2013 Annual Science Report

Massachusetts Institute of Technology Reporting  |  SEP 2012 – AUG 2013

Executive Summary

Members of the MIT Team have been working on some of the oldest fossil evidence of animals and applying studies of modern animal development to interpret these fossils. The goal is to understand how the interactions between changes in the physical environment, ecological interactions and in developmental mechanisms in evolutionary innovations lead to greater biological complexity.

Environmental change and evolutionary innovation:
In January 2013 The Cambrian Explosion: The Construction of Animal Biodiversity by Douglas Erwin and Jim Valentine was published (Roberts Publishing). The book argues that the origin and early diversification of animals can only be understood through integrating our understanding of changes in the physical environment (principally changes in ocean redox), the construction of networks of ecological interactions, and the growth of regulatory interactions in gene networks that control development.

Graduate Student Sarah Tweedt (University of Maryland, but working at NMNH) is examining the developmental morphospace of the Ediacaran and early panarthropods using a new approach to defining morphospace.

Post-doctoral fellow Marc Laflamme continued studying the preservation and systematics of Ediacaran forms and published the first detailed analysis of the transition between Ediacaran and earliest Cambrian organisms, evaluating proposals for a mass extinction at the end of the Ediacaran. We also began what we expect to be a series of field campaigns to find and study new Ediacaran-age localities in southern Namibia.

A study of the Ediacaran frond-like animals, led by David Jacobs and Marco Ghisalberti of the University of Western Australia, reconstructed flow-velocity profiles and vertical mixing using canopy flow models appropriate to the densities of the communities at Mistaken Point in Canada. Modeling of processes at organismal surfaces documents increasing nutrient uptake with height as a function of thinning of the diffusive boundary layer with increased velocity. The velocity profile, produced by canopy-flow in the community, generates an advantage for upward growth. Alternative models of upward growth advantage based on redox/resource gradients fail, given the efficiency of vertical mixing. They demonstrated that taller architecture affords a selective driver for osmotrhophic communities in environmental settings where phototropism cannot contribute to upward growth.

Kevin Peterson’s molecular sequence analyses suggest that complex animals actually arose nearly 200 million years before appearing in the fossil record. This disparity motivates an interesting question—why is it that we cannot detect complex life here on Earth for nearly 200 million years? And if we cannot detect it on Earth, what hope would we have on another planet? New research (Heimberg et al. 2008; Philippe et al. 2001; Tarver et al. 2013) suggests that a group of non-coding RNA genes—microRNAs—might be instrumental for the advent and maintenance of complexity in animals. Therefore, sequencing the genomes and the transcriptomes (the expressed component of the genome) from carefully chosen taxa might allow us to better understand the biology of animals that predated the Cambrian explosion.

To date, the Peterson lab has sequenced the genome and both the mRNA and miRNA transcriptomes of the chaetognath Parasaggita elegans. These analyses firmly and finally establish the phylogenetic position of chaetognaths as basal to the two major protostome clades (the lophotrochozoans and the ecydysozoans) and show that chaetognaths have lost very few miRNAs. This supports chaetognaths as relatively complex animals with no obvious signs of secondary simplification, highlighting the disparity between the origins of morphological complexity and its manifestation in the fossil record.


Emerging research on Neoproterozoic sedimentary successions by our team now suggests that much of the apparently sudden rise of animals manifested in the Ediacaran record was initiated by earlier events during the late Mesoproterozoic Era and Cryogenian Period (1200–650 Ma). Our work seeks to illuminate this time period by documenting the stratigraphy, isotopic records, fossil assemblages and biomarker contents of critical Meso- to Neoproterozoic transitions in well-preserved Proterozoic sections.

Geology, geochemistry and paleontology of Proterozoic sections of Canada and Russia:
Francis Macdonald has been conducting geological studies in northwestern Canada and providing context for newly-discovered vase-shaped microfossils (VSMs) in the Callison Lake Dolostone. Importantly, he directly dated the shale horizon in which these fossils occur with Re/Os to 739+/-6 Ma, a date indistinguishable from the U/Pb age constraint of 742+/-6 Ma on the VSMs in the Chuar Group in the Grand Canyon. In Namibia, team members Macdonald, Justin Strauss and Sara Pruss reported the discovery of large, complex trace fossils present in strata >5 Myrs older than the Precambrian-Cambrian boundary.

Phoebe Cohen has macerated or thin-sectioned over 120 samples from these sediments from Canada. Thus far, these samples have yielded intriguing, extremely well-preserved and diverse VSMs, believed to be the remains of testate (shell-forming) amoebae. Interestingly, these fossils are preserved not only in thin section, but also in macerated shale material: a new taphonomic window on this important Neoproterozoic fossil group.

Tanja Bosak has been investigating the environmental and taphonomic conditions during Mesoproterozoic, Neoproterozoic and Early Cambrian time, as recorded in the in the record of Cryogenian eukaryotes and the morphologies of sedimentary structures such as stromatolites and wrinkle structures. Alex Petroff, Tanja Bosak and Daniel Rothman published an article describing a model for the growth of conical stromatolites of all sizes by analyzing the geometry of their laminae. Giulio Mariotti has established an experimental system to test hypotheses coupling the morphology and cementation of sedimentary structures to the interactions among flow (waves and currents), sedimentary bedforms and microbial growth. These experiments also produced the first comprehensive model for the formation of wrinkle structures, enigmatic mm-scale features of many Ediacaran and Cambrian siliciclastic deposits in which impressions of macroscopic organisms and animals are also preserved.

Members of Andrew Knoll’s lab have discovered and analyzed a series of fossil assemblages deposited between 1100 and 800 million years ago and continued to show the relationship between evolution and environmental change on the early Earth. Ratti et al. (2013) reported the results of experiments that show how evolving eukaryophagic predators could have changed patterns of primary production, favoring eukaryotic algae over cyanobacterial phytoplankton.

Knoll’s group also discovered probable microfossils in metamorphosed Neoproterozoic shales from the Dalradian Supergroup, Scotland. They also linked latest Neoproterozoic oxygen rise and the ecological drivers of Cambrian animal diversification, showing via meta-analysis of ecological data from marine oxygen minimum zones that carnivory requires relatively high oxygen tensions.

The group also completed stratigraphic and geochemical research showing how the distinctive redox conditions of Ediacaran and Cambrian oceans help explain the exceptional fossil preservation by phosphate mineralization in beds of this age (Creveling et al., in press and submitted). Finally, Knoll and his colleagues completed critical reviews of stromatolites early eukaryotic evolution, early microbial evolution, the evolutionary relationship between animals and microbes and the physiological links between geological records of biological and environmental change.

David Johnston has conducted a geochemical study of the redox state of the late Precambrian world that also serves as a critical tie point for our upcoming work on Cryogenian ocean and atmospheric chemistry. This work entails extending similar tools to those we applied in the Ediacaran, as well as developing a new 17O system that will serve as a central measurement for the upcoming projects.

What emerges from a multi-proxy (Fe speciation, sulfur isotopes, major and trace element analyses) is a picture of a persistently anoxic and ferruginous Ediacaran ocean. The notable absence of geochemical evidence for prominent oxygenation challenges the idea of an Ediacaran jump in atmospheric oxygen, which in turn blurs the proposed link between animal evolution and local geochemical environments.

Other molecular paleontology:
Eric Alm and Greg Fournier have developed a theory of “gene transfer stratigraphy”, which can use a set of gene transfers to impose relative time calibrations within phylogenetic trees. Preliminary results using this new methodology for the time-calibration of archaeal evolution support a timing of the Last Common Ancestor and Origin of Life very early in planetary history, before the time of the proposed “Late Heavy Bombardment”. This provides evidence against models of impact frustration for the Origin of Life on early Earth.

In an attempt to improve phylogenetic analyses of gene trees, they have also investigated the presence of partial horizontal gene transfer within sequence datasets, and its impact on the inference of ancient evolutionary events. This method can reveal major sources of error in phylogenetic analyses.

Ann Pearson’s lab is addressing the question: Are hopanoids primarily remnants of primary producers or of heterotrophic consumers? Do they primarily come from free-living marine communities, or from shallow mats, tidal zone communities, or even terrigenous runoff? New methodologies and analyses of compound-specific carbon isotope data for hopanoids—to infer their sources in modern systems and as proxies for understanding ancient environments—are under development.

Roger Summons and collaborators have been exploring different organo-mineral associations in four distinct microbially-dominated environments comprising silica, gypsum and carbonate-depositing systems. A prime focus in this project was the origin and paleoenvironmental significance of ooids (spherical carbonate concretions), because ooids are common constituents of ancient carbonate rocks, many in the Precambrian, and can preserve isotopic and molecular records imparted by the microbial denizens of ancient coastlines. So far, our data suggest that ooids are colonized by a defined microbial community very similar to that forming associated stromatolites, and that these microbes likely mediate calcification.

The Proterozoic carbon isotopic record contains evidence of a series of large perturbations to the global carbon cycle, some or all of which may be associated with changes in atmospheric O2. Daniel Rothman is formulating a theoretical model to explain not only these disruptions, but also the permanent increase in O2 levels that occurred by the end of the Proterozoic.

MIT team members John Grotzinger, Andrew Knoll, Ralph Milliken, Dawn Sumner and Roger Summons, and members of their respective teams, are actively involved in both the continuing MER and new MSL missions to Mars.

The search for organic materials in extraterrestrial environments such as Mars is, by necessity, largely limited to remote techniques. Knoll, Milliken and Summons are analyzing shales and carbonates from well-preserved Proterozoic basins on Earth, with three goals in mind. First, they are gathering unprecedented data on the clay mineral content of ancient sedimentary successions on Earth. Second, they are analyzing the organic carbon content of the same rocks to understand the relationship between biomarker preservation and clay mineral content. And third, all samples are being analyzed by remote sensing instruments comparable to those that have flown or are contemplated for Mars missions, the idea being to provide ground truth for remote sensing inferences and exploring the relationship between clay mineralogy and organic carbon preservation in sedimentary rocks.

Ralph Milliken has been exploring the use of reflectance spectroscopy, which is a rapid, non-destructive technique, for assessing the presence and abundance of organic materials. Milliken and colleagues have measured over 100 rock powders that represent a wide range in age and depositional environment. Initial results show that organic absorption features are relatively easy to detect in samples dominated by clay minerals and/or Fe-oxides, where the latter become relatively transparent at longer wavelengths. However, the level of water content in the clays and/or the bulk sample affects the degree to which weak organic features can be identified. Additionally, the overlap between carbonate features near ~3.4 µm and organic features in this wavelength region make unambiguous detection of organics in carbonate-bearing samples difficult.

After a little more than a year on Mars, the Mars Science Laboratory Curiosity rover has discovered fine-grained sedimentary rocks, which are inferred to represent a habitable lake environment, whose chemistry indicates the presence of more neutral to alkaline conditions than the environments previous rovers explored. The science team has also determined the age of a Martian rock, found evidence the planet could have sustained microbial life, and taken radiation readings on the surface, which will help NASA create better models regarding the radiation environment for future astronauts.

Preservation of organic materials on Earth is most often associated with rapid mineralization of deposits. Kirsten Siebach’s research reports a set of large-scale boxwork structures in a sedimentary layer on Mount Sharp, Gale Crater’s central mound, which indicate extensive groundwater cementation and represent a possibly habitable environment where organic molecules may have been preserved.

In the Summons lab at MIT, Kristen Miller has been conducting analog experiments in an effort to understand the controls on the production of chlorohydrocarbons in Mars surface sediments and in the SAM instrument onboard Curiosity.

Andrew Knoll and John Grotzinger continue to serve on the MER science team, taking part in mission planning and the interpretation of data telemetered back from Mars. In recent progress, Opportunity has documented the oldest materials yet encountered on the mission, a volcanic and impact-related stratigraphy exposed within the inner rim of Endeavour crater that predates the sulfate-rich sandstones explored by Opportunity for some eight years. Knoll also participated in a second project to characterize and interpret Martian sandstones encountered by the Spirit rover.

In collaboration with the ASU team, we continued developing our interactive Virtual Field Trip (VFT) product, which allows teachers to take whole classrooms into astrobiologically significant remote regions worldwide. In June 2013, members of the MIT and ASU teams traveled to Shark Bay and the Pilbara regions of Western Australia to gather material for new VFTs, acquiring 13 location-based sphericals, 4 gigapans, 277 video clips, 5 quad copter flights, and well over 2,000 still photographs. We are developing learning modules for this new material, aligned to the Next Generation Science Standards and the undergraduate-level ASU online course “Habitable Worlds”.

During the Cambridge Science Festival in April 2013, we displayed our popular to-scale Geological Timeline walk signs and tours along the Charles River for 9 days. The MIT team has also been participating in the Cambridge Science Festival’s effort to reach populations not served by the annual festival, traveling to their communities throughout the year through a new program, Science on the Streets. With partners around MIT and Harvard, we expanded our successful teacher-scientist workshops into two consecutive sessions aimed at grades 4-8 and 9-12, respectively, and are working towards a significantly deeper evaluation of the resulting classroom visits, the primary goal of this program. In addition to this, many members of the MIT team participated in media interviews, classroom visits, and public presentations throughout the reporting period.