Baronchelli, A., Chater, N., Christiansen, M. H., Pastor-Satorras, R. (2013). "Evolution in a Changing Environment." PLoS One 8(1)
We propose a simple model for genetic adaptation to a changing environment, describing a fitness landscape characterized by two maxima. One is associated with "specialist'' individuals that are adapted to the environment; this maximum moves over time as the environment ...   [More]

Bedhomme, S., Lafforgue, G., Elena, S. F. (2013). "Genotypic but not Phenotypic Historical Contingency Revealed by Viral Experimental Evolution." BMC Evolutionary Biology 13
Background: The importance of historical contingency in determining the potential of viral populations to evolve has been largely unappreciated. Identifying the constraints imposed by past adaptations is, however, of importance for understanding many questions in evolutionary biology, such as the ...   [More]

Boyle, B., Hopkins, N., Lu, Z. Y., Garay, J. A. R., Mozzherin, D., Rees, T., Matasci, N., Narro, M. L., Piel, W. H., Mckay, S. J., Lowry, S., Freeland, C., Peet, R. K., Enquist, B. J. (2013). "The Taxonomic Name Resolution Service: An Online Tool for Automated Standardization of Plant Names." BMC Bioinformatics 14
Background: The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous ...   [More]

Braakman, R., Smith, E. (2013). "The Compositional and Evolutionary Logic of Metabolism." Physical Biology 10(1)
Metabolism is built on a foundation of organic chemistry, and employs structures and interactions at many scales. Despite these sources of complexity, metabolism also displays striking and robust regularities in the forms of modularity and hierarchy, which may be described ...   [More]

Caschera, F., Rasmussen, S., Hanczyc, M. M. (2013). "An Oil Droplet Division-Fusion Cycle." Chempluschem 78(1):52-54
Publisher's abstract: Well-oiled machine: Micro and macroscale self-assembled oil droplet structures are viable technologies for drug delivery as well as plausible models for self-replicating materials. When far from equilibrium, droplet systems can become dynamic and effect their own growth and ...   [More]

Clauset, A. (2013). "How Large Should Whales Be?." PLoS One 8(1)
The evolution and distribution of species body sizes for terrestrial mammals is well-explained by a macroevolutionary tradeoff between short-term selective advantages and long-term extinction risks from increased species body size, unfolding above the 2 g minimum size induced by thermoregulation ...   [More]

Dall'Asta, L., Caccioli, F., Beghe, D. (2013). "Fixation-Coexistence Transition in Spatial Populations." EPL 101(1)
alancing selection is a special case of frequency-dependent selection that is known to be the major force for the maintenance of biodiversity and polymorphism in natural populations. In finite populations, genetic drift eventually drives the population to fixation to the ...   [More]

Dangerman, A. T. C. J., Schellnhuber, H. J. (2013). "Energy Systems Transformation." PNAS 110(7):E549-$E558
The contemporary industrial metabolism is not sustainable. Critical problems arise at both the input and the output side of the complex: Although affordable fossil fuels and mineral resources are declining, the waste products of the current production and consumption schemes ...   [More]

DeLong, J. P., Burger, O., Hamilton, M. J. (2013). "The UN Medium Population Projection is an Unstable Equilibrium." Frontiers in Ecology and Environment 11(2):65-66
Press Release excerpt: “The upper limit suggested by the United Nations hardly represents a stable equilibrium,” Oskar Burger said. The results of the team’s model have now been published in the science magazine “Frontiers in Ecology and the Environment”. The ...   [More]

Gandon, S., Hochberg, M. E., Holt, R. D., Day, T. (2013). "What Limits the Evolutionary Emergence of Pathogens?." Philosophical Transactions of the Royal Society B - Biological Sciences 368(1610)
The ability of a pathogen to cause an epidemic when introduced in a new host population often relies on its ability to adapt to this new environment. Here, we give a brief overview of recent theoretical and empirical studies of ...   [More]

Ganusov, VV., De Boer, R. J. (2013). "A Mechanistic Model for Bromodeoxyuridine Dilution Naturally Explains Labelling Data of Self-Renewing T Cell Populations." Journal of the Royal Society Interface 10(78)
Bromodeoxyuridine (BrdU) is widely used in immunology to detect cell division, and several mathematical models have been proposed to estimate proliferation and death rates of lymphocytes from BrdU labelling and de-labelling curves. One problem in interpreting BrdU data is explaining ...   [More]

Gonzalez, A. L., Ronce, O., Ferriere, R., Hochberg, M. E. (2013). "Evolutionary Rescue: An Emerging Focus at the Intersection between Ecology and Evolution." Philosophical Transactions of the Royal Society B - Biological Sciences 368(1610)
There is concern that the rate of environmental change is now exceeding the capacity of many populations to adapt. Mitigation of biodiversity loss requires science that integrates both ecological and evolutionary responses of populations and communities to rapid environmental change, ...   [More]

Guy, T., Karny, M., Wolpert, D. H.. "Decision Making and Imperfection". Springer, 2013  [More]

Hellmuth, M., Hernandez-Rosales, M., Huber, K. T., Moulton, V., Stadler, P. F., Wieseke, N. (2013). "Orthology Relations, Symbolic Ultrametrics, and Cographs." Journal of Mathematical Biology 66(1-2):399-420
Orthology detection is an important problem in comparative and evolutionary genomics and, consequently, a variety of orthology detection methods have been devised in recent years. Although many of these methods are dependent on generating gene and/or species trees, it has ...   [More]

Hochberg, M. E., Thomas, F., Assenat, E., Hibner, U. (2013). "Preventive Evolutionary Medicine of Cancers." Evolutionary Applications 6(1):134-143 SI
Evolutionary theory predicts that once an individual reaches an age of sufficiently low Darwinian fitness, (s)he will have reduced chances of keeping cancerous lesions in check. While we clearly need to better understand the emergence of precursor states and early ...   [More]

Laflamme, M., Darroch, S. A. F., Tweedt, S. M., Peterson, K. J., Erwin, D. H. (2013). "The End of the Ediacara Biota: Extinction, Biotic Replacement, or Cheshire Cat?." Gondwana Research 23(2):558-573
The Ediacaran-Cambrian transition signals a drastic change in both diversity and ecosystem construction. The Ediacara biota (consisting of various metazoan stem lineages in addition to extinct eukaryotic clades) disappears, and is replaced by more familiar Cambrian and Paleozoic metazoan groups. ...   [More]

Lalic, J., Elena, S. F. (2013). "Epistasis between Mutations is Host-Dependent for an RNA virus." Biology Letters 9(1)
How, and to what extent, does the environment influence the way mutations interact? Do environmental changes affect both the sign and the magnitude of epistasis? Are there any correlations between environments in the variability, sign or magnitude of epistasis? Very ...   [More]

Langenberger, D., Cakir, M. V., Hoffmann, S., Stadler, P. F. (2013). "Dicer-Processed Small RNAs: Rules and Exceptions." Journal of Experimental Zoology Part B - Molecular and Developmental Evolution 320B(1):35-46
Canonical microRNAs are excised from their hairpin-shaped precursors by Dicer. In order to find possible exceptions to this rule and to identify additional substrates for Dicer processing we re-evaluate the small RNA sequencing data of the Dicer knockdown experiment in ...   [More]

Lehmann, J., Stadler, P. F., Krauss, V. (2013). "Near Intron Pairs and the Metazoan Tree." Molecular Phylogenetics and Evolution 66(3):811-823
Gene structure data can substantially advance our understanding of metazoan evolution and deliver an independent approach to resolve conflicts among existing hypotheses. Here, we used changes of spliceosomal intron positions as novel phylogenetic marker to reconstruct the animal tree. This ...   [More]

Liu, M. K. P., Hawkins, N., Ritchie, A. J., Ganusov, V. V., Whale, V., Brackenridge, S., Li, H., Pavlicek, J. W., Cai, F. P., Rose-Abrahams, M., Treurnicht, F. K., Hraber, P., Riou, C., Gray, C., Ferrari, G., Tanner, R., Ping, L. H., Anderson, J. A., Swanstrom, R., Chavi, C. B., Cohen, M. S., Karim, S. S. A., Haynes, B., Borrow, P., Perelson, A. S., Shaw, G. M., Hahn, B. H., Williamson, C., Korber, B. T., Gao, F., Self, S. G., McMichael, A., Goonetilleke, N. (2013). "Vertical T Cell Immunodominance and Epitope Entropy Determine HIV-1 Escape." Journal of Clinical Investigation 123(1):380-393
HIV-1 accumulates mutations in and around reactive epitopes to escape recognition and killing by CD8(+) T cells. Measurements of HIV-1 time to escape should therefore provide information on which parameters are most important for T cell-mediated in vivo control of ...   [More]

Lorz, A., Lorenzi, T., Hochberg, M. E., Clairambault, J., Perthame, B. (2013). "Populational Adaptivve Evolution, Chemotherapeutic Resisstance and Multiple Anti-Cancer Therapies." Esaim-Mathematical Modelling and Numerical Analysis - Modelisation Mathematique Et Analyse Enumerique 47(2):377-403
Resistance to chemotherapies, particularly to anticancer treatments, is an increasing medical concern. Among the many mechanisms at work in cancers, one of the most important is the selection of tumor cells expressing resistance genes or phenotypes. Motivated by the theory ...   [More]

Molnar, P. K., Kutz, S. J., Hoar, B. M., Dobson, A. P. (2013). "Metabolic Approaches to Understanding Climate Change Impacts on Seasonal Host-Macroparasite Dynamics." Ecology Letters 16(1):9-21
Climate change is expected to alter the dynamics of infectious diseases around the globe. Predictive models remain elusive due to the complexity of hostparasite systems and insufficient data describing how environmental conditions affect various system components. Here, we link hostmacroparasite ...   [More]

Moore, C. (2013). "Tetrahedral Tetris." American Scientist 101(1):3
Letter to the Editor   [More]

Nagy, B., Farmer, J. D., Bui, Q. M., Trancik, J. E. (2013). "Statistical Basis for Predicting Technological Progress." PLoS One 8(2)
Forecasting technological progress is of great interest to engineers, policy makers, and private investors. Several models have been proposed for predicting technological improvement, but how well do these models perform? An early hypothesis made by Theodore Wright in 1936 is ...   [More]

O'Dwyer, J. P. (2013). "The Dynamics of Adapting, Unregulated Populations and A Modified Fundamental Theorem." Journal of the Royal Society Interface 10(78)
A population in a novel environment will accumulate adaptive mutations over time, and the dynamics of this process depend on the underlying fitness landscape: the fitness of and mutational distance between possible genotypes in the population. Despite its fundamental importance ...   [More]

Pawar, S., Dell, A. I., Savage, V. M. (2013). "Does Consumption Rate Scale Superlinearly? Reply." Nature 493(7434):E2-E3   [More]

Ruiz, G., Tsallis, C. (2013). "Reply to Comment on "Towards a large deviation theory for strongly correlated systems"." Physics Letters A 377(6):491-495
The computational study commented by Touchette opens the door to a desirable generalization of standard large deviation theory for special, though ubiquitous, correlations. We focus on three interrelated aspects: (i) numerical results strongly suggest that the standard exponential probability law ...   [More]

Savage, V., Herman, A. B., West, G. B., Leu, K. (2013). "Using Fractal Geometry and Universal Growth Curves as Diagnostics for Comparing Tumor Vasculature and Metabolic Rate with Healthy Tissue and for Predicting Responses to Drug Therapies." Discrete and Continuous Dynamical Systems - Series B 18(4):1077-1108
Healthy vasculature exhibits a hierarchical branching structure in which, on average, vessel radius and length change systematically with branching order. In contrast, tumor vasculature exhibits less hierarchy and more variability in its branching patterns. Although differences in vasculature have been ...   [More]

Schindler, S., Breidbach, O., Jost, J. (2013). "Preferring the Fittest Mates: An Analytically Tractable Model." Journal of Theoretical Biology 317:30-38
We develop an analytically tractable model of female preference for fit mates. Our population-genetic model allows to trace the dynamics at both the individual and the population level. The preference for fit mates links ecological adaptation and mating success is ...   [More]

Smith, E., Foley, D. K., Good, B. H. (2013). "Unhedgeable Shocks and Statistical Economic Equilibrium." Economic Theory 52(1):187-235
We develop a statistical concept of economic equilibrium as the stationary distribution of a random walk on the exchange equilibrium set (the contract set) of a pure exchange economy induced by unhedgeable shocks that perturb the economy from the exchange ...   [More]

Thomas, F., Fisher, D., Fort, P., Marie, J. P., Daoust, S., Roche, B., Grunau, C., Cosseau, C., Mitta, G., Baghdiguian, S., Rousset, F., Lassus, P., Assenat, E., Gregoire, D., Misse, D., Lorz, A., Billy, F., Vainchenker, W., Delhommeau, F., Koscielny, S., Itzykson, R., Tang, R. P., Fava, F., Ballesta, A., Lepoutre, T., Krasinska, L., Dulic, V., Raynaud, P., Blache, P., Quittau-Prevostel, C., Vignal, E., Trauchessec, H., Perthame, B., Clairambault, J., Volpert, V., Solary, E., Hibner, U., Hochberg, M. E. (2013). "Applying Ecological and Evolutionary Theory to Cancer: A Long and Winding Road." Evolutionary Applications 6(1):1-10 SI
Since the mid 1970s, cancer has been described as a process of Darwinian evolution, with somatic cellular selection and evolution being the fundamental processes leading to malignancy and its many manifestations (neoangiogenesis, evasion of the immune system, metastasis, and resistance ...   [More]

Yoder, M. R., Van Aalsburg, J., Turcotte, D. L., Abaimov, S. G., Rundle, J. B. (2013). "Statistical Variability and Tokunaga Branching of Aftershock Sequences Utilizing BASS Model Simulations." Pure and Applied Geophysics 170(1-2):155-171
Aftershock statistics provide a wealth of data that can be used to better understand earthquake physics. Aftershocks satisfy scale-invariant Gutenberg-Richter (GR) frequency-magnitude statistics. They also satisfy Omori's law for power-law seismicity rate decay and BAyenth's law for maximum-magnitude scaling. The ...   [More]

Zinder, D., Bedford, T., Gupta, S., Pascual, M. (2013). "The Roles of Competition and Mutation in Shaping Antigenic and Genetic Diversity in Influenza." PLoS Pathogens 9(1)
Influenza A (H3N2) offers a well-studied, yet not fully understood, disease in terms of the interactions between pathogen population dynamics, epidemiology and genetics. A major open question is why the virus population is globally dominated by a single and very ...   [More]