Department of Biology

The mission of the Department of Biology is to combine internationally recognized research programs with a commitment to the very best in undergraduate and graduate education. Work in the Department is impressively interdisciplinary. For example, faculty research programs include the characterization of global ecosystem biology; the use of model systems to dissect gene expression, mammalian development, behavior, disease and evolution; and the development of genomics tools to study the architecture of gene expression and genome evolution. This research breadth allows the Department of Biology to tackle important questions in biology in an environment that encourages discussion and collaboration across different disciplines. From such strength the department has built outstanding research and educational programs in Ecology, Evolution & Biodiversity; the Molecular Basis of Behavior; Plant Science; Microbial Biology; Cell & Developmental Biology; Molecular Biology & Genetics and Genomics & Bioinformatics that are available for undergraduate, graduate and post-doctoral scientists.



Search results

Now showing 1 - 10 of 68
  • Publication
    Group Size and Social Conflict in Complex Societies
    (2014-02-01) Shen, Sheng-Feng; Akçay, Erol; Rubenstein, Dustin R
    Conflicts of interest over resources or reproduction among individuals in a social group have long been considered to result in automatic and universal costs to group living. However, exploring how social conflict varies with group size has produced mixed empirical results. Here we develop a model that generates alternative predictions for how social conflict should vary with group size depending on the type of benefits gained from being in a social group. We show that a positive relationship between social conflict and group size is favored when groups form primarily for the benefits of sociality but not when groups form mainly for accessing group-defended resources. Thus, increased social conflict in animal societies should not be viewed as an automatic cost of larger social groups. Instead, studying the relationship between social conflict and the types of grouping benefits will be crucial for understanding the evolution of complex societies.
  • Publication
    High Adenylyl Cyclase Activity and In Vivo cAMP Fluctuations in Corals Suggest Central Physiological Role
    (2013-03-05) Barott, Katie; Helman, Y.; Haramaty, L.; Barron, Megan E; Hess, K. C; Buck, J.; Levin, L. R; Tresguerres, Martin
    Corals are an ecologically and evolutionarily significant group, providing the framework for coral reef biodiversity while representing one of the most basal of metazoan phyla. However, little is known about fundamental signaling pathways in corals. Here we investigate the dynamics of cAMP, a conserved signaling molecule that can regulate virtually every physiological process. Bioinformatics revealed corals have both transmembrane and soluble adenylyl cyclases (AC). Endogenous cAMP levels in live corals followed a potential diel cycle, as they were higher during the day compared to the middle of the night. Coral homogenates exhibited some of the highest cAMP production rates ever to be recorded in any organism; this activity was inhibited by calcium ions and stimulated by bicarbonate. In contrast, zooxanthellae or mucus had >1000-fold lower AC activity. These results suggest that cAMP is an important regulator of coral physiology, especially in response to light, acid/base disturbances and inorganic carbon levels.
  • Publication
    Pathways to Social Evolution: Reciprocity, Relatedness, and Synergy
    (2014-08-01) Van Cleve, Jeremy; Akçay, Erol
    Many organisms live in populations structured by space and by class, exhibit plastic responses to their social partners, and are subject to nonadditive ecological and fitness effects. Social evolution theory has long recognized that all of these factors can lead to different selection pressures but has only recently attempted to synthesize how these factors interact. Using models for both discrete and continuous phenotypes, we show that analyzing these factors in a consistent framework reveals that they interact with one another in ways previously overlooked. Specifically, behavioral responses (reciprocity), genetic relatedness, and synergy interact in nontrivial ways that cannot be easily captured by simple summary indices of assortment. We demonstrate the importance of these interactions by showing how they have been neglected in previous synthetic models of social behavior both within and between species. These interactions also affect the level of behavioral responses that can evolve in the long run; proximate biological mechanisms are evolutionarily stable when they generate enough responsiveness relative to the level of responsiveness that exactly balances the ecological costs and benefits. Given the richness of social behavior across taxa, these interactions should be a boon for empirical research as they are likely crucial for describing the complex relationship linking ecology, demography, and social behavior.
  • Publication
    The Perfect Family: Decision Making in Biparental Care
    (2009-10-13) Akçay, Erol; Roughgarden, Joan
    Background Previous theoretical work on parental decisions in biparental care has emphasized the role of the conflict between evolutionary interests of parents in these decisions. A prominent prediction from this work is that parents should compensate for decreases in each other's effort, but only partially so. However, experimental tests that manipulate parents and measure their responses fail to confirm this prediction. At the same time, the process of parental decision making has remained unexplored theoretically. We develop a model to address the discrepancy between experiments and the theoretical prediction, and explore how assuming different decision making processes changes the prediction from the theory. Model Description We assume that parents make decisions in behavioral time. They have a fixed time budget, and allocate it between two parental tasks: provisioning the offspring and defending the nest. The proximate determinant of the allocation decisions are parents' behavioral objectives. We assume both parents aim to maximize the offspring production from the nest. Experimental manipulations change the shape of the nest production function. We consider two different scenarios for how parents make decisions: one where parents communicate with each other and act together (the perfect family), and one where they do not communicate, and act independently (the almost perfect family). Conclusions/Significance The perfect family model is able to generate all the types of responses seen in experimental studies. The kind of response predicted depends on the nest production function, i.e. how parents' allocations affect offspring production, and the type of experimental manipulation. In particular, we find that complementarity of parents' allocations promotes matching responses. In contrast, the relative responses do not depend on the type of manipulation in the almost perfect family model. These results highlight the importance of the interaction between nest production function and how parents make decisions, factors that have largely been overlooked in previous models.
  • Publication
    Immunolocalization of Proteins in Corals: The V-Type H+-ATPase Proton Pump
    (2015-09-05) Barott, Katie; Tresguerres, Martin
    Here we describe the immunolocalization of a membrane-bound proton pump, the V-type H+-ATPase (VHA), in tissues and isolated cells of scleractinian corals. Immunolocalization of coral proteins requires additional steps not required for various model organisms, such as decalcification of the coral skeleton for immunohistochemistry or removal of cells away from the skeleton for immunocytochemistry. The tissue and cell preparation techniques described here can be adapted for localization of other coral proteins, provided the appropriate validation steps have been taken for the primary antibodies and species of coral used. These techniques are important for improving our understanding of coral cell physiology.
  • Publication
    Social Inheritance Can Explain the Structure of Animal Social Networks
    (2015-01-01) Ilany, Amiyaal; Akçay, Erol
    The social network structure of animal populations has major implications to survival, reproductive success, sexual selection, and pathogen transmission. Recent studies showed in various species that the structure of social networks and individuals’ positions in it are influenced by individual traits such as sex, age, and social rank, and can be heritable between generations. But as of yet, no general theory of social network structure exists that can explain the diversity of social networks observed in nature, and serve as a null model for detecting species and population-specific factors. Here we propose such a general model of social network structure. We consider the emergence of network structure as a result of two types of social bond formation: via social inheritance, in which newborns are likely to bond with maternal contacts, and via forming bonds randomly. We compare model output to data from several species, showing that it can generate networks with properties such as those observed in real social systems. Our model demonstrates that some of the observed properties of social networks, such as heritability of network position or assortative associations, can be understood as a consequence of social inheritance. Our results highlight the need to consider the dynamic processes that generate social structure in order to explain patterns of variation in social networks.
  • Publication
    CoRAL: Predicting Non-Coding RNAs from Small RNA-Sequencing Data
    (2013-08-01) Leung, Yuk Y; Ryvkin, Paul; Ungar, Lyle H; Gregory, Brian D; Wang, Li-San
    The surprising observation that virtually the entire human genome is transcribed means we know little about the function of many emerging classes of RNAs, except their astounding diversities. Traditional RNA function prediction methods rely on sequence or alignment information, which are limited in their abilities to classify the various collections of non-coding RNAs (ncRNAs). To address this, we developed Classification of RNAs by Analysis of Length (CoRAL), a machine learning-based approach for classification of RNA molecules. CoRAL uses biologically interpretable features including fragment length and cleavage specificity to distinguish between different ncRNA populations. We evaluated CoRAL using genome-wide small RNA sequencing data sets from four human tissue types and were able to classify six different types of RNAs with ∼80% cross-validation accuracy. Analysis by CoRAL revealed that microRNAs, small nucleolar and transposon-derived RNAs are highly discernible and consistent across all human tissue types assessed, whereas long intergenic ncRNAs, small cytoplasmic RNAs and small nuclear RNAs show less consistent patterns. The ability to reliably annotate loci across tissue types demonstrates the potential of CoRAL to characterize ncRNAs using small RNA sequencing data in less well-characterized organisms.
  • Publication
    The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell
    (2017-02-20) Slabodnick, Mark M; Ruby, J. G; Reiff, Sarah B; Swart, Estienne C; Gosai, Sager J; Prabakaran, Sudhakaran; Witkowska, Ewa; Larue, Graham E; Gregory, Brian D; Nowacki, Mariusz; Derisi, Joseph; Roy, Scott W; Marshall, Wallace F; Sood, Pranidhi
    The giant, single-celled organism Stentor coeruleus has a long history as a model system for studying pattern formation and regeneration in single cells. Stentor [1, 2] is a heterotrichous ciliate distantly related to familiar ciliate models, such as Tetrahymena or Paramecium. The primary distinguishing feature of Stentor is its incredible size: a single cell is 1 mm long. Early developmental biologists, including T.H. Morgan [3], were attracted to the system because of its regenerative abilities—if large portions of a cell are surgically removed, the remnant reorganizes into a normal-looking but smaller cell with correct proportionality [2, 3]. These biologists were also drawn to Stentor because it exhibits a rich repertoire of behaviors, including light avoidance, mechanosensitive contraction, food selection, and even the ability to habituate to touch, a simple form of learning usually seen in higher organisms [4]. While early microsurgical approaches demonstrated a startling array of regenerative and morphogenetic processes in this single-celled organism, Stentor was never developed as a molecular model system. We report the sequencing of the Stentor coeruleus macronuclear genome and reveal key features of the genome. First, we find that Stentor uses the standard genetic code, suggesting that ciliate-specific genetic codes arose after Stentor branched from other ciliates. We also discover that ploidy correlates with Stentor’s cell size. Finally, in the Stentor genome, we discover the smallest spliceosomal introns reported for any species. The sequenced genome opens the door to molecular analysis of single-cell regeneration in Stentor.
  • Publication
    Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome
    (2012-11-01) Li, Fan; Vandivier, Lee E; Gregory, Brian D; Willmann, Matthew R; Chen, Ying
    The secondary structure of an RNA molecule plays an integral role in its maturation, regulation, and function. However, the global influence of this feature on plant gene expression is still largely unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach in conjunction with transcriptome-wide sequencing of rRNA-depleted (RNA sequencing), small RNA, and ribosome-bound RNA populations to investigate the impact of RNA secondary structure on gene expression regulation in Arabidopsis thaliana. From this analysis, we find that highly unpaired and paired RNAs are strongly correlated with euchromatic and heterochromatic epigenetic histone modifications, respectively, providing evidence that secondary structure is necessary for these RNA-mediated posttranscriptional regulatory pathways. Additionally, we uncover key structural patterns across protein-coding transcripts that indicate RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in this model plant. We further reveal that RNA folding is significantly anticorrelated with overall transcript abundance, which is often due to the increased propensity of highly structured mRNAs to be degraded and/or processed into small RNAs. Finally, we find that secondary structure affects mRNA translation, suggesting that this feature regulates plant gene expression at multiple levels. These findings provide a global assessment of RNA folding and its significant regulatory effects in a plant transcriptome.
  • Publication
    Biological Institutions: The Political Science of Animal Cooperation
    (2013-07-01) Akçay, Erol; Roughgarden, Joan; Fearon, James; Ferejohn, John; Weingast, Barry R
    Social evolution is one of the most rapidly developing areas in evolutionary biology. A main theme is the emergence of cooperation among organisms, including the factors that impede cooperation. Although animal societies seem to have no formal institutions, such as courts or legislatures, we argue that biology presents many examples where an interaction can properly be thought of as an informal institution, meaning there are evolved norms and structure to the interaction that enable parties to reach mutually beneficial outcomes. These informal institutions are embedded in the natural history of the interaction, in factors such as where and when parties interact, how long and how close they stay together, and so on. Institutional theory thus widens the scope of behavioral ecology by considering not only why animals evolve to choose the strategies they choose, but also asking both why it is that they find themselves in those particular interaction setups and how these particular interactions can be sustained. Institutions frequently enable interacting parties avoid inefficient outcomes and support efficient exchange among agents with conflicting interests. The main thesis of this paper is that the organization of many biological interactions can properly be understood as institutions that enable mutually beneficial outcomes to be achieved relative to an unstructured interaction. To do this, institutions resolve or regulate the conflicts of interests among parties. The way conflicts of interests affect the outcome depends on the structure of the interaction, which can create problems of commitment, coordination and private information. Institutional theory focuses on how to address each of these issues, typically focusing on the development of social norms, rules, and other constraints on individual behaviors. We illustrate our thesis with examples from cooperative breed and genes as within-body-mechanism-design.