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Project Reports

• Project 1: The Origin of Homochirality

  Small biological molecules are frequently chiral, meaning that they can exist in both right-handed and left-handed forms. The two forms are identical except for the mirror symmetry that they break, and so would be expected to participate in chemical reactions in a way that does not depend on their chirality. When assembled into polymers, the resulting chains would therefore be expected to consist of a mixture of right and left-handed forms of the small molecules, a so-called racemic state. The surprise is that this is not true for the molecules of life. All chiral amino acids used by biology are left-handed and all chiral sugars are right-handed. That is, they are homochiral. This project is concerned with trying to find an explanation for this ubiquitous phenomenon, a universal aspect of all life on Earth. The specific question that is addressed is whether homochirality is a generic phenomenon of living systems, one that would be anticipated to arise if life were found elsewhere in the universe. Or is it instead some frozen accident related to the specific way that life arose on Earth? This question has been hotly debated in one form or other for over a hundred years, certainly since the time that Lord Kelvin coined the term “homochirality”. It is important for the Illinois NASA Astrobiology Institute for Universal Biology, because it is one of the two most evident universal phenomena of all life on Earth, the other being the universal genetic code. The phenomenon is important for another reason. The magnitude of the homochirality is 100%. It is not a slight imbalance in the abundance of right-handed vs. left-handed molecules. Thus, it is an unambiguous signal to measure, either from biological samples or remotely due to the effects of homochirality on the scattering of light waves. Specifically, homochiral solutions or suspensions will affect the polarization plane of electromagnetic waves, and so can readily be detected through optical means. The most exciting possibility in this regard is that if homochirality can be firmly established as a biological phenomenon, then its presence can be used as a biosignature of non-terrestrial life.

  ROADMAP OBJECTIVES: 1.2 3.2 3.4 4.1 4.2 7.1 7.2

• Understanding Past Environments on Earth and Mars

  In this task we performed research to understand the evolution of habitable environments on Earth and Mars, both of which serve as potential analogs for habitable environments on extrasolar planets. We are expanding this line of work from past reports to span the entire histories of both planets. On Earth, we have sought to understand environments and time periods spanning the origins of life to the effects of human-generated greenhouse gas emissions on modern-day climate cycles. On Mars, we focus on the ancient conditions that could have allowed liquid water to be stable at the surface; on modern Mars, we focus on the debate on the presence, amount, and variability of methane in the Martian atmosphere.

  ROADMAP OBJECTIVES: 1.1 1.2 4.1 4.2 5.1 5.2 6.1

• Project 2: Function by Reduction: Do Extant Symbiont Enzymes Recapitulate Ancient Metabolic Generalists

  The origins of mitochondria and chloroplasts are two of the great unsolved mysteries in biology. It is now clear that these organelles used to be bacteria, but the evolutionary paths taken as they transitioned from bacteria to organelle are not well understood because they happened more than 1.5 billion years ago. Some insect endosymbionts have symbioses with bacteria which resemble organelles in many ways. We use these more recent symbioses as models to better understand the origins of organelles, one of the most critical events in the evolution of complex life.

  ROADMAP OBJECTIVES: 4.2 5.2 6.2

• Inv 3 – Planetary Disequilibria: Characterizing Ocean Worlds and Implications for Habitability

  INV 3 looks at how, where, and for how long might
disequilibria exist in icy worlds, and what that may imply in terms of
habitability. A major interest for this work is how ocean composition affects habitability. We are investigating chemistry behaves under conditions of pressure, temperature, and composition not found on Earth. Our simulations of deep ocean world chemistry couple with models for ocean dynamics, ocean ice interaction, and tectonics within the ice. We are examining each of these, how they interact, and how they relate to what future missions may discover. Members of our team are involved in missions to Mars, Jupiter’s moon Europa, Saturn, and Pluto. We are also involved in studies of exoplanets, and are working to understand how ocean worlds like Ganymede and Europa might provide analogues for more distant watery super-earths.

  ROADMAP OBJECTIVES: 1.1 1.2 2.2 3.1 4.2 6.2 7.1 7.2

• Project 3: Theory for the Darwinian Transition

  One of the key puzzles of astrobiology concerns the precision, uniqueness and rapidity of early evolution. In order for life to have evolved the main components of the modern cell as early 3.8 billion years ago, with a unique genetic code that is virtually optimal in terms of minimizing translational errors, the mode of evolution would have had to be different from the current vertical transmission of genes. We had shown in 2006 that the collective mechanism of horizontal gene transfer (HGT) is the only one capable of solving the puzzle of early evolution. The HGT means that the evolutionary process before LUCA can be thought of as a network of interactions rather than a tree, as would be the case in vertical gene transfer. The multiple connectivity of the network accelerates the evolution and allows rapid convergence to a unique, near-optimal genetic code. With all these advantages of HGT, why would it ever stop? Our project uses computer simulation of digital organisms in order to address these generic questions about the exit of life from the collective, progenote phase to the current era of vertically dominated evolution.

  This project is potentially important for understanding biosignatures of life. Even on Earth, we are familiar with the tree-like structure of individual organismal lineages. If life were a network, as we believe that it once was, the usual phylogenetic pattern of individuality and species would not apply. If we encounter life on other planets, we cannot be sure if it will be in the collective (progenote) phase or the vertical-dominated phase. Thus it is interesting to understand better the inexorability and timing of the Darwinian Transition.

  ROADMAP OBJECTIVES: 3.2 3.4 4.1 4.2 5.1 6.2

• ALTERNATIVE EARTH 3 – Oxygen Stasis and the Rise of Eukaryotes

  The importance of a full understanding of the controls on ocean-atmosphere O₂ levels during the mid-Proterozoic is difficult to overstate. The evolution of O₂ levels in the mid-Proterozoic ocean-atmosphere system forms the backdrop for the initial emergence and subsequent evolutionary stasis of eukaryotic life. Furthermore, it provides the possibility of a remarkably long period of Earth’s history during which many of the links among tectonics, climate, and life may have been short-circuited and/or amplified in unusual ways. Finally, it provides the preface that is essential reading for any story about the proximate causes of the subsequent emergence of complex life in the late Neoproterozoic. The central question in this regard is whether ocean-atmosphere O₂ levels were low enough to inhibit the evolution and ecological emergence of complex multicellular life, or must we seek mechanisms strictly associated with internal biology to explain this event—or both? Our developing framework for very low oxygen levels during the mid-Proterozoic in the deep ocean, shallow ocean, and atmosphere is the baseline against which the dramatic environmental, climatic, and biotic events and triggers of the later Proterozoic should be assessed.

  ROADMAP OBJECTIVES: 4.1 4.2 7.2

• Project 3: Consequences of recA Duplication for Recombination, Genome Stability and Fitness

  Homologous recombination (HR) – the exchange of genetic information between similar DNA molecules – is an ancient process that is central to the emergence of biological complexity, diversity and stability. Yet, it must be tightly regulated, as it is likewise an important source of destabilizing genomic rearrangements. Despite the importance of HR, we still have a poor understanding of the balance of these creative, stabilizing and destabilizing contributions to organismal fitness, complexity and genome evolution. We are using the extraordinary genome evolutionary dynamics and duplicated copies of the HR gene recA in the cyanobacterium Acaryochloris as a model to gain novel insights on the fitness consequences that emerge from the interplay between HR-mediated maintenance of genome stability, selectively favored gene duplications and non-adaptive genomic rearrangements.

  ROADMAP OBJECTIVES: 4.2 5.1 5.3 6.1 6.2

• Project 4: Experiment on Darwinian Transition

  Carl Woese proposed that life started as semi-autonomous subcellular forms named progenotes. The progenotes lacked cell membranes and readily exchanged information, suggesting that aspects of information processing had already been developed. Woese further hypothesized that certain early life processes crossed a Darwinian threshold, where incorporation of new components of a processes was not tolerated. We aim at determining whether translation, transcription, and replication have crossed the Darwinian threshold. To determine whether DNA replication has crossed the Darwinian Threshold, interchangeability of the DNA replication processivity factor known as the sliding clamp is being examined. It is only in the presence of the sliding clamp that DNA polymerases in extant organisms can gain the speed required to replicate their genomes. In Bacteria, the sliding clamp is the -subunit of Pol-III and in Archaea and Eukarya the functional homolog is proliferating cell nuclear antigen (PCNA). We have, therefore, expressed and purified a sliding clamp from each of the three domains of life (E. coli -subunit, M. acetivorans PCNA, and human PCNA). Sliding clamps are loaded in a clamp loader dependent manner; therefore, we have cloned, expressed and purified an archaeal clamp loader from M. acetivorans. Our next step is to determine whether an archaeal clamp loader can interact with each of the sliding clamps from the three domains of life and whether any of the interactions leads to loading of the sliding clamps onto DNA to orchestrate processive DNA synthesis.

  ROADMAP OBJECTIVES: 3.2 3.4 4.2

• Early Animals: Lipid Biosignatures

  We established the structures of two unusual steroid-related molecules that appear to be characteristic of Neoproterozoic ecosystems.

  We responded to an 2013 critique of the sponge biomarker hypothesis with a detailed rebutal. Currently, the most parsimonious interpretation of the presence of the unusual steroid, 24-isopropylcholestane, in Neoproterozoic sediments is that represents a molecular fossil of demosponges.

  We devolped a new approach to evaluating the diets of early hominins based on analyese of fecal sterols. We studied the fecal sterols of great apes and determined that they were distinct from the fecal sterols of Neandethals and modern humans (Sistiaga et al., 2015).

  ROADMAP OBJECTIVES: 3.2 4.2

• ALTERNATIVE EARTH 4 – the Rise of Complexity Amid Environmental Turmoil

  Climatic turmoil and major upheavals in global biogeochemical cycles characterize the latter part of the Proterozoic Eon, during the so-called Neoproterozoic (1,000–541 million years ago). The Neoproterozoic was marked by pronounced shifts in atmospheric composition—especially increased oxygen levels. This environmental instability provided the backdrop for the rise of complex life, including animals; however, limited empirical constraints have hindered attempts to untangle the cause-and-effect relationships among biological innovations, shifts in ecosystem complexity, and biogeochemical evolution. Likewise, still sparse coupled geochemical and paleontological records make it difficult to gauge whether the Neoproterozoic unfolded as a unidirectional march toward greater organismal complexity and higher oxygen levels, as traditionally envisioned, or whether dramatic swings in surface oxygen levels accompanied non-unidirectional ecological shifts. To resolve this debate, we are producing extensive, high-resolution records of oxygen levels and tracking the distribution, abundance, and impact of eukaryotic phytoplankton over this critical interval. Our central goal is to work synergistically with the Origins of Complexity NAI Team to better understand how the rise of complex life shaped planetary-scale biosignatures.

  ROADMAP OBJECTIVES: 4.1 4.2 7.2

• Project 5: Adaptation, Mutation Supply, and Evolution of Synergy in Biofilm Communities

  We will quantify the dynamics of adaptation and identify the mutational causes in evolving biofilms with high precision, and therefore illustrate how microbes colonizing a new surface can transform their environment and set the stage for primitive multicellularity. Biofilms resemble tissues in their subdivided labor, varied physical structure and shared metabolism. We predict that the stability of this ecological cooperation rests on population-genetic controls on selfish lineages associated with mutators, much as tissues are liable to selfish invasion by cancers.

  ROADMAP OBJECTIVES: 4.2 5.1 5.2 6.1 6.2

• Evolution of Precambrian Life and Primary Producers

  Life on Earth is sustained by photosynthesis, both on land and in the sea. New research provides novel perspectives on the evolution of diatoms, responsible for 25% of all photosynthesis in today’s oceans. Also, new fossils from Russia strengthen the relationship between early eukaryotes and environmental conditions in Proterozoic oceans.

  ROADMAP OBJECTIVES: 4.1 4.2 6.1

• Project 6: Life’s Diversity

  This project is on the theoretical modeling of life’s complexity and diversity, where we are modeling evolvability, diversity, and complexity in mathematical terms. Since these models are of high complexity, we are employing asymptotic and other approximate methods for their solution.

  ROADMAP OBJECTIVES: 4.2 6.2

• Early Animals: Evolution of Complex Multicellularity

  Oxygen availability has long been viewed as a principal deriver of Ediacaran-Cambrian animal diversification, yet quantitative constraints on oxygen history and physiological constraints on animal function at low pO2 have been limited. New statistical analyses of iron-sepciation data for Proterozoic and Paleozoic shales indicate that end-Proterozoic oxygen increase was limited, but physiologial insights from present day oxygen minimum zones indicate that oxygen levels may well have crossed the theshold reuqired from large diverse animals that include carnivores.

  ROADMAP OBJECTIVES: 4.1 4.2

• Project 6: The Evolution of Complexity via Multicellularity and Cellular Differentiation

  The evolution of multicellular organisms from single-celled ancestors set the stage for unprecedented increases in complexity, especially in land plants and animals. We have used the unicellular green alga Chlamydomonas reinhardtii to generate de novo origins of simple (undifferentiated) multicellularity in two separate experiments. Using these experimentally evolved algae, we will ascertain the genetic bases underlying the evolution of multicellularity, evaluate the role of genetic assimilation in the evolution of multicellularity, and observe the evolutionary origin of multicellular development in real time.

  ROADMAP OBJECTIVES: 4.2 5.1 6.2

• Project 7: Error Rate and the Origin and Early Evolution of Life

  Our project investigates the evolutionary relationship between rates of genetic mutation and genetic recombination. It addresses very general questions about the stability of heredity and the implications of that stability for adaptation and persistence of organisms. Such questions are likely to apply wherever and whenever life evolves. In prior theory work we have shown that the mutation rate of a population will tend towards ever-higher values in the absence of genetic recombination. Because mutation is the ultimate source of the variation required for the evolution of a population, it might be thought that a high mutation rate would enable more rapid evolutionary adaptation. We and others have shown, however, that too high a mutation rate can cause extinction of a population. Because early life probably had very high mutation rates, early life would have been at considerable risk of evolving a lethal mutation rate. This should have produced strong pressure for genetic recombination to evolve. In our project we are using experimental evolution, analytical theory, and computer simulations to test the effect that recombination has on mutation rate evolution, the effect that high mutation rates have on population adaptation and persistence, and the effect of mutation on the evolution of cooperation among life forms.

  ROADMAP OBJECTIVES: 4.2 5.2 6.2

• Project 7: Mining Archaeal Genomes for Signatures of Early Life: Comparison of Metabolic Genes in Methanogens

  Methanogens represent the largest diversity among the archaea and have the unique ability to generate methane from simple compounds such as carbon dioxide, acetate and methylamines which were common in the anaerobic environments of early Earth and perhaps Mars. Methane biosynthesis also requires the presence/uptake of important ions such as sulfates, sulfides, carbonates, phosphates, and various light metal ions. In this project, we are attempting to analyze the evolution of the methanogens’ central cellular functions of translation, transcription, replication, and metabolism. To accomplish this, we are constructing the metabolic and regulatory networks of Methanosarcina acetivorans, the most complex methanogen known, and using these models to establish a framework for studying the evolution of methanogens. Results will be tested through microfluidic studies using varying carbon and ion sources.

  ROADMAP OBJECTIVES: 1.1 2.1 3.1 3.2 3.3 3.4 4.1 4.2 5.1 5.2 5.3 6.1 6.2 7.1

• Early Animals: Taphonomic Controls on Fossil Record

  This project has focused on Neoproterozoic life with an emphasis on factors influencing fossil preservation. A combination of field and experimental approaches has been used to study preservation of Ediacara-type fossils and to test the prevailing ‘death-mask’ hypothesis that considers iron sulfides to have been a primary agent. Results so far indicate that ferruginization was a late-stage process and not consistent with this model suggesting an important role for early silicification. Initial experimental results show that microbial mats are prone to silicification and that their presence in association with invertebrate carcasses inhibits decay and enhances the preservation of soft-bodied organisms. An investigation of factors controlling the preservation of eukaryotic microfossils in Proterozoic rocks is also underway. Experimental data indicate that certain clays inhibit the growth of decay bacteria such as Pseudoaltermonas.

  New fossil assemblages from grey shales and cherts have been discovered from this same interval – a significant development because very few fossils have been described from rocks between the two Snowball Earth ice ages. The preponderance of exceptional preservations in the Cambrian and subsequent early Paleozoic may be explained in part by a delay in intense mixing of marine shelf sediments by bioturbators, which did not develop until the Devonian. This slow onset of thorough mixing may also have contributed to the late rise of sulfate in the oceans and a mid-Paleozoic drop in oxygen levels.

  ROADMAP OBJECTIVES: 4.1 4.2

• Project 8: The Evolution of the Eukaryote-Archaea Common Ancestor

  The goals of our lab with respect to the NAI project are to describe early evolutionary via genomic and cellular comparisons of diverse eukaryotes to diverse archaea. We are interested in comparing genomes from diverse free-living eukaryotes to investigate the origins and evolution of eukaryotic complexity. Evolutionary reconstructions of early eukaryotes are challenged by a lack of sufficient taxonomic sampling. Few genomes of free-living microbial eukaryotes are sequenced, despite their critical importance in ecology, evolution, and basic cellular biology. The real challenge to protistan genomics is actually quite mundane; it concerns the lack of available and cultivatable free-living protists (mainly heterotrophs) in the laboratory. Yet, a better understanding of the genomic content diverse eukaryotes facilitates the evolutionary analysis of archaeal genomes. To address these issues of poor taxonomic sampling of eukaryotic genomes, my lab has developed a molecular method to separate eukaryotic DNA from bacterial DNA. We have demonstrated conclusively that we can separate eukaryotic chromatin from a mixture of eukaryotic and bacterial genomic DNA. This method will be widely applicable to the study of protistan genomics. Currently, our lab is in the process of assembling and annotating ten eukaryotic genomes from my lab’s culture collection of over 100 amoeboid protists from diverse phylogenetic groups. Many of these amoeba represent novel phyla-level lineages of eukaryotes.

  One amoebal genome is form is Nuclearia sp., which is an amoeboid protist closely and a member of a primary “supergroup” of eukaryotes – the Optisthokonts. This supergroup includes all animals, fungi, and several types of unicellular or colonial protists including choanoflagllates. Thus, genomic analyses of Nuclearia will inform the evolution of complexity and multicelllularity in both Fungi and Animals.

  ROADMAP OBJECTIVES: 3.2 3.4 4.2 6.2

• Theoretical Integration: Evolutionary Dynamics of Ecosystems Controlled by Multiple Autonomous Genomes

  The work of Co-I Smith during 2015 centered on two aspects of the role of ecosystem feedback in determining the relations among fitness functions and the co-evolutionary dynamics of multiple genomes.

  The first task concerns the optimal degree of genomic autonomy to carry out the aggregate metabolic functions of an ecosystem: when is it preferable to combine the control of multiple pathways within a single genome, and when is splitting the control among multiple autonomous genomes more stable under coevolution?

  The second task concerns the stochastic dynamics and the descriptive statistics of populations evolving under the control of feedbacks from potentially-complex ecological stoichiometric constraints. It incorporates recent methods in computational chemistry to produce exactly solvable, and biologically relevant, models of complex stoichiometric constraint that couple multiple evolving lineages.

  ROADMAP OBJECTIVES: 4.2 5.2

• Rock Powered Life: Education and Communications

  The central theme of the Rock Powered Life research effort is to define how, where and when water/rock interactions release energy and how this energy is harvested to support microbial communities. These studies are of fundamental importance for improving understanding of how microbial life was supported on early Earth. Moreover, since similar reactions can be expected on any rocky planet with liquid water, these studies provide new constraints for predicting the distribution of life on other planetary bodies.

  The focus of our team – rock-hosted microbial ecosystems that are dependent on chemical rather than light energy – provides novel avenues to engage the next generation of astrobiologists and to disseminate knowledge to the broader public. Here we describe current and ongoing efforts by members of Rock Powered Life that are aimed at improving engagement and training in astrobiology. Of particular relevance are efforts to provide opportunities to provide underrepresented high school and undergraduate students hands on training opportnities in astrobiology-focused studies. We also describe advancements in Rock Powered Life’s digital-based information sharing technologies. Through these integrated team efforts we aim to attract and train future generations of astrobiologists and to provide greater access to the current knowledge base with which to understand the potential for life elsewhere on other planetary bodies.

  ROADMAP OBJECTIVES: 3.2 4.1 4.2 5.1 5.2 5.3 6.1 6.2

• The Long Wavelength Limit of Oxygenic Photosynthesis

  Oxygenic photosynthesis (OP) produces the strongest known biosignatures at the planetary scale on Earth: atmospheric oxygen and the spectral reflectance of vegetation. The pigment chlorophyll a was long considered the unique controller of both of these biosignatures, in its capability to enable water splitting to obtain electrons and thus produce oxygen as a biogenic gas, through spectral absorbance of light from the blue to 680 nm in the red. Then the discovery in 1996 of the cyanobacterium Acaryochloris marina shattered this conventional wisdom. A. marina was found to have replaced 93-97% of Chl a with Chl d, which enables it to perform oxygenic photosynthesis with much lower energy photons in the far-red/near-infrared. Since that first discovery in 1996, more far-red oxygenic phototrophs have been discovered, revealing a previously unsuspected diversity in the photosystems of oxygenic phototrophs. We seek to determine the long wavelength limit at which OP might remain viable and what factors affect the selection of that wavelength limit. This would clarify whether and how to look for OP adapted to the light from stars with a difference radiance spectrum from our Sun.

  Under this project in previous years and with other co-investigators, we spectrally quantified the thermodynamic efficiency of photon energy use in Acaryochloris marina str. MBIC11017, determined that its water-splitting wavelength is in the range 710-723 nm, and that it is more efficient than a Chl a cyanobacterium. The current focus of the project is to understand the adaptations of far-red/near-infrared (NIR) oxygenic photosynthetic organisms in general: in which environments they are competitive against chlorophyll a organisms, and what energetic shifts have been made in their photosynthetic reactions centers to enable their use of far-red/NIR photons. We are conducting field sampling and measurements to isolate new strains of far-red-utilizing oxygenic photosynthetic organisms, to quantify the spectral and temporal light regime in which they (and previously discovered strains) live in nature, and to use these light measurements to drive kinetic models of photon energy use to determine efficiency thresholds of survival.

  ROADMAP OBJECTIVES: 3.2 4.2 5.1 5.3 6.2 7.2

• Mars Analog Studies: Ice Covered Lakes on Earth and Mars

  Ice-covered lakes in Antarctica provide models for sedimentary processes on ancient Mars and microbial ecosystems for early Earth. Ice affects sedimentation because sand grains can be blown onto the ice, where they can eventually go through the ice into the lake below. Understanding the details of these processes and resulting sediments will allow us to better reconstruct details of lake environments and their implications for climate on early Mars. Early Earth ecosystems, and those on early Mars if life ever existed there, consist exclusively of microorganisms, which is also true for many Antarctic lakes. Thus, these lakes provide the opportunities to investigate ecological principles for early ecosystems. Data from the microbial mats in these lakes are providing insights into the growth of stromatolite, the geochemical impacts of oxygen-producing photosynthesis, and environments that may have promoted the early diversification of animals.

  ROADMAP OBJECTIVES: 2.1 4.1 4.2 5.1 5.2 6.1

• Project 9: Metapopulation Structure

  Although often modeled as a single well mixed populations, microbes in terrestrial systems likely exist as metapopulations, isolated but connected by infrequent migration. This can change the evolution of complexity, increasing the effect of genetic drift and decreasing the effect of selection. It can increase diversity and the rate at which complexity evolves. We have argued that metapopulation structure may have existed in early life and been responsible for the rapid evolution of LUCA and diversification across the tree of life. We investigate microbial genome evolution in metapopulations in Yellowstone National Park. We find that indeed they represent evidence for both natural selection and genetic drift shaping these populations.

  ROADMAP OBJECTIVES: 3.2 3.4 4.2 6.2

• Project 3A: Apatitic Latest Precambrian and Early Cambrian Fossils Provide Direct Evidence of Concentrations of Environmental Oxygen

  Means are not currently available to asses either quantitatively or semi-quantitatively the concentration of oxygen in Earth’s atmosphere over geological time. Despite this, the environmental availability of O₂ has been repeatedly postulated to be a cause of major changes in Earth’s biota, most particularly at the Precambrian-Cambrian boundary-defining “Cambrian Explosion of Life,” a time in Earth history when large deposits of phosphate-rich apatite were deposited in shallow basins worldwide. This study shows that substitution of Sm+3 in the Ca I and Ca II sites of fossil-permineralizing, -infilling, and -encrusting apatite can differentiate between oxic, dysoxic, an anoxic settings of apatite formation. Further studies are underway to date such apatite and establish its REE-substitution as a quantitative O₂ paleobarometer.

  ROADMAP OBJECTIVES: 4.1 4.2

• Eva Stüeken NPP Postdoc Report

  I study the non-marine sedimentary rock record to determine if lakes and rivers could have been important habitats for the early evolution of life on Earth. Our results suggest that the greater environmental diversity found in non-marine settings may enhance biological diversity. However, we cannot confirm previous conclusions that lakes were particularly suited for eukaryotic life. These findings may provide clues about potential biodiversity of other worlds that are characterized by smaller lake basins (e.g. early Mars) versus a global ocean (e.g. Europa).

  ROADMAP OBJECTIVES: 4.1 4.2 6.1

• Fullerenes and Mass Extinctions?

  A re-examination of past reports of the occurrence of fullerenes at mass extinction horizons, using proven extraction and analysis approaches, has failed to detect them. We conclude that fullerene cannot be used as a proxy for bolide impacts or mass extinction events.

  ROADMAP OBJECTIVES: 4.2 4.3

• Progress in the Elucidation of Microbial Biosignatures

  A number of discrete individual investigations have contributed to improved knowledge about the occurrence and interpretation of microbial molecular biosignatures across all geological timescales.

  A new analytical approach enabled a revised geologic distributions of fossilized biomarkers for anoxygenic sulfur bacteria. The prevalence of okenane and chlorobactane suggests that marine photic zone euxinia (PZE) was more intense and frequent in the geologic past. However, the presence of these compounds in some sediments and oils may also be a signature for basin restriction rather than one indicating more widespread marine anoxia.

  In a related work, pervasive photic zone euxinia and disruption of biogeochemical cycles was demonstrated for a sequence of rocks deposited on the northeastern Panthalassic Ocean during the end-Triassic extinction.

  A study of lipids and their isotopic compositions, combined with stable isotope probing experiments, demonstrated that streamer biofilm communities, which are a present in the high temperature zones of hydrothermal features of the Lower Geyser Basin of Yelowstone National Park, can alternate their metabolism between autotrophy and heterotrophy depending on substrate availability.

  Other collaborations with numerous colleagues resulted in documentation of lipid and isotopic biosignatures in cultured bacteria.

  ROADMAP OBJECTIVES: 3.2 4.2 5.1 5.2 5.3 6.1

• Early Animals: Modeling the Biotic-Abiotic Interface in the Early Evolution of Multicellular Form

  Multicellular organisms in the sea modify their local hydraulic environment. Modeling of the earliest-known multicellular communities of frond-like forms demonstrated that they were large enough and closely spaced enough to generate a distinctive canopy flow-regime. In this context diffusion at the surface of organism was limiting and height and attendant velocity exposure permitted escape from these limits (Ghisalberti et al. 2014). Building on these results, we are developing models of abiotic/biotic interactions at organismal surfaces, relevant to the morphology, development and orientation of other Neoproterozoic fossils. A subset of these are flat-lying forms such as Dickinsonia. These may interact with the sediment modifying redox gradients. Ultimately, this work will help illuminate how forms initially dependent on passive diffusion became more trophically, morphologically and behaviorally complex, during the diversification of animals.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 6.1

• Early Animals: Sensory Systems and Combinatorial Codes

  Understanding the evolution of integrated sensory organs—such as the eyes, ears and nose that develop in concert on our heads—is fundamental to understanding animal complexity. These are the features that permit movement and the environmental responses that characterize animals. We examine understudied early branches of the animal family tree, with a focus on the jellyfish Aurelia, to understand how the genetic regulation of sensory organs is conserved in some cases and evolves in others. Comparison of developmental regulation reveals how similar gene networks can be differentially modified and deployed, permitting the evolution of complex sensory systems. Jellyfish provide an ideal study system for the examination of the evolution of such sensory systems in animal evolution, as they are the most basal branch of the animal tree with multiple sensory modes, and these develop at multiple stages in a complex life history. This provides us the ability to compare and contrast within the broader cnidarian group to which jellyfish belong, and to the bilaterians, the broad group containing humans and most other animals. The application of genomic methods greatly enhances our ability to pursue these questions.

  ROADMAP OBJECTIVES: 4.1 4.2

• Taphonomy of Microbial Ecosystems

  We perform experiments to understand shapes, molecules and isotopic signals of microbial processes in modern and old sediments. Experimental studies of microbial interactions with sediments, ions in the solution and the flow help us elucidate mechanisms that may have shaped sandy surfaces and preserved fossils on these surfaces at the dawn of animal life. Culture-based studies of isotopic fractionations produced by microbial processes and microbial membrane lipids help us interpret corresponding signals in the rock record and modern environments.

  ROADMAP OBJECTIVES: 2.1 4.1 4.2 5.1 5.2 6.1 7.1 7.2

• Early Animals: The Origins of Biological Complexity

  We seek to understand the interactions of ecological, environmental and developmental processes that generate biological novelty and innovation, with particular emphasis on the events associated with the origin and early evolution of animals. The larger goal is to develop a general model of novelty (the origin of new organismal characters) and innovation (the ecological and evolutionary success of these novelties) and determine whether it applies through the history of life. Alternatively episodes of novelty and innovation may be dominated by historical contingency so that no general model can be developed.

  ROADMAP OBJECTIVES: 4.1 4.2

• Earth’s Evolving Nitrogen Cycle – Implications for Community Complexity and Stability

  This project examines nitrogen isotope patterns in Proterozoic and Paleozoic rocks, as part of a broader effort to understand the co-evolution of Earth’s redox cycles and marine ecosystems. The results are being incorporated into a growing framework of data and models that have as their primary objective to show how planetary geochemical cycles evolve with and/or help to record signatures of living systems – both microbial and complex. The project aims to yield a better understanding of the transition from primarily anoxic to primarily oxic deep oceans, and how that transition is mirrored in nutrient budgets (i.e., nitrogen) and the marine ecosystems that depend on the stability of these cycles. Understanding N-cycling throughout Earth’s history has critical implications for the evolution of complex marine ecosystems on geologic timescales.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 5.3 6.1

• Paleontological, Sedimentological, and Geochemical Investigations of the Mesoproterozoic-Neoproterozoic Transition

  As we learn more about the earliest evolutionary history of animals and other complex multicellular organisms, it becomes clearer that a satisfactory understanding of these events have to be set within the broader context of late Mesoproterozoic and Neoproterozoic biological and environmental change. To this end, several labs within our team have focused research effort of Mesoproterozoic and Neoproterozoic sedimentary successions. Over the reporting period, this has included stratigraphic and sedimentological fieldwork on rocks of this age in northwestern Canada, Death Valley, Mongolia, Peru, and anaylsis of drill cores from Russia, Congo and Zambia. Progress has also been made in new techniques for the discovery, description, and interpretation of Proterozoic microfossils, and several-fold improvements in the precision of oxygen-17 measurements, which can record the balance of atmospheric oxygen and carbon dioxide.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 6.1

• Early Animals: The Genomic Origins of Morphological Complexity

  Understanding the origins of life’s complexity here on Earth is paramount to finding it else-where in the universe. The fossil record indicates that complexity on Earth arose in a near geological moment – the famous Cambrian explosion – about 525 million years ago. However, molecular sequence analyses indicate that complex animals actually arose nearly 200 million years before they make their first appearance in the fossil record. This disparity between the advent of morphological complexity and its appearance in the fossil record 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 an-other distant Earth-like planet? Our research is focused on addressing this question by trying to obtain a better understanding of what encodes morphological complexity in the genome. Our research suggests that a group of non-coding RNA genes – microRNAs – might be instrumental for the advent and maintenance of complexity in animals, and therefore sequencing the genomes and the transcriptomes (the ex-pressed component of the genome) from carefully chosen taxa might allow us to better under-stand the biology of animals that predated the Cambrian explosion.

  ROADMAP OBJECTIVES: 4.2 4.3