sense for the immensity of geologic time and the antiquity of life. Six school and university classes signed up for tours, ranging from Cambridge public schools, the Prospect Hill Charter school and students from the Boston University English enrichment program. Tours were given by EPO Lead Cohen and other members of the MIT NAI team including graduate students, post docs, and faculty. Also, in collaboration with the Cambridge Science Festival, EPO lead Phoebe Cohen co-faciliated the Stories of Science Communication Workshop for graduate students in the Boston area on how to effectively communicate their research to public audiences.

We ran another in our series of successful Telling Your Story teacher-scientist partnership workshops in October of 2011. This workshop involved 27 K-12 teachers and 26 scientists (graduate students and post docs). Unlike our first workshop, this workshop expanded beyond the Earth and Spaces sciences to include other scientists in the Boston area, though we still recruited a number of graduate students and post docs from our MIT NAI team. The goals of the Telling Your Story program are threefold:
1) Create connections between local scientists and K-12 teachers.
2) Provide skills to scientists that they can take into K-12 classroom environments, and provide teachers with expectations for scientist visits.
3) Expose K-12 teachers to current research in the natural sciences.

During MIT’s winter session (IAP) of 2012, EPO Lead Phoebe Cohen taught a two week mini-course on Astrobiology for MIT undergraduate students. The class met for 10 consecutive days, 2 hours each day, and combined lectures and labs / active-learning activities including think-pair-share, hands on experiments, use of NAI-funded Virtual Field Trips, and a mock grant writing assignment. The course included multiple guest lectures from within the MIT astrobiology community and beyond, including a lecture by team PI Roger Summons, a lab tour by PI Tanja Bosak, and a skype lecture by Icy Moons PI Kevin Hand. The course was very successful and sparked interest in astrobiology for many of the 15 undergraduate students. There were also a few auditors in the class including a student from the MIT Science Writing program and a member of the local community.

The MIT NAI team continues to work on a suite of Virtual Field Trip products. In this endeavor we continued our collaboration with the ASU NAI team and the Australian Center for Astrobiology on the VFT to Flinders Range of Australia, and Shark Bay, Western Australia. The Flinders Range and Shark Bay VFT are now in a beta version and we are working towards evaluating the VFT as an effective teaching tool across a wide variety of audiences, from middle schools to colleges to informal learning environments. This process has involved a huge number of partners as we explore learning philosophies and work hard to create a product that will not only be engaging and entertaining, but educational as well.

Our specific role has focused on content creation, making sure the scientific data present in the VFT’s is accurate, and working with Geoffrey Bruce to develop questions and quizzes within the VFT’s that will challenge students and help them to learn the material while providing an engaging leaning environment. In addition, EPO Lead Cohen has been using the VFT’s in small in-person undergraduate courses and provides feedback on these uses to Bruce to further ensure that the VFT’s are applicable to a wide variety of audiences.

NAI funding has supported a post-doc, Dr Marc Laflamme, who will be moving in December to Univ. Toronto as an Assistant Professor

An NPP fellowship awarded to Dr Paula Welander has assisted her transition to independence as a researcher and she will take as a position as Assistant Professor of Geobiology at Stanford University on December 1, 2012.

Continuing team member and former postdoctoral fellow Phoebe Cohen has taken up her new post as Assistant Professor of Geosciences at Williams College.

Graduate student Jessica Creveling took up a postdoctoral Fellowship at Caltech.

Knoll is the editor or author of two new books with an astrobiological focus (Knoll et al., 2012, Morris et al., 2012) and will present the 2012 Howard Hughes Medical Institute Holiday Lectures, aimed to improve science education among high school students.

As noted above, Erwin and Valentine completed the first comprehensive book on the Cambrian explosion, which is due for release in early 2013. Dimitar Sasselov published his book on extra-solar planets, The Life of Super Earths, and completed a promotional tour that expounded, for the lay reader, on the main themes of Astrobiology.

Publications

  • Alegado, R. A., Grabenstatter, J. D., Zuzow, R., Morris, A., Huang, S. Y., Summons, R. E., & King, N. (2012). Algoriphagus machipongonensis sp. nov., co-isolated with a colonial choanoflagellate. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 63(Pt 1), 163–168. doi:10.1099/ijs.0.038646-0

  • Anderson, B. M., Pisani, D., Miller, A. I., & Peterson, K. J. (2011). The environmental affinities of marine higher taxa and possible biases in their first appearances in the fossil record. Geology, 39(10), 971–974. doi:10.1130/g32413.1

  • Beg, Q. K., Zampieri, M., Klitgord, N., Collins, S. B., Altafini, C., Serres, M. H., & Segre, D. (2012). Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis. Nucleic Acids Research, 40(15), 7132–7149. doi:10.1093/nar/gks467

  • Borucki, W. J., Koch, D. G., Batalha, N., Bryson, S. T., Rowe, J., Fressin, F., … Rapin, W. (2012). Kepler-22b: A 2.4 EARTH-RADIUS PLANET IN THE HABITABLE ZONE OF A SUN-LIKE STAR. The Astrophysical Journal, 745(2), 120. doi:10.1088/0004-637x/745/2/120

  • Bosak, T., Lahr, D. J. G., Pruss, S. B., MacDonald, F. A., Gooday, A. J., Dalton, L., & Matys, E. D. (2011). Possible early foraminiferans in post-Sturtian (716-635 Ma) cap carbonates. Geology, 40(1), 67–70. doi:10.1130/g32535.1

  • Campbell, L. I., Rota-Stabelli, O., Edgecombe, G. D., Marchioro, T., Longhorn, S. J., Telford, M. J., … Pisani, D. (2011). MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda. Proceedings of the National Academy of Sciences, 108(38), 15920–15924. doi:10.1073/pnas.1105499108

  • Campo-Paysaa, F., Sémon, M., Cameron, R. A., Peterson, K. J., & Schubert, M. (2011). microRNA complements in deuterostomes: origin and evolution of microRNAs. Evolution & Development, 13(1), 15–27. doi:10.1111/j.1525-142×.2010.00452.x

  • Chakrabarti, R., Knoll, A. H., Jacobsen, S. B., & Fischer, W. W. (2012). Si isotope variability in Proterozoic cherts. Geochimica et Cosmochimica Acta, 91, 187–201. doi:10.1016/j.gca.2012.05.025

  • Chiu, H-C., Marx, C. J., & Segre, D. (2012). Epistasis from functional dependence of fitness on underlying traits. Proceedings of the Royal Society B: Biological Sciences, 279(1745), 4156–4164. doi:10.1098/rspb.2012.1449

  • Cohen, P. A., & Knoll, A. H. (2012). Scale Microfossils from the Mid-Neoproterozoic Fifteenmile Group, Yukon Territory. Journal of Paleontology, 86(5), 775–800. doi:10.1666/11-138.1

  • Darroch, S. A. F., Laflamme, M., Schiffbauer, J. D., & Briggs, D. E. G. (2012). EXPERIMENTAL FORMATION OF A MICROBIAL DEATH MASK. PALAIOS, 27(5), 293–303. doi:10.2110/palo.2011.p11-059r

  • Erwin, D. H., Laflamme, M., Tweedt, S. M., Sperling, E. A., Pisani, D., & Peterson, K. J. (2011). The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals. Science, 334(6059), 1091–1097. doi:10.1126/science.1206375

  • Forney, D. C., & Rothman, D. H. (2012). Common structure in the heterogeneity of plant-matter decay. Journal of The Royal Society Interface, 9(74), 2255–2267. doi:10.1098/rsif.2012.0122

  • Forney, D. C., & Rothman, D. H. (2012). Inverse method for estimating respiration rates from decay time series. Biogeosciences Discuss., 9(3), 3795–3828. doi:10.5194/bgd-9-3795-2012

  • Fournier, G. P., Andam, C. P., Alm, E. J., & Peter Gogarten, J. (2011). Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life. Orig Life Evol Biosph, 41(6), 621–632. doi:10.1007/s11084-011-9261-2

  • Gold, D. A., & Jacobs, D. K. (2012). Stem cell dynamics in Cnidaria: are there unifying principles?. Dev Genes Evol, 223(1-2), 53–66. doi:10.1007/s00427-012-0429-1

  • Grosjean, E., Love, G. D., Kelly, A. E., Taylor, P. N., & Summons, R. E. (2012). Geochemical evidence for an Early Cambrian origin of the ‘Q’ oils and some condensates from north Oman. Organic Geochemistry, 45, 77–90. doi:10.1016/j.orggeochem.2011.12.006

  • Grotzinger, J. P., Crisp, J., Vasavada, A. R., Anderson, R. C., Baker, C. J., Barry, R., … Wiens, R. C. (2012). Mars Science Laboratory Mission and Science Investigation. Space Sci Rev, 170(1-4), 5–56. doi:10.1007/s11214-012-9892-2

  • Higgins, M. B., Robinson, R. S., Husson, J. M., Carter, S. J., & Pearson, A. (2012). Dominant eukaryotic export production during ocean anoxic events reflects the importance of recycled NH4+. Proceedings of the National Academy of Sciences, 109(7), 2269–2274. doi:10.1073/pnas.1104313109

  • Jacobs, C., & Segrè, D. (2012). Organization Principles in Genetic Interaction Networks. Advances in Experimental Medicine and Biology, None, 53–78. doi:10.1007/978-1-4614-3567-9_3

  • Johnston, D. T., MacDonald, F. A., Gill, B. C., Hoffman, P. F., & Schrag, D. P. (2012). Uncovering the Neoproterozoic carbon cycle. Nature, 483(7389), 320–323. doi:10.1038/nature10854

  • Johnston, D. T., Poulton, S. W., Goldberg, T., Sergeev, V. N., Podkovyrov, V., Vorob’eva, N. G., … Knoll, A. H. (2012). Late Ediacaran redox stability and metazoan evolution. Earth and Planetary Science Letters, 335-336, 25–35. doi:10.1016/j.epsl.2012.05.010

  • Kaltenegger, L., Miguel, Y., & Rugheimer, S. (2012). Rocky exoplanet characterization and atmospheres. International Journal of Astrobiology, 11(04), 297–307. doi:10.1017/s1473550412000134

  • Klepac-Ceraj, V., Hayes, C. A., Gilhooly, W. P., Lyons, T. W., Kolter, R., & Pearson, A. (2012). Microbial diversity under extreme euxinia: Mahoney Lake, Canada. Geobiology, 10(3), 223–235. doi:10.1111/j.1472-4669.2012.00317.x

  • Knoll, A. H., Canfield, D. E., & Konhauser, K. O. (2012). What is Geobiology?. Fundamentals of Geobiology, None, 1–4. doi:10.1002/9781118280874.ch1

  • Laflamme, M., Flude, L. I., & Narbonne, G. M. (2012). Ecological Tiering and the Evolution of a Stem: The Oldest Stemmed Frond from the Ediacaran of Newfoundland, Canada. Journal of Paleontology, 86(2), 193–200. doi:10.1666/11-044.1

  • Lyson, T. R., Sperling, E. A., Heimberg, A. M., Gauthier, J. A., King, B. L., & Peterson, K. J. (2011). MicroRNAs support a turtle + lizard clade. Biology Letters, 8(1), 104–107. doi:10.1098/rsbl.2011.0477

  • Nichols, S. A., Roberts, B. W., Richter, D. J., Fairclough, S. R., & King, N. (2012). Origin of metazoan cadherin diversity and the antiquity of the classical cadherin/ -catenin complex. Proceedings of the National Academy of Sciences, 109(32), 13046–13051. doi:10.1073/pnas.1120685109

  • Ono, S., Keller, N. S., Rouxel, O., & Alt, J. C. (2012). Sulfur-33 constraints on the origin of secondary pyrite in altered oceanic basement. Geochimica et Cosmochimica Acta, 87, 323–340. doi:10.1016/j.gca.2012.04.016

  • Petroff, A. P., Wu, T-D., Liang, B., Mui, J., Guerquin-Kern, J-L., Vali, H., … Bosak, T. (2011). Reaction–diffusion model of nutrient uptake in a biofilm: Theory and experiment. Journal of Theoretical Biology, 289, 90–95. doi:10.1016/j.jtbi.2011.08.004

  • Philippe, H., Brinkmann, H., Copley, R. R., Moroz, L. L., Nakano, H., Poustka, A. J., … Telford, M. J. (2011). Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature, 470(7333), 255–258. doi:10.1038/nature09676

  • Pisani, D., Feuda, R., Peterson, K. J., & Smith, A. B. (2012). Resolving phylogenetic signal from noise when divergence is rapid: A new look at the old problem of echinoderm class relationships. Molecular Phylogenetics and Evolution, 62(1), 27–34. doi:10.1016/j.ympev.2011.08.028

  • Rubidge, B. S., Erwin, D. H., Ramezani, J., Bowring, S. A., & De Klerk, W. J. (2013). High-precision temporal calibration of Late Permian vertebrate biostratigraphy: U-Pb zircon constraints from the Karoo Supergroup, South Africa. Geology, 41(3), 363–366. doi:10.1130/g33622.1

  • Schiffbauer, J. D., & Laflamme, M. (2012). LAGERSTATTEN THROUGH TIME: A COLLECTION OF EXCEPTIONAL PRESERVATIONAL PATHWAYS FROM THE TERMINAL NEOPROTEROZOIC THROUGH TODAY. PALAIOS, 27(5), 275–278. doi:10.2110/palo.2012.so3

  • Shen, S-Z., Crowley, J. L., Wang, Y., Bowring, S. A., Erwin, D. H., Sadler, P. M., … Jin, Y-G. (2011). Calibrating the End-Permian Mass Extinction. Science, 334(6061), 1367–1372. doi:10.1126/science.1213454

  • Sim, M. S., Ono, S., & Bosak, T. (2012). Effects of Iron and Nitrogen Limitation on Sulfur Isotope Fractionation during Microbial Sulfate Reduction. Applied and Environmental Microbiology, 78(23), 8368–8376. doi:10.1128/aem.01842-12

  • Sperling, E. A., Pisani, D., & Peterson, K. J. (2011). Molecular paleobiological insights into the origin of the Brachiopoda. Evolution & Development, 13(3), 290–303. doi:10.1111/j.1525-142×.2011.00480.x

  • Squyres, S. W., Arvidson, R. E., Bell, J. F., Calef, F., Clark, B. C., Cohen, B. A., … Zacny, K. (2012). Ancient Impact and Aqueous Processes at Endeavour Crater, Mars. Science, 336(6081), 570–576. doi:10.1126/science.1220476

  • Takashima, S., Gold, D., & Hartenstein, V. (2012). Stem cells and lineages of the intestine: a developmental and evolutionary perspective. Dev Genes Evol, 223(1-2), 85–102. doi:10.1007/s00427-012-0422-8

  • Tarver, J. E., Donoghue, P. C. J., & Peterson, K. J. (2012). Do miRNAs have a deep evolutionary history?. BioEssays, 34(10), 857–866. doi:10.1002/bies.201200055

  • Tsao, L. E., Robinson, R. S., Higgins, M. B., & Pearson, A. (2012). Nitrogen isotope ratio of cyanobacterial chlorophyll: Chemostat vs. batch culture. Organic Geochemistry, 49, 96–99. doi:10.1016/j.orggeochem.2012.06.001

  • Tziperman, E., Halevy, I., Johnston, D. T., Knoll, A. H., & Schrag, D. P. (2011). Biologically induced initiation of Neoproterozoic snowball-Earth events. Proceedings of the National Academy of Sciences, 108(37), 15091–15096. doi:10.1073/pnas.1016361108

  • Vinther, J., Sperling, E. A., Briggs, D. E. G., & Peterson, K. J. (2011). A molecular palaeobiological hypothesis for the origin of aplacophoran molluscs and their derivation from chiton-like ancestors. Proceedings of the Royal Society B: Biological Sciences, 279(1732), 1259–1268. doi:10.1098/rspb.2011.1773

  • Welander, P. V., & Summons, R. E. (2012). Discovery, taxonomic distribution, and phenotypic characterization of a gene required for 3-methylhopanoid production. Proceedings of the National Academy of Sciences, 109(32), 12905–12910. doi:10.1073/pnas.1208255109

  • Welander, P. V., Doughty, D. M., Wu, C-H., Mehay, S., Summons, R. E., & Newman, D. K. (2012). Identification and characterization of Rhodopseudomonas palustris TIE-1 hopanoid biosynthesis mutants. Geobiology, 10(2), 163–177. doi:10.1111/j.1472-4669.2011.00314.x

  • Wiegmann, B. M., Trautwein, M. D., Winkler, I. S., Barr, N. B., Kim, J-W., Lambkin, C., … Yeates, D. K. (2011). Episodic radiations in the fly tree of life. Proceedings of the National Academy of Sciences, 108(14), 5690–5695. doi:10.1073/pnas.1012675108

  • Winchell, C. J., & Jacobs, D. K. (2013). Expression of the Lhx genes apterous and lim1 in an errant polychaete: implications for bilaterian appendage evolution, neural development, and muscle diversification. EvoDevo, 4(1), 4. doi:10.1186/2041-9139-4-4

  • Copley, S.D. & Summons, R.E.  (2012, in Press).  Terran Metabolism: The First Billion Years.  In: Impey, C., Lunine, J. & José Funes, J. (Eds.).  Frontiers of Astrobiology.  Cambridge University Press.
  • Dornbos, S.Q., Clapham, M.E., Fraiser, M.L. & Laflamme, M.  (2012).  Lessons from the Fossil Record: The Ediacaran Radiation, the Cambrian Radiation, and the End-Permian Mass Extinction.  In: Solan, M., Aspden, R.J. & Paterson, D.M. (Eds.).  Marine Biodiversity Futures and Ecosystem Functioning frameworks, methodologies and integration.  Oxford: Oxford UP.
  • Erwin, D.H. & Tweedt, S.  (2012).  Ecosystem Engineering and the Ediacaran-Ordovician diversification of Metazoa.  Evolutionary Ecology, 26: 417-433.
  • Gaidos, E. & Knoll, A.H.  (2012).  Our evolving planet: from the dark ages to an evolutionary renaissance.  In: Lunine, J. & Impie, C. (Eds.).  Astrobiology.  Cambridge, UK: Cambridge University Press.
  • Grotzinger, J.P. & Milliken, R.E.  (2012).  The sedimentary rock record of Mars: distribution, origins, and global stratigraphy,.  In: Grotzinger, J.P. & Milliken, R.E. (Eds.).  SEPM Special Paper.
  • Halverson, G.P., MacDonald, F.A., Strauss, J.V., Smith, E.F., Cox, G.M. & Hubert-Theou, L.  (2011).  Updated definition and correlation of the lower Fifteenmile Group in the central and eastern Ogilvie Mountains.  In: MacFarlane, K.E. & Sack, P.J. (Eds.).  Yukon Exploration Geology 2011.  Whitehorse.
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