Coevolution of coloration and colour vision?

PubMed

Lind, Olle; Henze, Miriam J; Kelber, Almut; Osorio, Daniel

2017-07-05

The evolutionary relationship between signals and animal senses has broad significance, with potential consequences for speciation, and for the efficacy and honesty of biological communication. Here we outline current understanding of the diversity of colour vision in two contrasting groups: the phylogenetically conservative birds, and the more variable butterflies. Evidence for coevolution of colour signals and vision exists in both groups, but is limited to observations of phenotypic differences between visual systems, which might be correlated with coloration. Here, to illustrate how one might interpret the evolutionary significance of such differences, we used colour vision modelling based on an avian eye to evaluate the effects of variation in three key characters: photoreceptor spectral sensitivity, oil droplet pigmentation and the proportions of different photoreceptor types. The models predict that physiologically realistic changes in any one character will have little effect, but complementary shifts in all three can substantially affect discriminability of three types of natural spectra. These observations about the adaptive landscape of colour vision may help to explain the general conservatism of photoreceptor spectral sensitivities in birds. This approach can be extended to other types of eye and spectra to inform future work on coevolution of coloration and colour vision.This article is part of the themed issue 'Animal coloration: production, perception, function and application'. © 2017 The Author(s).

Coevolution between flight morphology, vertical stratification and sexual dimorphism: what can we learn from tropical butterflies?

PubMed

Graça, M B; Pequeno, P A C L; Franklin, E; Morais, J W

2017-10-01

Occurrence patterns are partly shaped by the affinity of species with habitat conditions. For winged organisms, flight-related attributes are vital for ecological performance. However, due to the different reproductive roles of each sex, we expect divergence in flight energy budget, and consequently different selection responses between sexes. We used tropical frugivorous butterflies as models to investigate coevolution between flight morphology, sex dimorphism and vertical stratification. We studied 94 species of Amazonian fruit-feeding butterflies sampled in seven sites across 3341 ha. We used wing-thorax ratio as a proxy for flight capacity and hierarchical Bayesian modelling to estimate stratum preference. We detected a strong phylogenetic signal in wing-thorax ratio in both sexes. Stouter fast-flying species preferred the canopy, whereas more slender slow-flying species preferred the understorey. However, this relationship was stronger in females than in males, suggesting that female phenotype associates more intimately with habitat conditions. Within species, males were stouter than females and sexual dimorphism was sharper in understorey species. Because trait-habitat relationships were independent from phylogeny, the matching between flight morphology and stratum preference is more likely to reflect adaptive radiation than shared ancestry. This study sheds light on the impact of flight and sexual dimorphism on the evolution and ecological adaptation of flying organisms. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Detection of significant protein coevolution.

PubMed

Ochoa, David; Juan, David; Valencia, Alfonso; Pazos, Florencio

2015-07-01

The evolution of proteins cannot be fully understood without taking into account the coevolutionary linkages entangling them. From a practical point of view, coevolution between protein families has been used as a way of detecting protein interactions and functional relationships from genomic information. The most common approach to inferring protein coevolution involves the quantification of phylogenetic tree similarity using a family of methodologies termed mirrortree. In spite of their success, a fundamental problem of these approaches is the lack of an adequate statistical framework to assess the significance of a given coevolutionary score (tree similarity). As a consequence, a number of ad hoc filters and arbitrary thresholds are required in an attempt to obtain a final set of confident coevolutionary signals. In this work, we developed a method for associating confidence estimators (P values) to the tree-similarity scores, using a null model specifically designed for the tree comparison problem. We show how this approach largely improves the quality and coverage (number of pairs that can be evaluated) of the detected coevolution in all the stages of the mirrortree workflow, independently of the starting genomic information. This not only leads to a better understanding of protein coevolution and its biological implications, but also to obtain a highly reliable and comprehensive network of predicted interactions, as well as information on the substructure of macromolecular complexes using only genomic information. The software and datasets used in this work are freely available at: http://csbg.cnb.csic.es/pMT/. pazos@cnb.csic.es Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Bats in the Classroom: A Conceptual Guide for Biology Teachers.

ERIC Educational Resources Information Center

Rankin, W. T.; Lewis, Norma G.

2002-01-01

Explains how to use bats to introduce different biological concepts such as classification and phylogeny, altruistic behavior, flight, coevolution, or physiological adaptations. Discusses common myths regarding bats and provides information on additional classroom materials. (YDS)

Coevolution can reverse predator–prey cycles

PubMed Central

Cortez, Michael H.; Weitz, Joshua S.

2014-01-01

A hallmark of Lotka–Volterra models, and other ecological models of predator–prey interactions, is that in predator–prey cycles, peaks in prey abundance precede peaks in predator abundance. Such models typically assume that species life history traits are fixed over ecologically relevant time scales. However, the coevolution of predator and prey traits has been shown to alter the community dynamics of natural systems, leading to novel dynamics including antiphase and cryptic cycles. Here, using an eco-coevolutionary model, we show that predator–prey coevolution can also drive population cycles where the opposite of canonical Lotka–Volterra oscillations occurs: predator peaks precede prey peaks. These reversed cycles arise when selection favors extreme phenotypes, predator offense is costly, and prey defense is effective against low-offense predators. We present multiple datasets from phage–cholera, mink–muskrat, and gyrfalcon–rock ptarmigan systems that exhibit reversed-peak ordering. Our results suggest that such cycles are a potential signature of predator–prey coevolution and reveal unique ways in which predator–prey coevolution can shape, and possibly reverse, community dynamics. PMID:24799689

Coevolution can reverse predator-prey cycles.

PubMed

Cortez, Michael H; Weitz, Joshua S

2014-05-20

A hallmark of Lotka-Volterra models, and other ecological models of predator-prey interactions, is that in predator-prey cycles, peaks in prey abundance precede peaks in predator abundance. Such models typically assume that species life history traits are fixed over ecologically relevant time scales. However, the coevolution of predator and prey traits has been shown to alter the community dynamics of natural systems, leading to novel dynamics including antiphase and cryptic cycles. Here, using an eco-coevolutionary model, we show that predator-prey coevolution can also drive population cycles where the opposite of canonical Lotka-Volterra oscillations occurs: predator peaks precede prey peaks. These reversed cycles arise when selection favors extreme phenotypes, predator offense is costly, and prey defense is effective against low-offense predators. We present multiple datasets from phage-cholera, mink-muskrat, and gyrfalcon-rock ptarmigan systems that exhibit reversed-peak ordering. Our results suggest that such cycles are a potential signature of predator-prey coevolution and reveal unique ways in which predator-prey coevolution can shape, and possibly reverse, community dynamics.

Duplicate Abalone Egg Coat Proteins Bind Sperm Lysin Similarly, but Evolve Oppositely, Consistent with Molecular Mimicry at Fertilization

PubMed Central

Aagaard, Jan E.; Springer, Stevan A.; Soelberg, Scott D.; Swanson, Willie J.

2013-01-01

Sperm and egg proteins constitute a remarkable paradigm in evolutionary biology: despite their fundamental role in mediating fertilization (suggesting stasis), some of these molecules are among the most rapidly evolving ones known, and their divergence can lead to reproductive isolation. Because of strong selection to maintain function among interbreeding individuals, interacting fertilization proteins should also exhibit a strong signal of correlated divergence among closely related species. We use evidence of such molecular co-evolution to target biochemical studies of fertilization in North Pacific abalone (Haliotis spp.), a model system of reproductive protein evolution. We test the evolutionary rates (d N/d S) of abalone sperm lysin and two duplicated egg coat proteins (VERL and VEZP14), and find a signal of co-evolution specific to ZP-N, a putative sperm binding motif previously identified by homology modeling. Positively selected residues in VERL and VEZP14 occur on the same face of the structural model, suggesting a common mode of interaction with sperm lysin. We test this computational prediction biochemically, confirming that the ZP-N motif is sufficient to bind lysin and that the affinities of VERL and VEZP14 are comparable. However, we also find that on phylogenetic lineages where lysin and VERL evolve rapidly, VEZP14 evolves slowly, and vice versa. We describe a model of sexual conflict that can recreate this pattern of anti-correlated evolution by assuming that VEZP14 acts as a VERL mimic, reducing the intensity of sexual conflict and slowing the co-evolution of lysin and VERL. PMID:23408913

Older partner selection promotes the prevalence of cooperation in evolutionary games.

PubMed

Yang, Guoli; Huang, Jincai; Zhang, Weiming

2014-10-21

Evolutionary games typically come with the interplays between evolution of individual strategy and adaptation to network structure. How these dynamics in the co-evolution promote (or obstruct) the cooperation is regarded as an important topic in social, economic, and biological fields. Combining spatial selection with partner choice, the focus of this paper is to identify which neighbour should be selected as a role to imitate during the process of co-evolution. Age, an internal attribute and kind of local piece of information regarding the survivability of the agent, is a significant consideration for the selection strategy. The analysis and simulations presented, demonstrate that older partner selection for strategy imitation could foster the evolution of cooperation. The younger partner selection, however, may decrease the level of cooperation. Our model highlights the importance of agent׳s age on the promotion of cooperation in evolutionary games, both efficiently and effectively. Copyright © 2014 Elsevier Ltd. All rights reserved.

New frontiers in the study of human cultural and genetic evolution.

PubMed

Ross, Cody T; Richerson, Peter J

2014-12-01

In this review, we discuss the dynamic linkages between culture and the genetic evolution of the human species. We begin by briefly describing the framework of gene-culture coevolutionary (or dual-inheritance) models for human evolutionary change. Until recently, the literature on gene-culture coevolution was composed primarily of mathematical models and formalized theory describing the complex dynamics underlying human behavior, adaptation, and technological evolution, but had little empirical support concerning genetics. The rapid progress in the fields of molecular genetics and genomics, however, is now providing the kinds of data needed to produce rich empirical support for gene-culture coevolutionary models. We briefly outline how theoretical and methodological progress in genome sciences has provided ways for the strength of selection on genes to be evaluated, and then outline how evidence of selection on several key genes can be directly linked to human cultural practices. We then describe some exciting new directions in the empirical study of gene-culture coevolution, and conclude with a discussion of the role of gene-culture evolutionary models in the future integration of medical, biological, and social sciences. Copyright © 2014 Elsevier Ltd. All rights reserved.

What language is the language-ready brain ready for?. Comment on "Towards a Computational Comparative Neuroprimatology: Framing the language-ready brain" by Michael A. Arbib

NASA Astrophysics Data System (ADS)

Croft, William

2016-03-01

Arbib's computational comparative neuroprimatology [1] is a welcome model for cognitive linguists, that is, linguists who ground their models of language in human cognition and language use in social interaction. Arbib argues that language emerged via biological and cultural coevolution [1]; linguistic knowledge is represented by constructions, and semantic representations of linguistic constructions are grounded in embodied perceptual-motor schemas (the mirror system hypothesis). My comments offer some refinements from a linguistic point of view.

A sense of life: computational and experimental investigations with models of biochemical and evolutionary processes.

PubMed

Mishra, Bud; Daruwala, Raoul-Sam; Zhou, Yi; Ugel, Nadia; Policriti, Alberto; Antoniotti, Marco; Paxia, Salvatore; Rejali, Marc; Rudra, Archisman; Cherepinsky, Vera; Silver, Naomi; Casey, William; Piazza, Carla; Simeoni, Marta; Barbano, Paolo; Spivak, Marina; Feng, Jiawu; Gill, Ofer; Venkatesh, Mysore; Cheng, Fang; Sun, Bing; Ioniata, Iuliana; Anantharaman, Thomas; Hubbard, E Jane Albert; Pnueli, Amir; Harel, David; Chandru, Vijay; Hariharan, Ramesh; Wigler, Michael; Park, Frank; Lin, Shih-Chieh; Lazebnik, Yuri; Winkler, Franz; Cantor, Charles R; Carbone, Alessandra; Gromov, Mikhael

2003-01-01

We collaborate in a research program aimed at creating a rigorous framework, experimental infrastructure, and computational environment for understanding, experimenting with, manipulating, and modifying a diverse set of fundamental biological processes at multiple scales and spatio-temporal modes. The novelty of our research is based on an approach that (i) requires coevolution of experimental science and theoretical techniques and (ii) exploits a certain universality in biology guided by a parsimonious model of evolutionary mechanisms operating at the genomic level and manifesting at the proteomic, transcriptomic, phylogenic, and other higher levels. Our current program in "systems biology" endeavors to marry large-scale biological experiments with the tools to ponder and reason about large, complex, and subtle natural systems. To achieve this ambitious goal, ideas and concepts are combined from many different fields: biological experimentation, applied mathematical modeling, computational reasoning schemes, and large-scale numerical and symbolic simulations. From a biological viewpoint, the basic issues are many: (i) understanding common and shared structural motifs among biological processes; (ii) modeling biological noise due to interactions among a small number of key molecules or loss of synchrony; (iii) explaining the robustness of these systems in spite of such noise; and (iv) cataloging multistatic behavior and adaptation exhibited by many biological processes.

The Role of Microbial Electron Transfer in the Coevolution of the Biosphere and Geosphere.

PubMed

Jelen, Benjamin I; Giovannelli, Donato; Falkowski, Paul G

2016-09-08

All life on Earth is dependent on biologically mediated electron transfer (i.e., redox) reactions that are far from thermodynamic equilibrium. Biological redox reactions originally evolved in prokaryotes and ultimately, over the first ∼2.5 billion years of Earth's history, formed a global electronic circuit. To maintain the circuit on a global scale requires that oxidants and reductants be transported; the two major planetary wires that connect global metabolism are geophysical fluids-the atmosphere and the oceans. Because all organisms exchange gases with the environment, the evolution of redox reactions has been a major force in modifying the chemistry at Earth's surface. Here we briefly review the discovery and consequences of redox reactions in microbes with a specific focus on the coevolution of life and geochemical phenomena.

Detecting Coevolution in and among Protein Domains

PubMed Central

Yeang, Chen-Hsiang; Haussler, David

2007-01-01

Correlated changes of nucleic or amino acids have provided strong information about the structures and interactions of molecules. Despite the rich literature in coevolutionary sequence analysis, previous methods often have to trade off between generality, simplicity, phylogenetic information, and specific knowledge about interactions. Furthermore, despite the evidence of coevolution in selected protein families, a comprehensive screening of coevolution among all protein domains is still lacking. We propose an augmented continuous-time Markov process model for sequence coevolution. The model can handle different types of interactions, incorporate phylogenetic information and sequence substitution, has only one extra free parameter, and requires no knowledge about interaction rules. We employ this model to large-scale screenings on the entire protein domain database (Pfam). Strikingly, with 0.1 trillion tests executed, the majority of the inferred coevolving protein domains are functionally related, and the coevolving amino acid residues are spatially coupled. Moreover, many of the coevolving positions are located at functionally important sites of proteins/protein complexes, such as the subunit linkers of superoxide dismutase, the tRNA binding sites of ribosomes, the DNA binding region of RNA polymerase, and the active and ligand binding sites of various enzymes. The results suggest sequence coevolution manifests structural and functional constraints of proteins. The intricate relations between sequence coevolution and various selective constraints are worth pursuing at a deeper level. PMID:17983264

Detecting sexually antagonistic coevolution with population crosses.

PubMed

Rowe, Locke; Cameron, Erin; Day, Troy

2003-10-07

The result of population crosses on traits such as mating rate, oviposition rate and survivorship are increasingly used to distinguish between modes of coevolution between the sexes. Two key hypotheses, erected from a verbal theory of sexually antagonistic coevolution, have been the subject of several recent tests. First, statistical interactions arising in population crosses are suggested to be indicative of a complex signal/receiver system. In the case of oviposition rates, an interaction between populations (x, y and z) would be indicated by the rank order of female oviposition rates achieved by x, y and z males changing depending upon the female (x, y or z) with which they mated. Second, under sexually antagonistic coevolution females will do 'best' when mated with their own males, where best is defined by the weakest response to the signal and the highest fitness. We test these hypotheses by crossing strains generated from a formal model of sexually antagonistic coevolution. Strains differ in the strength of natural selection acting on male and female traits. In our model, we assume sexually antagonistic coevolution of a single male signal and female receptor. The female receptor is treated as a preference function where both the slope and intercept of the function can evolve. Our results suggest that neither prediction is consistently supported. Interactions are not diagnostic of complex signal-receiver systems, and even under sexually antagonistic coevolution, females may do better mating with males of strains other than their own. These results suggest a reinterpretation of several recent experiments and have important implications for developing theories of speciation when sexually antagonistic coevolution is involved.

Coevolution of Glauber-like Ising dynamics and topology

NASA Astrophysics Data System (ADS)

Mandrà, Salvatore; Fortunato, Santo; Castellano, Claudio

2009-11-01

We study the coevolution of a generalized Glauber dynamics for Ising spins with tunable threshold and of the graph topology where the dynamics takes place. This simple coevolution dynamics generates a rich phase diagram in the space of the two parameters of the model, the threshold and the rewiring probability. The diagram displays phase transitions of different types: spin ordering, percolation, and connectedness. At variance with traditional coevolution models, in which all spins of each connected component of the graph have equal value in the stationary state, we find that, for suitable choices of the parameters, the system may converge to a state in which spins of opposite sign coexist in the same component organized in compact clusters of like-signed spins. Mean field calculations enable one to estimate some features of the phase diagram.

The potential for co-evolution of CO2-concentrating mechanisms and Rubisco in diatoms.

PubMed

Young, Jodi N; Hopkinson, Brian M

2017-06-01

Diatoms are a diverse group of unicellular algae that contribute significantly to global photosynthetic carbon fixation and export in the modern ocean, and are an important source of microfossils for paleoclimate reconstructions. Because of their importance in the environment, diatoms have been a focus of study on the physiology and ecophysiology of carbon fixation, in particular their CO2-concentrating mechanisms (CCMs) and Rubisco characteristics. While carbon fixation in diatoms is not as well understood as in certain model aquatic photoautotrophs, a greater number of species have been examined in diatoms. Recent work has highlighted a large diversity in the function, physiology, and kinetics of both the CCM and Rubisco between different diatom species. This diversity was unexpected since it has generally been assumed that CCMs and Rubiscos were similar within major algal lineages as the result of selective events deep in evolutionary history, and suggests a more recent co-evolution between the CCM and Rubisco within diatoms. This review explores our current understanding of the diatom CCM and highlights the diversity of both the CCM and Rubisco kinetics. We will suggest possible environmental, physiological, and evolutionary drivers for the co-evolution of the CCM and Rubisco in diatoms. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Evolutionary molecular medicine.

PubMed

Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

2012-05-01

Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

No correlation discerned between the periods of rise and dominance of simulated species in a model of biological evolution

NASA Astrophysics Data System (ADS)

Kuhnle, Alan

2009-11-01

In [1], Liow et al. discern a general feature of the occurrence trajectories of biological species: the periods of rise and fall of a typical species are about as long as the period of dominance. In this work, an individual-based model of biological evolution that was developed by Rikvold and Zia in [2] is investigated, but no analogous feature is observed in the simulated species populations. Instead, the periods of rise and fall of a simulated species cannot always be sensibly defined; when it does make sense to define these quantities, they are quite short and independent of the period of dominance. [4pt] [1] Liow, L. H., Skaug, H. J., Ergon, T., Schweder, T.: Global occurence trajectories of microfossils: Is the rise and persistence of species influenced by environmental volatility? Manuscript for Paleobiology, 5 Dec 2008 [0pt] [2] Rikvold, P.A., Zia, R.K.P.: Punctuated equilibria and 1/f noise in a biological coevolution model with individual-based dynamics. Physical Review E 68, 031913 (2003)

Self-organizing behavior in a lattice model for co-evolution of virus and immune systems

NASA Astrophysics Data System (ADS)

Izmailian, N. Sh.; Papoyan, Vl. V.; Priezzhev, V. B.; Hu, Chin-Kun

2007-04-01

We propose a lattice model for the co-evolution of a virus population and an adaptive immune system. We show that, under some natural assumptions, both probability distribution of the virus population and the distribution of activity of the immune system tend during the evolution to a self-organized critical state.

Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes.

PubMed

Theis, Kevin R; Dheilly, Nolwenn M; Klassen, Jonathan L; Brucker, Robert M; Baines, John F; Bosch, Thomas C G; Cryan, John F; Gilbert, Scott F; Goodnight, Charles J; Lloyd, Elisabeth A; Sapp, Jan; Vandenkoornhuyse, Philippe; Zilber-Rosenberg, Ilana; Rosenberg, Eugene; Bordenstein, Seth R

2016-01-01

Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization-what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.

Sex uncovered special issue: The ecology of sexual reproduction

PubMed Central

LIVELY, C. M.; MORRAN, L. T.

2014-01-01

Sexual reproduction is widely regarded as one of the major unexplained phenomena in biology. Nonetheless, while a general answer may remain elusive, considerable progress has been made in the last few decades. Here we fist review the genesis of, and support for, the major ecological hypotheses for biparental sexual reproduction. We then focus on the idea that host-parasite coevolution can favor cross fertilization over uniparental forms of reproduction, as this hypothesis currently has the most support from natural populations. We also review the results from experimental evolution studies, which tend to show that exposure to novel environments can select for higher levels of sexual reproduction, but that sex decreases in frequency after populations become adapted to the previously novel conditions. In contrast, experimental coevolution studies suggest that host-parasite interactions can lead to the long-term persistence of sex. Taken together, the evidence from natural populations and from laboratory experiments point to antagonistic coevolution as a potent and possibly ubiquitous force of selection favoring cross-fertilization and recombination. PMID:24617324

CMCpy: Genetic Code-Message Coevolution Models in Python

PubMed Central

Becich, Peter J.; Stark, Brian P.; Bhat, Harish S.; Ardell, David H.

2013-01-01

Code-message coevolution (CMC) models represent coevolution of a genetic code and a population of protein-coding genes (“messages”). Formally, CMC models are sets of quasispecies coupled together for fitness through a shared genetic code. Although CMC models display plausible explanations for the origin of multiple genetic code traits by natural selection, useful modern implementations of CMC models are not currently available. To meet this need we present CMCpy, an object-oriented Python API and command-line executable front-end that can reproduce all published results of CMC models. CMCpy implements multiple solvers for leading eigenpairs of quasispecies models. We also present novel analytical results that extend and generalize applications of perturbation theory to quasispecies models and pioneer the application of a homotopy method for quasispecies with non-unique maximally fit genotypes. Our results therefore facilitate the computational and analytical study of a variety of evolutionary systems. CMCpy is free open-source software available from http://pypi.python.org/pypi/CMCpy/. PMID:23532367

The role of epigenetics in host-parasite coevolution: lessons from the model host insects Galleria mellonella and Tribolium castaneum.

PubMed

Vilcinskas, Andreas

2016-08-01

Recent studies addressing experimental host-parasite coevolution and transgenerational immune priming in insects provide evidence for heritable shifts in host resistance or parasite virulence. These rapid reciprocal adaptations may thus be transferred to offspring generations by either genetic changes or mechanisms that do not involve changes in the germline DNA sequence. Epigenetic inheritance refers to changes in gene expression that are heritable across generations and mediated by epigenetic modifications passed from parents to offspring. Highlighting the role of epigenetics in host-parasite coevolution, this review discusses the involvement of DNA methylation, histone acetylation/deacetylation and microRNAs in the interactions between bacterial or fungal parasites and model host insects such as the greater wax moth Galleria mellonella and the red flour beetle Tribolium castaneum. These epigenetic mechanisms are thought to participate in generation-spanning transcriptional reprogramming in the host insect, often linking immunity with developmentally related gene expression and contributing to the heredity of acquired adaptations. It is proposed that the interactions during host-parasite coevolution can therefore be expanded beyond reciprocal genetic changes to include reciprocal epigenetic changes. Epigenetics is thus a promising and prospering field in the context of host-parasite coevolution. Copyright © 2016 The Author. Published by Elsevier GmbH.. All rights reserved.

Network Analysis Reveals the Recognition Mechanism for Mannose-binding Lectins

NASA Astrophysics Data System (ADS)

Zhao, Yunjie; Jian, Yiren; Zeng, Chen; Computational Biophysics Lab Team

The specific carbohydrate binding of mannose-binding lectin (MBL) protein in plants makes it a very useful molecular tool for cancer cell detection and other applications. The biological states of most MBL proteins are dimeric. Using dynamics network analysis on molecular dynamics (MD) simulations on the model protein of MBL, we elucidate the short- and long-range driving forces behind the dimer formation. The results are further supported by sequence coevolution analysis. We propose a general framework for deciphering the recognition mechanism underlying protein-protein interactions that may have potential applications in signaling pathways.

Are viruses alive? The replicator paradigm sheds decisive light on an old but misguided question

PubMed Central

Koonin, Eugene V.; Starokadomskyy, Petro

2016-01-01

The question whether or not “viruses are alive” has caused considerable debate over many years. Yet, the question is effectively without substance because the answer depends entirely on the definition of life or the state of “being alive” that is bound to be arbitrary. In contrast, the status of viruses among biological entities is readily defined within the replicator paradigm. All biological replicators form a continuum along the selfishness-cooperativity axis, from the completely selfish to fully cooperative forms. Within this range, typical, lytic viruses represent the selfish extreme whereas temperate viruses and various mobile elements occupy positions closer to the middle of the range. Selfish replicators not only belong to the biological realm but are intrinsic to any evolving system of replicators. No such system can evolve without the emergence of parasites, and moreover, parasites drive the evolution of biological complexity at multiple levels. The history of life is a story of parasite-host coevolution that includes both the incessant arms race and various forms of cooperation. All organisms are communities of interacting, coevolving replicators of different classes. A complete theory of replicator coevolution remains to be developed, but it appears likely that not only the differentiation between selfish and cooperative replicators but the emergence of the entire range of replication strategies, from selfish to cooperative, is intrinsic to biological evolution. PMID:26965225

Forced evolution in silico by artificial transposons and their genetic operators: The ant navigation problem.

PubMed

Zamdborg, Leonid; Holloway, David M; Merelo, Juan J; Levchenko, Vladimir F; Spirov, Alexander V

2015-06-10

Modern evolutionary computation utilizes heuristic optimizations based upon concepts borrowed from the Darwinian theory of natural selection. Their demonstrated efficacy has reawakened an interest in other aspects of contemporary biology as an inspiration for new algorithms. However, amongst the many excellent candidates for study, contemporary models of biological macroevolution attract special attention. We believe that a vital direction in this field must be algorithms that model the activity of "genomic parasites", such as transposons, in biological evolution. Many evolutionary biologists posit that it is the co-evolution of populations with their genomic parasites that permits the high efficiency of evolutionary searches found in the living world. This publication is our first step in the direction of developing a minimal assortment of algorithms that simulate the role of genomic parasites. Specifically, we started in the domain of genetic algorithms (GA) and selected the Artificial Ant Problem as a test case. This navigation problem is widely known as a classical benchmark test and possesses a large body of literature. We add new objects to the standard toolkit of GA - artificial transposons and a collection of operators that operate on them. We define these artificial transposons as a fragment of an ant's code with properties that cause it to stand apart from the rest. The minimal set of operators for transposons is a transposon mutation operator, and a transposon reproduction operator that causes a transposon to multiply within the population of hosts. An analysis of the population dynamics of transposons within the course of ant evolution showed that transposons are involved in the processes of propagation and selection of blocks of ant navigation programs. During this time, the speed of evolutionary search increases significantly. We concluded that artificial transposons, analogous to real transposons, are truly capable of acting as intelligent mutators that adapt in response to an evolutionary problem in the course of co-evolution with their hosts.

Forced evolution in silico by artificial transposons and their genetic operators: The ant navigation problem

PubMed Central

Zamdborg, Leonid; Holloway, David M.; Merelo, Juan J.; Levchenko, Vladimir F.; Spirov, Alexander V.

2015-01-01

Modern evolutionary computation utilizes heuristic optimizations based upon concepts borrowed from the Darwinian theory of natural selection. Their demonstrated efficacy has reawakened an interest in other aspects of contemporary biology as an inspiration for new algorithms. However, amongst the many excellent candidates for study, contemporary models of biological macroevolution attract special attention. We believe that a vital direction in this field must be algorithms that model the activity of “genomic parasites”, such as transposons, in biological evolution. Many evolutionary biologists posit that it is the co-evolution of populations with their genomic parasites that permits the high efficiency of evolutionary searches found in the living world. This publication is our first step in the direction of developing a minimal assortment of algorithms that simulate the role of genomic parasites. Specifically, we started in the domain of genetic algorithms (GA) and selected the Artificial Ant Problem as a test case. This navigation problem is widely known as a classical benchmark test and possesses a large body of literature. We add new objects to the standard toolkit of GA - artificial transposons and a collection of operators that operate on them. We define these artificial transposons as a fragment of an ant's code with properties that cause it to stand apart from the rest. The minimal set of operators for transposons is a transposon mutation operator, and a transposon reproduction operator that causes a transposon to multiply within the population of hosts. An analysis of the population dynamics of transposons within the course of ant evolution showed that transposons are involved in the processes of propagation and selection of blocks of ant navigation programs. During this time, the speed of evolutionary search increases significantly. We concluded that artificial transposons, analogous to real transposons, are truly capable of acting as intelligent mutators that adapt in response to an evolutionary problem in the course of co-evolution with their hosts. PMID:25767296

The Co-Evolution of Knowledge and Event Memory

ERIC Educational Resources Information Center

Nelson, Angela B.; Shiffrin, Richard M.

2013-01-01

We present a theoretical framework and a simplified simulation model for the co-evolution of knowledge and event memory, both termed SARKAE (Storing and Retrieving Knowledge and Events). Knowledge is formed through the accrual of individual events, a process that operates in tandem with the storage of individual event memories. In 2 studies, new…

Dueling biological and social contagions

PubMed Central

Fu, Feng; Christakis, Nicholas A.; Fowler, James H.

2017-01-01

Numerous models explore how a wide variety of biological and social phenomena spread in social networks. However, these models implicitly assume that the spread of one phenomenon is not affected by the spread of another. Here, we develop a model of “dueling contagions”, with a particular illustration of a situation where one is biological (influenza) and the other is social (flu vaccination). We apply the model to unique time series data collected during the 2009 H1N1 epidemic that includes information about vaccination, flu, and face-to-face social networks. The results show that well-connected individuals are more likely to get vaccinated, as are people who are exposed to friends who get vaccinated or are exposed to friends who get the flu. Our dueling contagion model suggests that other epidemiological models may be dramatically underestimating the R0 of contagions. It also suggests that the rate of vaccination contagion may be even more important than the biological contagion in determining the course of the disease. These results suggest that real world and online platforms that make it easier to see when friends have been vaccinated (personalized vaccination campaigns) and when they get the flu (personalized flu warnings) could have a large impact on reducing the severity of epidemics. They also suggest possible benefits from understanding the coevolution of many kinds of dueling contagions. PMID:28252663

Dueling biological and social contagions

NASA Astrophysics Data System (ADS)

Fu, Feng; Christakis, Nicholas A.; Fowler, James H.

2017-03-01

Numerous models explore how a wide variety of biological and social phenomena spread in social networks. However, these models implicitly assume that the spread of one phenomenon is not affected by the spread of another. Here, we develop a model of “dueling contagions”, with a particular illustration of a situation where one is biological (influenza) and the other is social (flu vaccination). We apply the model to unique time series data collected during the 2009 H1N1 epidemic that includes information about vaccination, flu, and face-to-face social networks. The results show that well-connected individuals are more likely to get vaccinated, as are people who are exposed to friends who get vaccinated or are exposed to friends who get the flu. Our dueling contagion model suggests that other epidemiological models may be dramatically underestimating the R0 of contagions. It also suggests that the rate of vaccination contagion may be even more important than the biological contagion in determining the course of the disease. These results suggest that real world and online platforms that make it easier to see when friends have been vaccinated (personalized vaccination campaigns) and when they get the flu (personalized flu warnings) could have a large impact on reducing the severity of epidemics. They also suggest possible benefits from understanding the coevolution of many kinds of dueling contagions.

Plastid-Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae.

PubMed

Weng, Mao-Lun; Ruhlman, Tracey A; Jansen, Robert K

2016-06-27

Plastids and mitochondria have many protein complexes that include subunits encoded by organelle and nuclear genomes. In animal cells, compensatory evolution between mitochondrial and nuclear-encoded subunits was identified and the high mitochondrial mutation rates were hypothesized to drive compensatory evolution in nuclear genomes. In plant cells, compensatory evolution between plastid and nucleus has rarely been investigated in a phylogenetic framework. To investigate plastid-nuclear coevolution, we focused on plastid ribosomal protein genes that are encoded by plastid and nuclear genomes from 27 Geraniales species. Substitution rates were compared for five sets of genes representing plastid- and nuclear-encoded ribosomal subunit proteins targeted to the cytosol or the plastid as well as nonribosomal protein controls. We found that nonsynonymous substitution rates (dN) and the ratios of nonsynonymous to synonymous substitution rates (ω) were accelerated in both plastid- (CpRP) and nuclear-encoded subunits (NuCpRP) of the plastid ribosome relative to control sequences. Our analyses revealed strong signals of cytonuclear coevolution between plastid- and nuclear-encoded subunits, in which nonsynonymous substitutions in CpRP and NuCpRP tend to occur along the same branches in the Geraniaceae phylogeny. This coevolution pattern cannot be explained by physical interaction between amino acid residues. The forces driving accelerated coevolution varied with cellular compartment of the sequence. Increased ω in CpRP was mainly due to intensified positive selection whereas increased ω in NuCpRP was caused by relaxed purifying selection. In addition, the many indels identified in plastid rRNA genes in Geraniaceae may have contributed to changes in plastid subunits. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Coevolution of game and network structure with adjustable linking

NASA Astrophysics Data System (ADS)

Qin, Shao-Meng; Zhang, Guo-Yong; Chen, Yong

2009-12-01

Most papers about the evolutionary game on graph assume the statistic network structure. However, in the real world, social interaction could change the relationship among people. And the change of social structure will also affect people’s strategies. We build a coevolution model of prisoner’s dilemma game and network structure to study the dynamic interaction in the real world. Differing from other coevolution models, players rewire their network connections according to the density of cooperation and other players’ payoffs. We use a parameter α to control the effect of payoff in the process of rewiring. Based on the asynchronous update rule and Monte Carlo simulation, we find that, when players prefer to rewire their links to those who are richer, the temptation can increase the cooperation density.

Estimation of plant disease severity visually, by digital photography and image analysis, and by hyperspectral imaging

USDA-ARS?s Scientific Manuscript database

Reliable, precise and accurate estimates of disease severity are important for predicting yield loss, monitoring and forecasting epidemics, for assessing crop germplasm for disease resistance, and for understanding fundamental biological processes including co-evolution. In some situations poor qual...

Our Social Roots: How Local Ecology Shapes Our Social Structures

NASA Astrophysics Data System (ADS)

Mace, Ruth

There is overwhelming evidence that wide-ranging aspects of human biology and human behavior can be considered as adaptations to different subsistence systems. Wider environmental and ecological correlates of behavioral and cultural traits are generally best understood as being mediated by differences in subsistence strategies. Modes of subsistence profoundly influence both human biology, as documented in genetic changes, and human social behavior and cultural norms, such as kinship, marriage, descent, wealth inheritance, and political systems. Thus both cultural and biological factors usually need to be considered together in studies of human evolutionary ecology, combined in specifically defined evolutionary models. Models of cultural adaptation to environmental conditions can be subjected to the same or similar tests that behavioral ecologists have used to seek evidence for adaptive behavior in other species. Phylogenetic comparative methods are proving useful, both for studying co-evolutionary hypotheses (cultural and/or gene-culture co-evolution), and for estimating ancestral states of prehistoric societies. This form of formal cross-cultural comparison is helping to put history back into anthropology, and helping us to understand cultural evolutionary processes at a number of levels.

Advances on plant-pathogen interactions from molecular toward systems biology perspectives.

PubMed

Peyraud, Rémi; Dubiella, Ullrich; Barbacci, Adelin; Genin, Stéphane; Raffaele, Sylvain; Roby, Dominique

2017-05-01

In the past 2 decades, progress in molecular analyses of the plant immune system has revealed key elements of a complex response network. Current paradigms depict the interaction of pathogen-secreted molecules with host target molecules leading to the activation of multiple plant response pathways. Further research will be required to fully understand how these responses are integrated in space and time, and exploit this knowledge in agriculture. In this review, we highlight systems biology as a promising approach to reveal properties of molecular plant-pathogen interactions and predict the outcome of such interactions. We first illustrate a few key concepts in plant immunity with a network and systems biology perspective. Next, we present some basic principles of systems biology and show how they allow integrating multiomics data and predict cell phenotypes. We identify challenges for systems biology of plant-pathogen interactions, including the reconstruction of multiscale mechanistic models and the connection of host and pathogen models. Finally, we outline studies on resistance durability through the robustness of immune system networks, the identification of trade-offs between immunity and growth and in silico plant-pathogen co-evolution as exciting perspectives in the field. We conclude that the development of sophisticated models of plant diseases incorporating plant, pathogen and climate properties represent a major challenge for agriculture in the future. © 2016 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

Niche construction game cancer cells play

NASA Astrophysics Data System (ADS)

Bergman, Aviv; Gligorijevic, Bojana

2015-10-01

Niche construction concept was originally defined in evolutionary biology as the continuous interplay between natural selection via environmental conditions and the modification of these conditions by the organism itself. Processes unraveling during cancer metastasis include construction of niches, which cancer cells use towards more efficient survival, transport into new environments and preparation of the remote sites for their arrival. Many elegant experiments were done lately illustrating, for example, the premetastatic niche construction, but there is practically no mathematical modeling done which would apply the niche construction framework. To create models useful for understanding niche construction role in cancer progression, we argue that a) genetic, b) phenotypic and c) ecological levels are to be included. While the model proposed here is phenomenological in its current form, it can be converted into a predictive outcome model via experimental measurement of the model parameters. Here we give an overview of an experimentally formulated problem in cancer metastasis and propose how niche construction framework can be utilized and broadened to model it. Other life science disciplines, such as host-parasite coevolution, may also benefit from niche construction framework adaptation, to satisfy growing need for theoretical considerations of data collected by experimental biology.

Niche construction game cancer cells play.

PubMed

Bergman, Aviv; Gligorijevic, Bojana

2015-10-01

Niche construction concept was originally defined in evolutionary biology as the continuous interplay between natural selection via environmental conditions and the modification of these conditions by the organism itself. Processes unraveling during cancer metastasis include construction of niches, which cancer cells use towards more efficient survival, transport into new environments and preparation of the remote sites for their arrival. Many elegant experiments were done lately illustrating, for example, the premetastatic niche construction, but there is practically no mathematical modeling done which would apply the niche construction framework. To create models useful for understanding niche construction role in cancer progression, we argue that a) genetic, b) phenotypic and c) ecological levels are to be included. While the model proposed here is phenomenological in its current form, it can be converted into a predictive outcome model via experimental measurement of the model parameters. Here we give an overview of an experimentally formulated problem in cancer metastasis and propose how niche construction framework can be utilized and broadened to model it. Other life science disciplines, such as host-parasite coevolution, may also benefit from niche construction framework adaptation, to satisfy growing need for theoretical considerations of data collected by experimental biology.

Non-parallel coevolution of sender and receiver in the acoustic communication system of treefrogs.

PubMed

Schul, Johannes; Bush, Sarah L

2002-09-07

Advertisement calls of closely related species often differ in quantitative features such as the repetition rate of signal units. These differences are important in species recognition. Current models of signal-receiver coevolution predict two possible patterns in the evolution of the mechanism used by receivers to recognize the call: (i) classical sexual selection models (Fisher process, good genes/indirect benefits, direct benefits models) predict that close relatives use qualitatively similar signal recognition mechanisms tuned to different values of a call parameter; and (ii) receiver bias models (hidden preference, pre-existing bias models) predict that if different signal recognition mechanisms are used by sibling species, evidence of an ancestral mechanism will persist in the derived species, and evidence of a pre-existing bias will be detectable in the ancestral species. We describe qualitatively different call recognition mechanisms in sibling species of treefrogs. Whereas Hyla chrysoscelis uses pulse rate to recognize male calls, Hyla versicolor uses absolute measurements of pulse duration and interval duration. We found no evidence of either hidden preferences or pre-existing biases. The results are compared with similar data from katydids (Tettigonia sp.). In both taxa, the data are not adequately explained by current models of signal-receiver coevolution.

Coevolution of Vertex Weights Resolves Social Dilemma in Spatial Networks.

PubMed

Shen, Chen; Chu, Chen; Guo, Hao; Shi, Lei; Duan, Jiangyan

2017-11-09

In realistic social system, the role or influence of each individual varies and adaptively changes in time in the population. Inspired by this fact, we thus consider a new coevolution setup of game strategy and vertex weight on a square lattice. In detail, we model the structured population on a square lattice, on which the role or influence of each individual is depicted by vertex weight, and the prisoner's dilemma game has been applied to describe the social dilemma of pairwise interactions of players. Through numerical simulation, we conclude that our coevolution setup can promote the evolution of cooperation effectively. Especially, there exists a moderate value of δ for each ε that can warrant an optimal resolution of social dilemma. For a further understanding of these results, we find that intermediate value of δ enables the strongest heterogeneous distribution of vertex weight. We hope our coevolution setup of vertex weight will provide new insight for the future research.

Host-parasite coevolution can promote the evolution of seed banking as a bet-hedging strategy.

PubMed

Verin, Mélissa; Tellier, Aurélien

2018-04-20

Seed (egg) banking is a common bet-hedging strategy maximizing the fitness of organisms facing environmental unpredictability by the delayed emergence of offspring. Yet, this condition often requires fast and drastic stochastic shifts between good and bad years. We hypothesize that the host seed banking strategy can evolve in response to coevolution with parasites because the coevolutionary cycles promote a gradually changing environment over longer times than seed persistence. We study the evolution of host germination fraction as a quantitative trait using both pairwise competition and multiple mutant competition methods, while the germination locus can be genetically linked or unlinked with the host locus under coevolution. In a gene-for-gene model of coevolution, hosts evolve a seed bank strategy under unstable coevolutionary cycles promoted by moderate to high costs of resistance or strong disease severity. Moreover, when assuming genetic linkage between coevolving and germination loci, the resistant genotype always evolves seed banking in contrast to susceptible hosts. Under a matching-allele interaction, both hosts' genotypes exhibit the same seed banking strategy irrespective of the genetic linkage between loci. We suggest host-parasite coevolution as an additional hypothesis for the evolution of seed banking as a temporal bet-hedging strategy. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning.

PubMed

Adhikari, Badri; Hou, Jie; Cheng, Jianlin

2018-03-01

In this study, we report the evaluation of the residue-residue contacts predicted by our three different methods in the CASP12 experiment, focusing on studying the impact of multiple sequence alignment, residue coevolution, and machine learning on contact prediction. The first method (MULTICOM-NOVEL) uses only traditional features (sequence profile, secondary structure, and solvent accessibility) with deep learning to predict contacts and serves as a baseline. The second method (MULTICOM-CONSTRUCT) uses our new alignment algorithm to generate deep multiple sequence alignment to derive coevolution-based features, which are integrated by a neural network method to predict contacts. The third method (MULTICOM-CLUSTER) is a consensus combination of the predictions of the first two methods. We evaluated our methods on 94 CASP12 domains. On a subset of 38 free-modeling domains, our methods achieved an average precision of up to 41.7% for top L/5 long-range contact predictions. The comparison of the three methods shows that the quality and effective depth of multiple sequence alignments, coevolution-based features, and machine learning integration of coevolution-based features and traditional features drive the quality of predicted protein contacts. On the full CASP12 dataset, the coevolution-based features alone can improve the average precision from 28.4% to 41.6%, and the machine learning integration of all the features further raises the precision to 56.3%, when top L/5 predicted long-range contacts are evaluated. And the correlation between the precision of contact prediction and the logarithm of the number of effective sequences in alignments is 0.66. © 2017 Wiley Periodicals, Inc.

On Design Mining: Coevolution and Surrogate Models.

PubMed

Preen, Richard J; Bull, Larry

2017-01-01

Design mining is the use of computational intelligence techniques to iteratively search and model the attribute space of physical objects evaluated directly through rapid prototyping to meet given objectives. It enables the exploitation of novel materials and processes without formal models or complex simulation. In this article, we focus upon the coevolutionary nature of the design process when it is decomposed into concurrent sub-design-threads due to the overall complexity of the task. Using an abstract, tunable model of coevolution, we consider strategies to sample subthread designs for whole-system testing and how best to construct and use surrogate models within the coevolutionary scenario. Drawing on our findings, we then describe the effective design of an array of six heterogeneous vertical-axis wind turbines.

Arms race between selfishness and policing: two-trait quantitative genetic model for caste fate conflict in eusocial Hymenoptera.

PubMed

Dobata, Shigeto

2012-12-01

Policing against selfishness is now regarded as the main force maintaining cooperation, by reducing costly conflict in complex social systems. Although policing has been studied extensively in social insect colonies, its coevolution against selfishness has not been fully captured by previous theories. In this study, I developed a two-trait quantitative genetic model of the conflict between selfish immature females (usually larvae) and policing workers in eusocial Hymenoptera over the immatures' propensity to develop into new queens. This model allows for the analysis of coevolution between genomes expressed in immatures and workers that collectively determine the immatures' queen caste fate. The main prediction of the model is that a higher level of polyandry leads to a smaller fraction of queens produced among new females through caste fate policing. The other main prediction of the present model is that, as a result of arms race, caste fate policing by workers coevolves with exaggerated selfishness of the immatures achieving maximum potential to develop into queens. Moreover, the model can incorporate genetic correlation between traits, which has been largely unexplored in social evolution theory. This study highlights the importance of understanding social traits as influenced by the coevolution of conflicting genomes. © 2012 The Author. Evolution© 2012 The Society for the Study of Evolution.

Holistic Darwinism: the new evolutionary paradigm and some implications for political science.

PubMed

Corning, Peter A

2008-03-01

Holistic Darwinism is a candidate name for a major paradigm shift that is currently underway in evolutionary biology and related disciplines. Important developments include (1) a growing appreciation for the fact that evolution is a multilevel process, from genes to ecosystems, and that interdependent coevolution is a ubiquitous phenomenon in nature; (2) a revitalization of group selection theory, which was banned (prematurely) from evolutionary biology over 30 years ago (groups may in fact be important evolutionary units); (3) a growing respect for the fact that the genome is not a "bean bag" (in biologist Ernst Mayr's caricature), much less a gladiatorial arena for competing selfish genes, but a complex, interdependent, cooperating system; (4) an increased recognition that symbiosis is an important phenomenon in nature and that symbiogenesis is a major source of innovation in evolution; (5) an array of new, more advanced game theory models, which support the growing evidence that cooperation is commonplace in nature and not a rare exception; (6) new research and theoretical work that stresses the role of nurture in evolution, including developmental processes, phenotypic plasticity, social information transfer (culture), and especially the role of behavioral innovations as pacemakers of evolutionary change (e.g., niche construction theory, which is concerned with the active role of organisms in shaping the evolutionary process, and gene-culture coevolution theory, which relates especially to the dynamics of human evolution); (7) and, not least, a broad effort to account for the evolution of biological complexity--from major transition theory to the "Synergism Hypothesis." Here I will briefly review these developments and will present a case for the proposition that this paradigm shift has profound implications for the social sciences, including specifically political theory, economic theory, and political science as a discipline. Interdependent superorganisms, it turns out, have played a major role in evolution--from eukaryotes to complex human societies.

Dilemma solving by the coevolution of networks and strategy in a 2 x 2 game.

PubMed

Tanimoto, Jun

2007-08-01

A 2 x 2 game model implemented by a coevolution mechanism of both networks and strategy, inspired by the work of Zimmermann and Eguiluz [Phys. Rev. E72, 056118 (2005)] is established. Network adaptation is the manner in which an existing link between two agents is destroyed and how a new one is established to replace it. The strategy is defined as whether an agent offers cooperation (C) or defection (D) . Both the networks and strategy are synchronously renovated in a simulation time step. A series of numerical experiments, considering various 2 x 2 game structures, reveals that the proposed coevolution mechanism can solve dilemmas in several game classes. The effect of solving a dilemma means mutual-cooperation reciprocity (R reciprocity), which is brought about by emerging several cooperative hub agents who have plenty of links. This effect can be primarily observed in game classes of the prisoner's dilemma and stag hunt. The coevolution mechanism, however, seems counterproductive for game classes of leader and hero, where the alternating reciprocity (ST reciprocity) is meaningful.

The evolution of reduced antagonism--A role for host-parasite coevolution.

PubMed

Gibson, A K; Stoy, K S; Gelarden, I A; Penley, M J; Lively, C M; Morran, L T

2015-11-01

Why do some host-parasite interactions become less antagonistic over evolutionary time? Vertical transmission can select for reduced antagonism. Vertical transmission also promotes coevolution between hosts and parasites. Therefore, we hypothesized that coevolution itself may underlie transitions to reduced antagonism. To test the coevolution hypothesis, we selected for reduced antagonism between the host Caenorhabditis elegans and its parasite Serratia marcescens. This parasite is horizontally transmitted, which allowed us to study coevolution independently of vertical transmission. After 20 generations, we observed a response to selection when coevolution was possible: reduced antagonism evolved in the copassaged treatment. Reduced antagonism, however, did not evolve when hosts or parasites were independently selected without coevolution. In addition, we found strong local adaptation for reduced antagonism between replicate host/parasite lines in the copassaged treatment. Taken together, these results strongly suggest that coevolution was critical to the rapid evolution of reduced antagonism. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Demographically idiosyncratic responses to climate change and rapid Pleistocene diversification of the walnut genus Juglans (Juglandaceae) revealed by whole-genome sequences

Treesearch

Wei-Ning Bai; Peng-Cheng Yan; Bo-Wen Zhang; Keith E. Woeste; Kui Lin; Da-Yong Zhang

2018-01-01

Whether species demography and diversification are driven primarily by extrinsic environmental changes such as climatic oscillations in the Quaternary or by intrinsic biological interactions like coevolution between antagonists is a matter of active debate. In fact, their relative importance can be assessed by tracking past population fluctuations over considerable...

Investigation of Dynamic Algorithms for Pattern Recognition Identified in Cerebral Cortex

DTIC Science & Technology

1991-12-02

oscillatory and possibly chaotic activity forin the actual cortical substrate of the diverse sensory, motor, and cognitive operations now studied in...September Neural Information Processing Systems - Natural and Synthetic, Denver, Colo., November 1989 U.C. San Diego, Cognitive Science Dept...Baird. Biologically applied neural networks may foster the co-evolution of neurobiology and cognitive psychology. Brain and Behavioral Sciences, 37

The genetic architecture of sexual conflict: male harm and female resistance in Callosobruchus maculatus.

PubMed

Gay, L; Brown, E; Tregenza, T; Pincheira-Donoso, D; Eady, P E; Vasudev, R; Hunt, J; Hosken, D J

2011-02-01

Males harm females during mating in a range of species. This harm is thought to evolve because it is directly or indirectly beneficial to the male, despite being costly to his mate. The resulting sexually antagonistic selection can cause sexual arms races. For sexually antagonistic co-evolution to occur, there must be genetic variation for traits involved in female harming and susceptibility to harm, but even then intersexual genetic correlations could facilitate or impede sexual co-evolution. Male Callosobruchus maculatus harm their mates during copulation by damaging the female's reproductive tract. However, there have been no investigations of the genetic variation in damage or in female susceptibility to damage, nor has the genetic covariance between these characters been assessed. Here, we use a full-sib/half-sib breeding design to show that male damage is heritable, whereas female susceptibility to damage is much less so. There is also a substantial positive genetic correlation between the two, suggesting that selection favouring damaging males will increase the prevalence of susceptible females. We also provide evidence consistent with intralocus sexual conflict in this species. © 2010 The Authors. Journal of Evolutionary Biology © 2010 European Society For Evolutionary Biology.

Assembly constraints drive co-evolution among ribosomal constituents.

PubMed

Mallik, Saurav; Akashi, Hiroshi; Kundu, Sudip

2015-06-23

Ribosome biogenesis, a central and essential cellular process, occurs through sequential association and mutual co-folding of protein-RNA constituents in a well-defined assembly pathway. Here, we construct a network of co-evolving nucleotide/amino acid residues within the ribosome and demonstrate that assembly constraints are strong predictors of co-evolutionary patterns. Predictors of co-evolution include a wide spectrum of structural reconstitution events, such as cooperativity phenomenon, protein-induced rRNA reconstitutions, molecular packing of different rRNA domains, protein-rRNA recognition, etc. A correlation between folding rate of small globular proteins and their topological features is known. We have introduced an analogous topological characteristic for co-evolutionary network of ribosome, which allows us to differentiate between rRNA regions subjected to rapid reconstitutions from those hindered by kinetic traps. Furthermore, co-evolutionary patterns provide a biological basis for deleterious mutation sites and further allow prediction of potential antibiotic targeting sites. Understanding assembly pathways of multicomponent macromolecules remains a key challenge in biophysics. Our study provides a 'proof of concept' that directly relates co-evolution to biophysical interactions during multicomponent assembly and suggests predictive power to identify candidates for critical functional interactions as well as for assembly-blocking antibiotic target sites. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Experimental Evolution with Caenorhabditis Nematodes

PubMed Central

Teotónio, Henrique; Estes, Suzanne; Phillips, Patrick C.; Baer, Charles F.

2017-01-01

The hermaphroditic nematode Caenorhabditis elegans has been one of the primary model systems in biology since the 1970s, but only within the last two decades has this nematode also become a useful model for experimental evolution. Here, we outline the goals and major foci of experimental evolution with C. elegans and related species, such as C. briggsae and C. remanei, by discussing the principles of experimental design, and highlighting the strengths and limitations of Caenorhabditis as model systems. We then review three exemplars of Caenorhabditis experimental evolution studies, underlining representative evolution experiments that have addressed the: (1) maintenance of genetic variation; (2) role of natural selection during transitions from outcrossing to selfing, as well as the maintenance of mixed breeding modes during evolution; and (3) evolution of phenotypic plasticity and its role in adaptation to variable environments, including host–pathogen coevolution. We conclude by suggesting some future directions for which experimental evolution with Caenorhabditis would be particularly informative. PMID:28592504

Coevolutionary modeling of protein sequences: Predicting structure, function, and mutational landscapes

NASA Astrophysics Data System (ADS)

Weigt, Martin

Over the last years, biological research has been revolutionized by experimental high-throughput techniques, in particular by next-generation sequencing technology. Unprecedented amounts of data are accumulating, and there is a growing request for computational methods unveiling the information hidden in raw data, thereby increasing our understanding of complex biological systems. Statistical-physics models based on the maximum-entropy principle have, in the last few years, played an important role in this context. To give a specific example, proteins and many non-coding RNA show a remarkable degree of structural and functional conservation in the course of evolution, despite a large variability in amino acid sequences. We have developed a statistical-mechanics inspired inference approach - called Direct-Coupling Analysis - to link this sequence variability (easy to observe in sequence alignments, which are available in public sequence databases) to bio-molecular structure and function. In my presentation I will show, how this methodology can be used (i) to infer contacts between residues and thus to guide tertiary and quaternary protein structure prediction and RNA structure prediction, (ii) to discriminate interacting from non-interacting protein families, and thus to infer conserved protein-protein interaction networks, and (iii) to reconstruct mutational landscapes and thus to predict the phenotypic effect of mutations. References [1] M. Figliuzzi, H. Jacquier, A. Schug, O. Tenaillon and M. Weigt ''Coevolutionary landscape inference and the context-dependence of mutations in beta-lactamase TEM-1'', Mol. Biol. Evol. (2015), doi: 10.1093/molbev/msv211 [2] E. De Leonardis, B. Lutz, S. Ratz, S. Cocco, R. Monasson, A. Schug, M. Weigt ''Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction'', Nucleic Acids Research (2015), doi: 10.1093/nar/gkv932 [3] F. Morcos, A. Pagnani, B. Lunt, A. Bertolino, D. Marks, C. Sander, R. Zecchina, J.N. Onuchic, T. Hwa, M. Weigt, ''Direct-coupling analysis of residue co-evolution captures native contacts across many protein families'', Proc. Natl. Acad. Sci. 108, E1293-E1301 (2011).

Evolution of female multiple mating: A quantitative model of the “sexually selected sperm” hypothesis

PubMed Central

Bocedi, Greta; Reid, Jane M

2015-01-01

Explaining the evolution and maintenance of polyandry remains a key challenge in evolutionary ecology. One appealing explanation is the sexually selected sperm (SSS) hypothesis, which proposes that polyandry evolves due to indirect selection stemming from positive genetic covariance with male fertilization efficiency, and hence with a male's success in postcopulatory competition for paternity. However, the SSS hypothesis relies on verbal analogy with “sexy-son” models explaining coevolution of female preferences for male displays, and explicit models that validate the basic SSS principle are surprisingly lacking. We developed analogous genetically explicit individual-based models describing the SSS and “sexy-son” processes. We show that the analogy between the two is only partly valid, such that the genetic correlation arising between polyandry and fertilization efficiency is generally smaller than that arising between preference and display, resulting in less reliable coevolution. Importantly, indirect selection was too weak to cause polyandry to evolve in the presence of negative direct selection. Negatively biased mutations on fertilization efficiency did not generally rescue runaway evolution of polyandry unless realized fertilization was highly skewed toward a single male, and coevolution was even weaker given random mating order effects on fertilization. Our models suggest that the SSS process is, on its own, unlikely to generally explain the evolution of polyandry. PMID:25330405

A coevolution analysis for identifying protein-protein interactions by Fourier transform.

PubMed

Yin, Changchuan; Yau, Stephen S-T

2017-01-01

Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees. The existing coevolution methods depend on multiple sequence alignments (MSA); however, the MSA-based coevolution methods often produce high false positive interactions. In this paper, we present a computational method using an alignment-free approach to accurately detect PPIs and reduce false positives. In the method, protein sequences are numerically represented by biochemical properties of amino acids, which reflect the structural and functional differences of proteins. Fourier transform is applied to the numerical representation of protein sequences to capture the dissimilarities of protein sequences in biophysical context. The method is assessed for predicting PPIs in Ebola virus. The results indicate strong coevolution between the protein pairs (NP-VP24, NP-VP30, NP-VP40, VP24-VP30, VP24-VP40, and VP30-VP40). The method is also validated for PPIs in influenza and E.coli genomes. Since our method can reduce false positive and increase the specificity of PPI prediction, it offers an effective tool to understand mechanisms of disease pathogens and find potential targets for drug design. The Python programs in this study are available to public at URL (https://github.com/cyinbox/PPI).

A coevolution analysis for identifying protein-protein interactions by Fourier transform

PubMed Central

Yin, Changchuan; Yau, Stephen S. -T.

2017-01-01

Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees. The existing coevolution methods depend on multiple sequence alignments (MSA); however, the MSA-based coevolution methods often produce high false positive interactions. In this paper, we present a computational method using an alignment-free approach to accurately detect PPIs and reduce false positives. In the method, protein sequences are numerically represented by biochemical properties of amino acids, which reflect the structural and functional differences of proteins. Fourier transform is applied to the numerical representation of protein sequences to capture the dissimilarities of protein sequences in biophysical context. The method is assessed for predicting PPIs in Ebola virus. The results indicate strong coevolution between the protein pairs (NP-VP24, NP-VP30, NP-VP40, VP24-VP30, VP24-VP40, and VP30-VP40). The method is also validated for PPIs in influenza and E.coli genomes. Since our method can reduce false positive and increase the specificity of PPI prediction, it offers an effective tool to understand mechanisms of disease pathogens and find potential targets for drug design. The Python programs in this study are available to public at URL (https://github.com/cyinbox/PPI). PMID:28430779

Invasion fitness for gene-culture co-evolution in family-structured populations and an application to cumulative culture under vertical transmission.

PubMed

Mullon, Charles; Lehmann, Laurent

2017-08-01

Human evolution depends on the co-evolution between genetically determined behaviors and socially transmitted information. Although vertical transmission of cultural information from parent to offspring is common in hominins, its effects on cumulative cultural evolution are not fully understood. Here, we investigate gene-culture co-evolution in a family-structured population by studying the invasion fitness of a mutant allele that influences a deterministic level of cultural information (e.g., amount of knowledge or skill) to which diploid carriers of the mutant are exposed in subsequent generations. We show that the selection gradient on such a mutant, and the concomitant level of cultural information it generates, can be evaluated analytically under the assumption that the cultural dynamic has a single attractor point, thereby making gene-culture co-evolution in family-structured populations with multigenerational effects mathematically tractable. We apply our result to study how genetically determined phenotypes of individual and social learning co-evolve with the level of adaptive information they generate under vertical transmission. We find that vertical transmission increases adaptive information due to kin selection effects, but when information is transmitted as efficiently between family members as between unrelated individuals, this increase is moderate in diploids. By contrast, we show that the way resource allocation into learning trades off with allocation into reproduction (the "learning-reproduction trade-off") significantly influences levels of adaptive information. We also show that vertical transmission prevents evolutionary branching and may therefore play a qualitative role in gene-culture co-evolutionary dynamics. More generally, our analysis of selection suggests that vertical transmission can significantly increase levels of adaptive information under the biologically plausible condition that information transmission between relatives is more efficient than between unrelated individuals. Copyright © 2017 Elsevier Inc. All rights reserved.

Practical aspects of protein co-evolution.

PubMed

Ochoa, David; Pazos, Florencio

2014-01-01

Co-evolution is a fundamental aspect of Evolutionary Theory. At the molecular level, co-evolutionary linkages between protein families have been used as indicators of protein interactions and functional relationships from long ago. Due to the complexity of the problem and the amount of genomic data required for these approaches to achieve good performances, it took a relatively long time from the appearance of the first ideas and concepts to the quotidian application of these approaches and their incorporation to the standard toolboxes of bioinformaticians and molecular biologists. Today, these methodologies are mature (both in terms of performance and usability/implementation), and the genomic information that feeds them large enough to allow their general application. This review tries to summarize the current landscape of co-evolution-based methodologies, with a strong emphasis on describing interesting cases where their application to important biological systems, alone or in combination with other computational and experimental approaches, allowed getting new insight into these.

Practical aspects of protein co-evolution

PubMed Central

Ochoa, David; Pazos, Florencio

2014-01-01

Co-evolution is a fundamental aspect of Evolutionary Theory. At the molecular level, co-evolutionary linkages between protein families have been used as indicators of protein interactions and functional relationships from long ago. Due to the complexity of the problem and the amount of genomic data required for these approaches to achieve good performances, it took a relatively long time from the appearance of the first ideas and concepts to the quotidian application of these approaches and their incorporation to the standard toolboxes of bioinformaticians and molecular biologists. Today, these methodologies are mature (both in terms of performance and usability/implementation), and the genomic information that feeds them large enough to allow their general application. This review tries to summarize the current landscape of co-evolution-based methodologies, with a strong emphasis on describing interesting cases where their application to important biological systems, alone or in combination with other computational and experimental approaches, allowed getting new insight into these. PMID:25364721

Computational evolution: taking liberties.

PubMed

Correia, Luís

2010-09-01

Evolution has, for a long time, inspired computer scientists to produce computer models mimicking its behavior. Evolutionary algorithm (EA) is one of the areas where this approach has flourished. EAs have been used to model and study evolution, but they have been especially developed for their aptitude as optimization tools for engineering. Developed models are quite simple in comparison with their natural sources of inspiration. However, since EAs run on computers, we have the freedom, especially in optimization models, to test approaches both realistic and outright speculative, from the biological point of view. In this article, we discuss different common evolutionary algorithm models, and then present some alternatives of interest. These include biologically inspired models, such as co-evolution and, in particular, symbiogenetics and outright artificial operators and representations. In each case, the advantages of the modifications to the standard model are identified. The other area of computational evolution, which has allowed us to study basic principles of evolution and ecology dynamics, is the development of artificial life platforms for open-ended evolution of artificial organisms. With these platforms, biologists can test theories by directly manipulating individuals and operators, observing the resulting effects in a realistic way. An overview of the most prominent of such environments is also presented. If instead of artificial platforms we use the real world for evolving artificial life, then we are dealing with evolutionary robotics (ERs). A brief description of this area is presented, analyzing its relations to biology. Finally, we present the conclusions and identify future research avenues in the frontier of computation and biology. Hopefully, this will help to draw the attention of more biologists and computer scientists to the benefits of such interdisciplinary research.

SuperDCA for genome-wide epistasis analysis.

PubMed

Puranen, Santeri; Pesonen, Maiju; Pensar, Johan; Xu, Ying Ying; Lees, John A; Bentley, Stephen D; Croucher, Nicholas J; Corander, Jukka

2018-05-29

The potential for genome-wide modelling of epistasis has recently surfaced given the possibility of sequencing densely sampled populations and the emerging families of statistical interaction models. Direct coupling analysis (DCA) has previously been shown to yield valuable predictions for single protein structures, and has recently been extended to genome-wide analysis of bacteria, identifying novel interactions in the co-evolution between resistance, virulence and core genome elements. However, earlier computational DCA methods have not been scalable to enable model fitting simultaneously to 10 4 -10 5 polymorphisms, representing the amount of core genomic variation observed in analyses of many bacterial species. Here, we introduce a novel inference method (SuperDCA) that employs a new scoring principle, efficient parallelization, optimization and filtering on phylogenetic information to achieve scalability for up to 10 5 polymorphisms. Using two large population samples of Streptococcus pneumoniae, we demonstrate the ability of SuperDCA to make additional significant biological findings about this major human pathogen. We also show that our method can uncover signals of selection that are not detectable by genome-wide association analysis, even though our analysis does not require phenotypic measurements. SuperDCA, thus, holds considerable potential in building understanding about numerous organisms at a systems biological level.

How to be a fig wasp.

PubMed

Weiblen, George D

2002-01-01

In the two decades since Janzen described how to be a fig, more than 200 papers have appeared on fig wasps (Agaonidae) and their host plants (Ficus spp., Moraceae). Fig pollination is now widely regarded as a model system for the study of coevolved mutualism, and earlier reviews have focused on the evolution of resource conflicts between pollinating fig wasps, their hosts, and their parasites. Fig wasps have also been a focus of research on sex ratio evolution, the evolution of virulence, coevolution, population genetics, host-parasitoid interactions, community ecology, historical biogeography, and conservation biology. This new synthesis of fig wasp research attempts to integrate recent contributions with the older literature and to promote research on diverse topics ranging from behavioral ecology to molecular evolution.

Gene–culture coevolution and the nature of human sociality

PubMed Central

Gintis, Herbert

2011-01-01

Human characteristics are the product of gene–culture coevolution, which is an evolutionary dynamic involving the interaction of genes and culture over long time periods. Gene–culture coevolution is a special case of niche construction. Gene–culture coevolution is responsible for human other-regarding preferences, a taste for fairness, the capacity to empathize and salience of morality and character virtues. PMID:21320901

Robustness of coevolution in resolving prisoner's dilemma games on interdependent networks subject to attack

NASA Astrophysics Data System (ADS)

Liu, Penghui; Liu, Jing

2017-08-01

Recently, coevolution between strategy and network structure has been established as a rule to resolve social dilemmas and reach optimal situations for cooperation. Many follow-up researches have focused on studying how coevolution helps networks reorganize to deter the defectors and many coevolution methods have been proposed. However, the robustness of the coevolution rules against attacks have not been studied much. Since attacks may directly influence the original evolutionary process of cooperation, the robustness should be an important index while evaluating the quality of a coevolution method. In this paper, we focus on investigating the robustness of an elementary coevolution method in resolving the prisoner's dilemma game upon the interdependent networks. Three different types of time-independent attacks, named as edge attacks, instigation attacks and node attacks have been employed to test its robustness. Through analyzing the simulation results obtained, we find this coevolution method is relatively robust against the edge attack and the node attack as it successfully maintains cooperation in the population over the entire attack range. However, when the instigation probability of the attacked individuals is large or the attack range of instigation attack is wide enough, coevolutionary rule finally fails in maintaining cooperation in the population.

Heuristic urban transportation network design method, a multilayer coevolution approach

NASA Astrophysics Data System (ADS)

Ding, Rui; Ujang, Norsidah; Hamid, Hussain bin; Manan, Mohd Shahrudin Abd; Li, Rong; Wu, Jianjun

2017-08-01

The design of urban transportation networks plays a key role in the urban planning process, and the coevolution of urban networks has recently garnered significant attention in literature. However, most of these recent articles are based on networks that are essentially planar. In this research, we propose a heuristic multilayer urban network coevolution model with lower layer network and upper layer network that are associated with growth and stimulate one another. We first use the relative neighbourhood graph and the Gabriel graph to simulate the structure of rail and road networks, respectively. With simulation we find that when a specific number of nodes are added, the total travel cost ratio between an expanded network and the initial lower layer network has the lowest value. The cooperation strength Λ and the changeable parameter average operation speed ratio Θ show that transit users' route choices change dramatically through the coevolution process and that their decisions, in turn, affect the multilayer network structure. We also note that the simulated relation between the Gini coefficient of the betweenness centrality, Θ and Λ have an optimal point for network design. This research could inspire the analysis of urban network topology features and the assessment of urban growth trends.

A Paradigm for Virus–Host Coevolution: Sequential Counter-Adaptations between Endogenous and Exogenous Retroviruses

PubMed Central

Arnaud, Frederick; Caporale, Marco; Varela, Mariana; Biek, Roman; Chessa, Bernardo; Alberti, Alberto; Golder, Matthew; Mura, Manuela; Zhang, Ya-ping; Yu, Li; Pereira, Filipe; DeMartini, James C; Leymaster, Kreg; Spencer, Thomas E; Palmarini, Massimo

2007-01-01

Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections of the host germline transmitted vertically from generation to generation. It is hypothesized that some ERVs are used by the host as restriction factors to block the infection of pathogenic retroviruses. Indeed, some ERVs efficiently interfere with the replication of related exogenous retroviruses. However, data suggesting that these mechanisms have influenced the coevolution of endogenous and/or exogenous retroviruses and their hosts have been more difficult to obtain. Sheep are an interesting model system to study retrovirus-host coevolution because of the coexistence in this animal species of two exogenous (i.e., horizontally transmitted) oncogenic retroviruses, Jaagsiekte sheep retrovirus and Enzootic nasal tumor virus, with highly related and biologically active endogenous retroviruses (enJSRVs). Here, we isolated and characterized the evolutionary history and molecular virology of 27 enJSRV proviruses. enJSRVs have been integrating in the host genome for the last 5–7 million y. Two enJSRV proviruses (enJS56A1 and enJSRV-20), which entered the host genome within the last 3 million y (before and during speciation within the genus Ovis), acquired in two temporally distinct events a defective Gag polyprotein resulting in a transdominant phenotype able to block late replication steps of related exogenous retroviruses. Both transdominant proviruses became fixed in the host genome before or around sheep domestication (∼ 9,000 y ago). Interestingly, a provirus escaping the transdominant enJSRVs has emerged very recently, most likely within the last 200 y. Thus, we determined sequentially distinct events during evolution that are indicative of an evolutionary antagonism between endogenous and exogenous retroviruses. This study strongly suggests that endogenization and selection of ERVs acting as restriction factors is a mechanism used by the host to fight retroviral infections. PMID:17997604

Non-Simian Foamy Viruses: Molecular Virology, Tropism and Prevalence and Zoonotic/Interspecies Transmission

PubMed Central

Kehl, Timo; Tan, Juan; Materniak, Magdalena

2013-01-01

Within the field of retrovirus, our knowledge of foamy viruses (FV) is still limited. Their unique replication strategy and mechanism of viral persistency needs further research to gain understanding of the virus-host interactions, especially in the light of the recent findings suggesting their ancient origin and long co-evolution with their nonhuman hosts. Unquestionably, the most studied member is the primate/prototype foamy virus (PFV) which was originally isolated from a human (designated as human foamy virus, HFV), but later identified as chimpanzee origin; phylogenetic analysis clearly places it among other Old World primates. Additionally, the study of non-simian animal FVs can contribute to a deeper understanding of FV-host interactions and development of other animal models. The review aims at highlighting areas of special interest regarding the structure, biology, virus-host interactions and interspecies transmission potential of primate as well as non-primate foamy viruses for gaining new insights into FV biology. PMID:24064793

Physical mode of bacteria and virus coevolution

NASA Astrophysics Data System (ADS)

Han, Pu; Niestemski, Liang; Deem, Michael

2013-03-01

Single-cell hosts such as bacteria or archaea possess an adaptive, heritable immune system that protects them from viral invasion. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences from viruses or plasmids. The sequences form what are called ``spacers'' in the CRISPR. Spacers in the CRISPR loci provide a record of the host and predator coevolution history. We develop a physical model to study the dynamics of this coevolution due to immune pressure. Hosts and viruses reproduce, die, and evolve due to viral infection pressure, host immune pressure, and mutation. We will discuss the differing effects of point mutation and recombination on CRISPR evolution. We will also discuss the effect of different spacer deletion mechanisms. We will describe population structure of hosts and viruses, how spacer diversity depends on position within CRISPR, and match of the CRISPR spacers to the virus population.

A Coupled Modeling Framework of the Co-evolution of Humans and Water: Case Study of Tarim River Basin, Western China

NASA Astrophysics Data System (ADS)

Liu, D.; Tian, F.; Lin, M.; Sivapalan, M.

2014-12-01

The complex interactions and feedbacks between humans and water are very essential issues but are poorly understood in the newly proposed discipline of socio-hydrology (Sivapalan et al., 2012). An exploratory model with the appropriate level of simplification can be valuable to improve our understanding of the co-evolution and self-organization of socio-hydrological systems driven by interactions and feedbacks operating at different scales. In this study, a simple coupled modeling framework for socio-hydrology co-evolution is developed for the Tarim River Basin in Western China, and is used to illustrate the explanatory power of such a model. The study area is the mainstream of the Tarim River, which is divided into two modeling units. The socio-hydrological system is composed of four parts, i.e., social sub-system, economic sub-system, ecological sub-system, and hydrological sub-system. In each modeling unit, four coupled ordinary differential equations are used to simulate the dynamics of the social sub-system represented by human population, the economic sub-system represented by irrigated crop area, the ecological sub-system represented by natural vegetation cover and the hydrological sub-system represented by stream discharge. The coupling and feedback processes of the four dominant sub-systems (and correspondingly four state variables) are integrated into several internal system characteristics interactively and jointly determined by themselves and by other coupled systems. For example, the stream discharge is coupled to the irrigated crop area by the colonization rate and mortality rate of the irrigated crop area in the upper reach and the irrigated area is coupled to stream discharge through irrigation water consumption. The co-evolution of the Tarim socio-hydrological system is then analyzed within this modeling framework to gain insights into the overall system dynamics and its sensitivity to the external drivers and internal system variables. In the modeling framework, the state of each subsystem is holistically described by one state variable and the framework is flexible enough to comprise more processes and constitutive relationships if they are needed to illustrate the interaction and feedback mechanisms of the human-water system.

The critical role of fire in catchment coevolution in South Eastern Australia

NASA Astrophysics Data System (ADS)

Nyman, P.; Inbar, A.; Lane, P. N. J.; Sheridan, G. J.

2016-12-01

Temperate south east Australian forested uplands are characterised by complex spatial patterns in forest types, soils and fire regimes, even within areas with similar geologies and landscape position. Preliminary measurements and experiments suggest that positive and negative feedbacks between the vegetation, fuels, fire frequency and soil erosion may control the coevolution of these observed system states. Here we propose the hypotheses that in this landscape post-fire soil erosion has played a dominant role in the coevolved system-state combinations of standing biomass, fire frequency and soil depth. To test the hypothesis a 1D simulation model was developed that links together an ecohydrological model to drive the biomass production and water and energy partitioning, a stochastic fire model that is controlled by climate, fuel load and moisture conditions, and a geomorphic model that controls soil production and fluvial and diffusive sediment transport rates. The model was calibrated to the range of existing observed quasi-equalibrium system-states of soil depth, standing biomass, fuel loading and fire frequency using field measurements from 12 instrumented eco-hydrologic microclimate research sites. The long-term partitioning of rainfall into evaporation, transpiration, and streamflow was calibrated against field and literature values. Fuel moisture and micro-climate variables were calibrated to the field microclimate stations. The calibrated model was able to reasonably replicate the observed quasi-equilibrium system-states and hydrologic outputs using current climate forcings operating over a 10,000 year period, providing confidence in the model structure and performance. The model was then used to test the hypothesis stated above, by alternatively including or excluding the post fire erosion process. An alternate hypothesis, whereby the observed system states are dominated by climate related differences in soil production rates was also tested in this way. The results support the hypothesis that feedbacks between fire, ecology, hydrology and geomorphology have played a critical role in the coevolution of south east Australian forested uplands. Similar pyro-eco-hydrologic feedbacks may play a critical role in catchment coevolution in other forested systems globally.

An emerging synthesis between community ecology and evolutionary biology.

PubMed

Johnson, Marc T J; Stinchcombe, John R

2007-05-01

A synthesis between community ecology and evolutionary biology is emerging that identifies how genetic variation and evolution within one species can shape the ecological properties of entire communities and, in turn, how community context can govern evolutionary processes and patterns. This synthesis incorporates research on the ecology and evolution within communities over short timescales (community genetics and diffuse coevolution), as well as macroevolutionary timescales (community phylogenetics and co-diversification of communities). As we discuss here, preliminary evidence supports the hypothesis that there is a dynamic interplay between ecology and evolution within communities, yet researchers have not yet demonstrated convincingly whether, and under what circumstances, it is important for biologists to bridge community ecology and evolutionary biology. Answering this question will have important implications for both basic and applied problems in biology.

Simulating the Effects of Cross-Generational Cultural Transmission on Language Change

NASA Astrophysics Data System (ADS)

Gong, Tao; Shuai, Lan

Language evolves in a socio-cultural environment. Apart from biological evolution and individual learning, cultural transmission also casts important influence on many aspects of language evolution. In this paper, based on the lexicon-syntax coevolution model, we extend the acquisition framework in our previous work to examine the roles of three forms of cultural transmission spanning the offspring, parent, and grandparent generations in language change. These transmissions are: those between the parent and offspring generations (PO), those within the offspring generation (OO), and those between the grandparent and offspring generations (GO). The simulation results of the considered model and relevant analyses illustrate not only the necessity of PO and OO transmissions for language change, thus echoing our previous findings, but also the importance of GO transmission, a form of cross-generational cultural transmission, on preserving the mutual understandability of the communal language across generations of individuals.

Niche construction, sources of selection and trait coevolution.

PubMed

Laland, Kevin; Odling-Smee, John; Endler, John

2017-10-06

Organisms modify and choose components of their local environments. This 'niche construction' can alter ecological processes, modify natural selection and contribute to inheritance through ecological legacies. Here, we propose that niche construction initiates and modifies the selection directly affecting the constructor, and on other species, in an orderly, directed and sustained manner. By dependably generating specific environmental states, niche construction co-directs adaptive evolution by imposing a consistent statistical bias on selection. We illustrate how niche construction can generate this evolutionary bias by comparing it with artificial selection. We suggest that it occupies the middle ground between artificial and natural selection. We show how the perspective leads to testable predictions related to: (i) reduced variance in measures of responses to natural selection in the wild; (ii) multiple trait coevolution, including the evolution of sequences of traits and patterns of parallel evolution; and (iii) a positive association between niche construction and biodiversity. More generally, we submit that evolutionary biology would benefit from greater attention to the diverse properties of all sources of selection.

Sex-biased dispersal, kin selection and the evolution of sexual conflict.

PubMed

Faria, Gonçalo S; Varela, Susana A M; Gardner, Andy

2015-10-01

There is growing interest in resolving the curious disconnect between the fields of kin selection and sexual selection. Rankin's (2011, J. Evol. Biol. 24, 71-81) theoretical study of the impact of kin selection on the evolution of sexual conflict in viscous populations has been particularly valuable in stimulating empirical research in this area. An important goal of that study was to understand the impact of sex-specific rates of dispersal upon the coevolution of male-harm and female-resistance behaviours. But the fitness functions derived in Rankin's study do not flow from his model's assumptions and, in particular, are not consistent with sex-biased dispersal. Here, we develop new fitness functions that do logically flow from the model's assumptions, to determine the impact of sex-specific patterns of dispersal on the evolution of sexual conflict. Although Rankin's study suggested that increasing male dispersal always promotes the evolution of male harm and that increasing female dispersal always inhibits the evolution of male harm, we find that the opposite can also be true, depending upon parameter values. © 2015 The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.

In love and war: altruism, norm formation, and two different types of group selection.

PubMed

van Veelen, Matthijs; Hopfensitz, Astrid

2007-12-21

We analyse simulations reported in "The co-evolution of individual behaviors and social institutions" by Bowles et al., 2003 in the Journal of Theoretical Biology 223, 135-147, and begin with distinguishing two types of group selection models. The literature does not provide different names for them, but they are shown to be fundamentally different and have quite different empirical implications. The working of the first one depends on the answer to the question "is the probability that you also are an altruist large enough", while the other needs an affirmative answer to "are our interests enough in line". The first one therefore can also be understood as a kin selection model, while the working of the second can also be described in terms of the direct benefits. The actual simulation model is a combination of the two. It is also a Markov chain, which has important implications for how the output data should be handled.

A matching-allele model explains host resistance to parasites.

PubMed

Luijckx, Pepijn; Fienberg, Harris; Duneau, David; Ebert, Dieter

2013-06-17

The maintenance of genetic variation and sex despite its costs has long puzzled biologists. A popular idea, the Red Queen Theory, is that under rapid antagonistic coevolution between hosts and their parasites, the formation of new rare host genotypes through sex can be advantageous as it creates host genotypes to which the prevailing parasite is not adapted. For host-parasite coevolution to lead to an ongoing advantage for rare genotypes, parasites should infect specific host genotypes and hosts should resist specific parasite genotypes. The most prominent genetics capturing such specificity are matching-allele models (MAMs), which have the key feature that resistance for two parasite genotypes can reverse by switching one allele at one host locus. Despite the lack of empirical support, MAMs have played a central role in the theoretical development of antagonistic coevolution, local adaptation, speciation, and sexual selection. Using genetic crosses, we show that resistance of the crustacean Daphnia magna against the parasitic bacterium Pasteuria ramosa follows a MAM. Simulation results show that the observed genetics can explain the maintenance of genetic variation and contribute to the maintenance of sex in the facultatively sexual host as predicted by the Red Queen Theory. Copyright © 2013 Elsevier Ltd. All rights reserved.

The accumulation of reproductive isolation in early stages of divergence supports a role for sexual selection.

PubMed

Martin, M D; Mendelson, T C

2016-04-01

Models of speciation by sexual selection propose that male-female coevolution leads to the rapid evolution of behavioural reproductive isolation. Here, we compare the strength of behavioural isolation to ecological isolation, gametic incompatibility and hybrid inviability in a group of dichromatic stream fishes. In addition, we examine whether any of these individual barriers, or a combined measure of total isolation, is predicted by body shape differences, male colour differences, environmental differences or genetic distance. Behavioural isolation reaches the highest values of any barrier and is significantly greater than ecological isolation. No individual reproductive barrier is associated with any of the predictor variables. However, marginally significant relationships between male colour and body shape differences with ecological and behavioural isolation are discussed. Differences in male colour and body shape predict total reproductive isolation between species; hierarchical partitioning of these two variables' effects suggests a stronger role for male colour differences. Together, these results suggest an important role for divergent sexual selection in darter speciation but raise new questions about the mechanisms of sexual selection at play and the role of male nuptial ornaments. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

A non-classical phase diagram for virus-bacterial co-evolution mediated by CRISPR

NASA Astrophysics Data System (ADS)

Han, Pu; Deem, Michael

CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. Due to the cost of CRISPR, bacteria can lose the acquired immunity. We will show an intriguing phase diagram of the virus extinction probability, which when the rate of losing the acquired immunity is small, is more complex than that of the classic predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape the recognition by CRISPR, and this co-evolution leads to a non-trivial phase structure that cannot be explained by the classical predator-prey model.

Limited ability driven phase transitions in the coevolution process in Axelrod's model

NASA Astrophysics Data System (ADS)

Wang, Bing; Han, Yuexing; Chen, Luonan; Aihara, Kazuyuki

2009-04-01

We study the coevolution process in Axelrod's model by taking into account of agents' abilities to access information, which is described by a parameter α to control the geographical range of communication. We observe two kinds of phase transitions in both cultural domains and network fragments, which depend on the parameter α. By simulation, we find that not all rewiring processes pervade the dissemination of culture, that is, a very limited ability to access information constrains the cultural dissemination, while an exceptional ability to access information aids the dissemination of culture. Furthermore, by analyzing the network characteristics at the frozen states, we find that there exists a stage at which the network develops to be a small-world network with community structures.

Coevolution of MHC genes (LMP/TAP/class Ia; NKT-class Ib; NKp30-B7H6): Lessons from cold-blooded vertebrates

PubMed Central

Ohta, Yuko; Flajnik, Martin F.

2015-01-01

Summary Comparative immunology provides the long view of what is conserved across all vertebrate taxa versus what is specific to particular organisms or group of organisms. Regarding the major histocompatibility complex (MHC) and coevolution, three striking cases have been revealed in cold-blooded vertebrates: lineages of class Ia antigen-processing and -presenting genes, evolutionary conservation of NKT-class Ib recognition, and the ancient emergence of the natural cytotoxicity receptor NKp30 and its ligand B7H6. While coevolution of transporter associated with antigen processing (TAP) and class Ia has been documented in endothermic birds and two mammals, lineages of LMP7 are restricted to ectotherms. The unambiguous discovery of natural killer T (NKT) cells in Xenopus demonstrated that NKT cells are not restricted to mammals and are likely to have emerged at the same time in evolution as classical α/β and γ/δ T cells. NK cell receptors evolve at a rapid rate, and orthologues are nearly impossible to identify in different vertebrate classes. By contrast, we have detected NKp30 in all gnathostomes, except in species where it was lost. The recently discovered ligand of NKp30, B7H6, shows strong signs of coevolution with NKp30 throughout evolution, i.e. coincident loss or expansion of both genes in some species. NKp30 also offers an attractive IgSF candidate for the invasion of the RAG transposon, which is believed to have initiated T-cell receptor/immunoglobulin adaptive immunity. Besides reviewing these intriguing features of MHC evolution and coevolution, we offer suggestions for future studies and propose a model for the primordial or proto MHC. PMID:26284468

Dynamical trade-offs arise from antagonistic coevolution and decrease intraspecific diversity.

PubMed

Huang, Weini; Traulsen, Arne; Werner, Benjamin; Hiltunen, Teppo; Becks, Lutz

2017-12-12

Trade-offs play an important role in evolution. Without trade-offs, evolution would maximize fitness of all traits leading to a "master of all traits". The shape of trade-offs has been shown to determine evolutionary trajectories and is often assumed to be static and independent of the actual evolutionary process. Here we propose that coevolution leads to a dynamical trade-off. We test this hypothesis in a microbial predator-prey system and show that the bacterial growth-defense trade-off changes from concave to convex, i.e., defense is effective and cheap initially, but gets costly when predators coevolve. We further explore the impact of such dynamical trade-offs by a novel mathematical model incorporating de novo mutations for both species. Predator and prey populations diversify rapidly leading to higher prey diversity when the trade-off is concave (cheap). Coevolution results in more convex (costly) trade-offs and lower prey diversity compared to the scenario where only the prey evolves.

Non-classical phase diagram for virus bacterial coevolution mediated by clustered regularly interspaced short palindromic repeats.

PubMed

Han, Pu; Deem, Michael W

2017-02-01

CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The condition for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this work, we show an intriguing phase diagram of the virus extinction probability, which is more complex than that of the classical predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape recognition by CRISPR. When bacteria have a small rate of deleting spacers, a new parameter region in which bacteria and viruses can coexist arises, and it leads to a more complex coexistence patten for bacteria and viruses. For example, when the virus mutation rate is low, the virus extinction probability changes non-montonically with the bacterial exposure rate. The virus and bacteria coevolution not only alters the virus extinction probability, but also changes the bacterial population structure. Additionally, we show that recombination is a successful strategy for viruses to escape from CRISPR recognition when viruses have multiple proto-spacers, providing support for a recombination-mediated escape mechanism suggested experimentally. Finally, we suggest that the re-entrant phase diagram, in which phages can progress through three phases of extinction and two phases of abundance at low spacer deletion rates as a function of exposure rate to bacteria, is an experimentally testable phenomenon. © 2017 The Author(s).

Mechanisms and Evidence of Genital Coevolution: The Roles of Natural Selection, Mate Choice, and Sexual Conflict

PubMed Central

Brennan, Patricia L.R.; Prum, Richard O.

2015-01-01

Genital coevolution between the sexes is expected to be common because of the direct interaction between male and female genitalia during copulation. Here we review the diverse mechanisms of genital coevolution that include natural selection, female mate choice, male–male competition, and how their interactions generate sexual conflict that can lead to sexually antagonistic coevolution. Natural selection on genital morphology will result in size coevolution to allow for copulation to be mechanically possible, even as other features of genitalia may reflect the action of other mechanisms of selection. Genital coevolution is explicitly predicted by at least three mechanisms of genital evolution: lock and key to prevent hybridization, female choice, and sexual conflict. Although some good examples exist in support of each of these mechanisms, more data on quantitative female genital variation and studies of functional morphology during copulation are needed to understand more general patterns. A combination of different approaches is required to continue to advance our understanding of genital coevolution. Knowledge of the ecology and behavior of the studied species combined with functional morphology, quantitative morphological tools, experimental manipulation, and experimental evolution have been provided in the best-studied species, all of which are invertebrates. Therefore, attention to vertebrates in any of these areas is badly needed. PMID:26134314

The importance of initial protection of conspicuous mutants for the coevolution of defense and aposematic signaling of the defense: a modeling study.

PubMed

Ruxton, Graeme D; Speed, Michael P; Broom, Mark

2007-09-01

Most models of the evolution of aposematic signaling assume (1) that the secondary defense being signaled is fixed, and (2) that conspicuous mutants arising in a population of defended individuals of cryptic appearance are initially protected from predation. Previous models of ours relaxed the first assumption, here we relax the second and compare with our earlier work to explore the consequences of initial protection from predation on the coevolution of secondary defense and aposematic signaling. As expected, we find that aposematic signaling evolves more easily if initial protection is available. Less obviously, the coevolved level of secondary defense should also be higher if initial protection is provided. Across species or populations, we predict that when initial protection occurs, then strength of aposematic signal should be correlated with the strength of the underlying secondary defense, whereas no such correlation should occur without initial protection. Finally, we demonstrate that species can invest heavily in a secondary defense and remain maximally cryptic (forgoing the advantages of aposematic signaling) and that within a species we should expect strong variation in appearance between populations but much less variation within populations. Hence, we demonstrate that whether conspicuous morphs receive initial protection from predation has powerful and potentially empirically detectible consequences for the coevolution of secondary defenses and aposematic signaling.

Biogeochemical Transformations in the History of the Ocean.

PubMed

Lenton, Timothy M; Daines, Stuart J

2017-01-03

The ocean has undergone several profound biogeochemical transformations in its 4-billion-year history, and these were an integral part of the coevolution of life and the planet. This review focuses on changes in ocean redox state as controlled by changes in biological activity, nutrient concentrations, and atmospheric O 2 . Motivated by disparate interpretations of available geochemical data, we aim to show how quantitative modeling-spanning microbial mats, shelf seas, and the open ocean-can help constrain past ocean biogeochemical redox states and show what caused transformations between them. We outline key controls on ocean redox structure and review pertinent proxies and their interpretation. We then apply this quantitative framework to three key questions: How did the origin of oxygenic photosynthesis transform ocean biogeochemistry? How did the Great Oxidation transform ocean biogeochemistry? And how was ocean biogeochemistry transformed in the Neoproterozoic-Paleozoic?

A protein coevolution method uncovers critical features of the Hepatitis C Virus fusion mechanism

PubMed Central

Douam, Florian; Mancip, Jimmy; Mailly, Laurent; Montserret, Roland; Ding, Qiang; Verhoeyen, Els; Baumert, Thomas F.; Ploss, Alexander; Carbone, Alessandra

2018-01-01

Amino-acid coevolution can be referred to mutational compensatory patterns preserving the function of a protein. Viral envelope glycoproteins, which mediate entry of enveloped viruses into their host cells, are shaped by coevolution signals that confer to viruses the plasticity to evade neutralizing antibodies without altering viral entry mechanisms. The functions and structures of the two envelope glycoproteins of the Hepatitis C Virus (HCV), E1 and E2, are poorly described. Especially, how these two proteins mediate the HCV fusion process between the viral and the cell membrane remains elusive. Here, as a proof of concept, we aimed to take advantage of an original coevolution method recently developed to shed light on the HCV fusion mechanism. When first applied to the well-characterized Dengue Virus (DENV) envelope glycoproteins, coevolution analysis was able to predict important structural features and rearrangements of these viral protein complexes. When applied to HCV E1E2, computational coevolution analysis predicted that E1 and E2 refold interdependently during fusion through rearrangements of the E2 Back Layer (BL). Consistently, a soluble BL-derived polypeptide inhibited HCV infection of hepatoma cell lines, primary human hepatocytes and humanized liver mice. We showed that this polypeptide specifically inhibited HCV fusogenic rearrangements, hence supporting the critical role of this domain during HCV fusion. By combining coevolution analysis and in vitro assays, we also uncovered functionally-significant coevolving signals between E1 and E2 BL/Stem regions that govern HCV fusion, demonstrating the accuracy of our coevolution predictions. Altogether, our work shed light on important structural features of the HCV fusion mechanism and contributes to advance our functional understanding of this process. This study also provides an important proof of concept that coevolution can be employed to explore viral protein mediated-processes, and can guide the development of innovative translational strategies against challenging human-tropic viruses. PMID:29505618

An integrated modeling framework for exploring flow regime and water quality changes with increasing biofuel crop production in the U.S. Corn Belt

NASA Astrophysics Data System (ADS)

Yaeger, Mary A.; Housh, Mashor; Cai, Ximing; Sivapalan, Murugesu

2014-12-01

To better address the dynamic interactions between human and hydrologic systems, we develop an integrated modeling framework that employs a System of Systems optimization model to emulate human development decisions which are then incorporated into a watershed model to estimate the resulting hydrologic impacts. The two models are run interactively to simulate the coevolution of coupled human-nature systems, such that reciprocal feedbacks between hydrologic processes and human decisions (i.e., human impacts on critical low flows and hydrologic impacts on human decisions on land and water use) can be assessed. The framework is applied to a Midwestern U.S. agricultural watershed, in the context of proposed biofuels development. This operation is illustrated by projecting three possible future coevolution trajectories, two of which use dedicated biofuel crops to reduce annual watershed nitrate export while meeting ethanol production targets. Imposition of a primary external driver (biofuel mandate) combined with different secondary drivers (water quality targets) results in highly nonlinear and multiscale responses of both the human and hydrologic systems, including multiple tradeoffs, impacting the future coevolution of the system in complex, heterogeneous ways. The strength of the hydrologic response is sensitive to the magnitude of the secondary driver; 45% nitrate reduction target leads to noticeable impacts at the outlet, while a 30% reduction leads to noticeable impacts that are mainly local. The local responses are conditioned by previous human-hydrologic modifications and their spatial relationship to the new biofuel development, highlighting the importance of past coevolutionary history in predicting future trajectories of change.

Collective evolution of cyanobacteria and cyanophages mediated by horizontal gene transfer

NASA Astrophysics Data System (ADS)

Shih, Hong-Yan; Rogers, Tim; Goldenfeld, Nigel

We describe a model for how antagonistic predator-prey coevolution can lead to mutualistic adaptation to an environment, as a result of horizontal gene transfer. Our model is a simple description of ecosystems such as marine cyanobacteria and their predator cyanophages, which carry photosynthesis genes. These genes evolve more rapidly in the virosphere than the bacterial pan-genome, and thus the bacterial population could potentially benefit from phage predation. By modeling both the barrier to predation and horizontal gene transfer, we study this balance between individual sacrifice and collective benefits. The outcome is an emergent mutualistic coevolution of improved photosynthesis capability, benefiting both bacteria and phage. This form of multi-level selection can contribute to niche stratification in the cyanobacteria-phage ecosystem. This work is supported in part by a cooperative agreement with NASA, Grant NNA13AA91A/A0018.

Mechanisms and Evidence of Genital Coevolution: The Roles of Natural Selection, Mate Choice, and Sexual Conflict.

PubMed

Brennan, Patricia L R; Prum, Richard O

2015-07-01

Genital coevolution between the sexes is expected to be common because of the direct interaction between male and female genitalia during copulation. Here we review the diverse mechanisms of genital coevolution that include natural selection, female mate choice, male-male competition, and how their interactions generate sexual conflict that can lead to sexually antagonistic coevolution. Natural selection on genital morphology will result in size coevolution to allow for copulation to be mechanically possible, even as other features of genitalia may reflect the action of other mechanisms of selection. Genital coevolution is explicitly predicted by at least three mechanisms of genital evolution: lock and key to prevent hybridization, female choice, and sexual conflict. Although some good examples exist in support of each of these mechanisms, more data on quantitative female genital variation and studies of functional morphology during copulation are needed to understand more general patterns. A combination of different approaches is required to continue to advance our understanding of genital coevolution. Knowledge of the ecology and behavior of the studied species combined with functional morphology, quantitative morphological tools, experimental manipulation, and experimental evolution have been provided in the best-studied species, all of which are invertebrates. Therefore, attention to vertebrates in any of these areas is badly needed. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Accurate Simulation and Detection of Coevolution Signals in Multiple Sequence Alignments

PubMed Central

Ackerman, Sharon H.; Tillier, Elisabeth R.; Gatti, Domenico L.

2012-01-01

Background While the conserved positions of a multiple sequence alignment (MSA) are clearly of interest, non-conserved positions can also be important because, for example, destabilizing effects at one position can be compensated by stabilizing effects at another position. Different methods have been developed to recognize the evolutionary relationship between amino acid sites, and to disentangle functional/structural dependencies from historical/phylogenetic ones. Methodology/Principal Findings We have used two complementary approaches to test the efficacy of these methods. In the first approach, we have used a new program, MSAvolve, for the in silico evolution of MSAs, which records a detailed history of all covarying positions, and builds a global coevolution matrix as the accumulated sum of individual matrices for the positions forced to co-vary, the recombinant coevolution, and the stochastic coevolution. We have simulated over 1600 MSAs for 8 protein families, which reflect sequences of different sizes and proteins with widely different functions. The calculated coevolution matrices were compared with the coevolution matrices obtained for the same evolved MSAs with different coevolution detection methods. In a second approach we have evaluated the capacity of the different methods to predict close contacts in the representative X-ray structures of an additional 150 protein families using only experimental MSAs. Conclusions/Significance Methods based on the identification of global correlations between pairs were found to be generally superior to methods based only on local correlations in their capacity to identify coevolving residues using either simulated or experimental MSAs. However, the significant variability in the performance of different methods with different proteins suggests that the simulation of MSAs that replicate the statistical properties of the experimental MSA can be a valuable tool to identify the coevolution detection method that is most effective in each case. PMID:23091608

New Measurement for Correlation of Co-evolution Relationship of Subsequences in Protein.

PubMed

Gao, Hongyun; Yu, Xiaoqing; Dou, Yongchao; Wang, Jun

2015-12-01

Many computational tools have been developed to measure the protein residues co-evolution. Most of them only focus on co-evolution for pairwise residues in a protein sequence. However, number of residues participate in co-evolution might be multiple. And some co-evolved residues are clustered in several distinct regions in primary structure. Therefore, the co-evolution among the adjacent residues and the correlation between the distinct regions offer insights into function and evolution of the protein and residues. Subsequence is used to represent the adjacent multiple residues in one distinct region. In the paper, co-evolution relationship in each subsequence is represented by mutual information matrix (MIM). Then, Pearson's correlation coefficient: R value is developed to measure the similarity correlation of two MIMs. MSAs from Catalytic Data Base (Catalytic Site Atlas, CSA) are used for testing. R value characterizes a specific class of residues. In contrast to individual pairwise co-evolved residues, adjacent residues without high individual MI values are found since the co-evolved relationship among them is similar to that among another set of adjacent residues. These subsequences possess some flexibility in the composition of side chains, such as the catalyzed environment.

Wing patterning genes and coevolution of Müllerian mimicry in Heliconius butterflies: Support from phylogeography, cophylogeny, and divergence times.

PubMed

Hoyal Cuthill, Jennifer F; Charleston, Michael

2015-12-01

Examples of long-term coevolution are rare among free-living organisms. Müllerian mimicry in Heliconius butterflies had been suggested as a key example of coevolution by early genetic studies. However, research over the last two decades has been dominated by the idea that the best-studied comimics, H. erato and H. melpomene, did not coevolve at all. Recently sequenced genes associated with wing color pattern phenotype offer a new opportunity to resolve this controversy. Here, we test the hypothesis of coevolution between H. erato and H. melpomene using Bayesian multilocus analysis of five color pattern genes and five neutral genetic markers. We first explore the extent of phylogenetic agreement versus conflict between the different genes. Coevolution is then tested against three aspects of the mimicry diversifications: phylogenetic branching patterns, divergence times, and, for the first time, phylogeographic histories. We show that all three lines of evidence are compatible with strict coevolution of the diverse mimicry wing patterns, contrary to some recent suggestions. Instead, these findings tally with a coevolutionary diversification driven primarily by the ecological force of Müllerian mimicry. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking

PubMed Central

Madaoui, Hocine; Guerois, Raphaël

2008-01-01

Protein surfaces are under significant selection pressure to maintain interactions with their partners throughout evolution. Capturing how selection pressure acts at the interfaces of protein–protein complexes is a fundamental issue with high interest for the structural prediction of macromolecular assemblies. We tackled this issue under the assumption that, throughout evolution, mutations should minimally disrupt the physicochemical compatibility between specific clusters of interacting residues. This constraint drove the development of the so-called Surface COmplementarity Trace in Complex History score (SCOTCH), which was found to discriminate with high efficiency the structure of biological complexes. SCOTCH performances were assessed not only with respect to other evolution-based approaches, such as conservation and coevolution analyses, but also with respect to statistically based scoring methods. Validated on a set of 129 complexes of known structure exhibiting both permanent and transient intermolecular interactions, SCOTCH appears as a robust strategy to guide the prediction of protein–protein complex structures. Of particular interest, it also provides a basic framework to efficiently track how protein surfaces could evolve while keeping their partners in contact. PMID:18511568

The causes of variation in the presence of genetic covariance between sexual traits and preferences.

PubMed

Fowler-Finn, Kasey D; Rodríguez, Rafael L

2016-05-01

Mating traits and mate preferences often show patterns of tight correspondence across populations and species. These patterns of apparent coevolution may result from a genetic association between traits and preferences (i.e. trait-preference genetic covariance). We review the literature on trait-preference covariance to determine its prevalence and potential biological relevance. Of the 43 studies we identified, a surprising 63% detected covariance. We test multiple hypotheses for factors that may influence the likelihood of detecting this covariance. The main predictor was the presence of genetic variation in mate preferences, which is one of the three main conditions required for the establishment of covariance. In fact, 89% of the nine studies where heritability of preference was high detected covariance. Variables pertaining to the experimental methods and type of traits involved in different studies did not greatly influence the detection of trait-preference covariance. Trait-preference genetic covariance appears to be widespread and therefore represents an important and currently underappreciated factor in the coevolution of traits and preferences. © 2015 Cambridge Philosophical Society.

Coevolution of parental investment and sexually selected traits drives sex-role divergence.

PubMed

Fromhage, Lutz; Jennions, Michael D

2016-08-18

Sex-role evolution theory attempts to explain the origin and direction of male-female differences. A fundamental question is why anisogamy, the difference in gamete size that defines the sexes, has repeatedly led to large differences in subsequent parental care. Here we construct models to confirm predictions that individuals benefit less from caring when they face stronger sexual selection and/or lower certainty of parentage. However, we overturn the widely cited claim that a negative feedback between the operational sex ratio and the opportunity cost of care selects for egalitarian sex roles. We further argue that our model does not predict any effect of the adult sex ratio (ASR) that is independent of the source of ASR variation. Finally, to increase realism and unify earlier models, we allow for coevolution between parental investment and investment in sexually selected traits. Our model confirms that small initial differences in parental investment tend to increase due to positive evolutionary feedback, formally supporting long-standing, but unsubstantiated, verbal arguments.

Coevolution of parental investment and sexually selected traits drives sex-role divergence

PubMed Central

Fromhage, Lutz; Jennions, Michael D.

2016-01-01

Sex-role evolution theory attempts to explain the origin and direction of male–female differences. A fundamental question is why anisogamy, the difference in gamete size that defines the sexes, has repeatedly led to large differences in subsequent parental care. Here we construct models to confirm predictions that individuals benefit less from caring when they face stronger sexual selection and/or lower certainty of parentage. However, we overturn the widely cited claim that a negative feedback between the operational sex ratio and the opportunity cost of care selects for egalitarian sex roles. We further argue that our model does not predict any effect of the adult sex ratio (ASR) that is independent of the source of ASR variation. Finally, to increase realism and unify earlier models, we allow for coevolution between parental investment and investment in sexually selected traits. Our model confirms that small initial differences in parental investment tend to increase due to positive evolutionary feedback, formally supporting long-standing, but unsubstantiated, verbal arguments. PMID:27535478

Solar radiation and landscape evolution: co-evolution of topography, vegetation, and erosion rates in a semi-arid ecosystem

NASA Astrophysics Data System (ADS)

Istanbulluoglu, Erkan; Yetemen, Omer

2016-04-01

In this study CHILD landscape evolution model (LEM) is used to study the role of solar radiation on the co-evolution of landscape morphology, vegetation patterns, and erosion rates in a central New Mexico catchment. In the study site north facing slopes (NFS) are characterized by steep diffusion-dominated planar hillslopes covered by co-exiting juniper pine and grass vegetation. South facing slopes (SFS) are characterized by shallow slopes and covered by sparse shrub vegetation. Measured short-term and Holocene-averaged erosion rates show higher soil loss on SFS than NFS. In this study CHILD LEM is first confirmed with ecohydrologic field data and used to systematically examine the co-evolution of topography, vegetation pattern, and erosion rates. Aspect- and network-control are identified as the two main topographic drivers of soil moisture and vegetation organization on the landscape. Landscape-scale and long-term implications of solar radiation driven ecohdrologic patterns emerged in modeled landscape: NFS supported denser vegetation cover and became steeper and planar, while on SFS vegetation grew sparser and slopes declined with more fluvial activity. At the landscape scale, these differential erosion processes led to asymmetric development of catchment forms, consistent with regional observations. While the general patterns of vegetation and topography were reproduced by the model using a stationary representation of the current climate, the observed differential Holocene erosion rates were captured by the model only when cyclic climate is used. This suggests sensitivity of Holocene erosion rates to long-term climate fluctuations.

Learning bias, cultural evolution of language, and the biological evolution of the language faculty.

PubMed

Smith, Kenny

2011-04-01

The biases of individual language learners act to determine the learnability and cultural stability of languages: learners come to the language learning task with biases which make certain linguistic systems easier to acquire than others. These biases are repeatedly applied during the process of language transmission, and consequently should effect the types of languages we see in human populations. Understanding the cultural evolutionary consequences of particular learning biases is therefore central to understanding the link between language learning in individuals and language universals, common structural properties shared by all the world’s languages. This paper reviews a range of models and experimental studies which show that weak biases in individual learners can have strong effects on the structure of socially learned systems such as language, suggesting that strong universal tendencies in language structure do not require us to postulate strong underlying biases or constraints on language learning. Furthermore, understanding the relationship between learner biases and language design has implications for theories of the evolution of those learning biases: models of gene-culture coevolution suggest that, in situations where a cultural dynamic mediates between properties of individual learners and properties of language in this way, biological evolution is unlikely to lead to the emergence of strong constraints on learning.

Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system

NASA Astrophysics Data System (ADS)

Han, Pu; Niestemski, Liang Ren; Barrick, Jeffrey E.; Deem, Michael W.

2013-04-01

Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences, called ‘spacers’ into its CRISPR system. Spacers in the CRISPR system provide a record of the history of bacteria and phage coevolution. We use a physical model to study the dynamics of this coevolution as it evolves stochastically over time. We focus on the impact of mutation and recombination on bacteria and phage evolution and evasion. We discuss the effect of different spacer deletion mechanisms on the coevolutionary dynamics. We make predictions about bacteria and phage population growth, spacer diversity within the CRISPR locus, and spacer protection against the phage population.

Extremal Optimization: Methods Derived from Co-Evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boettcher, S.; Percus, A.G.

1999-07-13

We describe a general-purpose method for finding high-quality solutions to hard optimization problems, inspired by self-organized critical models of co-evolution such as the Bak-Sneppen model. The method, called Extremal Optimization, successively eliminates extremely undesirable components of sub-optimal solutions, rather than ''breeding'' better components. In contrast to Genetic Algorithms which operate on an entire ''gene-pool'' of possible solutions, Extremal Optimization improves on a single candidate solution by treating each of its components as species co-evolving according to Darwinian principles. Unlike Simulated Annealing, its non-equilibrium approach effects an algorithm requiring few parameters to tune. With only one adjustable parameter, its performance provesmore » competitive with, and often superior to, more elaborate stochastic optimization procedures. We demonstrate it here on two classic hard optimization problems: graph partitioning and the traveling salesman problem.« less

Towards first principle medical diagnostics: on the importance of disease-disease and sign-sign interactions

NASA Astrophysics Data System (ADS)

Ramezanpour, Abolfazl; Mashaghi, Alireza

2017-07-01

A fundamental problem in medicine and biology is to assign states, e.g. healthy or diseased, to cells, organs or individuals. State assignment or making a diagnosis is often a nontrivial and challenging process and, with the advent of omics technologies, the diagnostic challenge is becoming more and more serious. The challenge lies not only in the increasing number of measured properties and dynamics of the system (e.g. cell or human body) but also in the co-evolution of multiple states and overlapping properties, and degeneracy of states. We develop, from first principles, a generic rational framework for state assignment in cell biology and medicine, and demonstrate its applicability with a few simple theoretical case studies from medical diagnostics. We show how disease-related statistical information can be used to build a comprehensive model that includes the relevant dependencies between clinical and laboratory findings (signs) and diseases. In particular, we include disease-disease and sign-sign interactions and study how one can infer the probability of a disease in a patient with given signs. We perform comparative analysis with simple benchmark models to check the performances of our models. We find that including interactions can significantly change the statistical importance of the signs and diseases. This first principles approach, as we show, facilitates the early diagnosis of disease by taking interactions into accounts, and enables the construction of consensus diagnostic flow charts. Additionally, we envision that our approach will find applications in systems biology, and in particular, in characterizing the phenome via the metabolome, the proteome, the transcriptome, and the genome.

The Landscape Evolution Observatory: a large-scale controllable infrastructure to study coupled Earth-surface processes

USGS Publications Warehouse

Pangle, Luke A.; DeLong, Stephen B.; Abramson, Nate; Adams, John; Barron-Gafford, Greg A.; Breshears, David D.; Brooks, Paul D.; Chorover, Jon; Dietrich, William E.; Dontsova, Katerina; Durcik, Matej; Espeleta, Javier; Ferré, T.P.A.; Ferriere, Regis; Henderson, Whitney; Hunt, Edward A.; Huxman, Travis E.; Millar, David; Murphy, Brendan; Niu, Guo-Yue; Pavao-Zuckerman, Mitch; Pelletier, Jon D.; Rasmussen, Craig; Ruiz, Joaquin; Saleska, Scott; Schaap, Marcel; Sibayan, Michael; Troch, Peter A.; Tuller, Markus; van Haren, Joost; Zeng, Xubin

2015-01-01

Zero-order drainage basins, and their constituent hillslopes, are the fundamental geomorphic unit comprising much of Earth's uplands. The convergent topography of these landscapes generates spatially variable substrate and moisture content, facilitating biological diversity and influencing how the landscape filters precipitation and sequesters atmospheric carbon dioxide. In light of these significant ecosystem services, refining our understanding of how these functions are affected by landscape evolution, weather variability, and long-term climate change is imperative. In this paper we introduce the Landscape Evolution Observatory (LEO): a large-scale controllable infrastructure consisting of three replicated artificial landscapes (each 330 m2 surface area) within the climate-controlled Biosphere 2 facility in Arizona, USA. At LEO, experimental manipulation of rainfall, air temperature, relative humidity, and wind speed are possible at unprecedented scale. The Landscape Evolution Observatory was designed as a community resource to advance understanding of how topography, physical and chemical properties of soil, and biological communities coevolve, and how this coevolution affects water, carbon, and energy cycles at multiple spatial scales. With well-defined boundary conditions and an extensive network of sensors and samplers, LEO enables an iterative scientific approach that includes numerical model development and virtual experimentation, physical experimentation, data analysis, and model refinement. We plan to engage the broader scientific community through public dissemination of data from LEO, collaborative experimental design, and community-based model development.

Co-evolution of transportation and land use : modeling historical dependencies in land use and transportation decision making.

DOT National Transportation Integrated Search

2009-11-01

The interaction between land use and transportation has long been the central issue in urban and regional planning. Models of such : interactions provide vital information to support many public policy decisions, such as land supply, infrastructure p...

Myxomatosis in Australia and Europe: a model for emerging infectious diseases.

PubMed

Kerr, Peter J

2012-03-01

Myxoma virus is a poxvirus naturally found in two American leporid (rabbit) species (Sylvilagus brasiliensis and Sylvilagus bachmani) in which it causes an innocuous localised cutaneous fibroma. However, in European rabbits (Oryctolagus cuniculus) the same virus causes the lethal disseminated disease myxomatosis. The introduction of myxoma virus into the European rabbit population in Australia in 1950 initiated the best known example of what happens when a novel pathogen jumps into a completely naïve new mammalian host species. The short generation time of the rabbit and their vast numbers in Australia meant evolution could be studied in real time. The carefully documented emergence of attenuated strains of virus that were more effectively transmitted by the mosquito vector and the subsequent selection of rabbits with genetic resistance to myxomatosis is the paradigm for pathogen virulence and host-pathogen coevolution. This natural experiment was repeated with the release of a separate strain of myxoma virus in France in 1952. The subsequent spread of the virus throughout Europe and its coevolution with the rabbit essentially paralleled what occurred in Australia. Detailed molecular studies on myxoma virus have dissected the role of virulence genes in the pathogenesis of myxomatosis and when combined with genomic data and reverse genetics should in future enable the understanding of the molecular evolution of the virus as it adapted to its new host. This review describes the natural history and evolution of myxoma virus together with the molecular biology and experimental pathogenesis studies that are informing our understanding of evolution of emerging diseases. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

Chasing the Patagonian sun: comparative thermal biology of Liolaemus lizards.

PubMed

Azócar, Débora Lina Moreno; Vanhooydonck, Bieke; Bonino, Marcelo F; Perotti, M Gabriela; Abdala, Cristian S; Schulte, James A; Cruz, Félix B

2013-04-01

The importance of the thermal environment for ectotherms and its relationship with thermal physiology and ecology is widely recognized. Several models have been proposed to explain the evolution of the thermal biology of ectotherms, but experimental studies have provided mixed support. Lizards from the Liolaemus goetschi group can be found along a wide latitudinal range across Argentina. The group is monophyletic and widely distributed, and therefore provides excellent opportunities to study the evolution of thermal biology. We studied thermal variables of 13 species of the L. goetschi group, in order to answer three questions. First, are aspects of the thermal biology of the L. goetschi group modelled by the environment or are they evolutionarily conservative? Second, have thermal characteristics of these animals co-evolved? And third, how do the patterns of co-evolution observed within the L. goetschi group compare to those in a taxonomically wider selection of species of Liolaemus? We collected data on 13 focal species and used species information of Liolaemus lizards available in the literature and additional data obtained by the authors. We tackled these questions using both conventional and phylogenetically based analyses. Our results show that lizards from the L. goetschi group and the genus Liolaemus in general vary in critical thermal minimum in relation to mean air temperature, and particularly the L. goetschi group shows that air temperature is associated with critical thermal range, as well as with body temperature. Although the effect of phylogeny cannot be ignored, our results indicate that these thermal biology aspects are modelled by cold environments of Patagonia, while other aspects (preferred body temperature and critical thermal maximum) are more conservative. We found evidence of co-evolutionary patterns between critical thermal minimum and preferred body temperature at both phylogenetic scales (the L. goetschi group and the extended sample of 68 Liolaemus species).

Autonomous Agent-Based Systems and Their Applications in Fluid Dynamics, Particle Separation, and Co-evolving Networks

NASA Astrophysics Data System (ADS)

Graeser, Oliver

This thesis comprises three parts, reporting research results in Fluid Dynamics (Part I), Particle Separation (Part II) and Co-evolving Networks (Part III). Part I deals with the simulation of fluid dynamics using the lattice-Boltzmann method. Microfluidic devices often feature two-dimensional, repetitive arrays. Flows through such devices are pressure-driven and confined by solid walls. We have defined new adaptive generalised periodic boundary conditions to represent the effects of outer solid walls, and are thus able to exploit the periodicity of the array by simulating the flow through one unit cell in lieu of the entire device. The so-calculated fully developed flow describes the flow through the entire array accurately, but with computational requirements that are reduced according to the dimensions of the array. Part II discusses the problem of separating macromolecules like proteins or DNA coils. The reliable separation of such molecules is a crucial task in molecular biology. The use of Brownian ratchets as mechanisms for the separation of such particles has been proposed and discussed during the last decade. Pressure-driven flows have so far been dismissed as possible driving forces for Brownian ratchets, as they do not generate ratchet asymmetry. We propose a microfluidic design that uses pressure-driven flows to create asymmetry and hence allows particle separation. The dependence of the asymmetry on various factors of the microfluidic geometry is discussed. We further exemplify the feasibility of our approach using Brownian dynamics simulations of particles of different sizes in such a device. The results show that ratchet-based particle separation using flows as the driving force is possible. Simulation results and ratchet theory predictions are in excellent agreement. Part III deals with the co-evolution of networks and dynamic models. A group of agents occupies the nodes of a network, which defines the relationship between these agents. The evolution of the agents is defined by the rules of the dynamic model and depends on the relationship between agents, i.e., the state of the network. In return, the evolution of the network depends on the state of the dynamic model. The concept is introduced through the adaptive SIS model. We show that the previously used criterion determining the critical infected fraction, i.e., the number of infected agents required to sustain the epidemic, is inappropriate for this model. We introduce a different criterion and show that the critical infected fraction so determined is in good agreement with results obtained by numerical simulations. We further discuss the concept of co-evolving dynamics using the Snowdrift Game as a model paradigm. Co-evolution occurs through agents cutting dissatisfied links and rewiring to other agents at random. The effect of co-evolution on the emergence of cooperation is discussed using a mean-field theory and numerical simulations. A transition between a connected and a disconnected, highly cooperative state of the system is observed, and explained using the mean-field model. Quantitative deviations regarding the level of cooperation in the disconnected regime can be fully resolved through an improved mean-field theory that includes the effect of random fluctuations into its model.

Memory-Based Multiagent Coevolution Modeling for Robust Moving Object Tracking

PubMed Central

Wang, Yanjiang; Qi, Yujuan; Li, Yongping

2013-01-01

The three-stage human brain memory model is incorporated into a multiagent coevolutionary process for finding the best match of the appearance of an object, and a memory-based multiagent coevolution algorithm for robust tracking the moving objects is presented in this paper. Each agent can remember, retrieve, or forget the appearance of the object through its own memory system by its own experience. A number of such memory-based agents are randomly distributed nearby the located object region and then mapped onto a 2D lattice-like environment for predicting the new location of the object by their coevolutionary behaviors, such as competition, recombination, and migration. Experimental results show that the proposed method can deal with large appearance changes and heavy occlusions when tracking a moving object. It can locate the correct object after the appearance changed or the occlusion recovered and outperforms the traditional particle filter-based tracking methods. PMID:23843739

Memory-based multiagent coevolution modeling for robust moving object tracking.

PubMed

Wang, Yanjiang; Qi, Yujuan; Li, Yongping

2013-01-01

The three-stage human brain memory model is incorporated into a multiagent coevolutionary process for finding the best match of the appearance of an object, and a memory-based multiagent coevolution algorithm for robust tracking the moving objects is presented in this paper. Each agent can remember, retrieve, or forget the appearance of the object through its own memory system by its own experience. A number of such memory-based agents are randomly distributed nearby the located object region and then mapped onto a 2D lattice-like environment for predicting the new location of the object by their coevolutionary behaviors, such as competition, recombination, and migration. Experimental results show that the proposed method can deal with large appearance changes and heavy occlusions when tracking a moving object. It can locate the correct object after the appearance changed or the occlusion recovered and outperforms the traditional particle filter-based tracking methods.

The hitchhiker's guide to altruism: gene-culture coevolution, and the internalization of norms.

PubMed

Gintis, Herbert

2003-02-21

An internal norm is a pattern of behavior enforced in part by internal sanctions, such as shame, guilt and loss of self-esteem, as opposed to purely external sanctions, such as material rewards and punishment. The ability to internalize norms is widespread among humans, although in some so-called "sociopaths", this capacity is diminished or lacking. Suppose there is one genetic locus that controls the capacity to internalize norms. This model shows that if an internal norm is fitness enhancing, then for plausible patterns of socialization, the allele for internalization of norms is evolutionarily stable. This framework can be used to model Herbert Simon's (1990) explanation of altruism, showing that altruistic norms can "hitchhike" on the general tendency of internal norms to be personally fitness-enhancing. A multi-level selection, gene-culture coevolution argument then explains why individually fitness-reducing internal norms are likely to be prosocial as opposed to socially harmful.

The coevolution of recognition and social behavior.

PubMed

Smead, Rory; Forber, Patrick

2016-05-26

Recognition of behavioral types can facilitate the evolution of cooperation by enabling altruistic behavior to be directed at other cooperators and withheld from defectors. While much is known about the tendency for recognition to promote cooperation, relatively little is known about whether such a capacity can coevolve with the social behavior it supports. Here we use evolutionary game theory and multi-population dynamics to model the coevolution of social behavior and recognition. We show that conditional harming behavior enables the evolution and stability of social recognition, whereas conditional helping leads to a deterioration of recognition ability. Expanding the model to include a complex game where both helping and harming interactions are possible, we find that conditional harming behavior can stabilize recognition, and thereby lead to the evolution of conditional helping. Our model identifies a novel hypothesis for the evolution of cooperation: conditional harm may have coevolved with recognition first, thereby helping to establish the mechanisms necessary for the evolution of cooperation.

The coevolution of recognition and social behavior

PubMed Central

Smead, Rory; Forber, Patrick

2016-01-01

Recognition of behavioral types can facilitate the evolution of cooperation by enabling altruistic behavior to be directed at other cooperators and withheld from defectors. While much is known about the tendency for recognition to promote cooperation, relatively little is known about whether such a capacity can coevolve with the social behavior it supports. Here we use evolutionary game theory and multi-population dynamics to model the coevolution of social behavior and recognition. We show that conditional harming behavior enables the evolution and stability of social recognition, whereas conditional helping leads to a deterioration of recognition ability. Expanding the model to include a complex game where both helping and harming interactions are possible, we find that conditional harming behavior can stabilize recognition, and thereby lead to the evolution of conditional helping. Our model identifies a novel hypothesis for the evolution of cooperation: conditional harm may have coevolved with recognition first, thereby helping to establish the mechanisms necessary for the evolution of cooperation. PMID:27225673

Mainstreaming Caenorhabditis elegans in experimental evolution.

PubMed

Gray, Jeremy C; Cutter, Asher D

2014-03-07

Experimental evolution provides a powerful manipulative tool for probing evolutionary process and mechanism. As this approach to hypothesis testing has taken purchase in biology, so too has the number of experimental systems that use it, each with its own unique strengths and weaknesses. The depth of biological knowledge about Caenorhabditis nematodes, combined with their laboratory tractability, positions them well for exploiting experimental evolution in animal systems to understand deep questions in evolution and ecology, as well as in molecular genetics and systems biology. To date, Caenorhabditis elegans and related species have proved themselves in experimental evolution studies of the process of mutation, host-pathogen coevolution, mating system evolution and life-history theory. Yet these organisms are not broadly recognized for their utility for evolution experiments and remain underexploited. Here, we outline this experimental evolution work undertaken so far in Caenorhabditis, detail simple methodological tricks that can be exploited and identify research areas that are ripe for future discovery.

Amino acid positions subject to multiple coevolutionary constraints can be robustly identified by their eigenvector network centrality scores.

PubMed

Parente, Daniel J; Ray, J Christian J; Swint-Kruse, Liskin

2015-12-01

As proteins evolve, amino acid positions key to protein structure or function are subject to mutational constraints. These positions can be detected by analyzing sequence families for amino acid conservation or for coevolution between pairs of positions. Coevolutionary scores are usually rank-ordered and thresholded to reveal the top pairwise scores, but they also can be treated as weighted networks. Here, we used network analyses to bypass a major complication of coevolution studies: For a given sequence alignment, alternative algorithms usually identify different, top pairwise scores. We reconciled results from five commonly-used, mathematically divergent algorithms (ELSC, McBASC, OMES, SCA, and ZNMI), using the LacI/GalR and 1,6-bisphosphate aldolase protein families as models. Calculations used unthresholded coevolution scores from which column-specific properties such as sequence entropy and random noise were subtracted; "central" positions were identified by calculating various network centrality scores. When compared among algorithms, network centrality methods, particularly eigenvector centrality, showed markedly better agreement than comparisons of the top pairwise scores. Positions with large centrality scores occurred at key structural locations and/or were functionally sensitive to mutations. Further, the top central positions often differed from those with top pairwise coevolution scores: instead of a few strong scores, central positions often had multiple, moderate scores. We conclude that eigenvector centrality calculations reveal a robust evolutionary pattern of constraints-detectable by divergent algorithms--that occur at key protein locations. Finally, we discuss the fact that multiple patterns coexist in evolutionary data that, together, give rise to emergent protein functions. © 2015 Wiley Periodicals, Inc.

Sexual conflict over the maintenance of sex: effects of sexually antagonistic coevolution for reproductive isolation of parthenogenesis.

PubMed

Kawatsu, Kazutaka

2013-01-01

Sexual reproduction involves many costs. Therefore, females acquiring a capacity for parthenogenetic (or asexual) reproduction will gain a reproductive advantage over obligately sexual females. In contrast, for males, any trait coercing parthenogens into sexual reproduction (male coercion) increases their fitness and should be under positive selection because parthenogenesis deprives them of their genetic contribution to future generations. Surprisingly, although such sexual conflict is a possible outcome whenever reproductive isolation is incomplete between parthenogens and the sexual ancestors, it has not been given much attention in the studies of the maintenance of sex. Using two mathematical models, I show here that the evolution of male coercion substantially favours the maintenance of sex even though a female barrier against the coercion can evolve. First, the model based on adaptive-dynamics theory demonstrates that the resultant antagonistic coevolution between male coercion and a female barrier fundamentally ends in either the prevalence of sex or the co-occurrence of two reproductive modes. This is because the coevolution between the two traits additionally involves sex-ratio selection, that is, an increase in parthenogenetic reproduction leads to a female-biased population sex ratio, which will enhance reproductive success of more coercive males and directly promotes the evolution of the coercion among males. Therefore, as shown by the individual-based model, the establishment of obligate parthenogenesis in the population requires the simultaneous evolution of strong reproductive isolation between males and parthenogens. These findings should shed light on the interspecific diversity of reproductive modes as well as help to explain the prevalence of sexual reproduction.

Sexual Conflict over the Maintenance of Sex: Effects of Sexually Antagonistic Coevolution for Reproductive Isolation of Parthenogenesis

PubMed Central

Kawatsu, Kazutaka

2013-01-01

Sexual reproduction involves many costs. Therefore, females acquiring a capacity for parthenogenetic (or asexual) reproduction will gain a reproductive advantage over obligately sexual females. In contrast, for males, any trait coercing parthenogens into sexual reproduction (male coercion) increases their fitness and should be under positive selection because parthenogenesis deprives them of their genetic contribution to future generations. Surprisingly, although such sexual conflict is a possible outcome whenever reproductive isolation is incomplete between parthenogens and the sexual ancestors, it has not been given much attention in the studies of the maintenance of sex. Using two mathematical models, I show here that the evolution of male coercion substantially favours the maintenance of sex even though a female barrier against the coercion can evolve. First, the model based on adaptive-dynamics theory demonstrates that the resultant antagonistic coevolution between male coercion and a female barrier fundamentally ends in either the prevalence of sex or the co-occurrence of two reproductive modes. This is because the coevolution between the two traits additionally involves sex-ratio selection, that is, an increase in parthenogenetic reproduction leads to a female-biased population sex ratio, which will enhance reproductive success of more coercive males and directly promotes the evolution of the coercion among males. Therefore, as shown by the individual-based model, the establishment of obligate parthenogenesis in the population requires the simultaneous evolution of strong reproductive isolation between males and parthenogens. These findings should shed light on the interspecific diversity of reproductive modes as well as help to explain the prevalence of sexual reproduction. PMID:23469150

Co-evolution of electric and telecommunications networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rivkin, S.R.

1998-05-01

There are potentially significant societal benefits in co-evolution between electricity and telecommunications in the areas of common infrastructure, accelerated deployment of distributed energy, tighter integration of information flow for energy management and distribution, and improved customer care. With due regard for natural processes that are more potent than any regulation and more real than any ideology, the gains from co-evolution would far outweigh the attenuated and speculative savings from restructuring of electricity that is too simplistic.

Co-evolution with chicken class I genes.

PubMed

Kaufman, Jim

2015-09-01

The concept of co-evolution (or co-adaptation) has a long history, but application at molecular levels (e.g., 'supergenes' in genetics) is more recent, with a consensus definition still developing. One interesting example is the chicken major histocompatibility complex (MHC). In contrast to typical mammals that have many class I and class I-like genes, only two classical class I genes, two CD1 genes and some non-classical Rfp-Y genes are known in chicken, and all are found on the microchromosome that bears the MHC. Rarity of recombination between the closely linked and polymorphic genes encoding classical class I and TAPs allows co-evolution, leading to a single dominantly expressed class I molecule in each MHC haplotype, with strong functional consequences in terms of resistance to infectious pathogens. Chicken tapasin is highly polymorphic, but co-evolution with TAP and class I genes remains unclear. T-cell receptors, natural killer (NK) cell receptors, and CD8 co-receptor genes are found on non-MHC chromosomes, with some evidence for co-evolution of surface residues and number of genes along the avian and mammalian lineages. Over even longer periods, co-evolution has been invoked to explain how the adaptive immune system of jawed vertebrates arose from closely linked receptor, ligand, and antigen-processing genes in the primordial MHC. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Darwin and the linguists: the coevolution of mind and language, part 2. The language-thought relationship.

PubMed

Alter, Stephen G

2008-03-01

This paper examines Charles Darwin's idea that language-use and humanity's unique cognitive abilities reinforced each other's evolutionary emergence-an idea Darwin sketched in his early notebooks, set forth in his Descent of man (1871), and qualified in Descent's second (1874) edition. Darwin understood this coevolution process in essentially Lockean terms, based on John Locke's hints about the way language shapes thinking itself. Ironically, the linguist Friedrich Max Müller attacked Darwin's human descent theory by invoking a similar thesis, the German romantic notion of an identity between language and thought. Although Darwin avoided outright contradiction, when he came to defend himself against Müller's attacks, he undercut some of his own argumentation in favor of the coevolution idea. That is, he found it difficult to counter Müller's argument while also making a case for coevolution. Darwin's efforts in this area were further complicated by British and American writers who held a naturalistic view of speech origins yet still taught that language had been invented by fully evolved homo sapiens, thus denying coevolution.

Mapping proteins in the presence of paralogs using units of coevolution

PubMed Central

2013-01-01

Background We study the problem of mapping proteins between two protein families in the presence of paralogs. This problem occurs as a difficult subproblem in coevolution-based computational approaches for protein-protein interaction prediction. Results Similar to prior approaches, our method is based on the idea that coevolution implies equal rates of sequence evolution among the interacting proteins, and we provide a first attempt to quantify this notion in a formal statistical manner. We call the units that are central to this quantification scheme the units of coevolution. A unit consists of two mapped protein pairs and its score quantifies the coevolution of the pairs. This quantification allows us to provide a maximum likelihood formulation of the paralog mapping problem and to cast it into a binary quadratic programming formulation. Conclusion CUPID, our software tool based on a Lagrangian relaxation of this formulation, makes it, for the first time, possible to compute state-of-the-art quality pairings in a few minutes of runtime. In summary, we suggest a novel alternative to the earlier available approaches, which is statistically sound and computationally feasible. PMID:24564758

Modeling viral coevolution: HIV multi-clonal persistence and competition dynamics

NASA Astrophysics Data System (ADS)

Bagnoli, F.; Liò, P.; Sguanci, L.

2006-07-01

The coexistence of different viral strains (quasispecies) within the same host are nowadays observed for a growing number of viruses, most notably HIV, Marburg and Ebola, but the conditions for the formation and survival of new strains have not yet been understood. We present a model of HIV quasispecies competition, which describes the conditions of viral quasispecies coexistence under different immune system conditions. Our model incorporates both T and B cells responses, and we show that the role of B cells is important and additive to that of T cells. Simulations of coinfection (simultaneous infection) and superinfection (delayed secondary infection) scenarios in the early stages (days) and in the late stages of the infection (years) are in agreement with emerging molecular biology findings. The immune response induces a competition among similar phenotypes, leading to differentiation (quasispeciation), escape dynamics and complex oscillations of viral strain abundance. We found that the quasispecies dynamics after superinfection or coinfection has time scales of several months and becomes even slower when the immune system response is weak. Our model represents a general framework to study the speed and distribution of HIV quasispecies during disease progression, vaccination and therapy.

Viruses and mobile elements as drivers of evolutionary transitions

PubMed Central

2016-01-01

The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of ‘public goods’. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host–parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431520

Viruses and mobile elements as drivers of evolutionary transitions.

PubMed

Koonin, Eugene V

2016-08-19

The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of 'public goods'. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host-parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions.This article is part of the themed issue 'The major synthetic evolutionary transitions'. © 2016 The Authors.

Coevolution in host-parasite systems: behavioural strategies of slave-making ants and their hosts.

PubMed

Foitzik, S; DeHeer, C J; Hunjan, D N; Herbers, J M

2001-06-07

Recently, avian brood parasites and their hosts have emerged as model systems for the study of host-parasite coevolution. However, empirical studies of the highly analogous social parasites, which use the workers of another eusocial species to raise their own young, have never explicitly examined the dynamics of these systems from a coevolutionary perspective. Here, we demonstrate interpopulational variation in behavioural interactions between a socially parasitic slave-maker ant and its host that is consistent with the expectations of host-parasite coevolution. Parasite pressure, as inferred by the size, abundance and raiding frequency of Protomognathus americanus colonies, was highest in a New York population of the host Leptothorax longispinosus and lowest in a West Virginia population. As host-parasite coevolutionary theory would predict, we found that the slave-makers and the hosts from New York were more effective at raiding and defending against raiders, respectively, than were conspecifics from the West Virginia population. Some of these variations in efficacy were brought about by apparently simple shifts in behaviour. These results demonstrate that defence mechanisms against social parasites can evolve, and they give the first indications of the existence of a coevolutionary arms race between a social parasite and its host.

A review of the latest concepts in molecular plant pathology and applications to potato breeding

USDA-ARS?s Scientific Manuscript database

Co-evolution between pathogens and plants has led to the development of a range of constitutive and inducible resistance mechanisms that help plants survive pathogen attack. Different models have been proposed to describe the plant immune system. The most popular current model indicates that plants ...

The coevolution of partner switching and strategy updating in non-excludable public goods game

NASA Astrophysics Data System (ADS)

Li, Yixiao; Shen, Bin

2013-10-01

Spatial public goods game is a popular metaphor to model the dilemma of collective cooperation on graphs, yet the non-excludable property of public goods has seldom been considered in previous models. Based upon a coevolutionary model where agents play public goods games and adjust their partnerships, the present model incorporates the non-excludable property of public goods: agents are able to adjust their participation in the games hosted by others, whereas they cannot exclude others from their own games. In the coevolution, a directed and dynamical network which represents partnerships among autonomous agents is evolved. We find that non-excludable property counteracts the positive effect of partner switching, i.e., the equilibrium level of cooperation is lower than that in the situation of excludable public goods game. Therefore, we study the effect of individual punishment that cooperative agents pay a personal cost to decrease benefits of those defective neighbors who participate in their hosted games. It is found that the cooperation level in the whole population is heightened in the presence of such a costly behavior.

An entropic model of Gaia.

PubMed

Arthur, R; Nicholson, A

2017-10-07

We modify the Tangled Nature Model of Christensen et. al. (2002) so that the agents affect the carrying capacity. This leads to a model of species-environment co-evolution where the system tends to have a larger carrying capacity with life than without. We discuss the model as an example of an entropic hierarchy and some implications for Gaia theory. Copyright © 2017 Elsevier Ltd. All rights reserved.

New thinking: the evolution of human cognition

PubMed Central

Heyes, Cecilia

2012-01-01

Humans are animals that specialize in thinking and knowing, and our extraordinary cognitive abilities have transformed every aspect of our lives. In contrast to our chimpanzee cousins and Stone Age ancestors, we are complex political, economic, scientific and artistic creatures, living in a vast range of habitats, many of which are our own creation. Research on the evolution of human cognition asks what types of thinking make us such peculiar animals, and how they have been generated by evolutionary processes. New research in this field looks deeper into the evolutionary history of human cognition, and adopts a more multi-disciplinary approach than earlier ‘Evolutionary Psychology’. It is informed by comparisons between humans and a range of primate and non-primate species, and integrates findings from anthropology, archaeology, economics, evolutionary biology, neuroscience, philosophy and psychology. Using these methods, recent research reveals profound commonalities, as well striking differences, between human and non-human minds, and suggests that the evolution of human cognition has been much more gradual and incremental than previously assumed. It accords crucial roles to cultural evolution, techno-social co-evolution and gene–culture co-evolution. These have produced domain-general developmental processes with extraordinary power—power that makes human cognition, and human lives, unique. PMID:22734052

New thinking: the evolution of human cognition.

PubMed

Heyes, Cecilia

2012-08-05

Humans are animals that specialize in thinking and knowing, and our extraordinary cognitive abilities have transformed every aspect of our lives. In contrast to our chimpanzee cousins and Stone Age ancestors, we are complex political, economic, scientific and artistic creatures, living in a vast range of habitats, many of which are our own creation. Research on the evolution of human cognition asks what types of thinking make us such peculiar animals, and how they have been generated by evolutionary processes. New research in this field looks deeper into the evolutionary history of human cognition, and adopts a more multi-disciplinary approach than earlier 'Evolutionary Psychology'. It is informed by comparisons between humans and a range of primate and non-primate species, and integrates findings from anthropology, archaeology, economics, evolutionary biology, neuroscience, philosophy and psychology. Using these methods, recent research reveals profound commonalities, as well striking differences, between human and non-human minds, and suggests that the evolution of human cognition has been much more gradual and incremental than previously assumed. It accords crucial roles to cultural evolution, techno-social co-evolution and gene-culture co-evolution. These have produced domain-general developmental processes with extraordinary power-power that makes human cognition, and human lives, unique.

Controlled experiments of hillslope co-evolution at the Biosphere 2 Landscape Evolution Observatory: toward prediction of coupled hydrological, biogeochemical, and ecological change

NASA Astrophysics Data System (ADS)

Volkmann, T. H. M.; Sengupta, A.; Pangle, L.; Abramson, N.; Barron-Gafford, G.; Breshears, D. D.; Bugaj, A.; Chorover, J.; Dontsova, K.; Durcik, M.; Ferre, T. P. A.; Harman, C. J.; Hunt, E.; Huxman, T. E.; Kim, M.; Maier, R. M.; Matos, K.; Alves Meira Neto, A.; Meredith, L. K.; Monson, R. K.; Niu, G. Y.; Pelletier, J. D.; Rasmussen, C.; Ruiz, J.; Saleska, S. R.; Schaap, M. G.; Sibayan, M.; Tuller, M.; Van Haren, J. L. M.; Wang, Y.; Zeng, X.; Troch, P. A.

2017-12-01

Understanding the process interactions and feedbacks among water, microbes, plants, and porous geological media is crucial for improving predictions of the response of Earth's critical zone to future climatic conditions. However, the integrated co-evolution of landscapes under change is notoriously difficult to investigate. Laboratory studies are typically limited in spatial and temporal scale, while field studies lack observational density and control. To bridge the gap between controlled lab and uncontrolled field studies, the University of Arizona - Biosphere 2 built a macrocosm experiment of unprecedented scale: the Landscape Evolution Observatory (LEO). LEO consists of three replicated, 330-m2 hillslope landscapes inside a 5000-m2 environmentally controlled facility. The engineered landscapes contain 1-m depth of basaltic tephra ground to homogenous loamy sand that will undergo physical, chemical, and mineralogical changes over many years. Each landscape contains a dense sensor network capable of resolving water, carbon, and energy cycling processes at sub-meter to whole-landscape scale. Embedded sampling devices allow for quantification of biogeochemical processes, and facilitate the use of chemical tracers applied with the artificial rainfall. LEO is now fully operational and intensive forcing experiments have been launched. While operating the massive infrastructure poses significant challenges, LEO has demonstrated the capacity of tracking multi-scale matter and energy fluxes at a level of detail impossible in field experiments. Initial sensor, sampler, and restricted soil coring data are already providing insights into the tight linkages between water flow, weathering, and (micro-) biological community development during incipient landscape evolution. Over the years to come, these interacting processes are anticipated to drive the model systems to increasingly complex states, potentially perturbed by changes in climatic forcing. By intensively monitoring the evolutionary trajectory, integrating data with models, and fostering community-wide collaborations, we envision that emergent landscape structures and functions can be linked and significant progress can be made toward predicting the coupled hydro-biogeochemical and ecological responses to global change.

A coupled modeling framework of the co-evolution of humans and water: case study of Tarim River Basin, western China

NASA Astrophysics Data System (ADS)

Liu, D.; Tian, F.; Lin, M.; Sivapalan, M.

2014-04-01

The complex interactions and feedbacks between humans and water are very essential issues but are poorly understood in the newly proposed discipline of socio-hydrology (Sivapalan et al., 2012). An exploratory model with the appropriate level of simplification can be valuable to improve our understanding of the co-evolution and self-organization of socio-hydrological systems driven by interactions and feedbacks operating at different scales. In this study, a simple coupled modeling framework for socio-hydrology co-evolution is developed for the Tarim River Basin in Western China, and is used to illustrate the explanatory power of such a model. The study area is the mainstream of the Tarim River, which is divided into two modeling units. The socio-hydrological system is composed of four parts, i.e. social sub-system, economic sub-system, ecological sub-system, and hydrological sub-system. In each modeling unit, four coupled ordinary differential equations are used to simulate the dynamics of the social sub-system represented by human population, the economic sub-system represented by irrigated crop area, the ecological sub-system represented by natural vegetation cover and the hydrological sub-system represented by stream discharge. The coupling and feedback processes of the four dominant sub-systems (and correspondingly four state variables) are integrated into several internal system characteristics interactively and jointly determined by themselves and by other coupled systems. For example, the stream discharge is coupled to the irrigated crop area by the colonization rate and mortality rate of the irrigated crop area in the upper reach and the irrigated area is coupled to stream discharge through irrigation water consumption. In a similar way, the stream discharge and natural vegetation cover are coupled together. The irrigated crop area is coupled to human population by the colonization rate and mortality rate of the population. The inflow of the lower reach is determined by the outflow from the upper reach. The natural vegetation cover in the lower reach is coupled to the outflow from the upper reach and governed by regional water resources management policy. The co-evolution of the Tarim socio-hydrological system is then analyzed within this modeling framework to gain insights into the overall system dynamics and its sensitivity to the external drivers and internal system variables. In the modeling framework, the state of each subsystem is holistically described by one state variable and the framework is flexible enough to comprise more processes and constitutive relationships if they are needed to illustrate the interaction and feedback mechanisms of the human-water system.

Coevolution of landesque capital intensive agriculture and sociopolitical hierarchy

PubMed Central

Sheehan, Oliver; Gray, Russell D.; Atkinson, Quentin D.

2018-01-01

One of the defining trends of the Holocene has been the emergence of complex societies. Two essential features of complex societies are intensive resource use and sociopolitical hierarchy. Although it is widely agreed that these two phenomena are associated cross-culturally and have both contributed to the rise of complex societies, the causality underlying their relationship has been the subject of longstanding debate. Materialist theories of cultural evolution tend to view resource intensification as driving the development of hierarchy, but the reverse order of causation has also been advocated, along with a range of intermediate views. Phylogenetic methods have the potential to test between these different causal models. Here we report the results of a phylogenetic study that modeled the coevolution of one type of resource intensification—the development of landesque capital intensive agriculture—with political complexity and social stratification in a sample of 155 Austronesian-speaking societies. We found support for the coevolution of landesque capital with both political complexity and social stratification, but the contingent and nondeterministic nature of both of these relationships was clear. There was no indication that intensification was the “prime mover” in either relationship. Instead, the relationship between intensification and social stratification was broadly reciprocal, whereas political complexity was more of a driver than a result of intensification. These results challenge the materialist view and emphasize the importance of both material and social factors in the evolution of complex societies, as well as the complex and multifactorial nature of cultural evolution. PMID:29555760

Coordinated Rates of Evolution between Interacting Plastid and Nuclear Genes in Geraniaceae

PubMed Central

Zhang, Jin; Ruhlman, Tracey A.; Sabir, Jamal; Blazier, J. Chris; Jansen, Robert K.

2015-01-01

Although gene coevolution has been widely observed within individuals and between different organisms, rarely has this phenomenon been investigated within a phylogenetic framework. The Geraniaceae is an attractive system in which to study plastid-nuclear genome coevolution due to the highly elevated evolutionary rates in plastid genomes. In plants, the plastid-encoded RNA polymerase (PEP) is a protein complex composed of subunits encoded by both plastid (rpoA, rpoB, rpoC1, and rpoC2) and nuclear genes (sig1-6). We used transcriptome and genomic data for 27 species of Geraniales in a systematic evaluation of coevolution between genes encoding subunits of the PEP holoenzyme. We detected strong correlations of dN (nonsynonymous substitutions) but not dS (synonymous substitutions) within rpoB/sig1 and rpoC2/sig2, but not for other plastid/nuclear gene pairs, and identified the correlation of dN/dS ratio between rpoB/C1/C2 and sig1/5/6, rpoC1/C2 and sig2, and rpoB/C2 and sig3 genes. Correlated rates between interacting plastid and nuclear sequences across the Geraniales could result from plastid-nuclear genome coevolution. Analyses of coevolved amino acid positions suggest that structurally mediated coevolution is not the major driver of plastid-nuclear coevolution. The detection of strong correlation of evolutionary rates between SIG and RNAP genes suggests a plausible explanation for plastome-genome incompatibility in Geraniaceae. PMID:25724640

Towards a richer evolutionary game theory

PubMed Central

McNamara, John M.

2013-01-01

Most examples of the application of evolutionary game theory to problems in biology involve highly simplified models. I contend that it is time to move on and include much more richness in models. In particular, more thought needs to be given to the importance of (i) between-individual variation; (ii) the interaction between individuals, and hence the process by which decisions are reached; (iii) the ecological and life-history context of the situation; (iv) the traits that are under selection, and (v) the underlying psychological mechanisms that lead to behaviour. I give examples where including variation between individuals fundamentally changes predicted outcomes of a game. Variation also selects for real-time responses, again resulting in changed outcomes. Variation can select for other traits, such as choosiness and social sensitivity. More generally, many problems involve coevolution of more than one trait. I identify situations where a reductionist approach, in which a game is isolated from is ecological setting, can be misleading. I also highlight the need to consider flexibility of behaviour, mental states and other issues concerned with the evolution of mechanism. PMID:23966616

Metabolic basis for the self-referential genetic code.

PubMed

Guimarães, Romeu Cardoso

2011-08-01

An investigation of the biosynthesis pathways producing glycine and serine was necessary to clarify an apparent inconsistency between the self-referential model (SRM) for the formation of the genetic code and the model of coevolution of encodings and of amino acid biosynthesis routes. According to the SRM proposal, glycine was the first amino acid encoded, followed by serine. The coevolution model does not state precisely which the first encodings were, only presenting a list of about ten early assignments including the derivation of glycine from serine-this being derived from the glycolysis intermediate glycerate, which reverses the order proposed by the self-referential model. Our search identified the glycine-serine pathway of syntheses based on one-carbon sources, involving activities of the glycine decarboxylase complex and its associated serine hydroxymethyltransferase, which is consistent with the order proposed by the self-referential model and supports its rationale for the origin of the genetic code: protein synthesis was developed inside an early metabolic system, serving the function of a sink of amino acids; the first peptides were glycine-rich and fit for the function of building the early ribonucleoproteins; glycine consumption in proteins drove the fixation of the glycine-serine pathway.

The Collective Knowledge of Social Tags: Direct and Indirect Influences on Navigation, Learning, and Information Processing

ERIC Educational Resources Information Center

Cress, Ulrike; Held, Christoph; Kimmerle, Joachim

2013-01-01

Tag clouds generated in social tagging systems can capture the collective knowledge of communities. Using as a basis spreading activation theories, information foraging theory, and the co-evolution model of cognitive and social systems, we present here a model for an "extended information scent," which proposes that both collective and individual…

Interfacing Network Simulations and Empirical Data

DTIC Science & Technology

2009-05-01

contraceptive innovations in the Cameroon. He found that real-world adoption rates did not follow simulation models when the network relationships were...Analysis of the Coevolution of Adolescents ’ Friendship Networks, Taste in Music, and Alcohol Consumption. Methodology, 2: 48-56. Tichy, N.M., Tushman

Coevolution of patch-type dependent emigration and patch-type dependent immigration.

PubMed

Weigang, Helene C

2017-08-07

The three phases of dispersal - emigration, transfer and immigration - are affecting each other and the former and latter decisions may depend on patch types. Despite the inevitable fact of the complexity of the dispersal process, patch-type dependencies of dispersal decisions modelled as emigration and immigration are usually missing in theoretical dispersal models. Here, I investigate the coevolution of patch-type dependent emigration and patch-type dependent immigration in an extended Hamilton-May model. The dispersing population inhabits a landscape structured into many patches of two types and disperses during a continuous-time season. The trait under consideration is a four dimensional vector consisting of two values for emigration probability from the patches and two values for immigration probability into the patches of each type. Using the adaptive dynamics approach I show that four qualitatively different dispersal strategies may evolve in different parameter regions, including a counterintuitive strategy, where patches of one type are fully dispersed from (emigration probability is one) but individuals nevertheless always immigrate into them during the dispersal season (immigration probability is one). I present examples of evolutionary branching in a wide parameter range, when the patches with high local death rate during the dispersal season guarantee a high expected disperser output. I find that two dispersal strategies can coexist after evolutionary branching: a strategy with full immigration only into the patches with high expected disperser output coexists with a strategy that immigrates into any patch. Stochastic simulations agree with the numerical predictions. Since evolutionary branching is also found when immigration evolves alone, the present study is adding coevolutionary constraints on the emigration traits and hence finds that the coevolution of a higher dimensional trait sometimes hinders evolutionary diversification. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular dynamics simulations and statistical coupling analysis reveal functional coevolution network of oncogenic mutations in the CDKN2A-CDK6 complex.

PubMed

Wang, Jingwen; Zhao, Yuqi; Wang, Yanjie; Huang, Jingfei

2013-01-16

Coevolution between proteins is crucial for understanding protein-protein interaction. Simultaneous changes allow a protein complex to maintain its overall structural-functional integrity. In this study, we combined statistical coupling analysis (SCA) and molecular dynamics simulations on the CDK6-CDKN2A protein complex to evaluate coevolution between proteins. We reconstructed an inter-protein residue coevolution network, consisting of 37 residues and 37 interactions. It shows that most of the coevolved residue pairs are spatially proximal. When the mutations happened, the stable local structures were broken up and thus the protein interaction was decreased or inhibited, with a following increased risk of melanoma. The identification of inter-protein coevolved residues in the CDK6-CDKN2A complex can be helpful for designing protein engineering experiments. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Adaptation and Coevolution on an Emergent Global Competitive Landscape

NASA Astrophysics Data System (ADS)

Fellman, Philip Vos; Post, Jonathan Vos; Wright, Roxana; Dasari, Usha

Notions of Darwinian selection have been implicit in economic theory for at least sixty years. Richard Nelson and Sidney Winter have argued that while evolutionary thinking was prevalent in prewar economics, the postwar Neoclassical school became almost entirely preoccupied with equilibrium conditions and their mathematical conditions. One of the problems with the economic interpretation of firm selection through competition has been a weak grasp on an incomplete scientific paradigm. As I.F. Price notes: "The biological metaphor has long lurked in the background of management theory largely because the message of 'survival of the fittest' (usually wrongly attributed to Charles Darwin rather than Herbert Spencer) provides a seemingly natural model for market competition (e.g. Alchian 1950, Merrell 1984, Henderson 1989, Moore 1993), without seriously challenging the underlying paradigms of what an organisation is." [1] In this paper we examine the application of dynamic fitness landscape models to economic theory, particularly the theory of technology substitution, drawing on recent work by Kauffman, Arthur, McKelvey, Nelson and Winter, and Windrum and Birchenhall. In particular we use Professor Post's early work with John Holland on the genetic algorithm to explain some of the key differences between static and dynamic approaches to economic modeling.

A comparison of biological and cultural evolution.

PubMed

Portin, Petter

2015-03-01

This review begins with a definition of biological evolution and a description of its general principles. This is followed by a presentation of the biological basis of culture, specifically the concept of social selection. Further, conditions for cultural evolution are proposed, including a suggestion for language being the cultural replicator corresponding to the concept of the gene in biological evolution. Principles of cultural evolution are put forward and compared to the principles of biological evolution. Special emphasis is laid on the principle of selection in cultural evolution, including presentation of the concept of cultural fitness. The importance of language as a necessary condition for cultural evolution is stressed. Subsequently, prime differences between biological and cultural evolution are presented, followed by a discussion on interaction of our genome and our culture. The review aims at contributing to the present discussion concerning the modern development of the general theory of evolution, for example by giving a tentative formulation of the necessary and sufficient conditions for cultural evolution, and proposing that human creativity and mind reading or theory of mind are motors specific for it. The paper ends with the notion of the still ongoing coevolution of genes and culture.

Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae.

PubMed

Zhang, Jin; Ruhlman, Tracey A; Sabir, Jamal; Blazier, J Chris; Jansen, Robert K

2015-03-01

Although gene coevolution has been widely observed within individuals and between different organisms, rarely has this phenomenon been investigated within a phylogenetic framework. The Geraniaceae is an attractive system in which to study plastid-nuclear genome coevolution due to the highly elevated evolutionary rates in plastid genomes. In plants, the plastid-encoded RNA polymerase (PEP) is a protein complex composed of subunits encoded by both plastid (rpoA, rpoB, rpoC1, and rpoC2) and nuclear genes (sig1-6). We used transcriptome and genomic data for 27 species of Geraniales in a systematic evaluation of coevolution between genes encoding subunits of the PEP holoenzyme. We detected strong correlations of dN (nonsynonymous substitutions) but not dS (synonymous substitutions) within rpoB/sig1 and rpoC2/sig2, but not for other plastid/nuclear gene pairs, and identified the correlation of dN/dS ratio between rpoB/C1/C2 and sig1/5/6, rpoC1/C2 and sig2, and rpoB/C2 and sig3 genes. Correlated rates between interacting plastid and nuclear sequences across the Geraniales could result from plastid-nuclear genome coevolution. Analyses of coevolved amino acid positions suggest that structurally mediated coevolution is not the major driver of plastid-nuclear coevolution. The detection of strong correlation of evolutionary rates between SIG and RNAP genes suggests a plausible explanation for plastome-genome incompatibility in Geraniaceae. © 2015 American Society of Plant Biologists. All rights reserved.

Suppressing disease spreading by using information diffusion on multiplex networks.

PubMed

Wang, Wei; Liu, Quan-Hui; Cai, Shi-Min; Tang, Ming; Braunstein, Lidia A; Stanley, H Eugene

2016-07-06

Although there is always an interplay between the dynamics of information diffusion and disease spreading, the empirical research on the systemic coevolution mechanisms connecting these two spreading dynamics is still lacking. Here we investigate the coevolution mechanisms and dynamics between information and disease spreading by utilizing real data and a proposed spreading model on multiplex network. Our empirical analysis finds asymmetrical interactions between the information and disease spreading dynamics. Our results obtained from both the theoretical framework and extensive stochastic numerical simulations suggest that an information outbreak can be triggered in a communication network by its own spreading dynamics or by a disease outbreak on a contact network, but that the disease threshold is not affected by information spreading. Our key finding is that there is an optimal information transmission rate that markedly suppresses the disease spreading. We find that the time evolution of the dynamics in the proposed model qualitatively agrees with the real-world spreading processes at the optimal information transmission rate.

An extension of the coevolution theory of the origin of the genetic code

PubMed Central

Di Giulio, Massimo

2008-01-01

Background The coevolution theory of the origin of the genetic code suggests that the genetic code is an imprint of the biosynthetic relationships between amino acids. However, this theory does not seem to attribute a role to the biosynthetic relationships between the earliest amino acids that evolved along the pathways of energetic metabolism. As a result, the coevolution theory is unable to clearly define the very earliest phases of genetic code origin. In order to remove this difficulty, I here suggest an extension of the coevolution theory that attributes a crucial role to the first amino acids that evolved along these biosynthetic pathways and to their biosynthetic relationships, even when defined by the non-amino acid molecules that are their precursors. Results It is re-observed that the first amino acids to evolve along these biosynthetic pathways are predominantly those codified by codons of the type GNN, and this observation is found to be statistically significant. Furthermore, the close biosynthetic relationships between the sibling amino acids Ala-Ser, Ser-Gly, Asp-Glu, and Ala-Val are not random in the genetic code table and reinforce the hypothesis that the biosynthetic relationships between these six amino acids played a crucial role in defining the very earliest phases of genetic code origin. Conclusion All this leads to the hypothesis that there existed a code, GNS, reflecting the biosynthetic relationships between these six amino acids which, as it defines the very earliest phases of genetic code origin, removes the main difficulty of the coevolution theory. Furthermore, it is here discussed how this code might have naturally led to the code codifying only for the domains of the codons of precursor amino acids, as predicted by the coevolution theory. Finally, the hypothesis here suggested also removes other problems of the coevolution theory, such as the existence for certain pairs of amino acids with an unclear biosynthetic relationship between the precursor and product amino acids and the collocation of Ala between the amino acids Val and Leu belonging to the pyruvate biosynthetic family, which the coevolution theory considered as belonging to different biosyntheses. Reviewers This article was reviewed by Rob Knight, Paul Higgs (nominated by Laura Landweber), and Eugene Koonin. PMID:18775066

Collapse of cooperation in evolving games.

PubMed

Stewart, Alexander J; Plotkin, Joshua B

2014-12-09

Game theory provides a quantitative framework for analyzing the behavior of rational agents. The Iterated Prisoner's Dilemma in particular has become a standard model for studying cooperation and cheating, with cooperation often emerging as a robust outcome in evolving populations. Here we extend evolutionary game theory by allowing players' payoffs as well as their strategies to evolve in response to selection on heritable mutations. In nature, many organisms engage in mutually beneficial interactions and individuals may seek to change the ratio of risk to reward for cooperation by altering the resources they commit to cooperative interactions. To study this, we construct a general framework for the coevolution of strategies and payoffs in arbitrary iterated games. We show that, when there is a tradeoff between the benefits and costs of cooperation, coevolution often leads to a dramatic loss of cooperation in the Iterated Prisoner's Dilemma. The collapse of cooperation is so extreme that the average payoff in a population can decline even as the potential reward for mutual cooperation increases. Depending upon the form of tradeoffs, evolution may even move away from the Iterated Prisoner's Dilemma game altogether. Our work offers a new perspective on the Prisoner's Dilemma and its predictions for cooperation in natural populations; and it provides a general framework to understand the coevolution of strategies and payoffs in iterated interactions.

Coevolution in host-parasite systems: behavioural strategies of slave-making ants and their hosts.

PubMed Central

Foitzik, S.; DeHeer, C. J.; Hunjan, D. N.; Herbers, J. M.

2001-01-01

Recently, avian brood parasites and their hosts have emerged as model systems for the study of host-parasite coevolution. However, empirical studies of the highly analogous social parasites, which use the workers of another eusocial species to raise their own young, have never explicitly examined the dynamics of these systems from a coevolutionary perspective. Here, we demonstrate interpopulational variation in behavioural interactions between a socially parasitic slave-maker ant and its host that is consistent with the expectations of host-parasite coevolution. Parasite pressure, as inferred by the size, abundance and raiding frequency of Protomognathus americanus colonies, was highest in a New York population of the host Leptothorax longispinosus and lowest in a West Virginia population. As host-parasite coevolutionary theory would predict, we found that the slave-makers and the hosts from New York were more effective at raiding and defending against raiders, respectively, than were conspecifics from the West Virginia population. Some of these variations in efficacy were brought about by apparently simple shifts in behaviour. These results demonstrate that defence mechanisms against social parasites can evolve, and they give the first indications of the existence of a coevolutionary arms race between a social parasite and its host. PMID:11375101

Socio-hydrologic perspectives of the co-evolution of humans and water in the Tarim River Basin, Western China: the Taiji-Tire Model

NASA Astrophysics Data System (ADS)

Liu, Y.; Tian, F.; Hu, H.; Sivapalan, M.

2013-10-01

This paper presents a historical socio-hydrological analysis of the Tarim Basin, Xinjiang Province, Western China, from the time of the opening of the Silk Road to the present. The analysis is aimed at exploring the historical co-evolution of coupled human-water systems and at identifying common patterns or organizing principles underpinning socio-hydrological systems (SHS). As a self-organized entity, the evolution of the human-water system in the Tarim Basin reached stable states for long periods of time, then punctuated by sudden shifts due to internal or external disturbances. In this study, we discuss three steady periods (i.e. natural, human exploitation, and degradation and recovery) and transitions in between during the past 2000 yr. During the "natural" stage that existed pre-18th century, with small-scale human society and sound environment, evolution of the SHS was mainly driven by natural environmental changes such as river channel migration and climate change. During the human exploitation stage, especially in the 19th and 20th centuries, it experienced rapid population growth, massive land reclamation and fast socio-economic development, and humans became the principal players of system evolution. By the 1970s, the Tarim Basin had evolved into a new regime with a vulnerable eco-hydrological system seemingly populated beyond its carrying capacity, and a human society that began to suffer from serious water shortages, land salinization and desertification. With intensified deterioration of river health and increased recognition of unsustainability of traditional development pattern, human intervention and recovery measures have been adopted. Since then, the basin has shown a reverse regime shift towards some healing of the environmental damage. Spatio-temporal variations of historical socio-hydrological co-evolution are classified into four types: primitive agricultural, traditional agricultural, industrial agricultural and urban SHSs. These co-evolutionary changes have been summarized in terms of the Taiji-Tire Model, a refinement of a special concept in Chinese philosophy, relating to the co-evolution of a system because of interactions among its components.

Host-to-host variation of ecological interactions in polymicrobial infections

NASA Astrophysics Data System (ADS)

Mukherjee, Sayak; Weimer, Kristin E.; Seok, Sang-Cheol; Ray, Will C.; Jayaprakash, C.; Vieland, Veronica J.; Swords, W. Edward; Das, Jayajit

2015-02-01

Host-to-host variability with respect to interactions between microorganisms and multicellular hosts are commonly observed in infection and in homeostasis. However, the majority of mechanistic models used to analyze host-microorganism relationships, as well as most of the ecological theories proposed to explain coevolution of hosts and microbes, are based on averages across a host population. By assuming that observed variations are random and independent, these models overlook the role of differences between hosts. Here, we analyze mechanisms underlying host-to-host variations of bacterial infection kinetics, using the well characterized experimental infection model of polymicrobial otitis media (OM) in chinchillas, in combination with population dynamic models and a maximum entropy (MaxEnt) based inference scheme. We find that the nature of the interactions between bacterial species critically regulates host-to-host variations in these interactions. Surprisingly, seemingly unrelated phenomena, such as the efficiency of individual bacterial species in utilizing nutrients for growth, and the microbe-specific host immune response, can become interdependent in a host population. The latter finding suggests a potential mechanism that could lead to selection of specific strains of bacterial species during the coevolution of the host immune response and the bacterial species.

Studying the co-evolution of protein families with the Mirrortree web server.

PubMed

Ochoa, David; Pazos, Florencio

2010-05-15

The Mirrortree server allows to graphically and interactively study the co-evolution of two protein families, and investigate their possible interactions and functional relationships in a taxonomic context. The server includes the possibility of starting from single sequences and hence it can be used by non-expert users. The web server is freely available at http://csbg.cnb.csic.es/mtserver. It was tested in the main web browsers. Adobe Flash Player is required at the client side to perform the interactive assessment of co-evolution. pazos@cnb.csic.es Supplementary data are available at Bioinformatics online.

Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins

NASA Astrophysics Data System (ADS)

Champeimont, Raphaël; Laine, Elodie; Hu, Shuang-Wei; Penin, Francois; Carbone, Alessandra

2016-05-01

A novel computational approach of coevolution analysis allowed us to reconstruct the protein-protein interaction network of the Hepatitis C Virus (HCV) at the residue resolution. For the first time, coevolution analysis of an entire viral genome was realized, based on a limited set of protein sequences with high sequence identity within genotypes. The identified coevolving residues constitute highly relevant predictions of protein-protein interactions for further experimental identification of HCV protein complexes. The method can be used to analyse other viral genomes and to predict the associated protein interaction networks.

The early phase of the SMBH-galaxy coevolution in low-z "young" galaxies

NASA Astrophysics Data System (ADS)

Nagao, Tohru

2014-01-01

It is now widely recognized that most galaxies have a supermassive black hole (SMBH) in their nucleus, and the evolution of SMBHs is closely related with that of their host galaxies (the SMBH-galaxy coevolution). This is suggested by the correlation in the mass of SMBHs and their host galaxies, that has been observed in low redshifts. However, the physics of the coevolution is totally unclear, that prevents us from complete understandings of the galaxy evolution. One possible strategy to tackle this issue is measuring the mass ratio between SMBHs and their host galaxies (M_BH/M_host) at high redshifs, since different scenarios predict different evolution of the ratio ofMBH/Mhost. However it is extremely challenging to measure the mass of the host of high-z quasars, given the faint surface brightness of the host at close to the glaring quasar nucleus. Here we propose a brand-new approach to assess the early phase of the SMBH-galaxy coevolution, by focusing on low-z AGN-hosting "young" galaxies. Specifically, we focus on some very metal-poor galaxies with broadline Balmer lines at z ~ 0.1 - 0.3. By examining the SMBH scaling relations in some low-z metal-poor AGNs through high-resolution IRCS imaging observations, we will discriminate various scenarios for the SMBH-galaxy coevolution.

Coevolution of landesque capital intensive agriculture and sociopolitical hierarchy.

PubMed

Sheehan, Oliver; Watts, Joseph; Gray, Russell D; Atkinson, Quentin D

2018-04-03

One of the defining trends of the Holocene has been the emergence of complex societies. Two essential features of complex societies are intensive resource use and sociopolitical hierarchy. Although it is widely agreed that these two phenomena are associated cross-culturally and have both contributed to the rise of complex societies, the causality underlying their relationship has been the subject of longstanding debate. Materialist theories of cultural evolution tend to view resource intensification as driving the development of hierarchy, but the reverse order of causation has also been advocated, along with a range of intermediate views. Phylogenetic methods have the potential to test between these different causal models. Here we report the results of a phylogenetic study that modeled the coevolution of one type of resource intensification-the development of landesque capital intensive agriculture-with political complexity and social stratification in a sample of 155 Austronesian-speaking societies. We found support for the coevolution of landesque capital with both political complexity and social stratification, but the contingent and nondeterministic nature of both of these relationships was clear. There was no indication that intensification was the "prime mover" in either relationship. Instead, the relationship between intensification and social stratification was broadly reciprocal, whereas political complexity was more of a driver than a result of intensification. These results challenge the materialist view and emphasize the importance of both material and social factors in the evolution of complex societies, as well as the complex and multifactorial nature of cultural evolution. Copyright © 2018 the Author(s). Published by PNAS.

Co-evolution of payoff strategy and interaction strategy in prisoner's dilemma game

NASA Astrophysics Data System (ADS)

Zhang, Kangjie; Cheng, Hongyan

2016-11-01

Co-evolutionary dynamical models, providing a realistic paradigm for investigating complex system, have been extensively studied. In this paper, the co-evolution of payoff strategy and interaction strategy is studied. Starting with an initial Gaussian distribution of payoff strategy r with the mean u and the variance q, we focus on the final distribution of the payoff strategy. We find that final distribution of the payoff strategy may display different structures depending on parameters. In the ranges u < - 1 and u > 3, the distribution displays a single-peak structure which is symmetric about r = u. The distribution manifests itself as a double-peak structure in the range - 1 < u < 3 although a fake three-peak structure shows up in range 1 < u < 2. The explanations on the formation of different types of payoff strategy distributions are presented.

Structures vibration control via Tuned Mass Dampers using a co-evolution Coral Reefs Optimization algorithm

NASA Astrophysics Data System (ADS)

Salcedo-Sanz, S.; Camacho-Gómez, C.; Magdaleno, A.; Pereira, E.; Lorenzana, A.

2017-04-01

In this paper we tackle a problem of optimal design and location of Tuned Mass Dampers (TMDs) for structures subjected to earthquake ground motions, using a novel meta-heuristic algorithm. Specifically, the Coral Reefs Optimization (CRO) with Substrate Layer (CRO-SL) is proposed as a competitive co-evolution algorithm with different exploration procedures within a single population of solutions. The proposed approach is able to solve the TMD design and location problem, by exploiting the combination of different types of searching mechanisms. This promotes a powerful evolutionary-like algorithm for optimization problems, which is shown to be very effective in this particular problem of TMDs tuning. The proposed algorithm's performance has been evaluated and compared with several reference algorithms in two building models with two and four floors, respectively.

Island emergence/subsidence histories and their bearing upon biological speciation in the Galápagos

NASA Astrophysics Data System (ADS)

Orellana Rovirosa, F.

2017-12-01

In the context of plate motion reconstructions for the Nazca, Cocos and South American plates in relation with the Galápagos hotspot, it is found that the age-depth dependence of bathymetry, dynamic topography due to the Galápagos plume, crustal relaxation, and magmatic production allow for us to estimate the subsidence of islands and seamounts along the Carnegie Ridge. Our estimates are partially based on geodynamic theory (fluid mechanics and elasticity), but also on detailed bathymetric observations and analysis. For the Carnegie Ridge saddle, we estimate subsidence of about 2 km occurring during the past 13 Ma. Because the present-day depths of the region are in the range 2-2.5 km, this assessment shows that the deepest region of the present-day Carnegie Ridge may have been above sea level when it was closer to the active hotspot, therefore providing habitat for land species for a few (<5) million years. Moreover, the migrating hotspot swell may have caused the emerging of different portions of the Carnegie Ridge on a spatio-temporal progression. A more sophisticated 3D numerical model including an asthenosphere and plume interacting with the overlying Nazca plate may provide an improved understanding of geological-biological co-evolution in the Galápagos-Carnegie Ridge.

The Beringian coevolution project: Holistic collections of mammals and associated parasites reveal novel perspectives on evolutionary and environmental change in the North

USGS Publications Warehouse

Cook, Joseph A.; Galbreath, Kurt E.; Campbell, Mariel; Carrière, Susanne; Colella, Jocelyn P.; Dawson, Natalie G.; Dunnum, Jonathan L.; Eckerlin, Ralph P.; Greiman, Stephen E.; Fedorov, Vadim B.; Haas, Genevieve M. S.; Haukisalmi, Voitto; Henttonen, Heikki; Hope, Andrew G.; Jackson, Donavan; Jung, Tom; Koehler, Anson V.; Kinsella, John M.; Krejsa, Dianna; Kutz, Susan J.; Liphardt, Schuyler; MacDonald, Stephen O.; Malaney, Jason L.; Makarikov, Arseny; Martin, Jon; McLean, Bryan S.; Mulders, Robert; Nyamsuren, Batsaikhan; Talbot, Sandra L.; Tkach, Vasyl V.; Tsvetkova, Albina; Toman, Heather M.; Waltari, Eric C.; Whitman, Jackson S.; Hoberg, Eric P.

2017-01-01

The Beringian Coevolution Project (BCP), a field program underway in the high northern latitudes since 1999, has focused on building key scientific infrastructure for integrated specimen-based studies on mammals and their associated parasites. BCP has contributed new insights across temporal and spatial scales into how ancient climate and environmental change have shaped faunas, emphasizing processes of assembly, persistence, and diversification across the vast Beringian region. BCP collections also represent baseline records of biotic diversity from across the northern high latitudes at a time of accelerated environmental change. These specimens and associated data form an unmatched resource for identifying hidden diversity, interpreting past responses to climate oscillations, documenting contemporary conditions, and anticipating outcomes for complex biological systems in a regime of ecological perturbation. Because of its dual focus on hosts and parasites, the BCP record also provides a foundation for comparative analyses that can document the effects of dynamic change on the geographic distribution, transmission dynamics, and emergence of pathogens. By using specific examples from carnivores, shrews, lagomorphs, rodents and their associated parasites, we demonstrate how broad, integrated field collections provide permanent infrastructure that informs policy decisions regarding human impact and the effect of climate change on natural populations.

The genetic basis of a plant–insect coevolutionary key innovation

PubMed Central

Wheat, Christopher W.; Vogel, Heiko; Wittstock, Ute; Braby, Michael F.; Underwood, Dessie; Mitchell-Olds, Thomas

2007-01-01

Ehrlich and Raven formally introduced the concept of stepwise coevolution using butterfly and angiosperm interactions in an attempt to account for the impressive biological diversity of these groups. However, many biologists currently envision butterflies evolving 50 to 30 million years (Myr) after the major angiosperm radiation and thus reject coevolutionary origins of butterfly biodiversity. The unresolved central tenet of Ehrlich and Raven's theory is that evolution of plant chemical defenses is followed closely by biochemical adaptation in insect herbivores, and that newly evolved detoxification mechanisms result in adaptive radiation of herbivore lineages. Using one of their original butterfly-host plant systems, the Pieridae, we identify a pierid glucosinolate detoxification mechanism, nitrile-specifier protein (NSP), as a key innovation. Larval NSP activity matches the distribution of glucosinolate in their host plants. Moreover, by using five different temporal estimates, NSP seems to have evolved shortly after the evolution of the host plant group (Brassicales) (≈10 Myr). An adaptive radiation of these glucosinolate-feeding Pierinae followed, resulting in significantly elevated species numbers compared with related clades. Mechanistic understanding in its proper historical context documents more ancient and dynamic plant–insect interactions than previously envisioned. Moreover, these mechanistic insights provide the tools for detailed molecular studies of coevolution from both the plant and insect perspectives. PMID:18077380

Infanticide as Sexual Conflict: Coevolution of Male Strategies and Female Counterstrategies

PubMed Central

Palombit, Ryne A.

2015-01-01

One of the earliest recognized forms of sexual conflict was infanticide by males, which imposes serious costs on female reproductive success. Here I review two bodies of evidence addressing coevolved strategies of males and females. The original sexual selection hypothesis arguing that infanticide improves male mating success by accelerating the return of females to fertilizable condition has been generally supported in some taxa—notably, some primates, carnivores, rodents, and cetaceans—but not in other taxa. One result of recent research has been to implicate other selective benefits of infanticide by males in various taxa from insects to birds to mammals, such as acquisition of breeding status or improvement of the female breeding condition. In some cases, however, the adaptive significance of male infanticide remains obscure. The second body of data I review is arguably the most important result of recent research: clarifying the possible female counterstrategies to infanticide. These potential counterstrategies span diverse biological systems, ranging from sexual behavior (e.g., polyandrous mating), to physiology (e.g., the Bruce effect), to individual behavior (e.g., maternal aggression), to social strategies (e.g., association with coalitionary defenders of either sex). Although much remains to be studied, these current data provide compelling evidence of sexually antagonistic coevolution surrounding the phenomenon of infanticide. PMID:25986557

Construct - A Multi-Agent Network Model for the Co-Evolution of Agents and Socio-Cultural Environments

DTIC Science & Technology

2004-05-01

grounded in structuration theory (Giddens, 1984), social information processing theory (Salancik and Pfeffer, 1978) and symbolic interactionism (Manis...and B. N. Meltzer. Symbolic interaction: A reader in social psychology. Boston: Allyn & Bacon. 1978 Mcpherson, J. M. and L. Smith-Lovin

Using Wikis for Learning and Knowledge Building: Results of an Experimental Study

ERIC Educational Resources Information Center

Kimmerle, Joachim; Moskaliuk, Johannes; Cress, Ulrike

2011-01-01

Computer-supported learning and knowledge building play an increasing role in online collaboration. This paper outlines some theories concerning the interplay between individual processes of learning and collaborative processes of knowledge building. In particular, it describes the co-evolution model that attempts to examine processes of learning…

Coevolution of CRISPR bacteria and phage in 2 dimensions

NASA Astrophysics Data System (ADS)

Han, Pu; Deem, Michael

2014-03-01

CRISPR (cluster regularly interspaced short palindromic repeats) is a newly discovered adaptive, heritable immune system of prokaryotes. It can prevent infection of prokaryotes by phage. Most bacteria and almost all archae have CRISPR. The CRISPR system incorporates short nucleotide sequences from viruses. These incorporated sequences provide a historical record of the host and predator coevolution. We simulate the coevolution of bacteria and phage in 2 dimensions. Each phage has multiple proto-spacers that the bacteria can incorporate. Each bacterium can store multiple spacers in its CRISPR. Phages can escape recognition by the CRISPR system via point mutation or recombination. We will discuss the different evolutionary consequences of point mutation or recombination on the coevolution of bacteria and phage. We will also discuss an intriguing ``dynamic phase transition'' in the number of phage as a function of time and mutation rate. We will show that due to the arm race between phages and bacteria, the frequency of spacers and proto-spacers in a population can oscillate quite rapidly.

Consumer co-evolution as an important component of the eco-evolutionary feedback.

PubMed

Hiltunen, Teppo; Becks, Lutz

2014-10-22

Rapid evolution in ecologically relevant traits has recently been recognized to significantly alter the interaction between consumers and their resources, a key interaction in all ecological communities. While these eco-evolutionary dynamics have been shown to occur when prey populations are evolving, little is known about the role of predator evolution and co-evolution between predator and prey in this context. Here, we investigate the role of consumer co-evolution for eco-evolutionary feedback in bacteria-ciliate microcosm experiments by manipulating the initial trait variation in the predator populations. With co-evolved predators, prey evolve anti-predatory defences faster, trait values are more variable, and predator and prey population sizes are larger at the end of the experiment compared with the non-co-evolved predators. Most importantly, differences in predator traits results in a shift from evolution driving ecology, to ecology driving evolution. Thus we demonstrate that predator co-evolution has important effects on eco-evolutionary dynamics.

The fossilized birth–death process for coherent calibration of divergence-time estimates

PubMed Central

Heath, Tracy A.; Huelsenbeck, John P.; Stadler, Tanja

2014-01-01

Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover patterns of coevolution and diversification. Because molecular sequence data are not informative on absolute time, external data—most commonly, fossil age estimates—are required to calibrate estimates of species divergence dates. For Bayesian divergence time methods, the common practice for calibration using fossil information involves placing arbitrarily chosen parametric distributions on internal nodes, often disregarding most of the information in the fossil record. We introduce the “fossilized birth–death” (FBD) process—a model for calibrating divergence time estimates in a Bayesian framework, explicitly acknowledging that extant species and fossils are part of the same macroevolutionary process. Under this model, absolute node age estimates are calibrated by a single diversification model and arbitrary calibration densities are not necessary. Moreover, the FBD model allows for inclusion of all available fossils. We performed analyses of simulated data and show that node age estimation under the FBD model results in robust and accurate estimates of species divergence times with realistic measures of statistical uncertainty, overcoming major limitations of standard divergence time estimation methods. We used this model to estimate the speciation times for a dataset composed of all living bears, indicating that the genus Ursus diversified in the Late Miocene to Middle Pliocene. PMID:25009181

Metabolic coevolution in the bacterial symbiosis of whiteflies and related plant sap-feeding insects

USDA-ARS?s Scientific Manuscript database

In animals dependent on intracellular bacteria with very small genomes, the host cell is adapted to support the function of its bacterial symbionts, but the molecular basis of these adaptations is poorly understood. We investigated the metabolic coevolution between the whitefly Bemisia tabaci and th...

[The nature of personality: a co-evolutionary perspective].

PubMed

Asendorpf, J B

1996-01-01

Personality psychologists' attempts to explain human diversity have traditionally focused upon processes of person-situation interaction, and genotype-environment interaction. The great variability of genotypes and environments within cultures has remained unexplained in these efforts. Which processes may be responsible for the genetic and environmental variability within cultures? Answers to this question are sought in processes of genetic-cultural coevolution: mutation and sexual recombination of genes, innovation and synthesis of memes (units of cultural transmission), genotype-->environment and meme-->environment effects, and frequency-dependent natural and cultural selection. This twofold evolutionary explanation of personality differences within cultures suggests that a solid foundation of personality psychology requires bridging biology and cultural science.

Landscape co-evolution and river discharge.

NASA Astrophysics Data System (ADS)

van der Velde, Ype; Temme, Arnaud

2015-04-01

Fresh water is crucial for society and ecosystems. However, our ability to secure fresh water resources under climatic and anthropogenic change is impaired by the complexity of interactions between human society, ecosystems, soils, and topography. These interactions cause landscape properties to co-evolve, continuously changing the flow paths of water through the landscape. These co-evolution driven flow path changes and their effect on river runoff are, to-date, poorly understood. In this presentation we introduce a spatially distributed landscape evolution model that incorporates growing vegetation and its effect on evapotranspiration, interception, infiltration, soil permeability, groundwater-surface water exchange and erosion. This landscape scale (10km2) model is calibrated to evolve towards well known empirical organising principles such as the Budyko curve and Hacks law under different climate conditions. To understand how positive and negative feedbacks within the model structure form complex landscape patterns of forests and peat bogs that resemble observed landscapes under humid and boreal climates, we analysed the effects of individual processes on the spatial distribution of vegetation and river peak and mean flows. Our results show that especially river peak flows and droughts decrease with increasing evolution of the landscape, which is a result that has direct implications for flood management.

Conservation of coevolving protein interfaces bridges prokaryote–eukaryote homologies in the twilight zone

PubMed Central

Rodriguez-Rivas, Juan; Marsili, Simone; Juan, David; Valencia, Alfonso

2016-01-01

Protein–protein interactions are fundamental for the proper functioning of the cell. As a result, protein interaction surfaces are subject to strong evolutionary constraints. Recent developments have shown that residue coevolution provides accurate predictions of heterodimeric protein interfaces from sequence information. So far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compiled. We explore the hypothesis that coevolution points to structurally conserved contacts at protein–protein interfaces, which can be reliably projected to homologous complexes with distantly related sequences. We introduce a domain-centered protocol to study the interplay between residue coevolution and structural conservation of protein–protein interfaces. We show that sequence-based coevolutionary analysis systematically identifies residue contacts at prokaryotic interfaces that are structurally conserved at the interface of their eukaryotic counterparts. In turn, this allows the prediction of conserved contacts at eukaryotic protein–protein interfaces with high confidence using solely mutational patterns extracted from prokaryotic genomes. Even in the context of high divergence in sequence (the twilight zone), where standard homology modeling of protein complexes is unreliable, our approach provides sequence-based accurate information about specific details of protein interactions at the residue level. Selected examples of the application of prokaryotic coevolutionary analysis to the prediction of eukaryotic interfaces further illustrate the potential of this approach. PMID:27965389

Collapse of cooperation in evolving games

PubMed Central

Stewart, Alexander J.; Plotkin, Joshua B.

2014-01-01

Game theory provides a quantitative framework for analyzing the behavior of rational agents. The Iterated Prisoner’s Dilemma in particular has become a standard model for studying cooperation and cheating, with cooperation often emerging as a robust outcome in evolving populations. Here we extend evolutionary game theory by allowing players’ payoffs as well as their strategies to evolve in response to selection on heritable mutations. In nature, many organisms engage in mutually beneficial interactions and individuals may seek to change the ratio of risk to reward for cooperation by altering the resources they commit to cooperative interactions. To study this, we construct a general framework for the coevolution of strategies and payoffs in arbitrary iterated games. We show that, when there is a tradeoff between the benefits and costs of cooperation, coevolution often leads to a dramatic loss of cooperation in the Iterated Prisoner’s Dilemma. The collapse of cooperation is so extreme that the average payoff in a population can decline even as the potential reward for mutual cooperation increases. Depending upon the form of tradeoffs, evolution may even move away from the Iterated Prisoner’s Dilemma game altogether. Our work offers a new perspective on the Prisoner’s Dilemma and its predictions for cooperation in natural populations; and it provides a general framework to understand the coevolution of strategies and payoffs in iterated interactions. PMID:25422421

Effect of heterogeneous investments on the evolution of cooperation in spatial public goods game.

PubMed

Huang, Keke; Wang, Tao; Cheng, Yuan; Zheng, Xiaoping

2015-01-01

Understanding the emergence of cooperation in spatial public goods game remains a grand challenge across disciplines. In most previous studies, it is assumed that the investments of all the cooperators are identical, and often equal to 1. However, it is worth mentioning that players are diverse and heterogeneous when choosing actions in the rapidly developing modern society and researchers have shown more interest to the heterogeneity of players recently. For modeling the heterogeneous players without loss of generality, it is assumed in this work that the investment of a cooperator is a random variable with uniform distribution, the mean value of which is equal to 1. The results of extensive numerical simulations convincingly indicate that heterogeneous investments can promote cooperation. Specifically, a large value of the variance of the random variable can decrease the two critical values for the result of behavioral evolution effectively. Moreover, the larger the variance is, the better the promotion effect will be. In addition, this article has discussed the impact of heterogeneous investments when the coevolution of both strategy and investment is taken into account. Comparing the promotion effect of coevolution of strategy and investment with that of strategy imitation only, we can conclude that the coevolution of strategy and investment decreases the asymptotic fraction of cooperators by weakening the heterogeneity of investments, which further demonstrates that heterogeneous investments can promote cooperation in spatial public goods game.

Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone.

PubMed

Rodriguez-Rivas, Juan; Marsili, Simone; Juan, David; Valencia, Alfonso

2016-12-27

Protein-protein interactions are fundamental for the proper functioning of the cell. As a result, protein interaction surfaces are subject to strong evolutionary constraints. Recent developments have shown that residue coevolution provides accurate predictions of heterodimeric protein interfaces from sequence information. So far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compiled. We explore the hypothesis that coevolution points to structurally conserved contacts at protein-protein interfaces, which can be reliably projected to homologous complexes with distantly related sequences. We introduce a domain-centered protocol to study the interplay between residue coevolution and structural conservation of protein-protein interfaces. We show that sequence-based coevolutionary analysis systematically identifies residue contacts at prokaryotic interfaces that are structurally conserved at the interface of their eukaryotic counterparts. In turn, this allows the prediction of conserved contacts at eukaryotic protein-protein interfaces with high confidence using solely mutational patterns extracted from prokaryotic genomes. Even in the context of high divergence in sequence (the twilight zone), where standard homology modeling of protein complexes is unreliable, our approach provides sequence-based accurate information about specific details of protein interactions at the residue level. Selected examples of the application of prokaryotic coevolutionary analysis to the prediction of eukaryotic interfaces further illustrate the potential of this approach.

A conceptual socio-hydrological model of the co-evolution of humans and water: case study of the Tarim River basin, western China

NASA Astrophysics Data System (ADS)

Liu, D.; Tian, F.; Lin, M.; Sivapalan, M.

2015-02-01

The complex interactions and feedbacks between humans and water are critically important issues but remain poorly understood in the newly proposed discipline of socio-hydrology (Sivapalan et al., 2012). An exploratory model with the appropriate level of simplification can be valuable for improving our understanding of the co-evolution and self-organization of socio-hydrological systems driven by interactions and feedbacks operating at different scales. In this study, a simplified conceptual socio-hydrological model based on logistic growth curves is developed for the Tarim River basin in western China and is used to illustrate the explanatory power of such a co-evolutionary model. The study area is the main stream of the Tarim River, which is divided into two modeling units. The socio-hydrological system is composed of four sub-systems, i.e., the hydrological, ecological, economic, and social sub-systems. In each modeling unit, the hydrological equation focusing on water balance is coupled to the other three evolutionary equations to represent the dynamics of the social sub-system (denoted by population), the economic sub-system (denoted by irrigated crop area ratio), and the ecological sub-system (denoted by natural vegetation cover), each of which is expressed in terms of a logistic growth curve. Four feedback loops are identified to represent the complex interactions among different sub-systems and different spatial units, of which two are inner loops occurring within each separate unit and the other two are outer loops linking the two modeling units. The feedback mechanisms are incorporated into the constitutive relations for model parameters, i.e., the colonization and mortality rates in the logistic growth curves that are jointly determined by the state variables of all sub-systems. The co-evolution of the Tarim socio-hydrological system is then analyzed with this conceptual model to gain insights into the overall system dynamics and its sensitivity to the external drivers and internal system variables. The results show a costly pendulum swing between a balanced distribution of socio-economic and natural ecologic resources among the upper and lower reaches and a highly skewed distribution towards the upper reach. This evolution is principally driven by the attitudinal changes occurring within water resources management policies that reflect the evolving community awareness of society to concerns regarding the ecology and environment.

Comparative modeling of coevolution in communities of unicellular organisms: adaptability and biodiversity.

PubMed

Lashin, Sergey A; Suslov, Valentin V; Matushkin, Yuri G

2010-06-01

We propose an original program "Evolutionary constructor" that is capable of computationally efficient modeling of both population-genetic and ecological problems, combining these directions in one model of required detail level. We also present results of comparative modeling of stability, adaptability and biodiversity dynamics in populations of unicellular haploid organisms which form symbiotic ecosystems. The advantages and disadvantages of two evolutionary strategies of biota formation--a few generalists' taxa-based biota formation and biodiversity-based biota formation--are discussed.

Decision making on fitness landscapes

NASA Astrophysics Data System (ADS)

Arthur, R.; Sibani, P.

2017-04-01

We discuss fitness landscapes and how they can be modified to account for co-evolution. We are interested in using the landscape as a way to model rational decision making in a toy economic system. We develop a model very similar to the Tangled Nature Model of Christensen et al. that we call the Tangled Decision Model. This is a natural setting for our discussion of co-evolutionary fitness landscapes. We use a Monte Carlo step to simulate decision making and investigate two different decision making procedures.

Smart health community: the hidden value of health information exchange.

PubMed

Ciriello, James N; Kulatilaka, Nalin

2010-12-01

Investments in health information technology are accelerating the digitization of medicine. The value from these investments, however, can grow beyond efficiencies by filling the information gaps between the various stakeholders. New work processes, governance structures, and relationships are needed for the coevolution of healthcare markets and business models. But coevolution is slow, hindered by the scarcity of incentives for legacy delivery systems and constrained by the prevailing patient-healthcare paradigm. The greater opportunity lies in wellness for individuals, families, communities, and society at large: a consumer-community paradigm. Capturing new value from this opportunity can start with investment in health information exchange and the creation of Smart Health Communities. By shifting the focus of exchange from public servant to value-added service provider, these communities can serve as a platform for a wider array of wellness services from consumer care, traditional healthcare, and research.

Integrating instance selection, instance weighting, and feature weighting for nearest neighbor classifiers by coevolutionary algorithms.

PubMed

Derrac, Joaquín; Triguero, Isaac; Garcia, Salvador; Herrera, Francisco

2012-10-01

Cooperative coevolution is a successful trend of evolutionary computation which allows us to define partitions of the domain of a given problem, or to integrate several related techniques into one, by the use of evolutionary algorithms. It is possible to apply it to the development of advanced classification methods, which integrate several machine learning techniques into a single proposal. A novel approach integrating instance selection, instance weighting, and feature weighting into the framework of a coevolutionary model is presented in this paper. We compare it with a wide range of evolutionary and nonevolutionary related methods, in order to show the benefits of the employment of coevolution to apply the techniques considered simultaneously. The results obtained, contrasted through nonparametric statistical tests, show that our proposal outperforms other methods in the comparison, thus becoming a suitable tool in the task of enhancing the nearest neighbor classifier.

Next step in the ongoing arms race between myxoma virus and wild rabbits in Australia is a novel disease phenotype

PubMed Central

Kerr, Peter J.; Cattadori, Isabella M.; Liu, June; Sim, Derek G.; Dodds, Jeff W.; Brooks, Jason W.; Kennett, Mary J.; Holmes, Edward C.

2017-01-01

In host–pathogen arms races, increases in host resistance prompt counteradaptation by pathogens, but the nature of that counteradaptation is seldom directly observed outside of laboratory models. The best-documented field example is the coevolution of myxoma virus (MYXV) in European rabbits. To understand how MYXV in Australia has continued to evolve in wild rabbits under intense selection for genetic resistance to myxomatosis, we compared the phenotypes of the progenitor MYXV and viral isolates from the 1950s and the 1990s in laboratory rabbits with no resistance. Strikingly, and unlike their 1950s counterparts, most virus isolates from the 1990s induced a highly lethal immune collapse syndrome similar to septic shock. Thus, the next step in this canonical case of coevolution after a species jump has been further escalation by the virus in the face of widespread host resistance. PMID:28808019

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martín-Navarro, Ignacio; Brodie, Jean P.; Romanowsky, Aaron J.

Coevolution between supermassive black holes (BH) and their host galaxies is universally adopted in models for galaxy formation. In the absence of feedback from active galactic nuclei (AGNs), simulated massive galaxies keep forming stars in the local universe. From an observational point of view, however, such coevolution remains unclear. We present a stellar population analysis of galaxies with direct BH mass measurements and the BH mass– σ relation as a working framework. We find that over-massive BH galaxies, i.e., galaxies lying above the best-fitting BH mass– σ line, tend to be older and more α -element-enhanced than under-massive BH galaxies.more » The scatter in the BH mass– σ –[ α /Fe] plane is significantly lower than that in the standard BH mass– σ relation. We interpret this trend as an imprint of AGN feedback on the star formation histories of massive galaxies.« less

Insights From Natural Host-Parasite Interactions: The Drosophila Model

PubMed Central

Keebaugh, Erin S.; Schlenke, Todd A.

2013-01-01

Immune responses against opportunistic pathogens have been extensively studied in Drosophila, leading to a detailed map of the genetics behind innate immunity networks including the Toll, Imd, Jak-Stat, and JNK pathways. However, immune mechanisms of other organisms, particularly plants, have primarily been investigated using natural pathogens. It was the use of natural pathogens in plant research that revealed the plant R/Avr system, a specialized immune response derived from antagonistic coevolution between plant immune proteins and their natural pathogens’ virulence proteins. Thus, we recommend that researchers begin to use natural Drosophila pathogens to identify novel immune mechanisms that may have arisen through antagonistic coevolution with common natural pathogens. In this review, we address the benefits of using natural pathogens in research, describe the known natural pathogens of Drosophila, and discuss exciting prospects for future research on select natural pathogens of Drosophila. PMID:23764256

Cultural evolutionary theory: How culture evolves and why it matters

PubMed Central

Creanza, Nicole; Kolodny, Oren; Feldman, Marcus W.

2017-01-01

Human cultural traits—behaviors, ideas, and technologies that can be learned from other individuals—can exhibit complex patterns of transmission and evolution, and researchers have developed theoretical models, both verbal and mathematical, to facilitate our understanding of these patterns. Many of the first quantitative models of cultural evolution were modified from existing concepts in theoretical population genetics because cultural evolution has many parallels with, as well as clear differences from, genetic evolution. Furthermore, cultural and genetic evolution can interact with one another and influence both transmission and selection. This interaction requires theoretical treatments of gene–culture coevolution and dual inheritance, in addition to purely cultural evolution. In addition, cultural evolutionary theory is a natural component of studies in demography, human ecology, and many other disciplines. Here, we review the core concepts in cultural evolutionary theory as they pertain to the extension of biology through culture, focusing on cultural evolutionary applications in population genetics, ecology, and demography. For each of these disciplines, we review the theoretical literature and highlight relevant empirical studies. We also discuss the societal implications of the study of cultural evolution and of the interactions of humans with one another and with their environment. PMID:28739941

Cultural evolutionary theory: How culture evolves and why it matters.

PubMed

Creanza, Nicole; Kolodny, Oren; Feldman, Marcus W

2017-07-24

Human cultural traits-behaviors, ideas, and technologies that can be learned from other individuals-can exhibit complex patterns of transmission and evolution, and researchers have developed theoretical models, both verbal and mathematical, to facilitate our understanding of these patterns. Many of the first quantitative models of cultural evolution were modified from existing concepts in theoretical population genetics because cultural evolution has many parallels with, as well as clear differences from, genetic evolution. Furthermore, cultural and genetic evolution can interact with one another and influence both transmission and selection. This interaction requires theoretical treatments of gene-culture coevolution and dual inheritance, in addition to purely cultural evolution. In addition, cultural evolutionary theory is a natural component of studies in demography, human ecology, and many other disciplines. Here, we review the core concepts in cultural evolutionary theory as they pertain to the extension of biology through culture, focusing on cultural evolutionary applications in population genetics, ecology, and demography. For each of these disciplines, we review the theoretical literature and highlight relevant empirical studies. We also discuss the societal implications of the study of cultural evolution and of the interactions of humans with one another and with their environment.

Co-evolution of cooperation and cognition: the impact of imperfect deliberation and context-sensitive intuition

PubMed Central

Kagan, Ari; Rand, David G.

2017-01-01

How does cognitive sophistication impact cooperation? We explore this question using a model of the co-evolution of cooperation and cognition. In our model, agents confront social dilemmas and coordination games, and make decisions using intuition or deliberation. Intuition is automatic and effortless, but relatively (although not necessarily completely) insensitive to context. Deliberation, conversely, is costly but relatively (although not necessarily perfectly) sensitive to context. We find that regardless of the sensitivity of intuition and imperfection of deliberation, deliberating undermines cooperation in social dilemmas, whereas deliberating can increase cooperation in coordination games if intuition is sufficiently sensitive. Furthermore, when coordination games are sufficiently likely, selection favours a strategy whose intuitive response ignores the contextual cues available and cooperates across contexts. Thus, we see how simple cognition can arise from active selection for simplicity, rather than just be forced to be simple due to cognitive constraints. Finally, we find that when deliberation is imperfect, the favoured strategy increases cooperation in social dilemmas (as a result of reducing deliberation) as the benefit of cooperation to the recipient increases. PMID:28330915

Understanding the "lethal" drivers of tumor-stroma co-evolution: emerging role(s) for hypoxia, oxidative stress and autophagy/mitophagy in the tumor micro-environment.

PubMed

Lisanti, Michael P; Martinez-Outschoorn, Ubaldo E; Chiavarina, Barbara; Pavlides, Stephanos; Whitaker-Menezes, Diana; Tsirigos, Aristotelis; Witkiewicz, Agnieszka; Lin, Zhao; Balliet, Renee; Howell, Anthony; Sotgia, Federica

2010-09-15

We have recently proposed a new model for understanding how tumors evolve. To achieve successful "Tumor-Stroma Co-Evolution", cancer cells induce oxidative stress in adjacent fibroblasts and possibly other stromal cells. Oxidative stress in the tumor stroma mimics the effects of hypoxia, under aerobic conditions, resulting in an excess production of reactive oxygen species (ROS). Excess stromal production of ROS drives the onset of an anti-oxidant defense in adjacent cancer cells, protecting them from apoptosis. Moreover, excess stromal ROS production has a "Bystander-Effect", leading to DNA damage and aneuploidy in adjacent cancer cells, both hallmarks of genomic instability. Finally, ROS-driven oxidative stress induces autophagy and mitophagy in the tumor micro-environment, leading to the stromal over-production of recycled nutrients (including energy-rich metabolites, such as ketones and L-lactate). These recycled nutrients or chemical building blocks then help drive mitochondrial biogenesis in cancer cells, thereby promoting the anabolic growth of cancer cells (via an energy imbalance). We also show that ketones and lactate help "fuel" tumor growth and cancer cell metastasis and can act as chemo-attractants for cancer cells. We have termed this new paradigm for accelerating tumor-stroma co-evolution, "The Autophagic Tumor Stroma Model of Cancer Cell Metabolism". Heterotypic signaling in cancer-associated fibroblasts activates the transcription factors HIF1alpha and NFκB, potentiating the onset of hypoxic and inflammatory response(s), which further upregulates the autophagic program in the stromal compartment. Via stromal autophagy, this hypoxic/inflammatory response may provide a new escape mechanism for cancer cells during anti-angiogenic therapy, further exacerbating tumor recurrence and metastasis.

A model for the coevolution of immunity and immune evasion in vector-borne diseases with implications for the epidemiology of malaria.

PubMed

Koella, Jacob C; Boëte, C

2003-05-01

We describe a model of host-parasite coevolution, where the interaction depends on the investments by the host in its immune response and by the parasite in its ability to suppress (or evade) its host's immune response. We base our model on the interaction between malaria parasites and their mosquito hosts and thus describe the epidemiological dynamics with the Macdonald-Ross equation of malaria epidemiology. The qualitative predictions of the model are most sensitive to the cost of the immune response and to the intensity of transmission. If transmission is weak or the cost of immunity is low, the system evolves to a coevolutionarily stable equilibrium at intermediate levels of investment (and, generally, at a low frequency of resistance). At a higher cost of immunity and as transmission intensifies, the system is not evolutionarily stable but rather cycles around intermediate levels of investment. At more intense transmission, neither host nor parasite invests any resources in dominating its partner so that no resistance is observed in the population. These results may help to explain the lack of encapsulated malaria parasites generally observed in natural populations of mosquito vectors, despite strong selection pressure for resistance in areas of very intense transmission.

Assessing sexual conflict in the Drosophila melanogaster laboratory model system

PubMed Central

Rice, William R; Stewart, Andrew D; Morrow, Edward H; Linder, Jodell E; Orteiza, Nicole; Byrne, Phillip G

2006-01-01

We describe a graphical model of interlocus coevolution used to distinguish between the interlocus sexual conflict that leads to sexually antagonistic coevolution, and the intrinsic conflict over mating rate that is an integral part of traditional models of sexual selection. We next distinguish the ‘laboratory island’ approach from the study of both inbred lines and laboratory populations that are newly derived from nature, discuss why we consider it to be one of the most fitting forms of laboratory analysis to study interlocus sexual conflict, and then describe four experiments using this approach with Drosophila melanogaster. The first experiment evaluates the efficacy of the laboratory model system to study interlocus sexual conflict by comparing remating rates of females when they are, or are not, provided with a spatial refuge from persistent male courtship. The second experiment tests for a lag-load in males that is due to adaptations that have accumulated in females, which diminish male-induced harm while simultaneously interfering with a male's ability to compete in the context of sexual selection. The third and fourth experiments test for a lag-load in females owing to direct costs from their interactions with males, and for the capacity for indirect benefits to compensate for these direct costs. PMID:16612888

The Beringian Coevolution Project: Holistic collections of mammals and associated parasites reveal novel perspectives on changing environments in the north

USDA-ARS?s Scientific Manuscript database

The Beringian Coevolution Project (BCP), a field program underway in the Arctic since 1999, has focused on building key scientific infrastructure for integrated specimen-based studies on mammals and their associated parasites. BCP has contributed new insights across temporal and spatial scales into...

The Coevolution of "Tyrannosaurus" & Its Prey: Could "Tyrannosaurus" Chase down & Kill a "Triceratops" for Lunch?

ERIC Educational Resources Information Center

May, S. Randolph

2014-01-01

Students will analyze the coevolution of the predator-prey relationships between "Tyrannosaurus rex" and its prey species using analyses of animal speeds from fossilized trackways, prey-animal armaments, adaptive behaviors, bite marks on prey-animal fossils, predator-prey ratios, and scavenger competition. The students will be asked to…

A discriminative test among the different theories proposed to explain the origin of the genetic code: the coevolution theory finds additional support.

PubMed

Giulio, Massimo Di

2018-05-19

A discriminative statistical test among the different theories proposed to explain the origin of the genetic code is presented. Gathering the amino acids into polarity and biosynthetic classes that are the first expression of the physicochemical theory of the origin of the genetic code and the second expression of the coevolution theory, these classes are utilized in the Fisher's exact test to establish their significance within the genetic code table. Linking to the rows and columns of the genetic code of probabilities that express the statistical significance of these classes, I have finally been in the condition to be able to calculate a χ value to link to both the physicochemical theory and to the coevolution theory that would express the corroboration level referred to these theories. The comparison between these two χ values showed that the coevolution theory is able to explain - in this strictly empirical analysis - the origin of the genetic code better than that of the physicochemical theory. Copyright © 2018 Elsevier B.V. All rights reserved.

Evidence for parasite-mediated selection during short-lasting toxic algal blooms.

PubMed

Blanquart, François; Valero, Myriam; Alves-de-Souza, Catharina; Dia, Aliou; Lepelletier, Frédéric; Bigeard, Estelle; Jeanthon, Christian; Destombe, Christophe; Guillou, Laure

2016-10-26

Parasites play a role in the control of transient algal blooms, but it is not known whether parasite-mediated selection results in coevolution of the host and the parasites over this short time span. We investigated the presence of coevolution between the toxic dinoflagellate Alexandrium minutum and two naturally occurring endoparasites during blooms lasting a month in two river estuaries, using cross-inoculation experiments across time and space. Higher parasite abundance was associated with a large daily reduction in relative A. minutum abundances, demonstrating strong parasite-mediated selection. There was genetic variability in infectivity in both parasite species, and in resistance in the host. We found no evidence for coevolution in one estuary; however, in the other estuary, we found high genetic diversity in the two parasite species, fluctuations in infectivity and suggestion that the two parasites are well adapted to their host, as in 'Red Queen' dynamics. Thus, coevolution is possible over the short time span of a bloom, but geographically variable, and may feedback on community dynamics. © 2016 The Authors.

Coevolution between Male and Female Genitalia in the Drosophila melanogaster Species Subgroup

PubMed Central

Yassin, Amir; Orgogozo, Virginie

2013-01-01

In contrast to male genitalia that typically exhibit patterns of rapid and divergent evolution among internally fertilizing animals, female genitalia have been less well studied and are generally thought to evolve slowly among closely-related species. As a result, few cases of male-female genital coevolution have been documented. In Drosophila, female copulatory structures have been claimed to be mostly invariant compared to male structures. Here, we re-examined male and female genitalia in the nine species of the D. melanogaster subgroup. We describe several new species-specific female genital structures that appear to coevolve with male genital structures, and provide evidence that the coevolving structures contact each other during copulation. Several female structures might be defensive shields against apparently harmful male structures, such as cercal teeth, phallic hooks and spines. Evidence for male-female morphological coevolution in Drosophila has previously been shown at the post-copulatory level (e.g., sperm length and sperm storage organ size), and our results provide support for male-female coevolution at the copulatory level. PMID:23451172

Socio-hydrologic perspectives of the co-evolution of humans and water in the Tarim River basin, Western China: the Taiji-Tire model

NASA Astrophysics Data System (ADS)

Liu, Y.; Tian, F.; Hu, H.; Sivapalan, M.

2014-04-01

This paper presents a historical socio-hydrological analysis of the Tarim River basin (TRB), Xinjiang Uyghur Autonomous Region, in Western China, from the time of the opening of the Silk Road to the present. The analysis is aimed at exploring the historical co-evolution of coupled human-water systems and at identifying common patterns or organizing principles underpinning socio-hydrological systems (SHS). As a self-organized entity, the evolution of the human-water system in the Tarim Basin reached stable states for long periods of time, but then was punctuated by sudden shifts due to internal or external disturbances. In this study, we discuss three stable periods (i.e., natural, human exploitation, and degradation and recovery) and the transitions in between during the past 2000 years. During the "natural" stage that existed pre-18th century, with small-scale human society and sound environment, evolution of the SHS was mainly driven by natural environmental changes such as river channel migration and climate change. During the human exploitation stage, especially in the 19th and 20th centuries, it experienced rapid population growth, massive land reclamation and fast socio-economic development, and humans became the principal players of system evolution. By the 1970s, the Tarim Basin had evolved into a new regime with a vulnerable eco-hydrological system seemingly populated beyond its carrying capacity, and a human society that began to suffer from serious water shortages, land salinization and desertification. With intensified deterioration of river health and increased recognition of unsustainability of traditional development patterns, human intervention and recovery measures have since been adopted. As a result, the basin has shown a reverse regime shift towards some healing of the environmental damage. Based on our analysis within TRB and a common theory of social development, four general types of SHSs are defined according to their characteristic spatio-temporal variations of historical co-evolution, including primitive agricultural, traditional agricultural, industrial agricultural, and urban SHSs. These co-evolutionary changes have been explained in the paper in terms of the Taiji-Tire model, a refinement of a special concept in Chinese philosophy, relating to the co-evolution of a system because of interactions among its components.

Seed dispersal in limber and southwestern white pine: Comparing core and peripheral populations

Treesearch

Diana F. Tomback; Sheridan Samano; Elizabeth L. Pruett; Anna W. Schoettle

2011-01-01

According to the geographic mosaic theory of coevolution (Thompson 2005), the potential for coevolutionary relationships between interacting species varies with the presence of other species within a community. This implies that the strength of coevolution between two species may vary geographically. In this study, we ask whether there is a shift in vertebrate seed...

Training with O (Observing) and T (Treatment) Teams in Live Supervision: Reflections in the Looking Glass.

ERIC Educational Resources Information Center

Roberts, Janine; And Others

1989-01-01

Describes process that six counselor trainees and two supervisors used with treatment and observation teams to examine their own coevolution as a therapeutic system using the Milan model of family therapy and Ericksonian hypnotherapy. Concludes with a discussion of advantages and pitfalls of this type of dual supervision. (Author/ABL)

Human and Machine Entanglement in the Digital Archive: Academic Libraries and Socio-Technical Change

ERIC Educational Resources Information Center

Manoff, Marlene

2015-01-01

This essay urges a broadening of the discourse of library and information science (LIS) to address the convergence of forces shaping the information environment. It proposes adopting a model from the field of science studies that acknowledges the interdependence and coevolution of social, cultural, and material phenomena. Digital archives and…

The Coevolution of Society and Multimedia Technology: Issues in Predicting the Future Innovation and Use of a Ubiquitous Technology.

ERIC Educational Resources Information Center

Stewart, James; Williams, Robin

1998-01-01

Criticizes "technologically deterministic" approaches, which seek to extrapolate social change from technological potential. Shows how a three-layer model of component, system, and application technologies can be used to integrate findings from the use and development of technology in specific sectors. Examines three cases of…

Conciliation biology: the eco-evolutionary management of permanently invaded biotic systems

PubMed Central

Carroll, Scott P

2011-01-01

Biotic invaders and similar anthropogenic novelties such as domesticates, transgenics, and cancers can alter ecology and evolution in environmental, agricultural, natural resource, public health, and medical systems. The resulting biological changes may either hinder or serve management objectives. For example, biological control and eradication programs are often defeated by unanticipated resistance evolution and by irreversibility of invader impacts. Moreover, eradication may be ill-advised when nonnatives introduce beneficial functions. Thus, contexts that appear to call for eradication may instead demand managed coexistence of natives with nonnatives, and yet applied biologists have not generally considered the need to manage the eco-evolutionary dynamics that commonly result from interactions of natives with nonnatives. Here, I advocate a conciliatory approach to managing systems where novel organisms cannot or should not be eradicated. Conciliatory strategies incorporate benefits of nonnatives to address many practical needs including slowing rates of resistance evolution, promoting evolution of indigenous biological control, cultivating replacement services and novel functions, and managing native–nonnative coevolution. Evolutionary links across disciplines foster cohesion essential for managing the broad impacts of novel biotic systems. Rather than signaling defeat, conciliation biology thus utilizes the predictive power of evolutionary theory to offer diverse and flexible pathways to more sustainable outcomes. PMID:25567967

Molybdenite Mineral Evolution: A Study Of Trace Elements Through Time

NASA Astrophysics Data System (ADS)

McMillan, M. M.; Downs, R. T.; Stein, H. J.; Zimmerman, A.; Beitscher, B. A.; Sverjensky, D. A.; Papineau, D.; Armstrong, J. T.; Hazen, R. M.

2010-12-01

Mineral evolution explores changes through time in Earth’s near-surface mineralogy, including diversity of species, relative abundances of species, and compositional ranges of major, minor and trace elements. Such studies elucidate the co-evolution of the geosphere and biosphere. Accordingly, we investigated trace and minor elements in molybdenite (MoS2) with known ages from 3 billion years to recent. Molybdenite, the commonest mineral of Mo, may prove to be a useful case study as a consequence of its presence in Earth’s early history, the effects of oxidation on Mo mobility, and the possible role of Mo mineral coevolution with biology via its role in the nitrogen fixation enzyme nitrogenase. We employed ICPMS, SEM and electron microprobe analyses to detect trace and minor elements. We detected significant amounts of Mn and Cu (~100 ppm) and greater amounts of Fe, W, and Re (to ~4000 ppm). Molybdenites commonly contain micro inclusions, resulting in local concentrations in otherwise homogeneous samples. Inhomogeneities in Fe, Zn and Sn concentrations, for example, point to the presence of pyrite, sphalerite and cassiterite inclusions, respectively. Analyses examined as a function of time reveal that samples containing significant concentrations (>200 ppm, compared to average values < 100 ppm) of W and Re formed primarily within the last billion years. These trends may reflect changes in the mobility of W and Re in oxic hydrothermal fluids at shallow crustal conditions following the Great Oxidation Event.

Lineage-specific expansion of IFIT gene family: an insight into coevolution with IFN gene family.

PubMed

Liu, Ying; Zhang, Yi-Bing; Liu, Ting-Kai; Gui, Jian-Fang

2013-01-01

In mammals, IFIT (Interferon [IFN]-induced proteins with Tetratricopeptide Repeat [TPR] motifs) family genes are involved in many cellular and viral processes, which are tightly related to mammalian IFN response. However, little is known about non-mammalian IFIT genes. In the present study, IFIT genes are identified in the genome databases from the jawed vertebrates including the cartilaginous elephant shark but not from non-vertebrates such as lancelet, sea squirt and acorn worm, suggesting that IFIT gene family originates from a vertebrate ancestor about 450 million years ago. IFIT family genes show conserved gene structure and gene arrangements. Phylogenetic analyses reveal that this gene family has expanded through lineage-specific and species-specific gene duplication. Interestingly, IFN gene family seem to share a common ancestor and a similar evolutionary mechanism; the function link of IFIT genes to IFN response is present early since the origin of both gene families, as evidenced by the finding that zebrafish IFIT genes are upregulated by fish IFNs, poly(I:C) and two transcription factors IRF3/IRF7, likely via the IFN-stimulated response elements (ISRE) within the promoters of vertebrate IFIT family genes. These coevolution features creates functional association of both family genes to fulfill a common biological process, which is likely selected by viral infection during evolution of vertebrates. Our results are helpful for understanding of evolution of vertebrate IFN system.

Habitability for Complex Life and the Development and Self-Limitations of the Biotic Enhancement of Weathering

NASA Astrophysics Data System (ADS)

Schwartzman, D. W.; Volk, T.

2014-12-01

We submit that the tightly coupled coevolution of biota and climate is a critical driver of the self-organization of the biosphere over geologic time. The long-term carbon biogeochemical cycle includes a major influence of biology relevant to climatic, namely the biotic enhancement of weathering (BEW). According to a meta-analysis of field and experimental evidence, the likely magnitude of the present BEW is roughly two orders of magnitude, the culmination of its progressive increase over geologic time. Within the context of modeling this long-term cycle, this value can be used to estimate the likely abiotic temperature history of the Earth's surface, assuming plausible initial temperatures, and histories of volcanic outgassing and continental crust growth. The result of this modeling is that the Earth would have been habitable for thermophilic life (growing above 50 deg C) for the past 4.4 billion years, but not for low-temperature life, including plants and animals. Hence biospheric cooling due to biotic actions allowed the emergence of complex life. Much larger increases in BEW are self-limiting, since the atmospheric CO2 level would plunge below the lower limit potentially for photosynthesis, thereby driving a decline in the biological productivity and global BEW, related to reduced plant and soil activities, with the system being kept at this threshold or going back to higher CO2 levels, with scenarios dependent on volcanic outgassing and solar inputs. We will present astrobiological implications of this modeling. References: Schwartzman D (1999, 2002) Life, Temperature, and the Earth: The Self Organizing Biosphere. Columbia Univ. Press; Schwartzman, D. (2013) Keynote: The Geobiology of Weathering: The 13th Hypothesis. Goldschmidt Conference. (Schwartzman D. and Brantley S. (2013) Mineral. Mag. 77(5): 2170); Volk T (1998) Gaia's Body: Toward a Physiology of Earth. Copernicus.

Effect of Heterogeneous Investments on the Evolution of Cooperation in Spatial Public Goods Game

PubMed Central

Huang, Keke; Wang, Tao; Cheng, Yuan; Zheng, Xiaoping

2015-01-01

Understanding the emergence of cooperation in spatial public goods game remains a grand challenge across disciplines. In most previous studies, it is assumed that the investments of all the cooperators are identical, and often equal to 1. However, it is worth mentioning that players are diverse and heterogeneous when choosing actions in the rapidly developing modern society and researchers have shown more interest to the heterogeneity of players recently. For modeling the heterogeneous players without loss of generality, it is assumed in this work that the investment of a cooperator is a random variable with uniform distribution, the mean value of which is equal to 1. The results of extensive numerical simulations convincingly indicate that heterogeneous investments can promote cooperation. Specifically, a large value of the variance of the random variable can decrease the two critical values for the result of behavioral evolution effectively. Moreover, the larger the variance is, the better the promotion effect will be. In addition, this article has discussed the impact of heterogeneous investments when the coevolution of both strategy and investment is taken into account. Comparing the promotion effect of coevolution of strategy and investment with that of strategy imitation only, we can conclude that the coevolution of strategy and investment decreases the asymptotic fraction of cooperators by weakening the heterogeneity of investments, which further demonstrates that heterogeneous investments can promote cooperation in spatial public goods game. PMID:25781345

Frontier mutualism: coevolutionary patterns at the northern range limit of the leaf-cutter ant–fungus symbiosis

PubMed Central

Mueller, Ulrich G.; Mikheyev, Alexander S.; Solomon, Scott E.; Cooper, Michael

2011-01-01

Tropical leaf-cutter ants cultivate the fungus Attamyces bromatificus in a many-to-one, diffuse coevolutionary relationship where ant and fungal partners re-associate frequently over time. To evaluate whether ant–Attamyces coevolution is more specific (tighter) in peripheral populations, we characterized the host-specificities of Attamyces genotypes at their northern, subtropical range limits (southern USA, Mexico and Cuba). Population-genetic patterns of northern Attamyces reveal features that have so far not been observed in the diffusely coevolving, tropical ant–Attamyces associations. These unique features include (i) cases of one-to-one ant–Attamyces specialization that tighten coevolution at the northern frontier; (ii) distributions of genetically identical Attamyces clones over large areas (up to 81 000 km2, approx. the area of Ireland, Austria or Panama); (iii) admixture rates between Attamyces lineages that appear lower in northern than in tropical populations; and (iv) long-distance gene flow of Attamyces across a dispersal barrier for leaf-cutter ants (ocean between mainland North America and Cuba). The latter suggests that Attamyces fungi may occasionally disperse independently of the ants, contrary to the traditional assumption that Attamyces fungi depend entirely on leaf-cutter queens for dispersal. Peripheral populations in Argentina or at mid-elevation sites in the Andes may reveal additional regional variants in ant–Attamyces coevolution. Studies of such populations are most likely to inform models of coextinctions of obligate mutualistic partners that are doubly stressed by habitat marginality and by environmental change. PMID:21389026

Plastid–Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae

PubMed Central

Weng, Mao-Lun; Ruhlman, Tracey A.; Jansen, Robert K.

2016-01-01

Plastids and mitochondria have many protein complexes that include subunits encoded by organelle and nuclear genomes. In animal cells, compensatory evolution between mitochondrial and nuclear-encoded subunits was identified and the high mitochondrial mutation rates were hypothesized to drive compensatory evolution in nuclear genomes. In plant cells, compensatory evolution between plastid and nucleus has rarely been investigated in a phylogenetic framework. To investigate plastid–nuclear coevolution, we focused on plastid ribosomal protein genes that are encoded by plastid and nuclear genomes from 27 Geraniales species. Substitution rates were compared for five sets of genes representing plastid- and nuclear-encoded ribosomal subunit proteins targeted to the cytosol or the plastid as well as nonribosomal protein controls. We found that nonsynonymous substitution rates (dN) and the ratios of nonsynonymous to synonymous substitution rates (ω) were accelerated in both plastid- (CpRP) and nuclear-encoded subunits (NuCpRP) of the plastid ribosome relative to control sequences. Our analyses revealed strong signals of cytonuclear coevolution between plastid- and nuclear-encoded subunits, in which nonsynonymous substitutions in CpRP and NuCpRP tend to occur along the same branches in the Geraniaceae phylogeny. This coevolution pattern cannot be explained by physical interaction between amino acid residues. The forces driving accelerated coevolution varied with cellular compartment of the sequence. Increased ω in CpRP was mainly due to intensified positive selection whereas increased ω in NuCpRP was caused by relaxed purifying selection. In addition, the many indels identified in plastid rRNA genes in Geraniaceae may have contributed to changes in plastid subunits. PMID:27190001

Web building and silk properties functionally covary among species of wolf spider.

PubMed

Lacava, Mariángeles; Camargo, Arley; Garcia, Luis F; Benamú, Marco A; Santana, Martin; Fang, Jian; Wang, Xungai; Blamires, Sean J

2018-04-15

Although phylogenetic studies have shown covariation between the properties of spider major ampullate (MA) silk and web building, both spider webs and silks are highly plastic so we cannot be sure whether these traits functionally covary or just vary across environments that the spiders occupy. As MaSp2-like proteins provide MA silk with greater extensibility, their presence is considered necessary for spider webs to effectively capture prey. Wolf spiders (Lycosidae) are predominantly non-web building, but a select few species build webs. We accordingly collected MA silk from two web-building and six non-web-building species found in semirural ecosystems in Uruguay to test whether the presence of MaSp2-like proteins (indicated by amino acid composition, silk mechanical properties and silk nanostructures) was associated with web building across the group. The web-building and non-web-building species were from disparate subfamilies so we estimated a genetic phylogeny to perform appropriate comparisons. For all of the properties measured, we found differences between web-building and non-web-building species. A phylogenetic regression model confirmed that web building and not phylogenetic inertia influences silk properties. Our study definitively showed an ecological influence over spider silk properties. We expect that the presence of the MaSp2-like proteins and the subsequent nanostructures improves the mechanical performance of silks within the webs. Our study furthers our understanding of spider web and silk co-evolution and the ecological implications of spider silk properties. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution.

PubMed

Burke, Jordan E; Longhurst, Adam D; Merkurjev, Daria; Sales-Lee, Jade; Rao, Beiduo; Moresco, James J; Yates, John R; Li, Jingyi Jessica; Madhani, Hiten D

2018-05-03

Tools to understand how the spliceosome functions in vivo have lagged behind advances in the structural biology of the spliceosome. Here, methods are described to globally profile spliceosome-bound pre-mRNA, intermediates, and spliced mRNA at nucleotide resolution. These tools are applied to three yeast species that span 600 million years of evolution. The sensitivity of the approach enables the detection of canonical and non-canonical events, including interrupted, recursive, and nested splicing. This application of statistical modeling uncovers independent roles for the size and position of the intron and the number of introns per transcript in substrate progression through the two catalytic stages. These include species-specific inputs suggestive of spliceosome-transcriptome coevolution. Further investigations reveal the ATP-dependent discard of numerous endogenous substrates after spliceosome assembly in vivo and connect this discard to intron retention, a form of splicing regulation. Spliceosome profiling is a quantitative, generalizable global technology used to investigate an RNP central to eukaryotic gene expression. Copyright © 2018 Elsevier Inc. All rights reserved.

Evolution-Based Functional Decomposition of Proteins

PubMed Central

Rivoire, Olivier; Reynolds, Kimberly A.; Ranganathan, Rama

2016-01-01

The essential biological properties of proteins—folding, biochemical activities, and the capacity to adapt—arise from the global pattern of interactions between amino acid residues. The statistical coupling analysis (SCA) is an approach to defining this pattern that involves the study of amino acid coevolution in an ensemble of sequences comprising a protein family. This approach indicates a functional architecture within proteins in which the basic units are coupled networks of amino acids termed sectors. This evolution-based decomposition has potential for new understandings of the structural basis for protein function. To facilitate its usage, we present here the principles and practice of the SCA and introduce new methods for sector analysis in a python-based software package (pySCA). We show that the pattern of amino acid interactions within sectors is linked to the divergence of functional lineages in a multiple sequence alignment—a model for how sector properties might be differentially tuned in members of a protein family. This work provides new tools for studying proteins and for generally testing the concept of sectors as the principal units of function and adaptive variation. PMID:27254668

Coevolution of nutrigenomics and society: ethical considerations.

PubMed

Korthals, Michiel

2011-12-01

To optimize the coevolution of nutrigenomics and society (ie, the reciprocal stimulation of both developments), I analyzed chances for a fruitful match between normative concepts and strategies of both developments. Nutrigenomics embodies ≥ 3 normative concepts. First, food is exclusively interpreted in terms of disease prevention. Second, striving for health is interpreted as the quantification of risks and prevention of diseases through positive food-gene interactions. The third normative idea is that disease prevention by the minimization of risks is an individual's task. My thesis was that these concepts of nutrigenomics would not easily match with concepts of food and health of various food styles in Western societies, which, for instance, parents in the case of metabolic programming endorse and with a philosophical view of the relation between food, health, and the meaning of life. Next, I reflected on the nonsynchronized coevolution of nutrigenomics and society because of this mismatch and introduced the concept of the fair representation of food styles in nutrigenomic developments. To synchronize and optimize the coevolution of nutrigenomics and society, I propose that the research policy of nutrigenomics should change to a research partnership with society on the basis of fair representation.

Sexually antagonistic coevolution for sexual harassment can act as a barrier to further invasions by parthenogenesis.

PubMed

Kawatsu, Kazutaka

2013-02-01

The assumption of a twofold cost of sex not only complicates the maintenance of sex but also sets conditions for sexual conflict: in organisms with the twofold cost, males often sexually harass females. Sexual harassment is detrimental to female fitness and thus might help maintain sexual populations if male harassment inflicts a harsher cost on parthenogens than on sexual females (asymmetric harassment cost). However, the generality of this concept is now considered doubtful because selective harassment of parthenogens results in loss of mating opportunities for males. Using three mathematical models, I show here that sexual harassment still can impose the asymmetric cost on parthenogens. First, I apply the Lotka-Volterra model to show the degree of asymmetric harassment cost that permits sex to be maintained stably in the population. Second, using adaptive dynamics, I examine whether sexually antagonistic coevolution for sexual harassment, which occurs only in sexual populations, can promote the asymmetric harassment cost. Finally, an individual-based model, which assumes a spatial structure unlike that in the other two, demonstrates that the asymmetric evolution of harassment cost prevents further invasions of parthenogens from different patches into sexual lineages; these mechanisms may account for allopatric distributions of sexual and parthenogenetic lineages as well as the maintenance of sex.

On meme--gene coevolution.

PubMed

Bull, L; Holland, O; Blackmore, S

2000-01-01

In this article we examine the effects of the emergence of a new replicator, memes, on the evolution of a pre-existing replicator, genes. Using a version of the NKCS model we examine the effects of increasing the rate of meme evolution in relation to the rate of gene evolution, for various degrees of interdependence between the two replicators. That is, the effects of memes' (suggested) more rapid rate of evolution in comparison to that of genes is investigated using a tunable model of coevolution. It is found that, for almost any degree of interdependence between the two replicators, as the rate of meme evolution increases, a phase transition-like dynamic occurs under which memes have a significantly detrimental effect on the evolution of genes, quickly resulting in the cessation of effective gene evolution. Conversely, the memes experience a sharp increase in benefit from increasing their rate of evolution. We then examine the effects of enabling genes to reduce the percentage of gene-detrimental evolutionary steps taken by memes. Here a critical region emerges as the comparative rate of meme evolution increases, such that if genes cannot effectively select memes a high percentage of the time, they suffer from meme evolution as if they had almost no selective capability.

Biomimicry of symbiotic multi-species coevolution for discrete and continuous optimization in RFID networks.

PubMed

Lin, Na; Chen, Hanning; Jing, Shikai; Liu, Fang; Liang, Xiaodan

2017-03-01

In recent years, symbiosis as a rich source of potential engineering applications and computational model has attracted more and more attentions in the adaptive complex systems and evolution computing domains. Inspired by different symbiotic coevolution forms in nature, this paper proposed a series of multi-swarm particle swarm optimizers called PS 2 Os, which extend the single population particle swarm optimization (PSO) algorithm to interacting multi-swarms model by constructing hierarchical interaction topologies and enhanced dynamical update equations. According to different symbiotic interrelationships, four versions of PS 2 O are initiated to mimic mutualism, commensalism, predation, and competition mechanism, respectively. In the experiments, with five benchmark problems, the proposed algorithms are proved to have considerable potential for solving complex optimization problems. The coevolutionary dynamics of symbiotic species in each PS 2 O version are also studied respectively to demonstrate the heterogeneity of different symbiotic interrelationships that effect on the algorithm's performance. Then PS 2 O is used for solving the radio frequency identification (RFID) network planning (RNP) problem with a mixture of discrete and continuous variables. Simulation results show that the proposed algorithm outperforms the reference algorithms for planning RFID networks, in terms of optimization accuracy and computation robustness.

Co-Evolution of User and Organizational Interfaces: A Longitudinal Case Study of WWW Dissemination of National Statistics.

ERIC Educational Resources Information Center

Marchionini, Gary

2002-01-01

Describes how user interfaces for the Bureau of Labor Statistics (BLS) web site evolved over a 5-year period along with the larger organizational interface and how this co-evolution has influenced the institution. Interviews with BLS staff and transaction log analysis are the foci of this study, as well as user information-seeking studies and user…

Differential susceptibility to plasticity: a 'missing link' between gene-culture co-evolution and neuropsychiatric spectrum disorders?

PubMed Central

2012-01-01

Brüne's proposal that erstwhile 'vulnerability' genes need to be reconsidered as 'plasticity' genes, given the potential for certain environments to yield increased positive function in the same domain as potential dysfunction, has implications for psychiatric nosology as well as a more dynamic understanding of the relationship between genes and culture. In addition to validating neuropsychiatric spectrum disorder nosologies by calling for similar methodological shifts in gene-environment-interaction studies, Brüne's position elevates the importance of environmental contexts - inclusive of socio-cultural variables - as mechanisms that contribute to clinical presentation. We assert that when models of susceptibility to plasticity and neuropsychiatric spectrum disorders are concomitantly considered, a new line of inquiry emerges into the co-evolution and co-determination of socio-cultural contexts and endophenotypes. This presents potentially unique opportunities, benefits, challenges, and responsibilities for research and practice in psychiatry. Please see related manuscript: http://www.biomedcentral.com/1741-7015/10/38 PMID:22510307

Differential susceptibility to plasticity: a 'missing link' between gene-culture co-evolution and neuropsychiatric spectrum disorders?

PubMed

Wurzman, Rachel; Giordano, James

2012-04-17

Brüne's proposal that erstwhile 'vulnerability' genes need to be reconsidered as 'plasticity' genes, given the potential for certain environments to yield increased positive function in the same domain as potential dysfunction, has implications for psychiatric nosology as well as a more dynamic understanding of the relationship between genes and culture. In addition to validating neuropsychiatric spectrum disorder nosologies by calling for similar methodological shifts in gene-environment-interaction studies, Brüne's position elevates the importance of environmental contexts - inclusive of socio-cultural variables - as mechanisms that contribute to clinical presentation. We assert that when models of susceptibility to plasticity and neuropsychiatric spectrum disorders are concomitantly considered, a new line of inquiry emerges into the co-evolution and co-determination of socio-cultural contexts and endophenotypes. This presents potentially unique opportunities, benefits, challenges, and responsibilities for research and practice in psychiatry. Please see related manuscript: http://www.biomedcentral.com/1741-7015/10/38.

The co-evolution of social institutions, demography, and large-scale human cooperation.

PubMed

Powers, Simon T; Lehmann, Laurent

2013-11-01

Human cooperation is typically coordinated by institutions, which determine the outcome structure of the social interactions individuals engage in. Explaining the Neolithic transition from small- to large-scale societies involves understanding how these institutions co-evolve with demography. We study this using a demographically explicit model of institution formation in a patch-structured population. Each patch supports both social and asocial niches. Social individuals create an institution, at a cost to themselves, by negotiating how much of the costly public good provided by cooperators is invested into sanctioning defectors. The remainder of their public good is invested in technology that increases carrying capacity, such as irrigation systems. We show that social individuals can invade a population of asocials, and form institutions that support high levels of cooperation. We then demonstrate conditions where the co-evolution of cooperation, institutions, and demographic carrying capacity creates a transition from small- to large-scale social groups. © 2013 John Wiley & Sons Ltd/CNRS.

Hydrologic Regulation of Plant Rooting Depth and Vice Versa

NASA Astrophysics Data System (ADS)

Fan, Y.; Miguez-Macho, G.

2017-12-01

How deep plant roots go and why may hold the answer to several questions regarding the co-evolution of terrestrial life and its environment. In this talk we explore how plant rooting depth responds to the hydrologic plumbing system in the soil/regolith/bedrocks, and vice versa. Through analyzing 2200 root observations of >1000 species along biotic (life form, genus) and abiotic (precipitation, soil, drainage) gradients, we found strong sensitivities of rooting depth to local soil water profiles determined by precipitation infiltration depth from the top (reflecting climate and soil), and groundwater table depth from below (reflecting topography-driven land drainage). In well-drained uplands, rooting depth follows infiltration depth; in waterlogged lowlands, roots stay shallow avoiding oxygen stress below the water table; in between, high productivity and drought can send roots many meters down to groundwater capillary fringe. We explore the global significance of this framework using an inverse model, and the implications to the coevolution of deep roots and the CZ in the Early-Mid Devonian when plants colonized the upland environments.

Persistence of host defence behaviour in the absence of avian brood parasitism

PubMed Central

Peer, Brian D.; Kuehn, Michael J.; Rothstein, Stephen I.; Fleischer, Robert C.

2011-01-01

The fate of host defensive behaviour in the absence of selection from brood parasitism is critical to long-term host–parasite coevolution. We investigated whether New World Bohemian waxwings Bombycilla garrulus that are allopatric from brown-headed cowbird Molothrus ater and common cuckoo Cuculus canorus parasitism have retained egg rejection behaviour. We found that egg rejection was expressed by 100 per cent of Bohemian waxwings. Our phylogeny revealed that Bohemian and Japanese waxwings Bombycilla japonica were sister taxa, and this clade was sister to the cedar waxwing Bombycilla cedrorum. In addition, there was support for a split between Old and New World Bohemian waxwings. Our molecular clock estimates suggest that egg rejection may have been retained for 2.8–3.0 Myr since New World Bohemian waxwings inherited it from their common ancestor with the rejecter cedar waxwings. These results support the ‘single trajectory’ model of host–brood parasite coevolution that once hosts evolve defences, they are retained, forcing parasites to become more specialized over time. PMID:21493623

Clustered marginalization of minorities during social transitions induced by co-evolution of behaviour and network structure

NASA Astrophysics Data System (ADS)

Schleussner, Carl-Friedrich; Donges, Jonathan F.; Engemann, Denis A.; Levermann, Anders

2016-08-01

Large-scale transitions in societies are associated with both individual behavioural change and restructuring of the social network. These two factors have often been considered independently, yet recent advances in social network research challenge this view. Here we show that common features of societal marginalization and clustering emerge naturally during transitions in a co-evolutionary adaptive network model. This is achieved by explicitly considering the interplay between individual interaction and a dynamic network structure in behavioural selection. We exemplify this mechanism by simulating how smoking behaviour and the network structure get reconfigured by changing social norms. Our results are consistent with empirical findings: The prevalence of smoking was reduced, remaining smokers were preferentially connected among each other and formed increasingly marginalized clusters. We propose that self-amplifying feedbacks between individual behaviour and dynamic restructuring of the network are main drivers of the transition. This generative mechanism for co-evolution of individual behaviour and social network structure may apply to a wide range of examples beyond smoking.

Host Jumps and Radiation, Not Co-Divergence Drives Diversification of Obligate Pathogens. A Case Study in Downy Mildews and Asteraceae.

PubMed

Choi, Young-Joon; Thines, Marco

2015-01-01

Even though the microevolution of plant hosts and pathogens has been intensely studied, knowledge regarding macro-evolutionary patterns is limited. Having the highest species diversity and host-specificity among Oomycetes, downy mildews are a useful a model for investigating long-term host-pathogen coevolution. We show that phylogenies of Bremia and Asteraceae are significantly congruent. The accepted hypothesis is that pathogens have diverged contemporarily with their hosts. But maximum clade age estimation and sequence divergence comparison reveal that congruence is not due to long-term coevolution but rather due to host-shift driven speciation (pseudo-cospeciation). This pattern results from parasite radiation in related hosts, long after radiation and speciation of the hosts. As large host shifts free pathogens from hosts with effector triggered immunity subsequent radiation and diversification in related hosts with similar innate immunity may follow, resulting in a pattern mimicking true co-divergence, which is probably limited to the terminal nodes in many pathogen groups.

Opinion diversity and community formation in adaptive networks

NASA Astrophysics Data System (ADS)

Yu, Y.; Xiao, G.; Li, G.; Tay, W. P.; Teoh, H. F.

2017-10-01

It is interesting and of significant importance to investigate how network structures co-evolve with opinions. In this article, we show that, a simple model integrating consensus formation, link rewiring, and opinion change allows complex system dynamics to emerge, driving the system into a dynamic equilibrium with the co-existence of diversified opinions. Specifically, similar opinion holders may form into communities yet with no strict community consensus; and rather than being separated into disconnected communities, different communities are connected by a non-trivial proportion of inter-community links. More importantly, we show that the complex dynamics may lead to different numbers of communities at the steady state with a given tolerance between different opinion holders. We construct a framework for theoretically analyzing the co-evolution process. Theoretical analysis and extensive simulation results reveal some useful insights into the complex co-evolution process, including the formation of dynamic equilibrium, the transition between different steady states with different numbers of communities, and the dynamics between opinion distribution and network modularity.

Host Jumps and Radiation, Not Co‐Divergence Drives Diversification of Obligate Pathogens. A Case Study in Downy Mildews and Asteraceae

PubMed Central

Choi, Young-Joon; Thines, Marco

2015-01-01

Even though the microevolution of plant hosts and pathogens has been intensely studied, knowledge regarding macro-evolutionary patterns is limited. Having the highest species diversity and host-specificity among Oomycetes, downy mildews are a useful a model for investigating long-term host-pathogen coevolution. We show that phylogenies of Bremia and Asteraceae are significantly congruent. The accepted hypothesis is that pathogens have diverged contemporarily with their hosts. But maximum clade age estimation and sequence divergence comparison reveal that congruence is not due to long-term coevolution but rather due to host-shift driven speciation (pseudo-cospeciation). This pattern results from parasite radiation in related hosts, long after radiation and speciation of the hosts. As large host shifts free pathogens from hosts with effector triggered immunity subsequent radiation and diversification in related hosts with similar innate immunity may follow, resulting in a pattern mimicking true co-divergence, which is probably limited to the terminal nodes in many pathogen groups. PMID:26230508

Coevolution of cooperation and network structure under natural selection

NASA Astrophysics Data System (ADS)

Yang, D.-P.; Lin, H.; Shuai, J. W.

2011-02-01

A coevolution model by coupling mortality and fertility selection is introduced to investigate the evolution of cooperation and network structure in the prisoner's dilemma game. The cooperation level goes through a continuous phase transition vs. defection temptation b for low mortality selection intensity β and through a discontinuous one for infinite β. The cooperation level is enhanced most at β≈1 for any b. The local and global properties of the network structure, such as cluster and cooperating k-core, are investigated for the understanding of cooperation evolution. Cooperation is promoted by forming a tight cooperating k-core at moderate β, but too large β will destroy the cooperating k-core rapidly resulting in a rapid drop of the cooperation level. Importantly, the infinite β changes the normalized sucker's payoff S from 0 to 1-b and its dynamics of the cooperation level undergoes a very slow power-law decay, which leads the evolution into the regime of neutral evolution.

Clustered marginalization of minorities during social transitions induced by co-evolution of behaviour and network structure.

PubMed

Schleussner, Carl-Friedrich; Donges, Jonathan F; Engemann, Denis A; Levermann, Anders

2016-08-11

Large-scale transitions in societies are associated with both individual behavioural change and restructuring of the social network. These two factors have often been considered independently, yet recent advances in social network research challenge this view. Here we show that common features of societal marginalization and clustering emerge naturally during transitions in a co-evolutionary adaptive network model. This is achieved by explicitly considering the interplay between individual interaction and a dynamic network structure in behavioural selection. We exemplify this mechanism by simulating how smoking behaviour and the network structure get reconfigured by changing social norms. Our results are consistent with empirical findings: The prevalence of smoking was reduced, remaining smokers were preferentially connected among each other and formed increasingly marginalized clusters. We propose that self-amplifying feedbacks between individual behaviour and dynamic restructuring of the network are main drivers of the transition. This generative mechanism for co-evolution of individual behaviour and social network structure may apply to a wide range of examples beyond smoking.

The species-area relationship and evolution.

PubMed

Lawson, Daniel; Jensen, Henrik Jeldtoft

2006-08-07

Models relating to the species-area curve usually assume the existence of species, and are concerned mainly with ecological timescales. We examine an individual-based model of co-evolution on a spatial lattice based on the tangled nature model in which species are emergent structures, and show that reproduction, mutation and dispersion by diffusion, with interaction via genotype space, produces power-law species-area relations as observed in ecological measurements at medium scales. We find that long-lasting co-evolutionary habitats form, allowing high diversity levels in a spatially homogenous system.

Bioaerosols in the Earth system: Climate, health, and ecosystem interactions

NASA Astrophysics Data System (ADS)

Fröhlich-Nowoisky, Janine; Kampf, Christopher J.; Weber, Bettina; Huffman, J. Alex; Pöhlker, Christopher; Andreae, Meinrat O.; Lang-Yona, Naama; Burrows, Susannah M.; Gunthe, Sachin S.; Elbert, Wolfgang; Su, Hang; Hoor, Peter; Thines, Eckhard; Hoffmann, Thorsten; Després, Viviane R.; Pöschl, Ulrich

2016-12-01

Aerosols of biological origin play a vital role in the Earth system, particularly in the interactions between atmosphere, biosphere, climate, and public health. Airborne bacteria, fungal spores, pollen, and other bioparticles are essential for the reproduction and spread of organisms across various ecosystems, and they can cause or enhance human, animal, and plant diseases. Moreover, they can serve as nuclei for cloud droplets, ice crystals, and precipitation, thus influencing the hydrological cycle and climate. The sources, abundance, composition, and effects of biological aerosols and the atmospheric microbiome are, however, not yet well characterized and constitute a large gap in the scientific understanding of the interaction and co-evolution of life and climate in the Earth system. This review presents an overview of the state of bioaerosol research, highlights recent advances, and outlines future perspectives in terms of bioaerosol identification, characterization, transport, and transformation processes, as well as their interactions with climate, health, and ecosystems, focusing on the role bioaerosols play in the Earth system.

Bioaerosols in the Earth system: Climate, health, and ecosystem interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fröhlich-Nowoisky, Janine; Kampf, Christopher J.; Weber, Bettina

Aerosols of biological origin play a vital role in the Earth system, particularly in the in-teractions between atmosphere, biosphere, climate, and public health. Airborne bacteria, fungal spores, pollen, and other bioparticles are essential for the reproduction and spread of organisms across various ecosystems, and they can cause or enhance human, animal, and plant diseases. Moreover, they can serve as nuclei for cloud droplets, ice crystals, and precipitation, thus influencing the hydrological cycle and climate. The actual formation, abundance, composition, and effects of biological aerosols and the atmospheric microbi-ome are, however, not yet well characterized and constitute a large gap inmore » the scientific understanding of the interaction and co-evolution of life and climate in the Earth system. This review presents an overview of the state of bioaerosol research and highlights recent advances in terms of bioaerosol identification, characterization, transport, and transfor-mation processes, as well as their interactions with climate, health, and ecosystems, focus-ing on the role bioaerosols play in the Earth system.« less

Sequence co-evolution gives 3D contacts and structures of protein complexes

PubMed Central

Hopf, Thomas A; Schärfe, Charlotta P I; Rodrigues, João P G L M; Green, Anna G; Kohlbacher, Oliver; Sander, Chris; Bonvin, Alexandre M J J; Marks, Debora S

2014-01-01

Protein–protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein–protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein–protein interaction networks and used for interaction predictions at residue resolution. DOI: http://dx.doi.org/10.7554/eLife.03430.001 PMID:25255213

Phylogenetic placement of an unusual coral mushroom challenges the classic hypothesis of strict coevolution in the Apterostigma pilosum group ant-fungus mutualism

Treesearch

Bryn T.M. Dentinger; D.Jean Lodge; Andrew B. Munkacsi; Dennis E. Desjardin; David J. McLaughlin

2009-01-01

The ~50 million-year-old fungus-farming ant mutualism is a classic example of coevolution, involving ants that subsist on asexual, fungal biomass, in turn propagating the fungus clonally through nest-to-nest transmission. Most mutualistic ants cultivate two closely related groups of gilled mushrooms, whereas one small group of ants in the genus ...

Coevolution study of mitochondria respiratory chain proteins: toward the understanding of protein--protein interaction.

PubMed

Yang, Ming; Ge, Yan; Wu, Jiayan; Xiao, Jingfa; Yu, Jun

2011-05-20

Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein--protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using "Mirror tree" method on the respiratory chain (RC) proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein--protein interaction in intra-complex and the binary protein--protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions (Wilcoxon test, p-value = 4.4 × 10(-6)). Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein--protein interaction. Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study. Copyright © 2011. Published by Elsevier Ltd.

Phylogenetic placement of an unusual coral mushroom challenges the classic hypothesis of strict coevolution in the apterostigma pilosum group ant-fungus mutualism.

PubMed

Dentinger, Bryn T M; Lodge, D Jean; Munkacsi, Andrew B; Desjardin, Dennis E; McLaughlin, David J

2009-08-01

The approximately 50 million-year-old fungus-farming ant mutualism is a classic example of coevolution, involving ants that subsist on asexual, fungal biomass, in turn propagating the fungus clonally through nest-to-nest transmission. Most mutualistic ants cultivate two closely related groups of gilled mushrooms, whereas one small group of ants in the genus Apterostigma cultivates a distantly related lineage comprised of the G2 and G4 groups. The G2 and G4 fungi were previously shown to form a monophyletic group sister to the thread-like coral mushroom family Pterulaceae. Here, we identify an enigmatic coral mushroom that produces both fertile and sterile fruiting structures as the closest free-living relative of the G4 fungi, challenging the monophyly of the Apterostigma-cultivated fungi for the first time. Both nonparametric bootstrap and Bayesian posterior probability support the node leading to the G4 cultivars and a free-living Pterula mushroom. These data suggest three scenarios that contradict the hypothesis of strict coevolution: (1) multiple domestications, (2) escape from domestication, (3) selection of single cultivar lineages from an ancestral mixed-fungus garden. These results illustrate how incomplete phylogenies for coevolved symbionts impede our understanding of the patterns and processes of coevolution.

On Cellular Darwinism: Mitochondria.

PubMed

Bull, Larry

2016-01-01

The significant role of mitochondria within cells is becoming increasingly clear. This letter uses the NKCS model of coupled fitness landscapes to explore aspects of organelle-nucleus coevolution. The phenomenon of mitochondrial diversity is allowed to emerge under a simple intracellular evolutionary process, including varying the relative rate of evolution by the organelle. It is shown how the conditions for the maintenance of more than one genetic variant of mitochondria are similar to those previously suggested as needed for the original symbiotic origins of the relationship using the NKCS model.

Tangled nature: a model of evolutionary ecology.

PubMed

Christensen, Kim; di Collobiano, Simone A; Hall, Matt; Jensen, Henrik J

2002-05-07

We discuss a simple model of co-evolution. In order to emphasize the effect of interaction between individuals, the entire population is subjected to the same physical environment. Species are emergent structures and extinction, origination and diversity are entirely a consequence of co-evolutionary interaction between individuals. For comparison, we consider both asexual and sexually reproducing populations. In either case, the system evolves through periods of hectic reorganization separated by periods of coherent stable coexistence. Copyright 2002 Elsevier Science Ltd. All rights reserved.

Sensory exploitation and sexual conflict

PubMed Central

Arnqvist, Göran

2006-01-01

Much of the literature on male–female coevolution concerns the processes by which male traits and female preferences for these can coevolve and be maintained by selection. There has been less explicit focus on the origin of male traits and female preferences. Here, I argue that it is important to distinguish origin from subsequent coevolution and that insights into the origin can help us appreciate the relative roles of various coevolutionary processes for the evolution of diversity in sexual dimorphism. I delineate four distinct scenarios for the origin of male traits and female preferences that build on past contributions, two of which are based on pre-existing variation in quality indicators among males and two on exploitation of pre-existing sensory biases among females. Recent empirical research, and theoretical models, suggest that origin by sensory exploitation has been widespread. I argue that this points to a key, but perhaps transient, role for sexually antagonistic coevolution (SAC) in the subsequent evolutionary elaboration of sexual traits, because (i) sensory exploitation is often likely to be initially costly for individuals of the exploited sex and (ii) the subsequent evolution of resistance to sensory exploitation should often be associated with costs due to selective constraints. A review of a few case studies is used to illustrate these points. Empirical data directly relevant to the costs of being sensory exploited and the costs of evolving resistance is largely lacking, and I stress that such data would help determining the general importance of sexual conflict and SAC for the evolution of sexual dimorphism. PMID:16612895

The arms race between heliconiine butterflies and Passiflora plants - new insights on an ancient subject.

PubMed

de Castro, Érika C P; Zagrobelny, Mika; Cardoso, Márcio Z; Bak, Søren

2018-02-01

Heliconiines are called passion vine butterflies because they feed exclusively on Passiflora plants during the larval stage. Many features of Passiflora and heliconiines indicate that they have radiated and speciated in association with each other, and therefore this model system was one of the first examples used to exemplify coevolution theory. Three major adaptations of Passiflora plants supported arguments in favour of their coevolution with heliconiines: unusual variation of leaf shape within the genus; the occurrence of yellow structures mimicking heliconiine eggs; and their extensive diversity of defence compounds called cyanogenic glucosides. However, the protection systems of Passiflora plants go beyond these three features. Trichomes, mimicry of pathogen infection through variegation, and production of extrafloral nectar to attract ants and other predators of their herbivores, are morphological defences reported in this plant genus. Moreover, Passiflora plants are well protected chemically, not only by cyanogenic glucosides, but also by other compounds such as alkaloids, flavonoids, saponins, tannins and phenolics. Heliconiines can synthesize cyanogenic glucosides themselves, and their ability to handle these compounds was probably one of the most crucial adaptations that allowed the ancestor of these butterflies to feed on Passiflora plants. Indeed, it has been shown that Heliconius larvae can sequester cyanogenic glucosides and alkaloids from their host plants and utilize them for their own benefit. Recently, it was discovered that Heliconius adults have highly accurate visual and chemosensory systems, and the expansion of brain structures that can process such information allows them to memorize shapes and display elaborate pre-oviposition behaviour in order to defeat visual barriers evolved by Passiflora species. Even though the heliconiine-Passiflora model system has been intensively studied, the forces driving host-plant preference in these butterflies remain unclear. New studies have shown that host-plant preference seems to be genetically controlled, but in many species there is some plasticity in this choice and preferences can even be induced. Although much knowledge regarding the coevolution of Passiflora plants and heliconiine butterflies has accumulated in recent decades, there remain many exciting unanswered questions concerning this model system. © 2017 Cambridge Philosophical Society.

Coevolution between Nuclear-Encoded DNA Replication, Recombination, and Repair Genes and Plastid Genome Complexity.

PubMed

Zhang, Jin; Ruhlman, Tracey A; Sabir, Jamal S M; Blazier, John Chris; Weng, Mao-Lun; Park, Seongjun; Jansen, Robert K

2016-02-17

Disruption of DNA replication, recombination, and repair (DNA-RRR) systems has been hypothesized to cause highly elevated nucleotide substitution rates and genome rearrangements in the plastids of angiosperms, but this theory remains untested. To investigate nuclear-plastid genome (plastome) coevolution in Geraniaceae, four different measures of plastome complexity (rearrangements, repeats, nucleotide insertions/deletions, and substitution rates) were evaluated along with substitution rates of 12 nuclear-encoded, plastid-targeted DNA-RRR genes from 27 Geraniales species. Significant correlations were detected for nonsynonymous (dN) but not synonymous (dS) substitution rates for three DNA-RRR genes (uvrB/C, why1, and gyrA) supporting a role for these genes in accelerated plastid genome evolution in Geraniaceae. Furthermore, correlation between dN of uvrB/C and plastome complexity suggests the presence of nucleotide excision repair system in plastids. Significant correlations were also detected between plastome complexity and 13 of the 90 nuclear-encoded organelle-targeted genes investigated. Comparisons revealed significant acceleration of dN in plastid-targeted genes of Geraniales relative to Brassicales suggesting this correlation may be an artifact of elevated rates in this gene set in Geraniaceae. Correlation between dN of plastid-targeted DNA-RRR genes and plastome complexity supports the hypothesis that the aberrant patterns in angiosperm plastome evolution could be caused by dysfunction in DNA-RRR systems. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Gene-culture coevolution in whales and dolphins.

PubMed

Whitehead, Hal

2017-07-24

Whales and dolphins (Cetacea) have excellent social learning skills as well as a long and strong mother-calf bond. These features produce stable cultures, and, in some species, sympatric groups with different cultures. There is evidence and speculation that this cultural transmission of behavior has affected gene distributions. Culture seems to have driven killer whales into distinct ecotypes, which may be incipient species or subspecies. There are ecotype-specific signals of selection in functional genes that correspond to cultural foraging behavior and habitat use by the different ecotypes. The five species of whale with matrilineal social systems have remarkably low diversity of mtDNA. Cultural hitchhiking, the transmission of functionally neutral genes in parallel with selective cultural traits, is a plausible hypothesis for this low diversity, especially in sperm whales. In killer whales the ecotype divisions, together with founding bottlenecks, selection, and cultural hitchhiking, likely explain the low mtDNA diversity. Several cetacean species show habitat-specific distributions of mtDNA haplotypes, probably the result of mother-offspring cultural transmission of migration routes or destinations. In bottlenose dolphins, remarkable small-scale differences in haplotype distribution result from maternal cultural transmission of foraging methods, and large-scale redistributions of sperm whale cultural clans in the Pacific have likely changed mitochondrial genetic geography. With the acceleration of genomics new results should come fast, but understanding gene-culture coevolution will be hampered by the measured pace of research on the socio-cultural side of cetacean biology.

Gene–culture coevolution in whales and dolphins

PubMed Central

Whitehead, Hal

2017-01-01

Whales and dolphins (Cetacea) have excellent social learning skills as well as a long and strong mother–calf bond. These features produce stable cultures, and, in some species, sympatric groups with different cultures. There is evidence and speculation that this cultural transmission of behavior has affected gene distributions. Culture seems to have driven killer whales into distinct ecotypes, which may be incipient species or subspecies. There are ecotype-specific signals of selection in functional genes that correspond to cultural foraging behavior and habitat use by the different ecotypes. The five species of whale with matrilineal social systems have remarkably low diversity of mtDNA. Cultural hitchhiking, the transmission of functionally neutral genes in parallel with selective cultural traits, is a plausible hypothesis for this low diversity, especially in sperm whales. In killer whales the ecotype divisions, together with founding bottlenecks, selection, and cultural hitchhiking, likely explain the low mtDNA diversity. Several cetacean species show habitat-specific distributions of mtDNA haplotypes, probably the result of mother–offspring cultural transmission of migration routes or destinations. In bottlenose dolphins, remarkable small-scale differences in haplotype distribution result from maternal cultural transmission of foraging methods, and large-scale redistributions of sperm whale cultural clans in the Pacific have likely changed mitochondrial genetic geography. With the acceleration of genomics new results should come fast, but understanding gene–culture coevolution will be hampered by the measured pace of research on the socio-cultural side of cetacean biology. PMID:28739936

Integrative analyses of leprosy susceptibility genes indicate a common autoimmune profile.

PubMed

Zhang, Deng-Feng; Wang, Dong; Li, Yu-Ye; Yao, Yong-Gang

2016-04-01

Leprosy is an ancient chronic infection in the skin and peripheral nerves caused by Mycobacterium leprae. The development of leprosy depends on genetic background and the immune status of the host. However, there is no systematic view focusing on the biological pathways, interaction networks and overall expression pattern of leprosy-related immune and genetic factors. To identify the hub genes in the center of leprosy genetic network and to provide an insight into immune and genetic factors contributing to leprosy. We retrieved all reported leprosy-related genes and performed integrative analyses covering gene expression profiling, pathway analysis, protein-protein interaction network, and evolutionary analyses. A list of 123 differentially expressed leprosy related genes, which were enriched in activation and regulation of immune response, was obtained in our analyses. Cross-disorder analysis showed that the list of leprosy susceptibility genes was largely shared by typical autoimmune diseases such as lupus erythematosus and arthritis, suggesting that similar pathways might be affected in leprosy and autoimmune diseases. Protein-protein interaction (PPI) and positive selection analyses revealed a co-evolution network of leprosy risk genes. Our analyses showed that leprosy associated genes constituted a co-evolution network and might undergo positive selection driven by M. leprae. We suggested that leprosy may be a kind of autoimmune disease and the development of leprosy is a matter of defect or over-activation of body immunity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Hydrologic Predictions in the Anthropocene: Exploration with Co-evolutionary Socio-hydrologic Models

NASA Astrophysics Data System (ADS)

Sivapalan, Murugesu; Tian, Fuqiang; Liu, Dengfeng

2013-04-01

Socio-hydrology studies the co-evolution and self-organization of humans in the hydrologic landscape, which requires a thorough understanding of the complex interactions between humans and water. On the one hand, the nature of water availability greatly impacts the development of society. On the other hand, humans can significantly alter the spatio-temporal distribution of water and in this way provide feedback to the society itself. The human-water system functions underlying such complex human-water interactions are not well understood. Exploratory models with the appropriate level of simplification in any given area can be valuable to understand these functions and the self-organization associated with socio-hydrology. In this study, a simple coupled modeling framework for socio-hydrology co-evolution is developed, and is used to illustrate the explanatory power of such models. In the Tarim River, humans depend heavily on agricultural production (other industries can be ignored for a start), and the social processes can be described principally by two variables, i.e., irrigated-area and human population. The eco-hydrological processes are expressed in terms of area under natural vegetation and stream discharge. The study area is the middle and the lower reaches of the Tarim River, which is divided into two modeling units, i.e. middle reach and lower reach. In each modeling unit, four ordinary differential equations are used to simulate the dynamics of the hydrological system represented by stream discharge, ecological system represented by area under natural vegetation, the economic system represented by irrigated area under agriculture and social system represented by human population. The four dominant variables are coupled together by several internal variables. For example, the stream discharge is coupled to irrigated area by the colonization rate and mortality rate of the irrigated area in the middle reach and the irrigated area is coupled to stream discharge by water used for irrigation. In a similar way, the stream discharge and natural vegetation are coupled together. The irrigated area is coupled to population by the colonization rate and mortality rate of the population. The discharge of the lower reach is determined by the discharge from the middle reach. The natural vegetation area in the lower reach is coupled to the discharge in the middle reach by water resources management policy. The co-evolution of the Tarim socio-hydrological system is then analyzed within this modeling framework to gain insights into the overall system dynamics and sensitivity to the external drivers and internal system variables.

Exploring gene-culture interactions: insights from handedness, sexual selection and niche-construction case studies.

PubMed

Laland, Kevin N

2008-11-12

Genes and culture represent two streams of inheritance that for millions of years have flowed down the generations and interacted. Genetic propensities, expressed throughout development, influence what cultural organisms learn. Culturally transmitted information, expressed in behaviour and artefacts, spreads through populations, modifying selection acting back on populations. Drawing on three case studies, I will illustrate how this gene-culture coevolution has played a critical role in human evolution. These studies explore (i) the evolution of handedness, (ii) sexual selection with a culturally transmitted mating preference, and (iii) cultural niche construction and human evolution. These analyses shed light on how genes and culture shape each other, and on the significance of feedback mechanisms between biological and cultural processes.

Herpesviruses and Their Host Cells: A Successful Liaison.

PubMed

Adler, Barbara; Sattler, Christine; Adler, Heiko

2017-03-01

During a long history of coevolution, herpesviruses have reached a fine-tuned balance with their hosts, allowing them to successfully persist and spread to new hosts without causing too much damage. Only under certain circumstances, as in neonates or immunocompromised individuals, they may cause serious diseases. The delicate balance between herpesviruses and their hosts results from interactions of a great variety of viral and cellular factors which together shape the tropism for a particular host, tissue, or cell. Understanding these interactions will provide insight into the viral life cycle and cell biology in general. Moreover, it will also facilitate comprehension of herpesvirus pathogenesis, enabling the development of new strategies to combat herpesviruses in cases where they cause disease. Copyright © 2016 Elsevier Ltd. All rights reserved.

Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life

PubMed Central

Wong, J. Tze-Fei; Ng, Siu-Kin; Mat, Wai-Kin; Hu, Taobo; Xue, Hong

2016-01-01

The origins of the components of genetic coding are examined in the present study. Genetic information arose from replicator induction by metabolite in accordance with the metabolic expansion law. Messenger RNA and transfer RNA stemmed from a template for binding the aminoacyl-RNA synthetase ribozymes employed to synthesize peptide prosthetic groups on RNAs in the Peptidated RNA World. Coevolution of the genetic code with amino acid biosynthesis generated tRNA paralogs that identify a last universal common ancestor (LUCA) of extant life close to Methanopyrus, which in turn points to archaeal tRNA introns as the most primitive introns and the anticodon usage of Methanopyrus as an ancient mode of wobble. The prediction of the coevolution theory of the genetic code that the code should be a mutable code has led to the isolation of optional and mandatory synthetic life forms with altered protein alphabets. PMID:26999216

Host-parasite coevolution: genetic variation in a virus population and the interaction with a host gene.

PubMed

Wilfert, L; Jiggins, F M

2010-07-01

Host-parasite coevolution is considered to be an important factor in maintaining genetic variation in resistance to pathogens. Drosophila melanogaster is naturally infected by the sigma virus, a vertically transmitted and host-specific pathogen. In fly populations, there is a large amount of genetic variation in the transmission rate from parent to offspring, much of which is caused by major-effect resistance polymorphisms. We have found that there are similarly high levels of genetic variation in the rate of paternal transmission among 95 different isolates of the virus as in the host. However, when we examined a transmission-blocking gene in the host, we found that it was effective across virus isolates. Therefore, the high levels of genetic variation observed in this system do not appear to be maintained because of coevolution resulting from interactions between this host gene and parasite genes.

The role of ecology, neutral processes and antagonistic coevolution in an apparent sexual arms race.

PubMed

Perry, Jennifer C; Garroway, Colin J; Rowe, Locke

2017-09-01

Some of the strongest examples of a sexual 'arms race' come from observations of correlated evolution in sexually antagonistic traits among populations. However, it remains unclear whether these cases truly represent sexually antagonistic coevolution; alternatively, ecological or neutral processes might also drive correlated evolution. To investigate these alternatives, we evaluated the contributions of intersex genetic correlations, ecological context, neutral genetic divergence and sexual coevolution in the correlated evolution of antagonistic traits among populations of Gerris incognitus water striders. We could not detect intersex genetic correlations for these sexually antagonistic traits. Ecological variation was related to population variation in the key female antagonistic trait (spine length, a defence against males), as well as body size. Nevertheless, population covariation between sexually antagonistic traits remained substantial and significant even after accounting for all of these processes. Our results therefore provide strong evidence for a contemporary sexual arms race. © 2017 John Wiley & Sons Ltd/CNRS.

From Charles Darwin's botanical country-house studies to modern plant biology.

PubMed

Kutschera, U; Briggs, W R

2009-11-01

As a student of theology at Cambridge University, Charles Darwin (1809-1882) attended the lectures of the botanist John S. Henslow (1796-1861). This instruction provided the basis for his life-long interest in plants as well as the species question. This was a major reason why in his book On the Origin of Species, which was published 150 years ago, Darwin explained his metaphorical phrase 'struggle for life' with respect to animals and plants. In this article, we review Darwin's botanical work with reference to the following topics: the struggle for existence in the vegetable kingdom with respect to the phytochrome-mediated shade avoidance response; the biology of flowers and Darwin's plant-insect co-evolution hypothesis; climbing plants and the discovery of action potentials; the power of movement in plants and Darwin's conflict with the German plant physiologist Julius Sachs; and light perception by growing grass coleoptiles with reference to the phototropins. Finally, we describe the establishment of the scientific discipline of Plant Biology that took place in the USA 80 years ago, and define this area of research with respect to Darwin's work on botany and the physiology of higher plants.

String Mining in Bioinformatics

NASA Astrophysics Data System (ADS)

Abouelhoda, Mohamed; Ghanem, Moustafa

Sequence analysis is a major area in bioinformatics encompassing the methods and techniques for studying the biological sequences, DNA, RNA, and proteins, on the linear structure level. The focus of this area is generally on the identification of intra- and inter-molecular similarities. Identifying intra-molecular similarities boils down to detecting repeated segments within a given sequence, while identifying inter-molecular similarities amounts to spotting common segments among two or multiple sequences. From a data mining point of view, sequence analysis is nothing but string- or pattern mining specific to biological strings. For a long time, this point of view, however, has not been explicitly embraced neither in the data mining nor in the sequence analysis text books, which may be attributed to the co-evolution of the two apparently independent fields. In other words, although the word "data-mining" is almost missing in the sequence analysis literature, its basic concepts have been implicitly applied. Interestingly, recent research in biological sequence analysis introduced efficient solutions to many problems in data mining, such as querying and analyzing time series [49,53], extracting information from web pages [20], fighting spam mails [50], detecting plagiarism [22], and spotting duplications in software systems [14].

String Mining in Bioinformatics

NASA Astrophysics Data System (ADS)

Abouelhoda, Mohamed; Ghanem, Moustafa

Sequence analysis is a major area in bioinformatics encompassing the methods and techniques for studying the biological sequences, DNA, RNA, and proteins, on the linear structure level. The focus of this area is generally on the identification of intra- and inter-molecular similarities. Identifying intra-molecular similarities boils down to detecting repeated segments within a given sequence, while identifying inter-molecular similarities amounts to spotting common segments among two or multiple sequences. From a data mining point of view, sequence analysis is nothing but string- or pattern mining specific to biological strings. For a long time, this point of view, however, has not been explicitly embraced neither in the data mining nor in the sequence analysis text books, which may be attributed to the co-evolution of the two apparently independent fields. In other words, although the word “data-mining” is almost missing in the sequence analysis literature, its basic concepts have been implicitly applied. Interestingly, recent research in biological sequence analysis introduced efficient solutions to many problems in data mining, such as querying and analyzing time series [49,53], extracting information from web pages [20], fighting spam mails [50], detecting plagiarism [22], and spotting duplications in software systems [14].

The co-evolution of total density profiles and central dark matter fractions in simulated early-type galaxies

NASA Astrophysics Data System (ADS)

Remus, Rhea-Silvia; Dolag, Klaus; Naab, Thorsten; Burkert, Andreas; Hirschmann, Michaela; Hoffmann, Tadziu L.; Johansson, Peter H.

2017-01-01

We present evidence from cosmological hydrodynamical simulations for a co-evolution of the slope of the total (dark and stellar) mass density profile, γtot, and the dark matter fraction within the half-mass radius, fDM, in early-type galaxies. The relation can be described as γtot = A fDM + B for all systems at all redshifts. The trend is set by the decreasing importance of gas dissipation towards lower redshifts and for more massive systems. Early-type galaxies are smaller, more concentrated, have lower fDM and steeper γtot at high redshifts and at lower masses for a given redshift; fDM and γtot are good indicators for growth by `dry' merging. The values for A and B change distinctively for different feedback models, and this relation can be used as a test for such models. A similar correlation exists between γtot and the stellar mass surface density Σ*. A model with weak stellar feedback and feedback from black holes is in best agreement with observations. All simulations, independent of the assumed feedback model, predict steeper γtot and lower fDM at higher redshifts. While the latter is in agreement with the observed trends, the former is in conflict with lensing observations, which indicate constant or decreasing γtot. This discrepancy is shown to be artificial: the observed trends can be reproduced from the simulations using observational methodology to calculate the total density slopes.

Vegetation controls on the maximum size of coastal dunes.

PubMed

Durán, Orencio; Moore, Laura J

2013-10-22

Coastal dunes, in particular foredunes, support a resilient ecosystem and reduce coastal vulnerability to storms. In contrast to dry desert dunes, coastal dunes arise from interactions between biological and physical processes. Ecologists have traditionally addressed coastal ecosystems by assuming that they adapt to preexisting dune topography, whereas geomorphologists have studied the properties of foredunes primarily in connection to physical, not biological, factors. Here, we study foredune development using an ecomorphodynamic model that resolves the coevolution of topography and vegetation in response to both physical and ecological factors. We find that foredune growth is eventually limited by a negative feedback between wind flow and topography. As a consequence, steady-state foredunes are scale invariant, which allows us to derive scaling relations for maximum foredune height and formation time. These relations suggest that plant zonation (in particular for strand "dune-building" species) is the primary factor controlling the maximum size of foredunes and therefore the amount of sand stored in a coastal dune system. We also find that aeolian sand supply to the dunes determines the timescale of foredune formation. These results offer a potential explanation for the empirical relation between beach type and foredune size, in which large (small) foredunes are found on dissipative (reflective) beaches. Higher waves associated with dissipative beaches increase the disturbance of strand species, which shifts foredune formation landward and thus leads to larger foredunes. In this scenario, plants play a much more active role in modifying their habitat and altering coastal vulnerability than previously thought.

Behavioural divergence, interfertility and speciation: a review.

PubMed

Pillay, Neville; Rymer, Tasmin L

2012-11-01

Behavioural compatibility between mates is fundamental for maintaining species boundaries and is achieved through appropriate communication between males and females. A breakdown in communication will lead to behavioural divergence and reduced interfertility. In this review, we summarise the current knowledge on male signals and female perception of these signals, integrating the literature from several taxa. We advocate that signaller-perceiver coevolution, which is usually under strong stabilising selection to enable mating, forms the basis of species-specific mate recognition systems. The mechanisms (phylogeny, geography, ecology, biology) shaping signaller-perceiver systems are briefly discussed to demonstrate the factors underpinning the evolution of signaller-perceiver couplings. Since divergence and diversification of communication systems is driven by changes in the mechanical properties of sensory pathways and morphology of sensory organs, we highlight signal modalities (auditory, olfactory, visual, tactile) and their importance in communication, particularly in mate selection. Next, using available examples and generating a stylised model, we suggest how disruption (biological, ecological, stochastic) of signaller-perceiver systems drives behavioural divergence and consequently results in reduced interfertility and speciation. Future studies should adopt an integrative approach, combining multiple parameters (phylogeny, adaptive utility of communication systems, genetics and biomechanical/biochemical properties of signals and perception) to explore how disruption of signaller-perceiver systems results in behavioural divergence and reduced interfertility. Finally, we question the impact that rapid environmental change will have on disruption of communication systems, potentially interfering with signaller-perceiver couplings. Copyright © 2012 Elsevier B.V. All rights reserved.

The evolutionary ecology of the Lygaeidae

PubMed Central

Burdfield-Steel, Emily R; Shuker, David M

2014-01-01

The Lygaeidae (sensu lato) are a highly successful family of true bugs found worldwide, yet many aspects of their ecology and evolution remain obscure or unknown. While a few species have attracted considerable attention as model species for the study of insect physiology, it is only relatively recently that biologists have begun to explore aspects of their behavior, life history evolution, and patterns of intra- and interspecific ecological interactions across more species. As a result though, a range of new phenotypes and opportunities for addressing current questions in evolutionary ecology has been uncovered. For example, researchers have revealed hitherto unexpectedly rich patterns of bacterial symbiosis, begun to explore the evolutionary function of the family's complex genitalia, and also found evidence of parthenogenesis. Here we review our current understanding of the biology and ecology of the group as a whole, focusing on several of the best-studied characteristics of the group, including aposematism (i.e., the evolution of warning coloration), chemical communication, sexual selection (especially, postcopulatory sexual selection), sexual conflict, and patterns of host-endosymbiont coevolution. Importantly, many of these aspects of lygaeid biology are likely to interact, offering new avenues for research, for instance into how the evolution of aposematism influences sexual selection. With the growing availability of genomic tools for previously “non-model” organisms, combined with the relative ease of keeping many of the polyphagous species in the laboratory, we argue that these bugs offer many opportunities for behavioral and evolutionary ecologists. PMID:25360267

The aminoacyl-tRNA synthetases had only a marginal role in the origin of the organization of the genetic code: Evidence in favor of the coevolution theory.

PubMed

Di Giulio, Massimo

2017-11-07

The coevolution theory of the origin of the genetic code suggests that the organization of the genetic code coevolved with the biosynthetic relationships between amino acids. The mechanism that allowed this coevolution was based on tRNA-like molecules on which-this theory-would postulate the biosynthetic transformations between amino acids to have occurred. This mechanism makes a prediction on how the role conducted by the aminoacyl-tRNA synthetases (ARSs), in the origin of the genetic code, should have been. Indeed, if the biosynthetic transformations between amino acids occurred on tRNA-like molecules, then there was no need to link amino acids to these molecules because amino acids were already charged on tRNA-like molecules, as the coevolution theory suggests. In spite of the fact that ARSs make the genetic code responsible for the first interaction between a component of nucleic acids and that of proteins, for the coevolution theory the role of ARSs should have been entirely marginal in the genetic code origin. Therefore, I have conducted a further analysis of the distribution of the two classes of ARSs and of their subclasses-in the genetic code table-in order to perform a falsification test of the coevolution theory. Indeed, in the case in which the distribution of ARSs within the genetic code would have been highly significant, then the coevolution theory would be falsified since the mechanism on which it is based would not predict a fundamental role of ARSs in the origin of the genetic code. I found that the statistical significance of the distribution of the two classes of ARSs in the table of the genetic code is low or marginal, whereas that of the subclasses of ARSs statistically significant. However, this is in perfect agreement with the postulates of the coevolution theory. Indeed, the only case of statistical significance-regarding the classes of ARSs-is appreciable for the CAG code, whereas for its complement-the UNN/NUN code-only a marginal significance is measurable. These two codes codify roughly for the two ARS classes, in particular, the CAG code for the class II while the UNN/NUN code for the class I. Furthermore, the subclasses of ARSs show a statistical significance of their distribution in the genetic code table. Nevertheless, the more sensible explanation for these observations would be the following. The observation that would link the two classes of ARSs to the CAG and UNN/NUN codes, and the statistical significance of the distribution of the subclasses of ARSs in the genetic code table, would be only a secondary effect due to the highly significant distribution of the polarity of amino acids and their biosynthetic relationships in the genetic code. That is to say, the polarity of amino acids and their biosynthetic relationships would have conditioned the evolution of ARSs so that their presence in the genetic code would have been detectable. Even if the ARSs would not have-on their own-influenced directly the evolutionary organization of the genetic code. In other words, the role that ARSs had in the origin of the genetic code would have been entirely marginal. This conclusion would be in perfect accord with the predictions of the coevolution theory. Conversely, this conclusion would be in contrast-at least partially-with the physicochemical theories of the origin of the genetic code because they would foresee an absolutely more active role of ARSs in the origin of the organization of the genetic code. Copyright © 2017 Elsevier Ltd. All rights reserved.

Coexistence via coevolution driven by reduced allelochemical effects and increased tolerance to competition between invasive and native plants.

PubMed

Huang, Fangfang; Lankau, Richard; Peng, Shaolin

2018-04-01

Coevolution can promote long-term coexistence of two competing species if selection acts to reduce the fitness inequality between competitors and/or strengthen negative frequency dependence within each population. However, clear coevolution between plant competitors has been rarely documented. Plant invasions offer opportunities to capture the process of coevolution. Here we investigated how the developing relationship between an invasive forb, Alliaria petiolata, and a native competitor, Pilea pumila, may affect their long-term coexistence, by testing the competitive effects of populations of varying lengths of co-occurrence on each other across a chronosequence of invasion history. Alliaria petiolata and P. pumila tended to develop greater tolerance to competition over invasion history. Their coexistence was promoted more by increases in stabilizing relative to equalizing processes. These changes likely stem in part from reductions in allelopathic traits in the invader and evolution of tolerance in the native. These results suggested that some native species can evolve tolerance against the competitive effects of strong invaders, which likely promoted their persistence in invaded communities. However, the potential for coevolutionary rescue of competing populations is likely to vary across native species, and evolutionary processes should not be expected to compensate for the ecological consequences of exotic invasions. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

The Red Queen in mitochondria: cyto-nuclear co-evolution, hybrid breakdown and human disease

PubMed Central

Chou, Jui-Yu; Leu, Jun-Yi

2015-01-01

Cyto-nuclear incompatibility, a specific form of Dobzhansky-Muller incompatibility caused by incompatible alleles between mitochondrial and nuclear genomes, has been suggested to play a critical role during speciation. Several features of the mitochondrial genome (mtDNA), including high mutation rate, dynamic genomic structure, and uniparental inheritance, make mtDNA more likely to accumulate mutations in the population. Once mtDNA has changed, the nuclear genome needs to play catch-up due to the intimate interactions between these two genomes. In two populations, if cyto-nuclear co-evolution is driven in different directions, it may eventually lead to hybrid incompatibility. Although cyto-nuclear incompatibility has been observed in a wide range of organisms, it remains unclear what type of mutations drives the co-evolution. Currently, evidence supporting adaptive mutations in mtDNA remains limited. On the other hand, it has been known that some mutations allow mtDNA to propagate more efficiently but compromise the host fitness (described as selfish mtDNA). Arms races between such selfish mtDNA and host nuclear genomes can accelerate cyto-nuclear co-evolution and lead to a phenomenon called the Red Queen Effect. Here, we discuss how the Red Queen Effect may contribute to the frequent observation of cyto-nuclear incompatibility and be the underlying driving force of some human mitochondrial diseases. PMID:26042149

Characterization of C-ring component assembly in flagellar motors from amino acid coevolution

PubMed Central

dos Santos, Ricardo Nascimento; Khan, Shahid

2018-01-01

Bacterial flagellar motility, an important virulence factor, is energized by a rotary motor localized within the flagellar basal body. The rotor module consists of a large framework (the C-ring), composed of the FliG, FliM and FliN proteins. FliN and FliM contacts the FliG torque ring to control the direction of flagellar rotation. We report that structure-based models constrained only by residue coevolution can recover the binding interface of atomic X-ray dimer complexes with remarkable accuracy (approx. 1 Å RMSD). We propose a model for FliM–FliN heterodimerization, which agrees accurately with homologous interfaces as well as in situ cross-linking experiments, and hence supports a proposed architecture for the lower portion of the C-ring. Furthermore, this approach allowed the identification of two discrete and interchangeable homodimerization interfaces between FliM middle domains that agree with experimental measurements and might be associated with C-ring directional switching dynamics triggered upon binding of CheY signal protein. Our findings provide structural details of complex formation at the C-ring that have been difficult to obtain with previous methodologies and clarify the architectural principle that underpins the ultra-sensitive allostery exhibited by this ring assembly that controls the clockwise or counterclockwise rotation of flagella. PMID:29892378

Coevolution of hydraulic, soil and vegetation processes in estuarine wetlands

NASA Astrophysics Data System (ADS)

Trivisonno, Franco; Rodriguez, Jose F.; Riccardi, Gerardo; Saco, Patricia; Stenta, Hernan

2014-05-01

Estuarine wetlands of south eastern Australia, typically display a vegetation zonation with a sequence mudflats - mangrove forest - saltmarsh plains from the seaward margin and up the topographic gradient. Estuarine wetlands are among the most productive ecosystems in the world, providing unique habitats for fish and many terrestrial species. They also have a carbon sequestration capacity that surpasess terrestrial forest. Estuarine wetlands respond to sea-level rise by vertical accretion and horizontal landward migration, in order to maintain their position in the tidal frame. In situations in which buffer areas for landward migration are not available, saltmarsh can be lost due to mangrove encroachment. As a result of mangrove invasion associated in part with raising estuary water levels and urbanisation, coastal saltmarsh in parts of south-eastern Australia has been declared an endangered ecological community. Predicting estuarine wetlands response to sea-level rise requires modelling the coevolving dynamics of water flow, soil and vegetation. This paper presents preliminary results of our recently developed numerical model for wetland dynamics in wetlands of the Hunter estuary of NSW. The model simulates continuous tidal inflow into the wetland, and accounts for the effect of varying vegetation types on flow resistance. Coevolution effects appear as vegetation types are updated based on their preference to prevailing hydrodynamic conditions. The model also considers that accretion values vary with vegetation type. Simulations are driven using local information collected over several years, which includes estuary water levels, accretion rates, soil carbon content, flow resistance and vegetation preference to hydraulic conditions. Model results predict further saltmarsh loss under current conditions of moderate increase of estuary water levels.

HIV-1 protease-substrate coevolution in nelfinavir resistance.

PubMed

Kolli, Madhavi; Ozen, Ayşegül; Kurt-Yilmaz, Nese; Schiffer, Celia A

2014-07-01

Resistance to various human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. The virus accumulates mutations within the protease (PR) that render the PIs less potent. Occasionally, Gag sequences also coevolve with mutations at PR cleavage sites contributing to drug resistance. In this study, we investigated the structural basis of coevolution of the p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations by determining crystal structures of wild-type and NFV-resistant HIV-1 protease in complex with p1-p6 substrate peptide variants with L449F and/or S451N. Alterations of residue 30's interaction with the substrate are compensated by the coevolving L449F and S451N cleavage site mutations. This interdependency in the PR-p1-p6 interactions enhances intermolecular contacts and reinforces the overall fit of the substrate within the substrate envelope, likely enabling coevolution to sustain substrate recognition and cleavage in the presence of PR resistance mutations. Resistance to human immunodeficiency virus type 1 (HIV-1) protease inhibitors challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. Mutations in HIV-1 protease selected under the pressure of protease inhibitors render the inhibitors less potent. Occasionally, Gag sequences also mutate and coevolve with protease, contributing to maintenance of viral fitness and to drug resistance. In this study, we investigated the structural basis of coevolution at the Gag p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations. Our structural analysis reveals the interdependency of protease-substrate interactions and how coevolution may restore substrate recognition and cleavage in the presence of protease drug resistance mutations. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Evaluating phylogenetic congruence in the post-genomic era.

PubMed

Leigh, Jessica W; Lapointe, François-Joseph; Lopez, Philippe; Bapteste, Eric

2011-01-01

Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for common descent. Existing methods for identifying incongruence or heterogeneity using character data were designed for data sets that are both small and expected to be rarely incongruent. At the same time, methods that assess incongruence using comparison of trees test a null hypothesis of uncorrelated tree structures, which may be inappropriate for phylogenomic studies. As such, they are ill-suited for the growing number of available genome sequences, most of which are from prokaryotes and viruses, either for phylogenomic analysis or for studies of the evolutionary forces and events that have shaped these genomes. Specifically, many existing methods scale poorly with large numbers of genes, cannot accommodate high levels of incongruence, and do not adequately model patterns of missing taxa for different markers. We propose the development of novel incongruence assessment methods suitable for the analysis of the molecular evolution of the vast majority of life and support the investigation of homogeneity of evolutionary process in cases where markers do not share identical tree structures.

Evaluating Phylogenetic Congruence in the Post-Genomic Era

PubMed Central

Leigh, Jessica W.; Lapointe, François-Joseph; Lopez, Philippe; Bapteste, Eric

2011-01-01

Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for common descent. Existing methods for identifying incongruence or heterogeneity using character data were designed for data sets that are both small and expected to be rarely incongruent. At the same time, methods that assess incongruence using comparison of trees test a null hypothesis of uncorrelated tree structures, which may be inappropriate for phylogenomic studies. As such, they are ill-suited for the growing number of available genome sequences, most of which are from prokaryotes and viruses, either for phylogenomic analysis or for studies of the evolutionary forces and events that have shaped these genomes. Specifically, many existing methods scale poorly with large numbers of genes, cannot accommodate high levels of incongruence, and do not adequately model patterns of missing taxa for different markers. We propose the development of novel incongruence assessment methods suitable for the analysis of the molecular evolution of the vast majority of life and support the investigation of homogeneity of evolutionary process in cases where markers do not share identical tree structures. PMID:21712432

Crowded growth leads to the spontaneous evolution of semistable coexistence in laboratory yeast populations.

PubMed

Frenkel, Evgeni M; McDonald, Michael J; Van Dyken, J David; Kosheleva, Katya; Lang, Gregory I; Desai, Michael M

2015-09-08

Identifying the mechanisms that create and maintain biodiversity is a central challenge in biology. Stable diversification of microbial populations often requires the evolution of differences in resource utilization. Alternatively, coexistence can be maintained by specialization to exploit spatial heterogeneity in the environment. Here, we report spontaneous diversification maintained by a related but distinct mechanism: crowding avoidance. During experimental evolution of laboratory Saccharomyces cerevisiae populations, we observed the repeated appearance of "adherent" (A) lineages able to grow as a dispersed film, in contrast to their crowded "bottom-dweller" (B) ancestors. These two types stably coexist because dispersal reduces interference competition for nutrients among kin, at the cost of a slower maximum growth rate. This tradeoff causes the frequencies of the two types to oscillate around equilibrium over the course of repeated cycles of growth, crowding, and dispersal. However, further coevolution of the A and B types can perturb and eventually destroy their coexistence over longer time scales. We introduce a simple mathematical model of this "semistable" coexistence, which explains the interplay between ecological and evolutionary dynamics. Because crowded growth generally limits nutrient access in biofilms, the mechanism we report here may be broadly important in maintaining diversity in these natural environments.

Do arms races punctuate evolutionary stasis? Unified insights from phylogeny, phylogeography and microevolutionary processes.

PubMed

Toju, Hirokazu; Sota, Teiji

2009-09-01

One of the major controversies in evolutionary biology concerns the processes underlying macroevolutionary patterns in which prolonged stasis is disrupted by rapid, short-term evolution that leads species to new adaptive zones. Recent advances in the understanding of contemporary evolution have suggested that such rapid evolution can occur in the wild as a result of environmental changes. Here, we examined a novel hypothesis that evolutionary stasis is punctuated by co-evolutionary arms races, which continuously alter adaptive peaks and landscapes. Based on the phylogeny of long-mouthed weevils in the genus Curculio, likelihood ratio tests showed that the macroevolutionary pattern of the weevils coincides with the punctuational evolution model. A coalescent analysis of a species, Curculio camelliae, the mouthpart of which has diverged considerably among populations because of an arms race with its host plant, further suggested that major evolutionary shifts had occurred within 7000 generations. Through a microevolutionary analysis of the species, we also found that natural selection acting through co-evolutionary interactions is potentially strong enough to drive rapid evolutionary shifts between adaptive zones. Overall, we posit that co-evolution is an important factor driving the history of organismal evolution.

Coevolving agent strategies and network topology for the public goods games

NASA Astrophysics Data System (ADS)

Zhang, C. Y.; Zhang, J. L.; Xie, G. M.; Wang, L.

2011-03-01

Much of human cooperation remains an evolutionary riddle. Coevolutionary public goods games in structured populations are studied where players can change from an unproductive public goods game to a productive one, by evaluating the productivity of the public goods games. In our model, each individual participates in games organized by its neighborhood plus by itself. Coevolution here refers to an evolutionary process entailing both deletion of existing links and addition of new links between agents that accompanies the evolution of their strategies. Furthermore, we investigate the effects of time scale separation of strategy and structure on cooperation level. This study presents the following: Foremost, we observe that high cooperation levels in public goods interactions are attained by the entangled coevolution of strategy and structure. Presented results also confirm that the resulting networks show many features of real systems, such as cooperative behavior and hierarchical clustering. The heterogeneity of the interaction network is held responsible for the observed promotion of cooperation. We hope our work may offer an explanation for the origin of large-scale cooperative behavior among unrelated individuals.

Host–parasite fluctuating selection in the absence of specificity

PubMed Central

Ashby, Ben; White, Andy; Bowers, Roger; Buckling, Angus; Koskella, Britt

2017-01-01

Fluctuating selection driven by coevolution between hosts and parasites is important for the generation of host and parasite diversity across space and time. Theory has focused primarily on infection genetics, with highly specific ‘matching-allele’ frameworks more likely to generate fluctuating selection dynamics (FSD) than ‘gene-for-gene’ (generalist–specialist) frameworks. However, the environment, ecological feedbacks and life-history characteristics may all play a role in determining when FSD occurs. Here, we develop eco-evolutionary models with explicit ecological dynamics to explore the ecological, epidemiological and host life-history drivers of FSD. Our key result is to demonstrate for the first time, to our knowledge, that specificity between hosts and parasites is not required to generate FSD. Furthermore, highly specific host–parasite interactions produce unstable, less robust stochastic fluctuations in contrast to interactions that lack specificity altogether or those that vary from generalist to specialist, which produce predictable limit cycles. Given the ubiquity of ecological feedbacks and the variation in the nature of specificity in host–parasite interactions, our work emphasizes the underestimated potential for host–parasite coevolution to generate fluctuating selection. PMID:29093222

Assembling the Tat protein translocase

PubMed Central

Alcock, Felicity; Stansfeld, Phillip J; Basit, Hajra; Habersetzer, Johann; Baker, Matthew AB; Palmer, Tracy; Wallace, Mark I; Berks, Ben C

2016-01-01

The twin-arginine protein translocation system (Tat) transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membranes of plant chloroplasts. The Tat transporter is assembled from multiple copies of the membrane proteins TatA, TatB, and TatC. We combine sequence co-evolution analysis, molecular simulations, and experimentation to define the interactions between the Tat proteins of Escherichia coli at molecular-level resolution. In the TatBC receptor complex the transmembrane helix of each TatB molecule is sandwiched between two TatC molecules, with one of the inter-subunit interfaces incorporating a functionally important cluster of interacting polar residues. Unexpectedly, we find that TatA also associates with TatC at the polar cluster site. Our data provide a structural model for assembly of the active Tat translocase in which substrate binding triggers replacement of TatB by TatA at the polar cluster site. Our work demonstrates the power of co-evolution analysis to predict protein interfaces in multi-subunit complexes. DOI: http://dx.doi.org/10.7554/eLife.20718.001 PMID:27914200

The RNA-world and co-evolution hypotheses and the origin of life: Implications, research strategies and perspectives

NASA Astrophysics Data System (ADS)

Lahav, Noam

1993-12-01

The applicability of the RNA-world and co-evolution hypotheses to the study of the very first stages of the origin of life is discussed. The discussion focuses on the basic differences between the two hypotheses and their implications, with regard to the reconstruction methodology, ribosome emergence, balance between ribozymes and protein enzymes, and their major difficulties. Additional complexities of the two hypotheses, such as membranes and the energy source of the first reactions, are not treated in the present work. A central element in the proposed experimental strategies is the study of the catalytic activities of very small peptides and RNA-like oligomers, according to existing, as well as to yet-to-be-invented scenarios of the two hypotheses under consideration. It is suggested that the noveldirected molecular evolution technology, andmolecular computational modeling, can be applied to this research. This strategy is assumed to be essential for the suggested goal of future studies of the origin of life, namely, the establishment of a ‘Primordial Darwinian entity’.

Clustered marginalization of minorities during social transitions induced by co-evolution of behaviour and network structure

PubMed Central

Schleussner, Carl-Friedrich; Donges, Jonathan F.; Engemann, Denis A.; Levermann, Anders

2016-01-01

Large-scale transitions in societies are associated with both individual behavioural change and restructuring of the social network. These two factors have often been considered independently, yet recent advances in social network research challenge this view. Here we show that common features of societal marginalization and clustering emerge naturally during transitions in a co-evolutionary adaptive network model. This is achieved by explicitly considering the interplay between individual interaction and a dynamic network structure in behavioural selection. We exemplify this mechanism by simulating how smoking behaviour and the network structure get reconfigured by changing social norms. Our results are consistent with empirical findings: The prevalence of smoking was reduced, remaining smokers were preferentially connected among each other and formed increasingly marginalized clusters. We propose that self-amplifying feedbacks between individual behaviour and dynamic restructuring of the network are main drivers of the transition. This generative mechanism for co-evolution of individual behaviour and social network structure may apply to a wide range of examples beyond smoking. PMID:27510641

The RNA-world and co-evolution hypothesis and the origin of life: Implications, research strategies and perspectives

NASA Technical Reports Server (NTRS)

Lahav, Noam

1993-01-01

The applicability of the RNA-world and co-evolution hypothesis to the study of the very first stages of the origin of life is discussed. The discussion focuses on the basic differences between the two hypotheses and their implications, with regard to the reconstruction methodology, ribosome emergence, balance between ribozymes and protein enzymes, and their major difficultites. Additional complexities of the two hypotheses, such as membranes and the energy source of the first reactions, are not treated in the present work. A central element in the proposed experimental strategies is the study of the catalytic activites of very small peptides and RNA-like oligomers, according to existing, as well as to yet-to-be-invented scenarios of the two hypothesis under consideration. It is suggested that the novel directed molecular evolution technology, and molecular computational modeling, can be applied to this research. This strategy is assumed to be essential for the suggested goal of future studies of the origin of life, namely, the establishment of a `Primordial Darwinian entity'.

Evolution of speech and evolution of language.

PubMed

de Boer, Bart

2017-02-01

Speech is the physical signal used to convey spoken language. Because of its physical nature, speech is both easier to compare with other species' behaviors and easier to study in the fossil record than other aspects of language. Here I argue that convergent fossil evidence indicates adaptations for complex vocalizations at least as early as the common ancestor of Neanderthals and modern humans. Furthermore, I argue that it is unlikely that language evolved separately from speech, but rather that gesture, speech, and song coevolved to provide both a multimodal communication system and a musical system. Moreover, coevolution must also have played a role by allowing both cognitive and anatomical adaptations to language and speech to evolve in parallel. Although such a coevolutionary scenario is complex, it is entirely plausible from a biological point of view.

Network analysis reveals the recognition mechanism for complex formation of mannose-binding lectins

NASA Astrophysics Data System (ADS)

Jian, Yiren; Zhao, Yunjie; Zeng, Chen

The specific carbohydrate binding of lectin makes the protein a powerful molecular tool for various applications including cancer cell detection due to its glycoprotein profile on the cell surface. Most biologically active lectins are dimeric. To understand the structure-function relation of lectin complex, it is essential to elucidate the short- and long-range driving forces behind the dimer formation. Here we report our molecular dynamics simulations and associated dynamical network analysis on a particular lectin, i.e., the mannose-binding lectin from garlic. Our results, further supported by sequence coevolution analysis, shed light on how different parts of the complex communicate with each other. We propose a general framework for deciphering the recognition mechanism underlying protein-protein interactions that may have potential applications in signaling pathways.

Cuckoos versus hosts in insects and birds: adaptations, counter-adaptations and outcomes.

PubMed

Kilner, Rebecca M; Langmore, Naomi E

2011-11-01

Avian parents and social insect colonies are victimized by interspecific brood parasites-cheats that procure costly care for their dependent offspring by leaving them in another species' nursery. Birds and insects defend themselves from attack by brood parasites; their defences in turn select counter-strategies in the parasite, thus setting in motion antagonistic co-evolution between the two parties. Despite their considerable taxonomic disparity, here we show striking parallels in the way that co-evolution between brood parasites and their hosts proceeds in insects and birds. First, we identify five types of co-evolutionary arms race from the empirical literature, which are common to both systems. These are: (a) directional co-evolution of weaponry and armoury; (b) furtiveness in the parasite countered by strategies in the host to expose the parasite; (c) specialist parasites mimicking hosts who escape by diversifying their genetic signatures; (d) generalist parasites mimicking hosts who escape by favouring signatures that force specialization in the parasite; and (e) parasites using crypsis to evade recognition by hosts who then simplify their signatures to make the parasite more detectable. Arms races a and c are well characterized in the theoretical literature on co-evolution, but the other types have received little or no formal theoretical attention. Empirical work suggests that hosts are doomed to lose arms races b and e to the parasite, in the sense that parasites typically evade host defences and successfully parasitize the nest. Nevertheless hosts may win when the co-evolutionary trajectory follows arms race a, c or d. Next, we show that there are four common outcomes of the co-evolutionary arms race for hosts. These are: (1) successful resistance; (2) the evolution of defence portfolios (or multiple lines of resistance); (3) acceptance of the parasite; and (4) tolerance of the parasite. The particular outcome is not determined by the type of preceding arms race but depends more on whether hosts or parasites control the co-evolutionary trajectory: tolerance is an outcome that parasites inflict on hosts, whereas the other three outcomes are more dependent on properties intrinsic to the host species. Finally, our review highlights considerable interspecific variation in the complexity and depth of host defence portfolios. Whether this variation is adaptive or merely reflects evolutionary lag is unclear. We propose an adaptive explanation, which centres on the relative strength of two opposing processes: strategy-facilitation, in which one line of host defence promotes the evolution of another form of resistance, and strategy-blocking, in which one line of defence may relax selection on another so completely that it causes it to decay. We suggest that when strategy-facilitation outweighs strategy-blocking, hosts will possess complex defence portfolios and we identify selective conditions in which this is likely to be the case. © 2011 The Authors. Biological Reviews © 2011 Cambridge Philosophical Society.

Co-evolution of upstream waves and accelerated ions at parallel shocks

NASA Astrophysics Data System (ADS)

Fujimoto, M.; Sugiyama, T.

2016-12-01

Shock waves in space plasmas have been considered as the agents for various particle acceleration phenomena. The basic idea behind shock acceleration is that particles are accelerated as they move back-and-forth across a shock front. Detailed studies of ion acceleration at the terrestrial bow shock have been performed, however, the restricted maximum energies attained prevent a straight-forward application of obtained knowledge to more energetic astrophysical situations. Here we show by a large-scale self-consistent particle simulation that the co-evolution of magnetic turbulence and accelerated ion population is the foundation for continuous operation of shock acceleration to ever higher energies. Magnetic turbulence is created by ions reflected back upstream of a parallel shock front. The co-evolution arises because more energetic ions excite waves of longer wavelengths, and because longer wavelength modes are capable of scattering (in the upstream) and reflecting (at the shock front) more energetic ions. Via carefully designed numerical experiments, we show very clearly that this picture is true.

Parallel arms races between garter snakes and newts involving tetrodotoxin as the phenotypic interface of coevolution.

PubMed

Brodie, Edmund D; Feldman, Chris R; Hanifin, Charles T; Motychak, Jeffrey E; Mulcahy, Daniel G; Williams, Becky L; Brodie, Edmund D

2005-02-01

Parallel "arms races" involving the same or similar phenotypic interfaces allow inference about selective forces driving coevolution, as well as the importance of phylogenetic and phenotypic constraints in coevolution. Here, we report the existence of apparent parallel arms races between species pairs of garter snakes and their toxic newt prey that indicate independent evolutionary origins of a key phenotype in the interface. In at least one area of sympatry, the aquatic garter snake, Thamnophis couchii, has evolved elevated resistance to the neurotoxin tetrodotoxin (TTX), present in the newt Taricha torosa. Previous studies have shown that a distantly related garter snake, Thamnophis sirtalis, has coevolved with another newt species that possesses TTX, Taricha granulosa. Patterns of within population variation and phenotypic tradeoffs between TTX resistance and sprint speed suggest that the mechanism of resistance is similar in both species of snake, yet phylogenetic evidence indicates the independent origins of elevated resistance to TTX.

Evolution of the CRISPR-Cas adaptive immunity systems in prokaryotes: models and observations on virus-host coevolution.

PubMed

Koonin, Eugene V; Wolf, Yuri I

2015-01-01

CRISPR-Cas is an adaptive immunity system in prokaryotes that functions via a unique mechanism which involves incorporation of foreign DNA fragments into CRISPR arrays and subsequent utilization of transcripts of these inserts (known as spacers) as guide RNAs to cleave the cognate selfish element genome. Multiple attempts have been undertaken to explore the coevolution of viruses and microbial hosts carrying CRISPR-Cas using mathematical models that employ either systems of differential equations or an agent-based approach, or combinations thereof. Analysis of these models reveals highly complex co-evolutionary dynamics that ensues from the combination of the heritability of the CRISPR-mediated adaptive immunity with the existence of different degrees of immunity depending on the number of cognate spacers and the cost of carrying a CRISPR-Cas locus. Depending on the details of the models, a variety of testable, sometimes conflicting predictions have been made on the dependence of the degree of immunity and the benefit of maintaining CRISPR-Cas on the abundance and diversity of hosts and viruses. Some of these predictions have already been directly validated experimentally. In particular, both the reality of the virus-host arms race, with viruses escaping resistance and hosts reacquiring it through the capture of new spacers, and the fitness cost of CRISPR-Cas due to the curtailment of beneficial HGT have been reproduced in the laboratory. However, to test the predictions of the models more specifically, detailed studies of coevolving populations of microbes and viruses both in nature and in the laboratory are essential. Such analyses are expected to yield disagreements with the predictions of the current, oversimplified models and to trigger a new round of theoretical developments.

Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways.

PubMed

Orlenko, Alena; Chi, Peter B; Liberles, David A

2017-05-25

Understanding the genotype-phenotype map is fundamental to our understanding of genomes. Genes do not function independently, but rather as part of networks or pathways. In the case of metabolic pathways, flux through the pathway is an important next layer of biological organization up from the individual gene or protein. Flux control in metabolic pathways, reflecting the importance of mutation to individual enzyme genes, may be evolutionarily variable due to the role of mutation-selection-drift balance. The evolutionary stability of rate limiting steps and the patterns of inter-molecular co-evolution were evaluated in a simulated pathway with a system out of equilibrium due to fluctuating selection, population size, or positive directional selection, to contrast with those under stabilizing selection. Depending upon the underlying population genetic regime, fluctuating population size was found to increase the evolutionary stability of rate limiting steps in some scenarios. This result was linked to patterns of local adaptation of the population. Further, during positive directional selection, as with more complex mutational scenarios, an increase in the observation of inter-molecular co-evolution was observed. Differences in patterns of evolution when systems are in and out of equilibrium, including during positive directional selection may lead to predictable differences in observed patterns for divergent evolutionary scenarios. In particular, this result might be harnessed to detect differences between compensatory processes and directional processes at the pathway level based upon evolutionary observations in individual proteins. Detecting functional shifts in pathways reflects an important milestone in predicting when changes in genotypes result in changes in phenotypes.

How Complex, Probable, and Predictable is Genetically Driven Red Queen Chaos?

PubMed

Duarte, Jorge; Rodrigues, Carla; Januário, Cristina; Martins, Nuno; Sardanyés, Josep

2015-12-01

Coevolution between two antagonistic species has been widely studied theoretically for both ecologically- and genetically-driven Red Queen dynamics. A typical outcome of these systems is an oscillatory behavior causing an endless series of one species adaptation and others counter-adaptation. More recently, a mathematical model combining a three-species food chain system with an adaptive dynamics approach revealed genetically driven chaotic Red Queen coevolution. In the present article, we analyze this mathematical model mainly focusing on the impact of species rates of evolution (mutation rates) in the dynamics. Firstly, we analytically proof the boundedness of the trajectories of the chaotic attractor. The complexity of the coupling between the dynamical variables is quantified using observability indices. By using symbolic dynamics theory, we quantify the complexity of genetically driven Red Queen chaos computing the topological entropy of existing one-dimensional iterated maps using Markov partitions. Co-dimensional two bifurcation diagrams are also built from the period ordering of the orbits of the maps. Then, we study the predictability of the Red Queen chaos, found in narrow regions of mutation rates. To extend the previous analyses, we also computed the likeliness of finding chaos in a given region of the parameter space varying other model parameters simultaneously. Such analyses allowed us to compute a mean predictability measure for the system in the explored region of the parameter space. We found that genetically driven Red Queen chaos, although being restricted to small regions of the analyzed parameter space, might be highly unpredictable.

Genetic architecture of resistance in Daphnia hosts against two species of host-specific parasites.

PubMed

Routtu, J; Ebert, D

2015-02-01

Understanding the genetic architecture of host resistance is key for understanding the evolution of host-parasite interactions. Evolutionary models often assume simple genetics based on few loci and strong epistasis. It is unknown, however, whether these assumptions apply to natural populations. Using a quantitative trait loci (QTL) approach, we explore the genetic architecture of resistance in the crustacean Daphnia magna to two of its natural parasites: the horizontally transmitted bacterium Pasteuria ramosa and the horizontally and vertically transmitted microsporidium Hamiltosporidium tvaerminnensis. These two systems have become models for studies on the evolution of host-parasite interactions. In the QTL panel used here, Daphnia's resistance to P. ramosa is controlled by a single major QTL (which explains 50% of the observed variation). Resistance to H. tvaerminnensis horizontal infections shows a signature of a quantitative trait based in multiple loci with weak epistatic interactions (together explaining 38% variation). Resistance to H. tvaerminnensis vertical infections, however, shows only one QTL (explaining 13.5% variance) that colocalizes with one of the QTLs for horizontal infections. QTLs for resistance to Pasteuria and Hamiltosporidium do not colocalize. We conclude that the genetics of resistance in D. magna are drastically different for these two parasites. Furthermore, we infer that based on these and earlier results, the mechanisms of coevolution differ strongly for the two host-parasite systems. Only the Pasteuria-Daphnia system is expected to follow the negative frequency-dependent selection (Red Queen) model. How coevolution works in the Hamiltosporidium-Daphnia system remains unclear.

Genetic architecture of resistance in Daphnia hosts against two species of host-specific parasites

PubMed Central

Routtu, J; Ebert, D

2015-01-01

Understanding the genetic architecture of host resistance is key for understanding the evolution of host–parasite interactions. Evolutionary models often assume simple genetics based on few loci and strong epistasis. It is unknown, however, whether these assumptions apply to natural populations. Using a quantitative trait loci (QTL) approach, we explore the genetic architecture of resistance in the crustacean Daphnia magna to two of its natural parasites: the horizontally transmitted bacterium Pasteuria ramosa and the horizontally and vertically transmitted microsporidium Hamiltosporidium tvaerminnensis. These two systems have become models for studies on the evolution of host–parasite interactions. In the QTL panel used here, Daphnia's resistance to P. ramosa is controlled by a single major QTL (which explains 50% of the observed variation). Resistance to H. tvaerminnensis horizontal infections shows a signature of a quantitative trait based in multiple loci with weak epistatic interactions (together explaining 38% variation). Resistance to H. tvaerminnensis vertical infections, however, shows only one QTL (explaining 13.5% variance) that colocalizes with one of the QTLs for horizontal infections. QTLs for resistance to Pasteuria and Hamiltosporidium do not colocalize. We conclude that the genetics of resistance in D. magna are drastically different for these two parasites. Furthermore, we infer that based on these and earlier results, the mechanisms of coevolution differ strongly for the two host–parasite systems. Only the Pasteuria–Daphnia system is expected to follow the negative frequency-dependent selection (Red Queen) model. How coevolution works in the Hamiltosporidium–Daphnia system remains unclear. PMID:25335558

A Simple General Model of Evolutionary Dynamics

NASA Astrophysics Data System (ADS)

Thurner, Stefan

Evolution is a process in which some variations that emerge within a population (of, e.g., biological species or industrial goods) get selected, survive, and proliferate, whereas others vanish. Survival probability, proliferation, or production rates are associated with the "fitness" of a particular variation. We argue that the notion of fitness is an a posteriori concept in the sense that one can assign higher fitness to species or goods that survive but one can generally not derive or predict fitness per se. Whereas proliferation rates can be measured, fitness landscapes, that is, the inter-dependence of proliferation rates, cannot. For this reason we think that in a physical theory of evolution such notions should be avoided. Here we review a recent quantitative formulation of evolutionary dynamics that provides a framework for the co-evolution of species and their fitness landscapes (Thurner et al., 2010, Physica A 389, 747; Thurner et al., 2010, New J. Phys. 12, 075029; Klimek et al., 2009, Phys. Rev. E 82, 011901 (2010). The corresponding model leads to a generic evolutionary dynamics characterized by phases of relative stability in terms of diversity, followed by phases of massive restructuring. These dynamical modes can be interpreted as punctuated equilibria in biology, or Schumpeterian business cycles (Schumpeter, 1939, Business Cycles, McGraw-Hill, London) in economics. We show that phase transitions that separate phases of high and low diversity can be approximated surprisingly well by mean-field methods. We demonstrate that the mathematical framework is suited to understand systemic properties of evolutionary systems, such as their proneness to collapse, or their potential for diversification. The framework suggests that evolutionary processes are naturally linked to self-organized criticality and to properties of production matrices, such as their eigenvalue spectra. Even though the model is phrased in general terms it is also practical in the sense that it's predictions can be used to understand a series of experimental data ranging from the fossil record to macroeconomic indices.

A coupled human-natural systems analysis of irrigated agriculture under changing climate

NASA Astrophysics Data System (ADS)

Giuliani, M.; Li, Y.; Castelletti, A.; Gandolfi, C.

2016-09-01

Exponentially growing water demands and increasingly uncertain hydrologic regimes due to changes in climate and land use are challenging the sustainability of agricultural water systems. Farmers must adapt their management strategies in order to secure food production and avoid crop failures. Investigating the potential for adaptation policies in agricultural systems requires accounting for their natural and human components, along with their reciprocal interactions. Yet this feedback is generally overlooked in the water resources systems literature. In this work, we contribute a novel modeling approach to study the coevolution of irrigated agriculture under changing climate, advancing the representation of the human component within agricultural systems by using normative meta-models to describe the behaviors of groups of farmers or institutional decisions. These behavioral models, validated against observational data, are then integrated into a coupled human-natural system simulation model to better represent both systems and their coevolution under future changing climate conditions, assuming the adoption of different policy adaptation options, such as cultivating less water demanding crops. The application to the pilot study of the Adda River basin in northern Italy shows that the dynamic coadaptation of water supply and demand allows farmers to avoid estimated potential losses of more than 10 M€/yr under projected climate changes, while unilateral adaptation of either the water supply or the demand are both demonstrated to be less effective. Results also show that the impact of the different policy options varies as function of drought intensity, with water demand adaptation outperforming water supply adaptation when drought conditions become more severe.

The Essential Role of Tick Salivary Glands and Saliva in Tick Feeding and Pathogen Transmission.

PubMed

Šimo, Ladislav; Kazimirova, Maria; Richardson, Jennifer; Bonnet, Sarah I

2017-01-01

As long-term pool feeders, ticks have developed myriad strategies to remain discreetly but solidly attached to their hosts for the duration of their blood meal. The critical biological material that dampens host defenses and facilitates the flow of blood-thus assuring adequate feeding-is tick saliva. Saliva exhibits cytolytic, vasodilator, anticoagulant, anti-inflammatory, and immunosuppressive activity. This essential fluid is secreted by the salivary glands, which also mediate several other biological functions, including secretion of cement and hygroscopic components, as well as the watery component of blood as regards hard ticks. When salivary glands are invaded by tick-borne pathogens, pathogens may be transmitted via saliva, which is injected alternately with blood uptake during the tick bite. Both salivary glands and saliva thus play a key role in transmission of pathogenic microorganisms to vertebrate hosts. During their long co-evolution with ticks and vertebrate hosts, microorganisms have indeed developed various strategies to exploit tick salivary molecules to ensure both acquisition by ticks and transmission, local infection and systemic dissemination within the vertebrate host.

The Essential Role of Tick Salivary Glands and Saliva in Tick Feeding and Pathogen Transmission

PubMed Central

Šimo, Ladislav; Kazimirova, Maria; Richardson, Jennifer; Bonnet, Sarah I.

2017-01-01

As long-term pool feeders, ticks have developed myriad strategies to remain discreetly but solidly attached to their hosts for the duration of their blood meal. The critical biological material that dampens host defenses and facilitates the flow of blood—thus assuring adequate feeding—is tick saliva. Saliva exhibits cytolytic, vasodilator, anticoagulant, anti-inflammatory, and immunosuppressive activity. This essential fluid is secreted by the salivary glands, which also mediate several other biological functions, including secretion of cement and hygroscopic components, as well as the watery component of blood as regards hard ticks. When salivary glands are invaded by tick-borne pathogens, pathogens may be transmitted via saliva, which is injected alternately with blood uptake during the tick bite. Both salivary glands and saliva thus play a key role in transmission of pathogenic microorganisms to vertebrate hosts. During their long co-evolution with ticks and vertebrate hosts, microorganisms have indeed developed various strategies to exploit tick salivary molecules to ensure both acquisition by ticks and transmission, local infection and systemic dissemination within the vertebrate host. PMID:28690983

The Vγ9Vδ2 T Cell Antigen Receptor and Butyrophilin-3 A1: Models of Interaction, the Possibility of Co-Evolution, and the Case of Dendritic Epidermal T Cells

PubMed Central

Karunakaran, Mohindar M.; Herrmann, Thomas

2014-01-01

Most circulating human gamma delta T cells are Vγ9Vδ2 T cells. Their hallmark is the expression of T cell antigen receptors (TCR) whose γ-chains show a Vγ9-JP (Vγ2-Jγ1.2) rearrangement and are paired with Vδ2-containing δ-chains, a dominant TCR configuration, which until recently seemed to occur in primates only. Vγ9Vδ2 T cells respond to phosphoantigens (PAg) such as (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), which is produced by many pathogens and isopentenyl pyrophosphate (IPP), which accumulates in certain tumors or cells treated with aminobisphosphonates such as zoledronate. A prerequisite for PAg-induced activation is the contact of Vγ9Vδ2 T cells with cells expressing butyrophilin-3 A1 (BTN3A1). We will first critically review models of how BTN3 might act in PAg-mediated Vγ9Vδ2 T cell activation and then address putative co-evolution of Vγ9, Vδ2, and BTN3 genes. In those rodent and lagomorphs used as animal models, all three genes are lost but a data-base analysis showed that they emerged together with placental mammals. A strong concomitant conservation of functional Vγ9, Vδ2, and BTN3 genes in other species suggests co-evolution of these three genes. A detailed analysis was performed for the new world camelid alpaca (Vicugna pacos). It provides an excellent candidate for a non-primate species with presumably functional Vγ9Vδ2 T cells since TCR rearrangements share features characteristic for PAg-reactive primate Vγ9Vδ2 TCR and proposed PAg-binding sites of BTN3A1 have been conserved. Finally, we analyze the possible functional relationship between the butyrophilin-family member Skint1 and the γδ TCR-V genes used by murine dendritic epithelial T cells (DETC). Among placental mammals, we identify five rodents, the cow, a bat, and the cape golden mole as the only species concomitantly possessing potentially functional homologs of murine Vγ3, Vδ4 genes, and Skint1 gene and suggest to search for DETC like cells in these species. PMID:25566259

Coevolved Mutations Reveal Distinct Architectures for Two Core Proteins in the Bacterial Flagellar Motor

PubMed Central

Pandini, Alessandro; Kleinjung, Jens; Rasool, Shafqat; Khan, Shahid

2015-01-01

Switching of bacterial flagellar rotation is caused by large domain movements of the FliG protein triggered by binding of the signal protein CheY to FliM. FliG and FliM form adjacent multi-subunit arrays within the basal body C-ring. The movements alter the interaction of the FliG C-terminal (FliGC) “torque” helix with the stator complexes. Atomic models based on the Salmonella entrovar C-ring electron microscopy reconstruction have implications for switching, but lack consensus on the relative locations of the FliG armadillo (ARM) domains (amino-terminal (FliGN), middle (FliGM) and FliGC) as well as changes during chemotaxis. The generality of the Salmonella model is challenged by the variation in motor morphology and response between species. We studied coevolved residue mutations to determine the unifying elements of switch architecture. Residue interactions, measured by their coevolution, were formalized as a network, guided by structural data. Our measurements reveal a common design with dedicated switch and motor modules. The FliM middle domain (FliMM) has extensive connectivity most simply explained by conserved intra and inter-subunit contacts. In contrast, FliG has patchy, complex architecture. Conserved structural motifs form interacting nodes in the coevolution network that wire FliMM to the FliGC C-terminal, four-helix motor module (C3-6). FliG C3-6 coevolution is organized around the torque helix, differently from other ARM domains. The nodes form separated, surface-proximal patches that are targeted by deleterious mutations as in other allosteric systems. The dominant node is formed by the EHPQ motif at the FliMMFliGM contact interface and adjacent helix residues at a central location within FliGM. The node interacts with nodes in the N-terminal FliGc α-helix triad (ARM-C) and FliGN. ARM-C, separated from C3-6 by the MFVF motif, has poor intra-network connectivity consistent with its variable orientation revealed by structural data. ARM-C could be the convertor element that provides mechanistic and species diversity. PMID:26561852

Sustainability, collapse and oscillations in a simple World-Earth model

NASA Astrophysics Data System (ADS)

Nitzbon, Jan; Heitzig, Jobst; Parlitz, Ulrich

2017-07-01

The Anthropocene is characterized by close interdependencies between the natural Earth system and the global human society, posing novel challenges to model development. Here we present a conceptual model describing the long-term co-evolution of natural and socio-economic subsystems of Earth. While the climate is represented via a global carbon cycle, we use economic concepts to model socio-metabolic flows of biomass and fossil fuels between nature and society. A well-being-dependent parametrization of fertility and mortality governs human population dynamics. Our analysis focuses on assessing possible asymptotic states of the Earth system for a qualitative understanding of its complex dynamics rather than quantitative predictions. Low dimension and simple equations enable a parameter-space analysis allowing us to identify preconditions of several asymptotic states and hence fates of humanity and planet. These include a sustainable co-evolution of nature and society, a global collapse and everlasting oscillations. We consider different scenarios corresponding to different socio-cultural stages of human history. The necessity of accounting for the ‘human factor’ in Earth system models is highlighted by the finding that carbon stocks during the past centuries evolved opposing to what would ‘naturally’ be expected on a planet without humans. The intensity of biomass use and the contribution of ecosystem services to human well-being are found to be crucial determinants of the asymptotic state in a (pre-industrial) biomass-only scenario without capital accumulation. The capitalistic, fossil-based scenario reveals that trajectories with fundamentally different asymptotic states might still be almost indistinguishable during even a centuries-long transient phase. Given current human population levels, our study also supports the claim that besides reducing the global demand for energy, only the extensive use of renewable energies may pave the way into a sustainable future.

Cooperation and charity in spatial public goods game under different strategy update rules

NASA Astrophysics Data System (ADS)

Li, Yixiao; Jin, Xiaogang; Su, Xianchuang; Kong, Fansheng; Peng, Chengbin

2010-03-01

Human cooperation can be influenced by other human behaviors and recent years have witnessed the flourishing of studying the coevolution of cooperation and punishment, yet the common behavior of charity is seldom considered in game-theoretical models. In this article, we investigate the coevolution of altruistic cooperation and egalitarian charity in spatial public goods game, by considering charity as the behavior of reducing inter-individual payoff differences. Our model is that, in each generation of the evolution, individuals play games first and accumulate payoff benefits, and then each egalitarian makes a charity donation by payoff transfer in its neighborhood. To study the individual-level evolutionary dynamics, we adopt different strategy update rules and investigate their effects on charity and cooperation. These rules can be classified into two global rules: random selection rule in which individuals randomly update strategies, and threshold selection rule where only those with payoffs below a threshold update strategies. Simulation results show that random selection enhances the cooperation level, while threshold selection lowers the threshold of the multiplication factor to maintain cooperation. When charity is considered, it is incapable in promoting cooperation under random selection, whereas it promotes cooperation under threshold selection. Interestingly, the evolution of charity strongly depends on the dispersion of payoff acquisitions of the population, which agrees with previous results. Our work may shed light on understanding human egalitarianism.

Stochastic eco-evolutionary model of a prey-predator community.

PubMed

Costa, Manon; Hauzy, Céline; Loeuille, Nicolas; Méléard, Sylvie

2016-02-01

We are interested in the impact of natural selection in a prey-predator community. We introduce an individual-based model of the community that takes into account both prey and predator phenotypes. Our aim is to understand the phenotypic coevolution of prey and predators. The community evolves as a multi-type birth and death process with mutations. We first consider the infinite particle approximation of the process without mutation. In this limit, the process can be approximated by a system of differential equations. We prove the existence of a unique globally asymptotically stable equilibrium under specific conditions on the interaction among prey individuals. When mutations are rare, the community evolves on the mutational scale according to a Markovian jump process. This process describes the successive equilibria of the prey-predator community and extends the polymorphic evolutionary sequence to a coevolutionary framework. We then assume that mutations have a small impact on phenotypes and consider the evolution of monomorphic prey and predator populations. The limit of small mutation steps leads to a system of two differential equations which is a version of the canonical equation of adaptive dynamics for the prey-predator coevolution. We illustrate these different limits with an example of prey-predator community that takes into account different prey defense mechanisms. We observe through simulations how these various prey strategies impact the community.

The genetic architecture of resistance to virus infection in Drosophila.

PubMed

Cogni, Rodrigo; Cao, Chuan; Day, Jonathan P; Bridson, Calum; Jiggins, Francis M

2016-10-01

Variation in susceptibility to infection has a substantial genetic component in natural populations, and it has been argued that selection by pathogens may result in it having a simpler genetic architecture than many other quantitative traits. This is important as models of host-pathogen co-evolution typically assume resistance is controlled by a small number of genes. Using the Drosophila melanogaster multiparent advanced intercross, we investigated the genetic architecture of resistance to two naturally occurring viruses, the sigma virus and DCV (Drosophila C virus). We found extensive genetic variation in resistance to both viruses. For DCV resistance, this variation is largely caused by two major-effect loci. Sigma virus resistance involves more genes - we mapped five loci, and together these explained less than half the genetic variance. Nonetheless, several of these had a large effect on resistance. Models of co-evolution typically assume strong epistatic interactions between polymorphisms controlling resistance, but we were only able to detect one locus that altered the effect of the main effect loci we had mapped. Most of the loci we mapped were probably at an intermediate frequency in natural populations. Overall, our results are consistent with major-effect genes commonly affecting susceptibility to infectious diseases, with DCV resistance being a near-Mendelian trait. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Coevolution of bed surface patchiness and channel morphology: 2. Numerical experiments

USGS Publications Warehouse

Nelson, Peter A.; McDonald, Richard R.; Nelson, Jonathan M.; Dietrich, William E.

2015-01-01

In gravel bed rivers, bed topography and the bed surface grain size distribution evolve simultaneously, but it is not clear how feedbacks between topography and grain sorting affect channel morphology. In this, the second of a pair of papers examining interactions between bed topography and bed surface sorting in gravel bed rivers, we use a two-dimensional morphodynamic model to perform numerical experiments designed to explore the coevolution of both free and forced bars and bed surface patches. Model runs were carried out on a computational grid simulating a 200 m long, 2.75 m wide, straight, rectangular channel, with an initially flat bed at a slope of 0.0137. Over five numerical experiments, we varied (a) whether an obstruction was present, (b) whether the sediment was a gravel mixture or a single size, and (c) whether the bed surface grain size feeds back on the hydraulic roughness field. Experiments with channel obstructions developed a train of alternate bars that became stationary and were connected to the obstruction. Freely migrating alternate bars formed in the experiments without channel obstructions. Simulations incorporating roughness feedbacks between the bed surface and flow field produced flatter, broader, and longer bars than simulations using constant roughness or uniform sediment. Our findings suggest that patches are not simply a by-product of bed topography, but they interact with the evolving bed and influence morphologic evolution.

Design Mining Interacting Wind Turbines.

PubMed

Preen, Richard J; Bull, Larry

2016-01-01

An initial study has recently been presented of surrogate-assisted evolutionary algorithms used to design vertical-axis wind turbines wherein candidate prototypes are evaluated under fan-generated wind conditions after being physically instantiated by a 3D printer. Unlike other approaches, such as computational fluid dynamics simulations, no mathematical formulations were used and no model assumptions were made. This paper extends that work by exploring alternative surrogate modelling and evolutionary techniques. The accuracy of various modelling algorithms used to estimate the fitness of evaluated individuals from the initial experiments is compared. The effect of temporally windowing surrogate model training samples is explored. A surrogate-assisted approach based on an enhanced local search is introduced; and alternative coevolution collaboration schemes are examined.

Some assembly required: evolutionary and systems perspectives on the mammalian reproductive system.

PubMed

Mordhorst, Bethany R; Wilson, Miranda L; Conant, Gavin C

2016-01-01

In this review, we discuss the way that insights from evolutionary theory and systems biology shed light on form and function in mammalian reproductive systems. In the first part of the review, we contrast the rapid evolution seen in some reproductive genes with the generally conservative nature of development. We discuss directional selection and coevolution as potential drivers of rapid evolution in sperm and egg proteins. Such rapid change is very different from the highly conservative nature of later embryo development. However, it is not unique, as some regions of the sex chromosomes also show elevated rates of evolutionary change. To explain these contradictory trends, we argue that it is not reproductive functions per se that induce rapid evolution. Rather, it is the fact that biotic interactions, such as speciation events and sexual conflict, have no evolutionary endpoint and hence can drive continuous evolutionary changes. Returning to the question of sex chromosome evolution, we discuss the way that recent advances in evolutionary genomics and systems biology and, in particular, the development of a theory of gene balance provide a better understanding of the evolutionary patterns seen on these chromosomes. We end the review with a discussion of a surprising and incompletely understood phenomenon observed in early embryos: namely the Warburg effect, whereby glucose is fermented to lactate and alanine rather than respired to carbon dioxide. We argue that evolutionary insights, from both yeasts and tumor cells, help to explain the Warburg effect, and that new metabolic modeling approaches are useful in assessing the potential sources of the effect.

Life’s Order, Complexity, Organization, and Its Thermodynamic–Holistic Imperatives

PubMed Central

Egel, Richard

2012-01-01

In memoriam Jeffrey S. Wicken (1942–2002)—the evolutionarily minded biochemist, who in the 1970/80s strived for a synthesis of biological and physical theories to fathom the tentative origins of life. Several integrative concepts are worth remembering from Wicken’s legacy. (i) Connecting life’s origins and complex organization to a preexisting physical world demands a thermodynamically sound transition. (ii) Energetic ‘charging’ of the prebiosphere must precede the emergence of biological organization. (iii) Environmental energy gradients are exploited progressively, approaching maximum interactive structure and minimum dissipation. (iv) Dynamic self-assembly of prebiotic organic matter is driven by hydrophobic tension between water and amphiphilic building blocks, such as aggregating peptides from non-polar amino acids and base stacking in nucleic acids. (v) The dynamics of autocatalytic self-organization are facilitated by a multiplicity of weak interactions, such as hydrogen bonding, within and between macromolecular assemblies. (vi) The coevolution of (initially uncoded) proteins and nucleic acids in energy-coupled and metabolically active so-called ‘microspheres’ is more realistic as a kinetic transition model of primal biogenesis than ‘hypercycle replication’ theories for nucleic acid replicators on their own. All these considerations blend well with the current understanding that sunlight UV-induced photo-electronic excitation of colloidal metal sulfide particles appears most suitable as a prebiotic driver of organic synthesis reactions, in tight cooperation with organic, phase-separated, catalytic ‘microspheres’. On the ‘continuist vs. miraculist’ schism described by Iris Fry for origins-of-life considerations (Table 1), Wicken was a fervent early protagonist of holistic ‘continuist’ views and agenda. PMID:25371269

On Budyko curve as a consequence of climate-soil-vegetation equilibrium hypothesis

NASA Astrophysics Data System (ADS)

Pande, S.

2012-04-01

A hypothesis that Budyko curve is a consequence of stable equilibriums of climate-soil-vegetation co-evolution is tested at biome scale. We assume that i) distribution of vegetation, soil and climate within a biome is a distribution of equilibriums of similar soil-vegetation dynamics and that this dynamics is different across different biomes and ii) soil and vegetation are in dynamic equilibrium with climate while in static equilibrium with each other. In order to test the hypothesis, a two stage regression is considered using MOPEX/Hydrologic Synthesis Project dataset for basins in eastern United States. In the first stage, multivariate regression (Seemingly Unrelated Regression) is performed for each biome with soil (estimated porosity and slope of soil water retention curve) and vegetation characteristics (5-week NDVI gradient) as dependent variables and aridity index, vegetation and soil characteristics as independent variables for respective dependent variables. The regression residuals of the first stage along with aridity index then serve as second stage independent variables while actual vaporization to precipitation ratio (vapor index) serving as dependent variable. Insignificance, if revealed, of a first stage parameter allows us to reject the role of corresponding soil or vegetation characteristics in the co-evolution hypothesis. Meanwhile the significance of second stage regression parameter corresponding to a first stage residual allow us to reject the hypothesis that Budyko curve is a locus "solely" of climate-soil-vegetation co-evolution equilibrium points. Results suggest lack of evidence for soil-vegetation co-evolution in Prairies and Mixed/SouthEast Forests (unlike in Deciduous Forests) though climate plays a dominant role in explaining within biome soil and vegetation characteristics across all the biomes. Preliminary results indicate absence of effects beyond climate-soil-vegetation co-evolution in explaining the ratio of annual total minimum monthly flows to precipitation in Deciduous Forests though other three biome types show presence of effects beyond co-evolutionary. Such an analysis can yield insights into the nature of hydrologic change when assessed along the Budyko curve as well as non co-evolutionary effects such as anthropogenic effects on basin scale annual water balances.

Endophytic Epichloë species and their grass hosts: from evolution to applications.

PubMed

Saikkonen, Kari; Young, Carolyn A; Helander, Marjo; Schardl, Christopher L

2016-04-01

The closely linked fitness of the Epichloë symbiont and the host grass is presumed to align the coevolution of the species towards specialization and mutually beneficial cooperation. Ecological observations demonstrating that Epichloë-grass symbioses can modulate grassland ecosystems via both above- and belowground ecosystem processes support this. In many cases the detected ecological importance of Epichloë species is directly or indirectly linked to defensive mutualism attributable to alkaloids of fungal-origin. Now, modern genetic and molecular techniques enable the precise studies on evolutionary origin of endophytic Epichloë species, their coevolution with host grasses and identification the genetic variation that explains phenotypic diversity in ecologically relevant characteristics of Epichloë-grass associations. Here we briefly review the most recent findings in these areas of research using the present knowledge of the genetic variation that explains the biosynthetic pathways driving the diversity of alkaloids produced by the endophyte. These findings underscore the importance of genetic interplay between the fungus and the host in shaping their coevolution and ecological role in both natural grass ecosystems, and in the agricultural arena.

Sequence, structure and function relationships in flaviviruses as assessed by evolutive aspects of its conserved non-structural protein domains.

PubMed

da Fonseca, Néli José; Lima Afonso, Marcelo Querino; Pedersolli, Natan Gonçalves; de Oliveira, Lucas Carrijo; Andrade, Dhiego Souto; Bleicher, Lucas

2017-10-28

Flaviviruses are responsible for serious diseases such as dengue, yellow fever, and zika fever. Their genomes encode a polyprotein which, after cleavage, results in three structural and seven non-structural proteins. Homologous proteins can be studied by conservation and coevolution analysis as detected in multiple sequence alignments, usually reporting positions which are strictly necessary for the structure and/or function of all members in a protein family or which are involved in a specific sub-class feature requiring the coevolution of residue sets. This study provides a complete conservation and coevolution analysis on all flaviviruses non-structural proteins, with results mapped on all well-annotated available sequences. A literature review on the residues found in the analysis enabled us to compile available information on their roles and distribution among different flaviviruses. Also, we provide the mapping of conserved and coevolved residues for all sequences currently in SwissProt as a supplementary material, so that particularities in different viruses can be easily analyzed. Copyright © 2017 Elsevier Inc. All rights reserved.

Within-host co-evolution of chronic viruses and the adaptive immune system

NASA Astrophysics Data System (ADS)

Nourmohammad, Armita

We normally think of evolution occurring in a population of organisms, in response to their external environment. Rapid evolution of cellular populations also occurs within our bodies, as the adaptive immune system works to eliminate infection. Some pathogens, such as HIV, are able to persist in a host for extended periods of time, during which they also evolve to evade the immune response. In this talk I will introduce an analytical framework for the rapid co-evolution of B-cell and viral populations, based on the molecular interactions between them. Since the co-evolution of antibodies and viruses is perpetually out of equilibrium, I will show how to quantify the amount of adaptation in each of the two populations by analysis of their co-evolutionary history. I will discuss the consequences of competition between lineages of antibodies, and characterize the fate of a given lineage dependent on the state of the antibody and viral populations. In particular, I will discuss the conditions for emergence of highly potent broadly neutralizing antibodies, which are now recognized as critical for designing an effective vaccine against HIV.

Cooperation enhanced by the coevolution of teaching activity in evolutionary prisoner's dilemma games with voluntary participation.

PubMed

Shen, Chen; Chu, Chen; Geng, Yini; Jin, Jiahua; Chen, Fei; Shi, Lei

2018-01-01

Voluntary participation, as an additional strategy involved in repeated games, has been proved to be an efficient way to promote the evolution of cooperation theoretically and empirically. Besides, current studies show that the coevolution of teaching activity can promote cooperation. Thus, inspired by aforementioned above, we investigate the effect of coevolution of teaching activity on the evolution of cooperation for prisoner's dilemma game with voluntary participation: when the focal player successfully enforces its strategy on the opponent, his teaching ability will get an increase. Through numerical simulation, we have shown that voluntary participation could effectively promote the fraction of cooperation, which is also affected by the value of increment. Furthermore, we investigate the influence of the increment value on the density of different strategies and find that there exists an optimal increment value that plays an utmost role on the evolutionary dynamics. With regard to this observation, we unveil that an optimal value of increment can lead to strongest heterogeneity in agents' teaching ability, further promoting the evolution of cooperation.

Human niche construction in interdisciplinary focus

PubMed Central

Kendal, Jeremy; Tehrani, Jamshid J.; Odling-Smee, John

2011-01-01

Niche construction is an endogenous causal process in evolution, reciprocal to the causal process of natural selection. It works by adding ecological inheritance, comprising the inheritance of natural selection pressures previously modified by niche construction, to genetic inheritance in evolution. Human niche construction modifies selection pressures in environments in ways that affect both human evolution, and the evolution of other species. Human ecological inheritance is exceptionally potent because it includes the social transmission and inheritance of cultural knowledge, and material culture. Human genetic inheritance in combination with human cultural inheritance thus provides a basis for gene–culture coevolution, and multivariate dynamics in cultural evolution. Niche construction theory potentially integrates the biological and social aspects of the human sciences. We elaborate on these processes, and provide brief introductions to each of the papers published in this theme issue. PMID:21320894

Life cycle specialization of filamentous pathogens - colonization and reproduction in plant tissues.

PubMed

Haueisen, Janine; Stukenbrock, Eva H

2016-08-01

Filamentous plant pathogens explore host tissues to obtain nutrients for growth and reproduction. Diverse strategies for tissue invasion, defense manipulation, and colonization of inter and intra-cellular spaces have evolved. Most research has focused on effector molecules, which are secreted to manipulate plant immunity and facilitate infection. Effector genes are often found to evolve rapidly in response to the antagonistic host-pathogen co-evolution but other traits are also subject to adaptive evolution during specialization to the anatomy, biochemistry and ecology of different plant hosts. Although not directly related to virulence, these traits are important components of specialization but little is known about them. We present and discuss specific life cycle traits that facilitate exploration of plant tissues and underline the importance of increasing our insight into the biology of plant pathogens. Copyright © 2016. Published by Elsevier Ltd.

An Airway Network Flow Assignment Approach Based on an Efficient Multiobjective Optimization Framework

PubMed Central

Zhang, Xuejun; Lei, Jiaxing

2015-01-01

Considering reducing the airspace congestion and the flight delay simultaneously, this paper formulates the airway network flow assignment (ANFA) problem as a multiobjective optimization model and presents a new multiobjective optimization framework to solve it. Firstly, an effective multi-island parallel evolution algorithm with multiple evolution populations is employed to improve the optimization capability. Secondly, the nondominated sorting genetic algorithm II is applied for each population. In addition, a cooperative coevolution algorithm is adapted to divide the ANFA problem into several low-dimensional biobjective optimization problems which are easier to deal with. Finally, in order to maintain the diversity of solutions and to avoid prematurity, a dynamic adjustment operator based on solution congestion degree is specifically designed for the ANFA problem. Simulation results using the real traffic data from China air route network and daily flight plans demonstrate that the proposed approach can improve the solution quality effectively, showing superiority to the existing approaches such as the multiobjective genetic algorithm, the well-known multiobjective evolutionary algorithm based on decomposition, and a cooperative coevolution multiobjective algorithm as well as other parallel evolution algorithms with different migration topology. PMID:26180840

Classification as clustering: a Pareto cooperative-competitive GP approach.

PubMed

McIntyre, Andrew R; Heywood, Malcolm I

2011-01-01

Intuitively population based algorithms such as genetic programming provide a natural environment for supporting solutions that learn to decompose the overall task between multiple individuals, or a team. This work presents a framework for evolving teams without recourse to prespecifying the number of cooperating individuals. To do so, each individual evolves a mapping to a distribution of outcomes that, following clustering, establishes the parameterization of a (Gaussian) local membership function. This gives individuals the opportunity to represent subsets of tasks, where the overall task is that of classification under the supervised learning domain. Thus, rather than each team member representing an entire class, individuals are free to identify unique subsets of the overall classification task. The framework is supported by techniques from evolutionary multiobjective optimization (EMO) and Pareto competitive coevolution. EMO establishes the basis for encouraging individuals to provide accurate yet nonoverlaping behaviors; whereas competitive coevolution provides the mechanism for scaling to potentially large unbalanced datasets. Benchmarking is performed against recent examples of nonlinear SVM classifiers over 12 UCI datasets with between 150 and 200,000 training instances. Solutions from the proposed coevolutionary multiobjective GP framework appear to provide a good balance between classification performance and model complexity, especially as the dataset instance count increases.

Coevolution of Information Sharing and Implementation of Evidence-Based Practices Among North American Tobacco Cessation Quitlines

PubMed Central

Saul, Jessie E.; Lemaire, Robin H.; Valente, Thomas W.; Leischow, Scott J.

2015-01-01

Objectives. We examined the coevolution of information sharing and implementation of evidence-based practices among US and Canadian tobacco cessation quitlines within the North American Quitline Consortium (NAQC). Methods. Web-based surveys were used to collect data from key respondents representing each of 74 participating funders of NAQC quitlines during the summer and fall of 2009, 2010, and 2011. We used stochastic actor-based models to estimate changes in information sharing and practice implementation in the NAQC network. Results. Funders were more likely to share information within their own country and with funders that contracted with the same service provider. Funders contracting with larger service providers shared less information but implemented significantly more practices. Funders connected to larger numbers of tobacco control researchers more often received information from other funders. Intensity of ties to the NAQC network administrative organization did not influence funders’ decisions to share information or implement practices. Conclusions. Our findings show the importance of monitoring the NAQC network over time. We recommend increased cross-border information sharing and sharing of information between funders contracting with different and smaller service providers. PMID:26180993

Computing the origin and evolution of the ribosome from its structure — Uncovering processes of macromolecular accretion benefiting synthetic biology

PubMed Central

Caetano-Anollés, Gustavo; Caetano-Anollés, Derek

2015-01-01

Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. Phylogenetic trees of protein structural domains and proteomes and their molecular functions were built from a genomic census of millions of encoded proteins and associated terminal Gene Ontology terms. Trees reveal a ‘metabolic-first’ origin of proteins, the late development of translation, and a patchwork distribution of proteins in biological networks mediated by molecular recruitment. Similarly, the natural history of ancient RNA molecules inferred from trees of molecular substructures built from a census of molecular features shows patchwork-like accretion patterns. Ideographic analyses of ribosomal history uncover the early appearance of structures supporting mRNA decoding and tRNA translocation, the coevolution of ribosomal proteins and RNA, and a first evolutionary transition that brings ribosomal subunits together into a processive protein biosynthetic complex. Nomothetic structural biology studies of tertiary interactions and ancient insertions in rRNA complement these findings, once concentric layering assumptions are removed. Patterns of coaxial helical stacking reveal a frustrated dynamics of outward and inward ribosomal growth possibly mediated by structural grafting. The early rise of the ribosomal ‘turnstile’ suggests an evolutionary transition in natural biological computation. Results make explicit the need to understand processes of molecular growth and information transfer of macromolecules. PMID:27096056

Exploring the co-evolution of marine ecology and environment in silico

NASA Astrophysics Data System (ADS)

Ridgwell, A.

2015-12-01

Species do not live in isolation, but adapt and ultimately, evolve, in relationship with other species as well as with their chemical and physical environment. In the marine environment, this interaction is intimately two-way - the surface biogeochemical environment modulates the makeup of the pelagic ecosystem, yet at the same time, the ecosystem assemblage, by setting the strength of the biological pump and ultimately, in regulating the carbon and nutrient inventory of the ocean and atmospheric pCO2, influences the surface geochemical environment. Feedbacks, both negative and positive, must therefore exist between plankton ecology and global biogeochemical cycles. This has implications for understanding the geological record and particularly the response and recovery of marine ecosystems following major environmental perturbation, but also complicates making projections of future ocean changes. To address a coupled system such as this, new numerical tools are needed as traditional 'functional type' marine ecosystem models are generally incapable of accounting for short-term adaptation, let alone long-term evolution. What is needed is the combination of a plankton model able to simulate a highly diverse ecology plus 'genetic' mutation (changes in trait value(s)) and extinction, *and* an Earth system model capable of simulating long-term evolution of the climatology and geochemistry of the ocean. The Earth system model 'cGENIE' - http://mycgenie.seao2.org generally fills the second criteria, so for this presentation I will focus on the structure of the ecosystem model, the associated methodology, and numerical techniques for dealing with what will turn out to be an exceptionally large number of ocean tracers. If you are really lucky, there may even be some preliminary results :)

Multiple Phase Transitions in the Culture Dissemination

NASA Astrophysics Data System (ADS)

Wang, Bing; Han, Yuexing; Chen, Luonan; Aihara, Kazuyuki

We study the coevolution process in the Axelrod’s model with the consideration of agents’ abilities to access to the information. With a parameter to control the ability of communication, we observe two kinds of phase transitions both for cultural domains and network fragments, respectively. With the simulation results, we find the relationship between the critical value and the controlled parameter. The results indicate that the powerful ability to access to the information benefits the dissemination of culture in the system.

Question 6: coevolution theory of the genetic code: a proven theory.

PubMed

Wong, Jeffrey Tze-Fei

2007-10-01

The coevolution theory proposes that primordial proteins consisted only of those amino acids readily obtainable from the prebiotic environment, representing about half the twenty encoded amino acids of today, and the missing amino acids entered the system as the code expanded along with pathways of amino acid biosynthesis. The isolation of genetic code mutants, and the antiquity of pretran synthesis revealed by the comparative genomics of tRNAs and aminoacyl-tRNA synthetases, have combined to provide a rigorous proof of the four fundamental tenets of the theory, thus solving the riddle of the structure of the universal genetic code.

The co-evolution of microstructure features in self-ion irradiated HT9 at very high damage levels

NASA Astrophysics Data System (ADS)

Getto, E.; Vancoevering, G.; Was, G. S.

2017-02-01

Understanding the void swelling and phase evolution of reactor structural materials at very high damage levels is essential to maintaining safety and longevity of components in Gen IV fast reactors. A combination of ion irradiation and modeling was utilized to understand the microstructure evolution of ferritic-martensitic alloy HT9 at high dpa. Self-ion irradiation experiments were performed on alloy HT9 to determine the co-evolution of voids, dislocations and precipitates up to 650 dpa at 460 °C. Modeling of microstructure evolution was conducted using the modified Radiation Induced Microstructure Evolution (RIME) model, which utilizes a mean field rate theory approach with grouped cluster dynamics. Irradiations were performed with 5 MeV raster-scanned Fe2+ ions on samples pre-implanted with 10 atom parts per million He. The swelling, dislocation and precipitate evolution at very high dpa was determined using Analytical Electron Microscopy in Scanning Transmission Electron Microscopy (STEM) mode. Experimental results were then interpreted using the RIME model. A microstructure consisting only of dislocations and voids is insufficient to account for the swelling evolution observed experimentally at high damage levels in a complicated microstructure such as irradiated alloy HT9. G phase was found to have a minimal effect on either void or dislocation evolution. M2X played two roles; a variable biased sink for defects, and as a vehicle for removal of carbon from solution, thus promoting void growth. When accounting for all microstructure interactions, swelling at high damage levels is a dynamic process that continues to respond to other changes in the microstructure as long as they occur.

Coevolution of bed surface patchiness and channel morphology: 1. Mechanisms of forced patch formation

USGS Publications Warehouse

Nelson, Peter A.; McDonald, Richard R.; Nelson, Jonathan M.; Dietrich, William E.

2015-01-01

Riverbeds frequently display a spatial structure where the sediment mixture composing the channel bed has been sorted into discrete patches of similar grain size. Even though patches are a fundamental feature in gravel bed rivers, we have little understanding of how patches form, evolve, and interact. Here we present a two-dimensional morphodynamic model that is used to examine in greater detail the mechanisms responsible for the development of forced bed surface patches and the coevolution of bed morphology and bed surface patchiness. The model computes the depth-averaged channel hydrodynamics, mixed-grain-size sediment transport, and bed evolution by coupling the river morphodynamic model Flow and Sediment Transport with Morphological Evolution of Channels (FaSTMECH) with a transport relation for gravel mixtures and the mixed-grain-size Exner equation using the active layer assumption. To test the model, we use it to simulate a flume experiment in which the bed developed a sequence of alternate bars and temporally and spatially persistent forced patches with a general pattern of coarse bar tops and fine pools. Cross-stream sediment flux causes sediment to be exported off of bars and imported into pools at a rate that balances downstream gradients in the streamwise sediment transport rate, allowing quasi-steady bar-pool topography to persist. The relative importance of lateral gravitational forces on the cross-stream component of sediment transport is a primary control on the amplitude of the bars. Because boundary shear stress declines as flow shoals over the bars, the lateral sediment transport is increasingly size selective and leads to the development of coarse bar tops and fine pools.

A New Framework for Analysis of Coevolutionary Systems-Directed Graph Representation and Random Walks.

PubMed

Chong, Siang Yew; Tiňo, Peter; He, Jun; Yao, Xin

2017-11-20

Studying coevolutionary systems in the context of simplified models (i.e., games with pairwise interactions between coevolving solutions modeled as self plays) remains an open challenge since the rich underlying structures associated with pairwise-comparison-based fitness measures are often not taken fully into account. Although cyclic dynamics have been demonstrated in several contexts (such as intransitivity in coevolutionary problems), there is no complete characterization of cycle structures and their effects on coevolutionary search. We develop a new framework to address this issue. At the core of our approach is the directed graph (digraph) representation of coevolutionary problems that fully captures structures in the relations between candidate solutions. Coevolutionary processes are modeled as a specific type of Markov chains-random walks on digraphs. Using this framework, we show that coevolutionary problems admit a qualitative characterization: a coevolutionary problem is either solvable (there is a subset of solutions that dominates the remaining candidate solutions) or not. This has an implication on coevolutionary search. We further develop our framework that provides the means to construct quantitative tools for analysis of coevolutionary processes and demonstrate their applications through case studies. We show that coevolution of solvable problems corresponds to an absorbing Markov chain for which we can compute the expected hitting time of the absorbing class. Otherwise, coevolution will cycle indefinitely and the quantity of interest will be the limiting invariant distribution of the Markov chain. We also provide an index for characterizing complexity in coevolutionary problems and show how they can be generated in a controlled manner.

Revitalization of plant growth promoting rhizobacteria for sustainable development in agriculture.

PubMed

Gouda, Sushanto; Kerry, Rout George; Das, Gitishree; Paramithiotis, Spiros; Shin, Han-Seung; Patra, Jayanta Kumar

2018-01-01

The progression of life in all forms is not only dependent on agricultural and food security but also on the soil characteristics. The dynamic nature of soil is a direct manifestation of soil microbes, bio-mineralization, and synergistic co-evolution with plants. With the increase in world's population the demand for agriculture yield has increased tremendously and thereby leading to large scale production of chemical fertilizers. Since the use of fertilizers and pesticides in the agricultural fields have caused degradation of soil quality and fertility, thus the expansion of agricultural land with fertile soil is near impossible, hence researchers and scientists have sifted their attention for a safer and productive means of agricultural practices. Plant growth promoting rhizobacteria (PGPR) has been functioning as a co-evolution between plants and microbes showing antagonistic and synergistic interactions with microorganisms and the soil. Microbial revitalization using plant growth promoters had been achieved through direct and indirect approaches like bio-fertilization, invigorating root growth, rhizoremediation, disease resistance etc. Although, there are a wide variety of PGPR and its allies, their role and usages for sustainable agriculture remains controversial and restricted. There is also variability in the performance of PGPR that may be due to various environmental factors that might affect their growth and proliferation in the plants. These gaps and limitations can be addressed through use of modern approaches and techniques such as nano-encapsulation and micro-encapsulation along with exploring multidisciplinary research that combines applications in biotechnology, nanotechnology, agro biotechnology, chemical engineering and material science and bringing together different ecological and functional biological approaches to provide new formulations and opportunities with immense potential. Copyright © 2017 Elsevier GmbH. All rights reserved.

Evolution of photorespiration from cyanobacteria to land plants, considering protein phylogenies and acquisition of carbon concentrating mechanisms.

PubMed

Hagemann, Martin; Kern, Ramona; Maurino, Veronica G; Hanson, David T; Weber, Andreas P M; Sage, Rowan F; Bauwe, Hermann

2016-05-01

Photorespiration and oxygenic photosynthesis are intimately linked processes. It has been shown that under the present day atmospheric conditions cyanobacteria and all eukaryotic phototrophs need functional photorespiration to grow autotrophically. The question arises as to when this essential partnership evolved, i.e. can we assume a coevolution of both processes from the beginning or did photorespiration evolve later to compensate for the generation of 2-phosphoglycolate (2PG) due to Rubisco's oxygenase reaction? This question is mainly discussed here using phylogenetic analysis of proteins involved in the 2PG metabolism and the acquisition of different carbon concentrating mechanisms (CCMs). The phylogenies revealed that the enzymes involved in the photorespiration of vascular plants have diverse origins, with some proteins acquired from cyanobacteria as ancestors of the chloroplasts and others from heterotrophic bacteria as ancestors of mitochondria in the plant cell. Only phosphoglycolate phosphatase was found to originate from Archaea. Notably glaucophyte algae, the earliest branching lineage of Archaeplastida, contain more photorespiratory enzymes of cyanobacterial origin than other algal lineages or land plants indicating a larger initial contribution of cyanobacterial-derived proteins to eukaryotic photorespiration. The acquisition of CCMs is discussed as a proxy for assessing the timing of periods when photorespiratory activity may have been enhanced. The existence of CCMs also had marked influence on the structure and function of photorespiration. Here, we discuss evidence for an early and continuous coevolution of photorespiration, CCMs and photosynthesis starting from cyanobacteria via algae, to land plants. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Co-evolution and symbiont replacement shaped the symbiosis between adelgids (Hemiptera: Adelgidae) and their bacterial symbionts.

PubMed

Toenshoff, Elena R; Gruber, Daniela; Horn, Matthias

2012-05-01

The Adelgidae (Insecta: Hemiptera), a small group of insects, are known as severe pests on various conifers of the northern hemisphere. Despite of this, little is known about their bacteriocyte-associated endosymbionts, which are generally important for the biology and ecology of plant sap-sucking insects. Here, we investigated the adelgid species complexes Adelges laricis/tardus, Adelges abietis/viridis and Adelges cooleyi/coweni, identified based on their coI and ef1alpha genes. Each of these insect groups harboured two phylogenetically different bacteriocyte-associated symbionts belonging to the Betaproteobacteria and the Gammaproteobacteria, respectively, as inferred from phylogenetic analyses of 16S rRNA gene sequences and demonstrated by fluorescence in situ hybridization. The betaproteobacterial symbionts of all three adelgid complexes ('Candidatus Vallotia tarda', 'Candidatus Vallotia virida' and 'Candidatus Vallotia cooleyia') share a common ancestor and show a phylogeny congruent with that of their respective hosts. Similarly, there is evidence for co-evolution between the gammaproteobacterial symbionts ('Candidatus Profftia tarda', 'Candidatus Profftia virida') and A. laricis/tardus and A. abietis/viridis. In contrast, the gammaproteobacterial symbiont of A. cooleyi/coweni ('Candidatus Gillettellia cooleyia') is different from that of the other two adelgids but shows a moderate relationship to the symbiont 'Candidatus Ecksteinia adelgidicola' of A. nordmannianae/piceae. All symbionts were present in all adelgid populations and life stages analysed, suggesting vertical transmission from mother to offspring. In sharp contrast to their sister group, the aphids, adelgids do not consistently contain a single obligate (primary) symbiont but have acquired phylogenetically different bacterial symbionts during their evolution, which included multiple infections and symbiont replacement. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Metabolic Coevolution in the Bacterial Symbiosis of Whiteflies and Related Plant Sap-Feeding Insects.

PubMed

Luan, Jun-Bo; Chen, Wenbo; Hasegawa, Daniel K; Simmons, Alvin M; Wintermantel, William M; Ling, Kai-Shu; Fei, Zhangjun; Liu, Shu-Sheng; Douglas, Angela E

2015-09-15

Genomic decay is a common feature of intracellular bacteria that have entered into symbiosis with plant sap-feeding insects. This study of the whitefly Bemisia tabaci and two bacteria (Portiera aleyrodidarum and Hamiltonella defensa) cohoused in each host cell investigated whether the decay of Portiera metabolism genes is complemented by host and Hamiltonella genes, and compared the metabolic traits of the whitefly symbiosis with other sap-feeding insects (aphids, psyllids, and mealybugs). Parallel genomic and transcriptomic analysis revealed that the host genome contributes multiple metabolic reactions that complement or duplicate Portiera function, and that Hamiltonella may contribute multiple cofactors and one essential amino acid, lysine. Homologs of the Bemisia metabolism genes of insect origin have also been implicated in essential amino acid synthesis in other sap-feeding insect hosts, indicative of parallel coevolution of shared metabolic pathways across multiple symbioses. Further metabolism genes coded in the Bemisia genome are of bacterial origin, but phylogenetically distinct from Portiera, Hamiltonella and horizontally transferred genes identified in other sap-feeding insects. Overall, 75% of the metabolism genes of bacterial origin are functionally unique to one symbiosis, indicating that the evolutionary history of metabolic integration in these symbioses is strongly contingent on the pattern of horizontally acquired genes. Our analysis, further, shows that bacteria with genomic decay enable host acquisition of complex metabolic pathways by multiple independent horizontal gene transfers from exogenous bacteria. Specifically, each horizontally acquired gene can function with other genes in the pathway coded by the symbiont, while facilitating the decay of the symbiont gene coding the same reaction. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Phase-specific Geochemistry of Ni: a Tracer of Geosphere-Biosphere Co-evolution?

NASA Astrophysics Data System (ADS)

Ciscato, E. R.; Vance, D.; Bontognali, T. R. R.; Poulton, S.

2016-12-01

Metalloproteome analyses and culturing studies have suggested that trace metals, such as Cu, Fe, Mo, Ni, and Zn, were selectively utilized by different organisms and specific metabolisms throughout the evolution of the biosphere. Methanogens have a particular requirement for Ni and culturing studies have shown that they fractionate Ni isotopes upon uptake. It is not clear, however, whether a resulting Ni isotopic signal can be preserved in the geological record. We have developed a new approach that enables us to analyze phase-specific authigenic trace metal enrichments, and their respective isotopic signatures, in (predominantly organic-rich) sediments from the geological record. An acid digestion step followed by high-pressure ashing allows us to separate an `organic matter + Pyrite' phase from an `HF-extractable' phase. We have applied this approach to investigate the distribution of Ni isotopes in a variety of modern sediments, including organic-rich sediments from upwelling margins and a hypersaline lagoonal setting where methanogenesis is likely to be an active process. Preliminary results on geological record samples show a δ60Ni for the `HF-extractable' phases that agrees with the average continental crust, whereas the `organic matter + Pyrite' phases are heavier and shifted in the direction of modern seawater. By combining this data with our δ60Ni dataset from modern sediments, we investigate the dynamics of Ni cycling in environments with different O2 and H2S availabilities both in the modern and throughout the past 3.2 billion years. Our phase-specific δ60Ni record is of instrumental importance in determining whether a biologically induced fractionation imparted by methanogens is indeed observable, and if it can be used as a biosignature for tracing the predominance of methanogenic pathways throughout the co-evolution of the geosphere and biosphere.

The Co-Evolution of Life & Environment, and the Astrobiological Quest

NASA Astrophysics Data System (ADS)

Cabrol, N. A.

2016-12-01

Physicochemical and environmental conditions determine the range of possible biogeochemistries on planets and moons. Yet, the Earth shows that as soon as life took hold, it modified its environment, from the mineralogy of sediments to the global composition of the atmosphere. In their evolution, life and environment are intertwined and cannot be separated. This coevolution is one of the most fundamental concepts in astrobiology, one that is central to our understanding of what, where, and how to search for life beyond Earth. In that quest, Mars will be the first destination for planetary missions seeking biosignatures. Both Earth and Mars had shared traits during the Archean/Noachian period. However, for Mars, the impact of a different environmental evolution on the development of life and the preservation of biosignatures remains unclear. In addition to an irreversible global climate change, Mars always had greater environmental variability than Earth due to its astronomical characteristics. Biological evolution, if any, would have had to proceed in this distinct context. If parallels can be drawn, the major metabolisms supporting Earth's biogeochemical cycles had evolved early. Understanding the succession of physical and environmental processes and their combination in the first 700 million years of Mars history is, therefore, essential to envision possible metabolisms, adaptation strategies life would have required to survive changes, and the biosignatures that could still be preserved today. Ultimately, the astrobiological significance of exploring Mars is also about teaching us invaluable lessons about the uniqueness of each planetary experiment, regardless of similarities. Beyond the Solar System, this notion can be expanded to the search for earth-like exoplanets, and for what it means to search for life as we know it, simple or complex.

Working with lay people in health service research: a model of co-evolution based on complexity theory.

PubMed

Kernick, David; Mitchell, Annie

2010-01-01

Involving lay researchers is an important part of Government policy in the United Kingdom within the context of the National Health Service. Here we draw upon insights from complexity theory to suggest a model that we call consensual qualitative research where lay researchers and professionals are co-producers of knowledge. The focus of attention is on understanding and facilitating the patterns that emerge from non-linear interaction at a local level. We describe some core principles that can facilitate the development of such a model and conclude that the resources in terms of time and effort that such an approach requires, should not be underestimated.

Reduction of female copulatory damage by resilin represents evidence for tolerance in sexual conflict

PubMed Central

Michels, Jan; Gorb, Stanislav N.; Reinhardt, Klaus

2015-01-01

Intergenomic evolutionary conflicts increase biological diversity. In sexual conflict, female defence against males is generally assumed to be resistance, which, however, often leads to trait exaggeration but not diversification. Here, we address whether tolerance, a female defence mechanism known from interspecific conflicts, exists in sexual conflict. We examined the traumatic insemination of female bed bugs via cuticle penetration by males, a textbook example of sexual conflict. Confocal laser scanning microscopy revealed large proportions of the soft and elastic protein resilin in the cuticle of the spermalege, the female defence organ. Reduced tissue damage and haemolymph loss were identified as adaptive female benefits from resilin. These did not arise from resistance because microindentation showed that the penetration force necessary to breach the cuticle was significantly lower at the resilin-rich spermalege than at other cuticle sites. Furthermore, a male survival analysis indicated that the spermalege did not impose antagonistic selection on males. Our findings suggest that the specific spermalege material composition evolved to tolerate the traumatic cuticle penetration. They demonstrate the importance of tolerance in sexual conflict and genitalia evolution, extend fundamental coevolution and speciation models and contribute to explaining the evolution of complexity. We propose that tolerance can drive trait diversity. PMID:25673297

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jennings, Ryan de Montmollin; Moran, James J.; Jay, Zackary J.

Biological fixation of CO 2 is the primary mechanism of C reduction in natural systems, and provides a diverse suite of organic compounds utilized by chemoorganoheterotrophs. The extent and mechanisms of CO 2 fixation were evaluated across a comprehensive set of high-temperature, chemotrophic microbial communities in Yellowstone National Park by combining metagenomic and stable 13C isotope analyses. Fifteen geothermal sites representing three distinct habitat types (iron-oxide mats, anoxic sulfur sediments, and filamentous ‘streamer’ communities) were investigated. Genes of the 3-hydroxypropionate/4-hydroxybutyrate, dicarboxylate/4-hydroxybutyrate, and reverse tricarboxylic acid CO 2 fixation pathways were identified in assembled genome sequence corresponding to the predominant Crenarchaeotamore » and Aquificales observed across this habitat range. Stable 13C analyses of dissolved inorganic and organic C (DIC, DOC), and possible landscape C sources were used to interpret the 13C content of microbial community samples. Isotope mixing models showed that the minimum amounts of autotrophic C in microbial biomass were > 50 % in the majority of communities analyzed, but were also dependent on the amounts of heterotrophy and/or accumulation of landscape C. Furthermore, the significance of CO 2 as a C source in these communities provides a foundation for understanding metabolic linkages among autotrophs and heterotrophs, community assembly and succession, and the likely coevolution of deeply-branching thermophiles.« less

Reduction of female copulatory damage by resilin represents evidence for tolerance in sexual conflict.

PubMed

Michels, Jan; Gorb, Stanislav N; Reinhardt, Klaus

2015-03-06

Intergenomic evolutionary conflicts increase biological diversity. In sexual conflict, female defence against males is generally assumed to be resistance, which, however, often leads to trait exaggeration but not diversification. Here, we address whether tolerance, a female defence mechanism known from interspecific conflicts, exists in sexual conflict. We examined the traumatic insemination of female bed bugs via cuticle penetration by males, a textbook example of sexual conflict. Confocal laser scanning microscopy revealed large proportions of the soft and elastic protein resilin in the cuticle of the spermalege, the female defence organ. Reduced tissue damage and haemolymph loss were identified as adaptive female benefits from resilin. These did not arise from resistance because microindentation showed that the penetration force necessary to breach the cuticle was significantly lower at the resilin-rich spermalege than at other cuticle sites. Furthermore, a male survival analysis indicated that the spermalege did not impose antagonistic selection on males. Our findings suggest that the specific spermalege material composition evolved to tolerate the traumatic cuticle penetration. They demonstrate the importance of tolerance in sexual conflict and genitalia evolution, extend fundamental coevolution and speciation models and contribute to explaining the evolution of complexity. We propose that tolerance can drive trait diversity. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Association and Host Selectivity in Multi-Host Pathogens

PubMed Central

Malpica, José M.; Sacristán, Soledad; Fraile, Aurora; García-Arenal, Fernando

2006-01-01

The distribution of multi-host pathogens over their host range conditions their population dynamics and structure. Also, host co-infection by different pathogens may have important consequences for the evolution of hosts and pathogens, and host-pathogen co-evolution. Hence it is of interest to know if the distribution of pathogens over their host range is random, or if there are associations between hosts and pathogens, or between pathogens sharing a host. To analyse these issues we propose indices for the observed patterns of host infection by pathogens, and for the observed patterns of co-infection, and tests to analyse if these patterns conform to randomness or reflect associations. Applying these tests to the prevalence of five plant viruses on 21 wild plant species evidenced host-virus associations: most hosts and viruses were selective for viruses and hosts, respectively. Interestingly, the more host-selective viruses were the more prevalent ones, suggesting that host specialisation is a successful strategy for multi-host pathogens. Analyses also showed that viruses tended to associate positively in co-infected hosts. The developed indices and tests provide the tools to analyse how strong and common are these associations among different groups of pathogens, which will help to understand and model the population biology of multi-host pathogens. PMID:17183670

Predicting language diversity with complex networks.

PubMed

Raducha, Tomasz; Gubiec, Tomasz

2018-01-01

We analyze the model of social interactions with coevolution of the topology and states of the nodes. This model can be interpreted as a model of language change. We propose different rewiring mechanisms and perform numerical simulations for each. Obtained results are compared with the empirical data gathered from two online databases and anthropological study of Solomon Islands. We study the behavior of the number of languages for different system sizes and we find that only local rewiring, i.e. triadic closure, is capable of reproducing results for the empirical data in a qualitative manner. Furthermore, we cancel the contradiction between previous models and the Solomon Islands case. Our results demonstrate the importance of the topology of the network, and the rewiring mechanism in the process of language change.

Identification of an ancestral resistance gene cluster involved in the coevolution process between Phaseolus vulgaris and its fungal pathogen Colletotrichum lindemuthianum.

PubMed

Geffroy, V; Sicard, D; de Oliveira, J C; Sévignac, M; Cohen, S; Gepts, P; Neema, C; Langin, T; Dron, M

1999-09-01

The recent cloning of plant resistance (R) genes and the sequencing of resistance gene clusters have shed light on the molecular evolution of R genes. However, up to now, no attempt has been made to correlate this molecular evolution with the host-pathogen coevolution process at the population level. Cross-inoculations were carried out between 26 strains of the fungal pathogen Colletotrichum lindemuthianum and 48 Phaseolus vulgaris plants collected in the three centers of diversity of the host species. A high level of diversity for resistance against the pathogen was revealed. Most of the resistance specificities were overcome in sympatric situations, indicating an adaptation of the pathogen to the local host. In contrast, plants were generally resistant to allopatric strains, suggesting that R genes that were efficient against exotic strains but had been overcome locally were maintained in the plant genome. These results indicated that coevolution processes between the two protagonists led to a differentiation for resistance in the three centers of diversity of the host. To improve our understanding of the molecular evolution of these different specificities, a recombinant inbred (RI) population derived from two representative genotypes of the Andean (JaloEEP558) and Mesoamerican (BAT93) gene pools was used to map anthracnose specificities. A gene cluster comprising both Andean (Co-y; Co-z) and Mesoamerican (Co-9) host resistance specificities was identified, suggesting that this locus existed prior to the separation of the two major gene pools of P. vulgaris. Molecular analysis revealed a high level of complexity at this locus. It harbors 11 restriction fragment length polymorphisms when R gene analog (RGA) clones are used. The relationship between the coevolution process and diversification of resistance specificities at resistance gene clusters is discussed.

Impact of two specialist insect herbivores on reproduction of horse nettle, Solanum carolinense.

PubMed

Wise, Michael J; Sacchi, Christopher F

1996-10-01

The frequency of coevolution as a process of strong mutual interaction between a single plant and herbivore species has been questioned in light of more commonly observed, complex relationships between a plant and a suite of herbivore species. Despite recognition of the possibility of diffuse coevolution, relatively few studies have examined ecological responses of plants to herbivores in complex associations. We studied the impact of two specialist herbivores, the horse nettle beetle, Leptinotarsa juncta, and the eggplant flea beetle, Epitrix fuscula, on reproduction of their host, Solanum carolinense. Our study involved field and controlled-environment experimental tests of the impact on sexual and potential asexual reproduction of attack by individuals of the two herbivore species, individually and in combination. Field tests demonstrated that under normal levels of phytophagous insect attack, horse nettle plants experienced a reduction in fruit production of more than 75% compared with plants from which insects were excluded. In controlled-environment experiments using enclosure-exclosure cages, the horse nettle's two principal herbivores, the flea beetle and the horse nettle beetle, caused decreases in sexual reproduction similar to those observed in the field, and a reduction in potential asexual reproduction, represented by root biomass. Attack by each herbivore reduced the numbers of fruits produced, and root growth, when feeding in isolation. When both species were feeding together, fruit production, but not root growth, was lower than when either beetle species fed alone. Ecological interactions between horse nettle and its two primary herbivores necessary for diffuse coevolution to occur were evident from an overall analysis of the statistical interactions between the two herbivores for combined assessment of fruit and vegetative traits. For either of these traits alone, the interactions necessary to promote diffuse coevolution apparently were lacking.

Evolutionary Diversification of Prey and Predator Species Facilitated by Asymmetric Interactions

PubMed Central

Zu, Jian; Wang, Jinliang; Huang, Gang

2016-01-01

We investigate the influence of asymmetric interactions on coevolutionary dynamics of a predator-prey system by using the theory of adaptive dynamics. We assume that the defense ability of prey and the attack ability of predators all can adaptively evolve, either caused by phenotypic plasticity or by behavioral choice, but there are certain costs in terms of their growth rate or death rate. The coevolutionary model is constructed from a deterministic approximation of random mutation-selection process. To sum up, if prey’s trade-off curve is globally weakly concave, then five outcomes of coevolution are demonstrated, which depend on the intensity and shape of asymmetric predator-prey interactions and predator’s trade-off shape. Firstly, we find that if there is a weakly decelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species may occur, but after branching further coevolution may lead to extinction of the predator species with a larger trait value. However, if there is a weakly accelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species is also possible and after branching the dimorphic predator can evolutionarily stably coexist with a monomorphic prey species. Secondly, if the asymmetric interactions become a little strong, then prey and predators will evolve to an evolutionarily stable equilibrium, at which they can stably coexist on a long-term timescale of evolution. Thirdly, if there is a weakly accelerating cost and a relatively strongly accelerating benefit for prey species, then evolutionary branching in the prey species is possible and the finally coevolutionary outcome contains a dimorphic prey and a monomorphic predator species. Fourthly, if the asymmetric interactions become more stronger, then predator-prey coevolution may lead to cycles in both traits and equilibrium population densities. The Red Queen dynamic is a possible outcome under asymmetric predator-prey interactions. PMID:27685540

Evolutionary Diversification of Prey and Predator Species Facilitated by Asymmetric Interactions.

PubMed

Zu, Jian; Wang, Jinliang; Huang, Gang

We investigate the influence of asymmetric interactions on coevolutionary dynamics of a predator-prey system by using the theory of adaptive dynamics. We assume that the defense ability of prey and the attack ability of predators all can adaptively evolve, either caused by phenotypic plasticity or by behavioral choice, but there are certain costs in terms of their growth rate or death rate. The coevolutionary model is constructed from a deterministic approximation of random mutation-selection process. To sum up, if prey's trade-off curve is globally weakly concave, then five outcomes of coevolution are demonstrated, which depend on the intensity and shape of asymmetric predator-prey interactions and predator's trade-off shape. Firstly, we find that if there is a weakly decelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species may occur, but after branching further coevolution may lead to extinction of the predator species with a larger trait value. However, if there is a weakly accelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species is also possible and after branching the dimorphic predator can evolutionarily stably coexist with a monomorphic prey species. Secondly, if the asymmetric interactions become a little strong, then prey and predators will evolve to an evolutionarily stable equilibrium, at which they can stably coexist on a long-term timescale of evolution. Thirdly, if there is a weakly accelerating cost and a relatively strongly accelerating benefit for prey species, then evolutionary branching in the prey species is possible and the finally coevolutionary outcome contains a dimorphic prey and a monomorphic predator species. Fourthly, if the asymmetric interactions become more stronger, then predator-prey coevolution may lead to cycles in both traits and equilibrium population densities. The Red Queen dynamic is a possible outcome under asymmetric predator-prey interactions.

The evolution of phenotypes and genetic parameters under preferential mating

PubMed Central

Roff, Derek A; Fairbairn, Daphne J

2014-01-01

This article extends and adds more realism to Lande's analytical model for evolution under mate choice by using individual-based simulations in which females sample a finite number of males and the genetic architecture of the preference and preferred trait evolves. The simulations show that the equilibrium heritabilities of the preference and preferred trait and the genetic correlation between them (rG), depend critically on aspects of the mating system (the preference function, mode of mate choice, choosiness, and number of potential mates sampled), the presence or absence of natural selection on the preferred trait, and the initial genetic parameters. Under some parameter combinations, preferential mating increased the heritability of the preferred trait, providing a possible resolution for the lek paradox. The Kirkpatrick–Barton approximation for rG proved to be biased downward, but the realized genetic correlations were also low, generally <0.2. Such low values of rG indicate that coevolution of the preference and preferred trait is likely to be very slow and subject to significant stochastic variation. Lande's model accurately predicted the incidence of runaway selection in the simulations, except where preferences were relative and the preferred trait was subject to natural selection. In these cases, runaways were over- or underestimated, depending on the number of males sampled. We conclude that rapid coevolution of preferences and preferred traits is unlikely in natural populations, but that the parameter combinations most conducive to it are most likely to occur in lekking species. PMID:25077025

Evolutionary Musicology Meets Embodied Cognition: Biocultural Coevolution and the Enactive Origins of Human Musicality.

PubMed

van der Schyff, Dylan; Schiavio, Andrea

2017-01-01

Despite evolutionary musicology's interdisciplinary nature, and the diverse methods it employs, the field has nevertheless tended to divide into two main positions. Some argue that music should be understood as a naturally selected adaptation, while others claim that music is a product of culture with little or no relevance for the survival of the species. We review these arguments, suggesting that while interesting and well-reasoned positions have been offered on both sides of the debate, the nature-or-culture (or adaptation vs. non-adaptation) assumptions that have traditionally driven the discussion have resulted in a problematic either/or dichotomy. We then consider an alternative "biocultural" proposal that appears to offer a way forward. As we discuss, this approach draws on a range of research in theoretical biology, archeology, neuroscience, embodied and ecological cognition, and dynamical systems theory (DST), positing a more integrated model that sees biological and cultural dimensions as aspects of the same evolving system. Following this, we outline the enactive approach to cognition, discussing the ways it aligns with the biocultural perspective. Put simply, the enactive approach posits a deep continuity between mind and life, where cognitive processes are explored in terms of how self-organizing living systems enact relationships with the environment that are relevant to their survival and well-being. It highlights the embodied and ecologically situated nature of living agents, as well as the active role they play in their own developmental processes. Importantly, the enactive approach sees cognitive and evolutionary processes as driven by a range of interacting factors, including the socio-cultural forms of activity that characterize the lives of more complex creatures such as ourselves. We offer some suggestions for how this approach might enhance and extend the biocultural model. To conclude we briefly consider the implications of this approach for practical areas such as music education.

Evolutionary Musicology Meets Embodied Cognition: Biocultural Coevolution and the Enactive Origins of Human Musicality

PubMed Central

van der Schyff, Dylan; Schiavio, Andrea

2017-01-01

Despite evolutionary musicology's interdisciplinary nature, and the diverse methods it employs, the field has nevertheless tended to divide into two main positions. Some argue that music should be understood as a naturally selected adaptation, while others claim that music is a product of culture with little or no relevance for the survival of the species. We review these arguments, suggesting that while interesting and well-reasoned positions have been offered on both sides of the debate, the nature-or-culture (or adaptation vs. non-adaptation) assumptions that have traditionally driven the discussion have resulted in a problematic either/or dichotomy. We then consider an alternative “biocultural” proposal that appears to offer a way forward. As we discuss, this approach draws on a range of research in theoretical biology, archeology, neuroscience, embodied and ecological cognition, and dynamical systems theory (DST), positing a more integrated model that sees biological and cultural dimensions as aspects of the same evolving system. Following this, we outline the enactive approach to cognition, discussing the ways it aligns with the biocultural perspective. Put simply, the enactive approach posits a deep continuity between mind and life, where cognitive processes are explored in terms of how self-organizing living systems enact relationships with the environment that are relevant to their survival and well-being. It highlights the embodied and ecologically situated nature of living agents, as well as the active role they play in their own developmental processes. Importantly, the enactive approach sees cognitive and evolutionary processes as driven by a range of interacting factors, including the socio-cultural forms of activity that characterize the lives of more complex creatures such as ourselves. We offer some suggestions for how this approach might enhance and extend the biocultural model. To conclude we briefly consider the implications of this approach for practical areas such as music education. PMID:29033780

Sexual selection and the evolution of secondary sexual traits: sex comb evolution in Drosophila.

PubMed

Snook, Rhonda R; Gidaszewski, Nelly A; Chapman, Tracey; Simmons, Leigh W

2013-04-01

Sexual selection can drive rapid evolutionary change in reproductive behaviour, morphology and physiology. This often leads to the evolution of sexual dimorphism, and continued exaggerated expression of dimorphic sexual characteristics, although a variety of other alternative selection scenarios exist. Here, we examined the evolutionary significance of a rapidly evolving, sexually dimorphic trait, sex comb tooth number, in two Drosophila species. The presence of the sex comb in both D. melanogaster and D. pseudoobscura is known to be positively related to mating success, although little is yet known about the sexually selected benefits of sex comb structure. In this study, we used experimental evolution to test the idea that enhancing or eliminating sexual selection would lead to variation in sex comb tooth number. However, the results showed no effect of either enforced monogamy or elevated promiscuity on this trait. We discuss several hypotheses to explain the lack of divergence, focussing on sexually antagonistic coevolution, stabilizing selection via species recognition and nonlinear selection. We discuss how these are important, but relatively ignored, alternatives in understanding the evolution of rapidly evolving sexually dimorphic traits. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

The function and evolution of male and female genitalia in Phyllophaga Harris scarab beetles (Coleoptera: Scarabaeidae).

PubMed

Richmond, M P; Park, J; Henry, C S

2016-11-01

Genitalia diversity in insects continues to fuel investigation of the function and evolution of these dynamic structures. Whereas most studies have focused on variation in male genitalia, an increasing number of studies on female genitalia have uncovered comparable diversity among females, but often at a much finer morphological scale. In this study, we analysed the function and evolution of male and female genitalia in Phyllophaga scarab beetles, a group in which both sexes exhibit genitalic diversity. To document the interaction between male and female structures during mating, we dissected flash-frozen mating pairs from three Phyllophaga species and investigated fine-scale morphology using SEM. We then reconstructed ancestral character states using a species tree inferred from mitochondrial and nuclear loci to elucidate and compare the evolutionary history of male and female genitalia. Our dissections revealed an interlocking mechanism of the female pubic process and male parameres that appears to improve the mechanical fit of the copulatory position. The comparative analyses, however, did not support coevolution of male and female structures and showed more erratic evolution of the female genitalia relative to males. By studying a group that exhibits obvious female genitalic diversity, we were able to demonstrate the relevance of female reproductive morphology in studies of male genital diversity. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Sexual conflict over parental care promotes the evolution of sex differences in care and the ability to care

PubMed Central

McNamara, John M.; Wolf, Max

2015-01-01

Strong asymmetries in parental care, with one sex providing more care than the other, are widespread across the animal kingdom. At present, two factors are thought to ultimately cause sex differences in care: certainty of parentage and sexual selection. By contrast, we here show that the coevolution of care and the ability to care can result in strong asymmetries in both the ability to care and the level of care, even in the absence of these factors. While the coevolution of care and the ability to care does not predict which sex evolves to care more than the other, once other factors give rise to even the slightest differences in the cost and benefits of care between the sexes (e.g. differences in certainty in parentage), a clear directionality emerges; the sex with the lower cost or higher benefit of care evolves both to be more able to care and to provide much higher levels of care than the other sex. Our findings suggest that the coevolution of levels of care and the ability to care may be a key factor underlying the evolution of sex differences in care. PMID:25694618

Selection on an antagonistic behavioral trait can drive rapid genital coevolution in the burying beetle, Nicrophorus vespilloides

PubMed Central

Hopwood, Paul E.; Head, Megan L.; Jordan, Eleanor J.; Carter, Mauricio J.; Davey, Emma; Moore, Allen J.; Royle, Nick J.

2016-01-01

Male and female genital morphology varies widely across many taxa, and even among populations. Disentangling potential sources of selection on genital morphology is problematic because each sex is predicted to respond to adaptations in the other due to reproductive conflicts of interest. To test how variation in this sexual conflict trait relates to variation in genital morphology we used our previously developed artificial selection lines for high and low repeated mating rates. We selected for high and low repeated mating rates using monogamous pairings to eliminate contemporaneous female choice and male–male competition. Male and female genital shape responded rapidly to selection on repeated mating rate. High and low mating rate lines diverged from control lines after only 10 generations of selection. We also detected significant patterns of male and female genital shape coevolution among selection regimes. We argue that because our selection lines differ in sexual conflict, these results support the hypothesis that sexually antagonistic coevolution can drive the rapid divergence of genital morphology. The greatest divergence in morphology corresponded with lines in which the resolution of sexual conflict over mating rate was biased in favor of male interests. PMID:27144373

Socio-hydrologic Perspectives of the Co-evolution of Humans and Water in the Tarim River Basin, Western China

NASA Astrophysics Data System (ADS)

Liu, Ye; Tian, Fuqiang; Hu, Heping; Liu, Dengfeng; Sivapalan, Murugesu

2013-04-01

Socio-hydrology studies the co-evolution of coupled human-water systems, which is of great importance for long-term sustainable water resource management in basins suffering from serious eco-environmental degradation. Process socio-hydrology can benefit from the exploring the patterns of historical co-evolution of coupled human-water systems as a way to discovering the organizing principles that may underpin their co-evolution. As a self-organized entity, the human-water system in a river basin would evolve into certain steady states over a sufficiently long time but then could also experience sudden shifts due to internal or external disturbances that exceed system thresholds. In this study, we discuss three steady states (also called stages in the social sciences, including natural, human exploitation and recovery stages) and transitions between these during the past 1500 years in the Tarim River Basin of Western China, which a rich history of civilization including its place in the famous Silk Road that connected China to Europe. Specifically, during the natural stage with a sound environment that existed before the 19th century, shifts in the ecohydrological regime were mainly caused by environmental changes such river channel migration and climate change. During the human exploitation stages in the 5th and again in the 19th-20th centuries, however, humans gradually became the main drivers for system evolution, during which the basin experienced rapid population growth, fast socio-economic development and intense human activities. By the 1970s, after 200 years of colonization, the Tarim River Basin evolved into a new regime with vulnerable ecosystem and water system, and suffered from serious water shortages and desertification. Human society then began to take a critical look into the effects of their activities and reappraise the impact of human development on the ecohydrological system, which eventually led the basin into a treatment and recovery stage. Since then, the basin has shown a reverse trend of regime shift towards healing of the environmental damage that was inflicted in the previous stage of human development. In this paper we analyze the recasting effect of human activities on the water system and provide explanations on how human activities influence the co-evolution of human-water system from a broader perspective.

Toward immunogenetic studies of amphibian chytridiomycosis: Linking innate and acquired immunity

USGS Publications Warehouse

Richmond, J.Q.; Savage, Anna E.; Zamudio, Kelly R.; Rosenblum, E.B.

2009-01-01

Recent declines in amphibian diversity and abundance have contributed significantly to the global loss of biodiversity. The fungal disease chytridiomycosis is widely considered to be a primary cause of these declines, yet the critical question of why amphibian species differ in susceptibility remains unanswered. Considerable evidence links environmental conditions and interspecific variability of the innate immune system to differential infection responses, but other sources of individual, population, or species-typical variation may also be important. In this article we review the preliminary evidence supporting a role for acquired immune defenses against chytridiomycosis, and advocate for targeted investigation of genes controlling acquired responses, as well as those that functionally bridge the innate and acquired immune systems. Immunogenetic data promise to answer key questions about chytridiomycosis susceptibility and host-pathogen coevolution, and will draw much needed attention to the importance of considering evolutionary processes in amphibian conservation management and practice. ?? 2009 by American Institute of Biological Sciences.

LINE-1 protein localization and functional dynamics during the cell cycle

PubMed Central

Wudzinska, Aleksandra; Sun, Xiaoji; Andrade, Joshua; Nayak, Shruti; Kahler, David J; Badri, Sana; LaCava, John; Ueberheide, Beatrix; Yun, Chi Y; Fenyö, David

2018-01-01

LINE-1/L1 retrotransposon sequences comprise 17% of the human genome. Among the many classes of mobile genetic elements, L1 is the only autonomous retrotransposon that still drives human genomic plasticity today. Through its co-evolution with the human genome, L1 has intertwined itself with host cell biology. However, a clear understanding of L1’s lifecycle and the processes involved in restricting its insertion and intragenomic spread remains elusive. Here we identify modes of L1 proteins’ entrance into the nucleus, a necessary step for L1 proliferation. Using functional, biochemical, and imaging approaches, we also show a clear cell cycle bias for L1 retrotransposition that peaks during the S phase. Our observations provide a basis for novel interpretations about the nature of nuclear and cytoplasmic L1 ribonucleoproteins (RNPs) and the potential role of DNA replication in L1 retrotransposition. PMID:29309036

Meta genome-wide network from functional linkages of genes in human gut microbial ecosystems.

PubMed

Ji, Yan; Shi, Yixiang; Wang, Chuan; Dai, Jianliang; Li, Yixue

2013-03-01

The human gut microbial ecosystem (HGME) exerts an important influence on the human health. In recent researches, meta-genomics provided deep insights into the HGME in terms of gene contents, metabolic processes and genome constitutions of meta-genome. Here we present a novel methodology to investigate the HGME on the basis of a set of functionally coupled genes regardless of their genome origins when considering the co-evolution properties of genes. By analyzing these coupled genes, we showed some basic properties of HGME significantly associated with each other, and further constructed a protein interaction map of human gut meta-genome to discover some functional modules that may relate with essential metabolic processes. Compared with other studies, our method provides a new idea to extract basic function elements from meta-genome systems and investigate complex microbial environment by associating its biological traits with co-evolutionary fingerprints encoded in it.

Predicting protein folding rate change upon point mutation using residue-level coevolutionary information.

PubMed

Mallik, Saurav; Das, Smita; Kundu, Sudip

2016-01-01

Change in folding kinetics of globular proteins upon point mutation is crucial to a wide spectrum of biological research, such as protein misfolding, toxicity, and aggregations. Here we seek to address whether residue-level coevolutionary information of globular proteins can be informative to folding rate changes upon point mutations. Generating residue-level coevolutionary networks of globular proteins, we analyze three parameters: relative coevolution order (rCEO), network density (ND), and characteristic path length (CPL). A point mutation is considered to be equivalent to a node deletion of this network and respective percentage changes in rCEO, ND, CPL are found linearly correlated (0.84, 0.73, and -0.61, respectively) with experimental folding rate changes. The three parameters predict the folding rate change upon a point mutation with 0.031, 0.045, and 0.059 standard errors, respectively. © 2015 Wiley Periodicals, Inc.

Evolution of angiosperm seed disperser mutualisms: the timing of origins and their consequences for coevolutionary interactions between angiosperms and frugivores.

PubMed

Eriksson, Ove

2016-02-01

The origins of interactions between angiosperms and fruit-eating seed dispersers have attracted much attention following a seminal paper on this topic by Tiffney (1984). This review synthesizes evidence pertaining to key events during the evolution of angiosperm-frugivore interactions and suggests some implications of this evidence for interpretations of angiosperm-frugivore coevolution. The most important conclusions are: (i) the diversification of angiosperm seed size and fleshy fruits commenced around 80 million years ago (Mya). The diversity of seed sizes, fruit sizes and fruit types peaked in the Eocene around 55 to 50 Mya. During this first phase of the interaction, angiosperms and animals evolving frugivory expanded into niche space not previously utilized by these groups, as frugivores and previously not existing fruit traits appeared. From the Eocene until the present, angiosperm-frugivore interactions have occurred within a broad frame of existing niche space, as defined by fruit traits and frugivory, motivating a separation of the angiosperm-frugivore interactions into two phases, before and after the peak in the early Eocene. (ii) The extinct multituberculates were probably the most important frugivores during the early radiation phase of angiosperm seeds and fleshy fruits. Primates and rodents are likely to have been important in the latter part of this first phase. (iii) Flying frugivores, birds and bats, evolved during the second phase, mainly during the Oligocene and Miocene, thus exploiting an existing diversity of fleshy fruits. (iv) A drastic climate shift around the Eocene-Oligocene boundary (around 34 Mya) resulted in more semi-open woodland vegetation, creating patchily occurring food resources for frugivores. This promoted evolution of a 'flying frugivore niche' exploited by birds and bats. In particular, passerines became a dominant frugivore group worldwide. (v) Fleshy fruits evolved at numerous occasions in many angiosperm families, and many of the originations of fleshy fruits occurred well after the peak in the early Eocene. (vi) During periods associated with environmental change altering coevolutionary networks and opening of niche space, reciprocal coevolution may result in strong directional selection formative for both fruit and frugivore evolution. Further evidence is needed to test this hypothesis. Based on the abundance of plant lineages with various forms of fleshy fruits, and the diversity of frugivores, it is suggested that periods of rapid coevolution in angiosperms and frugivores occurred numerous times during the 80 million years of angiosperm-frugivore evolution. © 2014 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

Biology, Pest Status, Microbiome and Control of Kudzu Bug (Hemiptera: Heteroptera: Plataspidae): A New Invasive Pest in the U.S.

PubMed Central

Dhammi, Anirudh; van Krestchmar, Jaap B.; Ponnusamy, Loganathan; Bacheler, Jack S.; Reisig, Dominic D.; Herbert, Ames; Del Pozo-Valdivia, Alejandro I.; Roe, R. Michael

2016-01-01

Soybean is an important food crop, and insect integrated pest management (IPM) is critical to the sustainability of this production system. In recent years, the introduction into the United States of the kudzu bug currently identified as Megacopta cribraria (F.), poses a threat to soybean production. The kudzu bug was first discovered in the state of Georgia, U.S. in 2009 and since then has spread to most of the southeastern states. Because it was not found in the North American subcontinent before this time, much of our knowledge of this insect comes from research done in its native habitat. However, since the U.S. introduction, studies have been undertaken to improve our understanding of the kudzu bug basic biology, microbiome, migration patterns, host selection and management in its expanding new range. Researchers are not only looking at developing IPM strategies for the kudzu bug in soybean, but also at its unique relationship with symbiotic bacteria. Adult females deposit bacterial packets with their eggs, and the neonates feed on these packets to acquire the bacteria, Candidatus Ishikawaella capsulata. The kudzu bug should be an informative model to study the co-evolution of insect function and behavior with that of a single bacteria species. We review kudzu bug trapping and survey methods, the development of bioassays for insecticide susceptibility, insecticide efficacy, host preferences, impact of the pest on urban environments, population expansion, and the occurrence of natural enemies. The identity of the kudzu bug in the U.S. is not clear. We propose that the kudzu bug currently accepted as M. cribraria in the U.S. is actually Megacopta punctatissima, with more work needed to confirm this hypothesis. PMID:27649166

Yet More “Weeds” in the Garden: Fungal Novelties from Nests of Leaf-Cutting Ants

PubMed Central

Augustin, Juliana O.; Groenewald, Johannes Z.; Nascimento, Robson J.; Mizubuti, Eduardo S. G.; Barreto, Robert W.; Elliot, Simon L.; Evans, Harry C.

2013-01-01

Background Symbiotic relationships modulate the evolution of living organisms in all levels of biological organization. A notable example of symbiosis is that of attine ants (Attini; Formicidae: Hymenoptera) and their fungal cultivars (Lepiotaceae and Pterulaceae; Agaricales: Basidiomycota). In recent years, this mutualism has emerged as a model system for studying coevolution, speciation, and multitrophic interactions. Ubiquitous in this ant-fungal symbiosis is the “weedy” fungus Escovopsis (Hypocreales: Ascomycota), known only as a mycoparasite of attine fungal gardens. Despite interest in its biology, ecology and molecular phylogeny—noting, especially, the high genetic diversity encountered—which has led to a steady flow of publications over the past decade, only two species of Escovopsis have formally been described. Methods and Results We sampled from fungal gardens and garden waste (middens) of nests of the leaf-cutting ant genus Acromyrmex in a remnant of subtropical Atlantic rainforest in Minas Gerais, Brazil. In culture, distinct morphotypes of Escovopsis sensu lato were recognized. Using both morphological and molecular analyses, three new species of Escovopsis were identified. These are described and illustrated herein—E. lentecrescens, E. microspora, and E. moelleri—together with a re-description of the genus and the type species, E. weberi. The new genus Escovopsioides is erected for a fourth morphotype. We identify, for the first time, a mechanism for horizontal transmission via middens. Conclusions The present study makes a start at assigning names and formal descriptions to these specific fungal parasites of attine nests. Based on the results of this exploratory and geographically-restricted survey, we expect there to be many more species of the genus Escovopsis and its relatives associated with nests of both the lower and higher Attini throughout their neotropical range, as suggested in previous studies. PMID:24376525

Host-parasite coevolution beyond the nestling stage? Mimicry of host fledglings by the specialist screaming cowbird.

PubMed

De Mársico, María C; Gantchoff, Mariela G; Reboreda, Juan C

2012-09-07

Egg mimicry by obligate avian brood parasites and host rejection of non-mimetic eggs are well-known textbook examples of host-parasite coevolution. By contrast, reciprocal adaptations and counteradaptations beyond the egg stage in brood parasites and their hosts have received less attention. The screaming cowbird (Molothrus rufoaxillaris) is a specialist obligate brood parasite whose fledglings look identical to those of its primary host, the baywing (Agelaioides badius). Such a resemblance has been proposed as an adaptation in response to host discrimination against odd-looking young, but evidence supporting this idea is scarce. Here, we examined this hypothesis by comparing the survival rates of young screaming cowbirds and non-mimetic shiny cowbirds (Molothrus bonariensis) cross-fostered to baywing nests and quantifying the similarity in plumage colour and begging calls between host and cowbird fledglings. Shiny cowbirds suffered higher post-fledging mortality rates (83%) than screaming cowbirds (0%) owing to host rejection. Visual modelling revealed that screaming cowbirds, but not shiny cowbirds, were indistinguishable from host young in plumage colour. Similarly, screaming cowbirds matched baywings' begging calls more closely than shiny cowbirds. Our results strongly support the occurrence of host fledgling mimicry in screaming cowbirds and suggest a role of visual and vocal cues in fledgling discrimination by baywings.

The interplay between social networks and culture: theoretically and among whales and dolphins.

PubMed

Cantor, Mauricio; Whitehead, Hal

2013-05-19

Culture is increasingly being understood as a driver of mammalian phenotypes. Defined as group-specific behaviour transmitted by social learning, culture is shaped by social structure. However, culture can itself affect social structure if individuals preferentially interact with others whose behaviour is similar, or cultural symbols are used to mark groups. Using network formalism, this interplay can be depicted by the coevolution of nodes and edges together with the coevolution of network topology and transmission patterns. We review attempts to model the links between the spread, persistence and diversity of culture and the network topology of non-human societies. We illustrate these processes using cetaceans. The spread of socially learned begging behaviour within a population of bottlenose dolphins followed the topology of the social network, as did the evolution of the song of the humpback whale between breeding areas. In three bottlenose dolphin populations, individuals preferentially associated with animals using the same socially learned foraging behaviour. Homogeneous behaviour within the tight, nearly permanent social structures of the large matrilineal whales seems to result from transmission bias, with cultural symbols marking social structures. We recommend the integration of studies of culture and society in species for which social learning is an important determinant of behaviour.

The interplay between social networks and culture: theoretically and among whales and dolphins

PubMed Central

Cantor, Mauricio; Whitehead, Hal

2013-01-01

Culture is increasingly being understood as a driver of mammalian phenotypes. Defined as group-specific behaviour transmitted by social learning, culture is shaped by social structure. However, culture can itself affect social structure if individuals preferentially interact with others whose behaviour is similar, or cultural symbols are used to mark groups. Using network formalism, this interplay can be depicted by the coevolution of nodes and edges together with the coevolution of network topology and transmission patterns. We review attempts to model the links between the spread, persistence and diversity of culture and the network topology of non-human societies. We illustrate these processes using cetaceans. The spread of socially learned begging behaviour within a population of bottlenose dolphins followed the topology of the social network, as did the evolution of the song of the humpback whale between breeding areas. In three bottlenose dolphin populations, individuals preferentially associated with animals using the same socially learned foraging behaviour. Homogeneous behaviour within the tight, nearly permanent social structures of the large matrilineal whales seems to result from transmission bias, with cultural symbols marking social structures. We recommend the integration of studies of culture and society in species for which social learning is an important determinant of behaviour. PMID:23569288

Host–parasite coevolution beyond the nestling stage? Mimicry of host fledglings by the specialist screaming cowbird

PubMed Central

De Mársico, María C.; Gantchoff, Mariela G.; Reboreda, Juan C.

2012-01-01

Egg mimicry by obligate avian brood parasites and host rejection of non-mimetic eggs are well-known textbook examples of host–parasite coevolution. By contrast, reciprocal adaptations and counteradaptations beyond the egg stage in brood parasites and their hosts have received less attention. The screaming cowbird (Molothrus rufoaxillaris) is a specialist obligate brood parasite whose fledglings look identical to those of its primary host, the baywing (Agelaioides badius). Such a resemblance has been proposed as an adaptation in response to host discrimination against odd-looking young, but evidence supporting this idea is scarce. Here, we examined this hypothesis by comparing the survival rates of young screaming cowbirds and non-mimetic shiny cowbirds (Molothrus bonariensis) cross-fostered to baywing nests and quantifying the similarity in plumage colour and begging calls between host and cowbird fledglings. Shiny cowbirds suffered higher post-fledging mortality rates (83%) than screaming cowbirds (0%) owing to host rejection. Visual modelling revealed that screaming cowbirds, but not shiny cowbirds, were indistinguishable from host young in plumage colour. Similarly, screaming cowbirds matched baywings' begging calls more closely than shiny cowbirds. Our results strongly support the occurrence of host fledgling mimicry in screaming cowbirds and suggest a role of visual and vocal cues in fledgling discrimination by baywings. PMID:22648157

Biomechanical Diversity of Mating Structures among Harvestmen Species Is Consistent with a Spectrum of Precopulatory Strategies

PubMed Central

Burns, Mercedes; Shultz, Jeffrey W.

2015-01-01

Diversity in reproductive structures is frequently explained by selection acting at individual to generational timescales, but interspecific differences predicted by such models (e.g., female choice or sexual conflict) are often untestable in a phylogenetic framework. An alternative approach focuses on clade- or function-specific hypotheses that predict evolutionary patterns in terms neutral to specific modes of sexual selection. Here we test a hypothesis that diversity of reproductive structures in leiobunine harvestmen (daddy longlegs) of eastern North America reflects two sexually coevolved but non-overlapping precopulatory strategies, a primitive solicitous strategy (females enticed by penis-associated nuptial gifts), and a multiply derived antagonistic strategy (penis exerts mechanical force against armature of the female pregenital opening). Predictions of sexual coevolution and fidelity to precopulatory categories were tested using 10 continuously varying functional traits from 28 species. Multivariate analyses corroborated sexual coevolution but failed to partition species by precopulatory strategy, with multiple methods placing species along a spectrum of mechanical antagonistic potential. These findings suggest that precopulatory features within species reflect different co-occurring levels of solicitation and antagonism, and that gradualistic evolutionary pathways exist between extreme strategies. The ability to quantify antagonistic potential of precopulatory structures invites comparison with ecological variables that may promote evolutionary shifts in precopulatory strategies. PMID:26352413

Biomechanical Diversity of Mating Structures among Harvestmen Species Is Consistent with a Spectrum of Precopulatory Strategies.

PubMed

Burns, Mercedes; Shultz, Jeffrey W

2015-01-01

Diversity in reproductive structures is frequently explained by selection acting at individual to generational timescales, but interspecific differences predicted by such models (e.g., female choice or sexual conflict) are often untestable in a phylogenetic framework. An alternative approach focuses on clade- or function-specific hypotheses that predict evolutionary patterns in terms neutral to specific modes of sexual selection. Here we test a hypothesis that diversity of reproductive structures in leiobunine harvestmen (daddy longlegs) of eastern North America reflects two sexually coevolved but non-overlapping precopulatory strategies, a primitive solicitous strategy (females enticed by penis-associated nuptial gifts), and a multiply derived antagonistic strategy (penis exerts mechanical force against armature of the female pregenital opening). Predictions of sexual coevolution and fidelity to precopulatory categories were tested using 10 continuously varying functional traits from 28 species. Multivariate analyses corroborated sexual coevolution but failed to partition species by precopulatory strategy, with multiple methods placing species along a spectrum of mechanical antagonistic potential. These findings suggest that precopulatory features within species reflect different co-occurring levels of solicitation and antagonism, and that gradualistic evolutionary pathways exist between extreme strategies. The ability to quantify antagonistic potential of precopulatory structures invites comparison with ecological variables that may promote evolutionary shifts in precopulatory strategies.

Co-evolution and thresholds in arid floodplain wetland ecosystems.

NASA Astrophysics Data System (ADS)

Sandi, Steven; Rodriguez, Jose; Riccardi, Gerardo; Wen, Li; Saintilan, Neil

2017-04-01

Vegetation in arid floodplain wetlands consist of water dependent and flood tolerant species that rely on periodical floods in order to maintain healthy conditions. The floodplain often consist of a complex system of marshes, swamps and lagoons interconnected by a network of streams and poorly defined rills. Over time, feedbacks develop between vegetation and flow paths producing areas of flow obstruction and flow concentration, which combined with depositional and erosional process lead to a continuous change on the position and characteristics of inundation areas. This coevolution of flow paths and vegetation can reach a threshold that triggers major channel transformations and abandonment of wetland areas, in a process that is irreversible. The Macquarie Marshes is a floodplain wetland complex in the semi-arid region of north western NSW, Australia. The site is characterised by a low-gradient topography that leads to channel breakdown processes where the river network becomes practically non-existent and the flow extends over large areas of wetland that later re-join and reform channels exiting the system. Due to a combination of climatic and anthropogenic pressures, the wetland ecosystem in the Macquarie Marshes has deteriorated over the past few decades. This has been linked to decreasing inundation frequencies and extent, with whole areas of flood dependent species such as Water Couch and Common Reed undergoing complete succession to terrestrial species and dryland. In this presentation we provide an overview of an ecogeomorphological model that we have developed in order to simulate the complex dynamics of the marshes. The model combines hydrodynamic, vegetation and channel evolution modules. We focus on the vegetation component of the model and the transitional rules to predict wetland invasion by terrestrial vegetation.

Metallicity gradients in local field star-forming galaxies: insights on inflows, outflows, and the coevolution of gas, stars and metals

NASA Astrophysics Data System (ADS)

Ho, I.-Ting; Kudritzki, Rolf-Peter; Kewley, Lisa J.; Zahid, H. Jabran; Dopita, Michael A.; Bresolin, Fabio; Rupke, David S. N.

2015-04-01

We present metallicity gradients in 49 local field star-forming galaxies. We derive gas-phase oxygen abundances using two widely adopted metallicity calibrations based on the [O III]/Hβ, [N II]/Hα, and [N II]/[O II] line ratios. The two derived metallicity gradients are usually in good agreement within ± 0.14 dex R_{25}^{-1} (R25 is the B-band iso-photoal radius), but the metallicity gradients can differ significantly when the ionization parameters change systematically with radius. We investigate the metallicity gradients as a function of stellar mass (8 < log (M*/M⊙) < 11) and absolute B-band luminosity (-16 > MB > -22). When the metallicity gradients are expressed in dex kpc-1, we show that galaxies with lower mass and luminosity, on average, have steeper metallicity gradients. When the metallicity gradients are expressed in dex R_{25}^{-1}, we find no correlation between the metallicity gradients, and stellar mass and luminosity. We provide a local benchmark metallicity gradient of field star-forming galaxies useful for comparison with studies at high redshifts. We investigate the origin of the local benchmark gradient using simple chemical evolution models and observed gas and stellar surface density profiles in nearby field spiral galaxies. Our models suggest that the local benchmark gradient is a direct result of the coevolution of gas and stellar disc under virtually closed-box chemical evolution when the stellar-to-gas mass ratio becomes high (≫0.3). These models imply low current mass accretion rates ( ≲ 0.3 × SFR), and low-mass outflow rates ( ≲ 3 × SFR) in local field star-forming galaxies.

Co-Evolution of Opinion and Strategy in Persuasion Dynamics:. AN Evolutionary Game Theoretical Approach

NASA Astrophysics Data System (ADS)

Ding, Fei; Liu, Yun; Li, Yong

In this paper, a new model of opinion formation within the framework of evolutionary game theory is presented. The model simulates strategic situations when people are in opinion discussion. Heterogeneous agents adjust their behaviors to the environment during discussions, and their interacting strategies evolve together with opinions. In the proposed game, we take into account payoff discount to join a discussion, and the situation that people might drop out of an unpromising game. Analytical and emulational results show that evolution of opinion and strategy always tend to converge, with utility threshold, memory length, and decision uncertainty parameters influencing the convergence time. The model displays different dynamical regimes when we set differently the rule when people are at a loss in strategy.

Exploring social structure effect on language evolution based on a computational model

NASA Astrophysics Data System (ADS)

Gong, Tao; Minett, James; Wang, William

2008-06-01

A compositionality-regularity coevolution model is adopted to explore the effect of social structure on language emergence and maintenance. Based on this model, we explore language evolution in three experiments, and discuss the role of a popular agent in language evolution, the relationship between mutual understanding and social hierarchy, and the effect of inter-community communications and that of simple linguistic features on convergence of communal languages in two communities. This work embodies several important interactions during social learning, and introduces a new approach that manipulates individuals' probabilities to participate in social interactions to study the effect of social structure. We hope it will stimulate further theoretical and empirical explorations on language evolution in a social environment.

Predicting language diversity with complex networks

PubMed Central

Gubiec, Tomasz

2018-01-01

We analyze the model of social interactions with coevolution of the topology and states of the nodes. This model can be interpreted as a model of language change. We propose different rewiring mechanisms and perform numerical simulations for each. Obtained results are compared with the empirical data gathered from two online databases and anthropological study of Solomon Islands. We study the behavior of the number of languages for different system sizes and we find that only local rewiring, i.e. triadic closure, is capable of reproducing results for the empirical data in a qualitative manner. Furthermore, we cancel the contradiction between previous models and the Solomon Islands case. Our results demonstrate the importance of the topology of the network, and the rewiring mechanism in the process of language change. PMID:29702699

The E-MOSAICS project: simulating the formation and co-evolution of galaxies and their star cluster populations

NASA Astrophysics Data System (ADS)

Pfeffer, Joel; Kruijssen, J. M. Diederik; Crain, Robert A.; Bastian, Nate

2018-04-01

We introduce the MOdelling Star cluster population Assembly In Cosmological Simulations within EAGLE (E-MOSAICS) project. E-MOSAICS incorporates models describing the formation, evolution, and disruption of star clusters into the EAGLE galaxy formation simulations, enabling the examination of the co-evolution of star clusters and their host galaxies in a fully cosmological context. A fraction of the star formation rate of dense gas is assumed to yield a cluster population; this fraction and the population's initial properties are governed by the physical properties of the natal gas. The subsequent evolution and disruption of the entire cluster population are followed accounting for two-body relaxation, stellar evolution, and gravitational shocks induced by the local tidal field. This introductory paper presents a detailed description of the model and initial results from a suite of 10 simulations of ˜L⋆ galaxies with disc-like morphologies at z = 0. The simulations broadly reproduce key observed characteristics of young star clusters and globular clusters (GCs), without invoking separate formation mechanisms for each population. The simulated GCs are the surviving population of massive clusters formed at early epochs (z ≳ 1-2), when the characteristic pressures and surface densities of star-forming gas were significantly higher than observed in local galaxies. We examine the influence of the star formation and assembly histories of galaxies on their cluster populations, finding that (at similar present-day mass) earlier-forming galaxies foster a more massive and disruption-resilient cluster population, while galaxies with late mergers are capable of forming massive clusters even at late cosmic epochs. We find that the phenomenological treatment of interstellar gas in EAGLE precludes the accurate modelling of cluster disruption in low-density environments, but infer that simulations incorporating an explicitly modelled cold interstellar gas phase will overcome this shortcoming.

A Novel Application of Synthetic Biology and Directed Evolution to Engineer Phage-based Antibiotics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Meiye

The emergence of multiple drug resistant bacteria poses threats to human health, agriculture and food safety. Annually over 100,000 deaths and up to $20 billion loss to the U.S. economy are attributed to multiple drug resistant bacteria. With only four new chemical antibiotics in the drug development pipeline, we are in dire need of new solutions to address the emerging threat of multiple drug resistance. We propose a paradigm-changing approach to address the multi-drug resistant bacteria problem by utilizing Synthetic Biology (SynBio) methodologies to create and evolve “designer” bacteriophages or phages – viruses that specifically infect bacteria – to infectmore » and kill newly emerging pathogenic bacterial strains WITHOUT the need for chemical antibiotics. A major advantage of using phage to combat pathogenic bacteria is that phages can co-evolve with their bacterial host, and Sandia can be the first in the world to establish an industrial scale Synthetic Biology pipeline for phage directed evolution for safe, targeted, customizable solution to bacterial drug resistance. Since there is no existing phage directed evolution effort within or outside of Sandia, this proposal is suitable as a high-risk LDRD effort to create the first pipeline for such an endeavor. The high potential reward nature of this proposal will be the immediate impact in decontamination and restoration of surfaces and infrastructure, with longer term impact in human or animal therapeutics. The synthetic biology and screening approaches will lead to fundamental knowledge of phage/bacteria co-evolution, making Sandia a world leader in directed evolution of bacteriophages.« less

Social evolution. Oxytocin-gaze positive loop and the coevolution of human-dog bonds.

PubMed

Nagasawa, Miho; Mitsui, Shouhei; En, Shiori; Ohtani, Nobuyo; Ohta, Mitsuaki; Sakuma, Yasuo; Onaka, Tatsushi; Mogi, Kazutaka; Kikusui, Takefumi

2015-04-17

Human-like modes of communication, including mutual gaze, in dogs may have been acquired during domestication with humans. We show that gazing behavior from dogs, but not wolves, increased urinary oxytocin concentrations in owners, which consequently facilitated owners' affiliation and increased oxytocin concentration in dogs. Further, nasally administered oxytocin increased gazing behavior in dogs, which in turn increased urinary oxytocin concentrations in owners. These findings support the existence of an interspecies oxytocin-mediated positive loop facilitated and modulated by gazing, which may have supported the coevolution of human-dog bonding by engaging common modes of communicating social attachment. Copyright © 2015, American Association for the Advancement of Science.

Coevolution of dependency distance, hierarchical structure and word order. Comment on "Dependency distance: a new perspective on syntactic patterns in natural languages" by Haitao Liu et al.

NASA Astrophysics Data System (ADS)

Jing, Yingqi

2017-07-01

Exploring the relationships between structural rules and their linearization constraints have been a central issue in formal syntax and linguistic typology [1]. Liu et al. give a historical overview of the investigation of dependency distance minimization (DDM) in various fields, and specify its potential connections with the graphic patterns of syntactic structure and the linear ordering of words and constituents in real sentences [2]. This comment focuses on discussing the relations between dependency distance (DD), hierarchical structure and word order, and advocates further study on the coevolution of these traits in language histories.

Comparative ribotyping of Staphylococcus intermedius isolated from members of the Canoidea gives possible evidence for host-specificity and co-evolution of bacteria and hosts.

PubMed

Aarestrup, F M

2001-07-01

A total of 41 Staphylococcus intermedius isolates were isolated from skin of healthy members of six phylogenetic groups within the Canoidea (the dog family, skunk subfamily, weasel subfamily, racoon family, red panda and bear family) of different geographical origin and compared by EcoRI ribotyping and cluster analysis. The S. intermedius isolates from the different families and subfamilies clustered together in separate groups, almost completely following the phylogenetic relationship of the animal hosts. These ribotype data indicate host-specificity of different types of S. intermedius and suggest co-evolution between the animal hosts within the Canoidea and S. intermedius.

Agent based modeling of the coevolution of hostility and pacifism

NASA Astrophysics Data System (ADS)

Dalmagro, Fermin; Jimenez, Juan

2015-01-01

We propose a model based on a population of agents whose states represent either hostile or peaceful behavior. Randomly selected pairs of agents interact according to a variation of the Prisoners Dilemma game, and the probabilities that the agents behave aggressively or not are constantly updated by the model so that the agents that remain in the game are those with the highest fitness. We show that the population of agents oscillate between generalized conflict and global peace, without either reaching a stable state. We then use this model to explain some of the emergent behaviors in collective conflicts, by comparing the simulated results with empirical data obtained from social systems. In particular, using public data reports we show how the model precisely reproduces interesting quantitative characteristics of diverse types of armed conflicts, public protests, riots and strikes.

Co-Evolutions of Ecosystems, Societies, and Economy in Dryland Asia

NASA Astrophysics Data System (ADS)

Chen, Jiquan; Ouyang, Zutao; John, Ranjeet; Dong, Gang; Fan, Peilei

2015-04-01

This presentation aims at the interactive changes of the natural system (NS) and the human system (HS) as well as the feedbacks in time and space for dryland Asia where multiple administrative units from several countries experience similar climates, ecosystems, cultures, and traditions but different governments, land uses, economic development, and demographic changes (e.g., ethnical composition). We compiled and examined the changes in major measures for ecosystems (e.g., PAR, LAI, GPP, ET), economy (GDP, export/import, EGS), and human demography (e.g., population, health, education) between 1981 through 2011 (30+ variables) for six Central Asian countries (Afghanistan, Turkmenistan, Tajikistan, Uzbekistan, Kazakhstan, Kyrgyzstan) and two East Asian countries (Mongolia and China). Particular attention was made to understand the co-evolutions of the ratios between the elements of HS and NS, such as: GDP: GPP, PET: FWW, R: PDSI, EGS: GPP, etc., so that feedbacks and interactions can be empirically studied. Spatial and temporal changes of each measure, as well as their ratios, were quantified to highlight the relative contributions of human activities (e.g., policy) and biophysical changes (e.g., climate). We found some tight connections between the HS and NS variables, but the co-evolutions have to be understood in the context of governments, policy, and other major institutional shifts.

Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.

PubMed

Ochoa, David; García-Gutiérrez, Ponciano; Juan, David; Valencia, Alfonso; Pazos, Florencio

2013-01-27

A widespread family of methods for studying and predicting protein interactions using sequence information is based on co-evolution, quantified as similarity of phylogenetic trees. Part of the co-evolution observed between interacting proteins could be due to co-adaptation caused by inter-protein contacts. In this case, the co-evolution is expected to be more evident when evaluated on the surface of the proteins or the internal layers close to it. In this work we study the effect of incorporating information on predicted solvent accessibility to three methods for predicting protein interactions based on similarity of phylogenetic trees. We evaluate the performance of these methods in predicting different types of protein associations when trees based on positions with different characteristics of predicted accessibility are used as input. We found that predicted accessibility improves the results of two recent versions of the mirrortree methodology in predicting direct binary physical interactions, while it neither improves these methods, nor the original mirrortree method, in predicting other types of interactions. That improvement comes at no cost in terms of applicability since accessibility can be predicted for any sequence. We also found that predictions of protein-protein interactions are improved when multiple sequence alignments with a richer representation of sequences (including paralogs) are incorporated in the accessibility prediction.

Coevolution of antibiotic production and counter-resistance in soil bacteria.

PubMed

Laskaris, Paris; Tolba, Sahar; Calvo-Bado, Leo; Wellington, Elizabeth M; Wellington, Liz

2010-03-01

We present evidence for the coexistence and coevolution of antibiotic resistance and biosynthesis genes in soil bacteria. The distribution of the streptomycin (strA) and viomycin (vph) resistance genes was examined in Streptomyces isolates. strA and vph were found either within a biosynthetic gene cluster or independently. Streptomyces griseus strains possessing the streptomycin cluster formed part of a clonal complex. All S. griseus strains possessing solely strA belonged to two clades; both were closely related to the streptomycin producers. Other more distantly related S. griseus strains did not contain strA. S. griseus strains with only vph also formed two clades, but they were more distantly related to the producers and to one another. The expression of the strA gene was constitutive in a resistance-only strain whereas streptomycin producers showed peak strA expression in late log phase that correlates with the switch on of streptomycin biosynthesis. While there is evidence that antibiotics have diverse roles in nature, our data clearly support the coevolution of resistance in the presence of antibiotic biosynthetic capability within closely related soil dwelling bacteria. This reinforces the view that, for some antibiotics at least, the primary role is one of antibiosis during competition in soil for resources.

Selection on an antagonistic behavioral trait can drive rapid genital coevolution in the burying beetle, Nicrophorus vespilloides.

PubMed

Hopwood, Paul E; Head, Megan L; Jordan, Eleanor J; Carter, Mauricio J; Davey, Emma; Moore, Allen J; Royle, Nick J

2016-06-01

Male and female genital morphology varies widely across many taxa, and even among populations. Disentangling potential sources of selection on genital morphology is problematic because each sex is predicted to respond to adaptations in the other due to reproductive conflicts of interest. To test how variation in this sexual conflict trait relates to variation in genital morphology we used our previously developed artificial selection lines for high and low repeated mating rates. We selected for high and low repeated mating rates using monogamous pairings to eliminate contemporaneous female choice and male-male competition. Male and female genital shape responded rapidly to selection on repeated mating rate. High and low mating rate lines diverged from control lines after only 10 generations of selection. We also detected significant patterns of male and female genital shape coevolution among selection regimes. We argue that because our selection lines differ in sexual conflict, these results support the hypothesis that sexually antagonistic coevolution can drive the rapid divergence of genital morphology. The greatest divergence in morphology corresponded with lines in which the resolution of sexual conflict over mating rate was biased in favor of male interests. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

The evolution of floral scent and olfactory preferences in pollinators: coevolution or pre-existing bias?

PubMed

Schiestl, Florian P; Dötterl, Stefan

2012-07-01

Coevolution is thought to be a major factor in shaping plant-pollinator interactions. Alternatively, plants may have evolved traits that fitted pre-existing preferences or morphologies in the pollinators. Here, we test these two scenarios in the plant family of Araceae and scarab beetles (Coleoptera, Scarabaeidae) as pollinators. We focused on floral volatile organic compounds (VOCs) and production/detection of VOCs by scarab beetles. We found phylogenetic structure in the production/detection of methoxylated aromatics in scarabs, but not plants. Within the plants, most of the compounds showed a well-supported pattern of correlated evolution with scarab-beetle pollination. In contrast, the scarabs showed no correlation between VOC production/detection and visitation to Araceae flowers, with the exception of the VOC skatole. Moreover, many VOCs were found in nonpollinating beetle groups (e.g., Melolonthinae) that are ancestors of pollinating scarabs. Importantly, none of the tested VOCs were found to have originated in pollinating taxa. Our analysis indicates a Jurassic origin of VOC production/detection in scarabs, but a Cretaceous/Paleocene origin of floral VOCs in plants. Therefore, we argue against coevolution, instead supporting the scenario of sequential evolution of floral VOCs in Araceae driven by pre-existing bias of pollinators. © 2012 The Author(s).

Host specificity and coevolution of Flavobacteriaceae endosymbionts within the siphonous green seaweed Bryopsis.

PubMed

Hollants, Joke; Leliaert, Frederik; Verbruggen, Heroen; De Clerck, Olivier; Willems, Anne

2013-06-01

The siphonous green seaweed Bryopsis harbors complex intracellular bacterial communities. Previous studies demonstrated that certain species form close, obligate associations with Flavobacteriaceae. A predominant imprint of host evolutionary history on the presence of these bacteria suggests a highly specialized association. In this study we elaborate on previous results by expanding the taxon sampling and testing for host-symbiont coevolution Therefore, we optimized a PCR protocol to directly and specifically amplify Flavobacteriaceae endosymbiont 16S rRNA gene sequences, which allowed us to screen a large number of algal samples without the need for cultivation or surface sterilization. We analyzed 146 Bryopsis samples, and 92 additional samples belonging to the Bryopsidales and other orders within the class Ulvophyceae. Results indicate that the Flavobacteriaceae endosymbionts are restricted to Bryopsis, and only occur within specific, warm-temperate and tropical clades of the genus. Statistical analyses (AMOVA) demonstrate a significant non-random host-symbiont association. Comparison of bacterial 16S rRNA and Bryopsis rbcL phylogenies, however, reveal complex host-symbiont evolutionary associations, whereby closely related hosts predominantly harbor genetically similar endosymbionts. Bacterial genotypes are rarely confined to a single Bryopsis species and most Bryopsis species harbored several Flavobacteriaceae, obscuring a clear pattern of coevolution. Copyright © 2013 Elsevier Inc. All rights reserved.

Beyond neutral and forbidden links: morphological matches and the assembly of mutualistic hawkmoth-plant networks.

PubMed

Sazatornil, Federico D; Moré, Marcela; Benitez-Vieyra, Santiago; Cocucci, Andrea A; Kitching, Ian J; Schlumpberger, Boris O; Oliveira, Paulo E; Sazima, Marlies; Amorim, Felipe W

2016-11-01

A major challenge in evolutionary ecology is to understand how co-evolutionary processes shape patterns of interactions between species at community level. Pollination of flowers with long corolla tubes by long-tongued hawkmoths has been invoked as a showcase model of co-evolution. Recently, optimal foraging models have predicted that there might be a close association between mouthparts' length and the corolla depth of the visited flowers, thus favouring trait convergence and specialization at community level. Here, we assessed whether hawkmoths more frequently pollinate plants with floral tube lengths similar to their proboscis lengths (morphological match hypothesis) against abundance-based processes (neutral hypothesis) and ecological trait mismatches constraints (forbidden links hypothesis), and how these processes structure hawkmoth-plant mutualistic networks from five communities in four biogeographical regions of South America. We found convergence in morphological traits across the five communities and that the distribution of morphological differences between hawkmoths and plants is consistent with expectations under the morphological match hypothesis in three of the five communities. In the two remaining communities, which are ecotones between two distinct biogeographical areas, interactions are better predicted by the neutral hypothesis. Our findings are consistent with the idea that diffuse co-evolution drives the evolution of extremely long proboscises and flower tubes, and highlight the importance of morphological traits, beyond the forbidden links hypothesis, in structuring interactions between mutualistic partners, revealing that the role of niche-based processes can be much more complex than previously known. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

Generalized antifungal activity and 454-screening of Pseudonocardia and Amycolatopsis bacteria in nests of fungus-growing ants.

PubMed

Sen, Ruchira; Ishak, Heather D; Estrada, Dora; Dowd, Scot E; Hong, Eunki; Mueller, Ulrich G

2009-10-20

In many host-microbe mutualisms, hosts use beneficial metabolites supplied by microbial symbionts. Fungus-growing (attine) ants are thought to form such a mutualism with Pseudonocardia bacteria to derive antibiotics that specifically suppress the coevolving pathogen Escovopsis, which infects the ants' fungal gardens and reduces growth. Here we test 4 key assumptions of this Pseudonocardia-Escovopsis coevolution model. Culture-dependent and culture-independent (tag-encoded 454-pyrosequencing) surveys reveal that several Pseudonocardia species and occasionally Amycolatopsis (a close relative of Pseudonocardia) co-occur on workers from a single nest, contradicting the assumption of a single pseudonocardiaceous strain per nest. Pseudonocardia can occur on males, suggesting that Pseudonocardia could also be horizontally transmitted during mating. Pseudonocardia and Amycolatopsis secretions kill or strongly suppress ant-cultivated fungi, contradicting the previous finding of a growth-enhancing effect of Pseudonocardia on the cultivars. Attine ants therefore may harm their own cultivar if they apply pseudonocardiaceous secretions to actively growing gardens. Pseudonocardia and Amycolatopsis isolates also show nonspecific antifungal activities against saprotrophic, endophytic, entomopathogenic, and garden-pathogenic fungi, contrary to the original report of specific antibiosis against Escovopsis alone. We conclude that attine-associated pseudonocardiaceous bacteria do not exhibit derived antibiotic properties to specifically suppress Escovopsis. We evaluate hypotheses on nonadaptive and adaptive functions of attine integumental bacteria, and develop an alternate conceptual framework to replace the prevailing Pseudonocardia-Escovopsis coevolution model. If association with Pseudonocardia is adaptive to attine ants, alternate roles of such microbes could include the protection of ants or sanitation of the nest.

Generalized antifungal activity and 454-screening of Pseudonocardia and Amycolatopsis bacteria in nests of fungus-growing ants

PubMed Central

Sen, Ruchira; Ishak, Heather D.; Estrada, Dora; Dowd, Scot E.; Hong, Eunki; Mueller, Ulrich G.

2009-01-01

In many host-microbe mutualisms, hosts use beneficial metabolites supplied by microbial symbionts. Fungus-growing (attine) ants are thought to form such a mutualism with Pseudonocardia bacteria to derive antibiotics that specifically suppress the coevolving pathogen Escovopsis, which infects the ants' fungal gardens and reduces growth. Here we test 4 key assumptions of this Pseudonocardia-Escovopsis coevolution model. Culture-dependent and culture-independent (tag-encoded 454-pyrosequencing) surveys reveal that several Pseudonocardia species and occasionally Amycolatopsis (a close relative of Pseudonocardia) co-occur on workers from a single nest, contradicting the assumption of a single pseudonocardiaceous strain per nest. Pseudonocardia can occur on males, suggesting that Pseudonocardia could also be horizontally transmitted during mating. Pseudonocardia and Amycolatopsis secretions kill or strongly suppress ant-cultivated fungi, contradicting the previous finding of a growth-enhancing effect of Pseudonocardia on the cultivars. Attine ants therefore may harm their own cultivar if they apply pseudonocardiaceous secretions to actively growing gardens. Pseudonocardia and Amycolatopsis isolates also show nonspecific antifungal activities against saprotrophic, endophytic, entomopathogenic, and garden-pathogenic fungi, contrary to the original report of specific antibiosis against Escovopsis alone. We conclude that attine-associated pseudonocardiaceous bacteria do not exhibit derived antibiotic properties to specifically suppress Escovopsis. We evaluate hypotheses on nonadaptive and adaptive functions of attine integumental bacteria, and develop an alternate conceptual framework to replace the prevailing Pseudonocardia-Escovopsis coevolution model. If association with Pseudonocardia is adaptive to attine ants, alternate roles of such microbes could include the protection of ants or sanitation of the nest. PMID:19805175

On the Supermassive Black Hole-Galaxy Coevolution

NASA Astrophysics Data System (ADS)

Hegde, Sahil; Zhang, Shawn; Rodriguez, Aldo; Primack, Joel R.

2017-01-01

In recent years, a major focus of astronomy has been the study of the effects of supermassive black holes (SMBH) on their host galaxies. Recent results have found strong correlations between SMBH mass and host galaxy properties, most notably in the bulge velocity dispersion and galaxy stellar mass. We utilize these relations along with a novel convolution method to construct number density models of different galaxy properties. Using these models, we compare two fundamental methods for constructing a black hole mass function (BHMF) with the M⊙-σ and M⊙-M* relations. With these methods, we estimate the redshift evolution of the BHMF and, based on that, compare mass growth histories of central black holes and their host galaxies. Additionally, we utilize a data compilation of over 500 galaxies with individual measurements of galaxy properties (BH mass, stellar velocity dispersion, stellar mass, etc.) and classify galaxies by their morphologies in order to shed light on the controversial Shankar et al. (2016) argument that observations are biased in favor of massive SMBHs. We find that such a bias has little impact on the SMBH-galaxy relations.We conclude that the galaxy sample is a fair representation of the local universe and argue that our BH number density and scaling relations can be employed in the future to constrain relevant mechanisms for galaxy formation. We emphasize that this is the most comprehensive and accurate study of SMBH-galaxy coevolution as of now. Most of this work was carried out by high school students working under the auspices of the Science Internship Program at UC Santa Cruz.

An experimental and computational evolution-based method to study a mode of co-evolution of overlapping open reading frames in the AAV2 viral genome.

PubMed

Kawano, Yasuhiro; Neeley, Shane; Adachi, Kei; Nakai, Hiroyuki

2013-01-01

Overlapping open reading frames (ORFs) in viral genomes undergo co-evolution; however, how individual amino acids coded by overlapping ORFs are structurally, functionally, and co-evolutionarily constrained remains difficult to address by conventional homologous sequence alignment approaches. We report here a new experimental and computational evolution-based methodology to address this question and report its preliminary application to elucidating a mode of co-evolution of the frame-shifted overlapping ORFs in the adeno-associated virus (AAV) serotype 2 viral genome. These ORFs encode both capsid VP protein and non-structural assembly-activating protein (AAP). To show proof of principle of the new method, we focused on the evolutionarily conserved QVKEVTQ and KSKRSRR motifs, a pair of overlapping heptapeptides in VP and AAP, respectively. In the new method, we first identified a large number of capsid-forming VP3 mutants and functionally competent AAP mutants of these motifs from mutant libraries by experimental directed evolution under no co-evolutionary constraints. We used Illumina sequencing to obtain a large dataset and then statistically assessed the viability of VP and AAP heptapeptide mutants. The obtained heptapeptide information was then integrated into an evolutionary algorithm, with which VP and AAP were co-evolved from random or native nucleotide sequences in silico. As a result, we demonstrate that these two heptapeptide motifs could exhibit high degeneracy if coded by separate nucleotide sequences, and elucidate how overlap-evoked co-evolutionary constraints play a role in making the VP and AAP heptapeptide sequences into the present shape. Specifically, we demonstrate that two valine (V) residues and β-strand propensity in QVKEVTQ are structurally important, the strongly negative and hydrophilic nature of KSKRSRR is functionally important, and overlap-evoked co-evolution imposes strong constraints on serine (S) residues in KSKRSRR, despite high degeneracy of the motifs in the absence of co-evolutionary constraints.

The Phylogenetic Signature Underlying ATP Synthase c-Ring Compliance

DOE PAGES

Pandini, Alessandro; Kleinjung, Jens; Taylor, Willie R.; ...

2015-09-01

The proton-driven ATP synthase (F OF 1) is comprised of two rotary, stepping motors (F O and F 1) coupled by an elastic power transmission. The elastic compliance resides in the rotor module that includes the membrane-embedded FO c-ring. Proton transport by FO is firmly coupled to the rotation of the c-ring relative to other F O subunits (ab 2). It drives ATP synthesis. We used a computational method to investigate the contribution of the c-ring to the total elastic compliance. We performed principal component analysis of conformational ensembles built using distance constraints from the bovine mitochondrial c-ring x-ray structure.more » Angular rotary twist, the dominant ring motion, was estimated to show that the c-ring accounted in part for the measured compliance. Ring rotation was entrained to rotation of the external helix within each hairpin-shaped c-subunit in the ring. Ensembles of monomer and dimers extracted from complete c-rings showed that the coupling between collective ring and the individual subunit motions was independent of the size of the c-ring, which varies between organisms. Molecular determinants were identified by covariance analysis of residue coevolution and structural-alphabet-based local dynamics correlations. The residue coevolution gave a readout of subunit architecture. The dynamic couplings revealed that the hinge for both ring and subunit helix rotations was constructed from the proton-binding site and the adjacent glycine motif (IB-GGGG) in the midmembrane plane. IB-GGGG motifs were linked by long-range couplings across the ring, while intrasubunit couplings connected the motif to the conserved cytoplasmic loop and adjacent segments. The correlation with principal collective motions shows that the couplings underlie both ring rotary and bending motions. Noncontact couplings between IB-GGGG motifs matched the coevolution signal as well as contact couplings. The residue coevolution reflects the physiological importance of the dynamics that may link proton transfer to ring compliance.« less

Inter-genomic sexual conflict drives antagonistic coevolution in harvester ants

PubMed Central

Herrmann, Michael; Cahan, Sara Helms

2014-01-01

The reproductive interests of males and females are not always aligned, leading to sexual conflict over parental investment, rate of reproduction and mate choice. Traits that increase the genetic interests of one sex often occur at the expense of the other, selecting for counter-adaptations leading to antagonistic coevolution. Reproductive conflict is not limited to intraspecific interactions; interspecific hybridization can produce pronounced sexual conflict between males and females of different species, but it is unclear whether such conflict can drive sexually antagonistic coevolution between reproductively isolated genomes. We tested for hybridization-driven sexually antagonistic adaptations in queens and males of the socially hybridogenetic ‘J’ lineages of Pogonomyrmex harvester ants, whose mating system promotes hybridization in queens but selects against it in males. We conducted no-choice mating assays to compare patterns of mating behaviour and sperm transfer between inter- and intra-lineage pairings. There was no evidence for mate discrimination on the basis of pair type, and the total quantity of sperm transferred did not differ between intra- and inter-lineage pairs; however, further dissection of the sperm transfer process into distinct mechanistic components revealed significant, and opposing, cryptic manipulation of copulatory investment by both sexes. Males of both lineages increased their rate of sperm transfer to high-fitness intra-lineage mates, with a stronger response in the rarer lineage for whom mating mistakes are the most likely. By contrast, the total duration of copulation for intra-lineage mating pairs was significantly shorter than for inter-lineage crosses, suggesting that queens respond to prevent excessive sperm loading by prematurely terminating copulation. These findings demonstrate that sexual conflict can lead to antagonistic coevolution in both intra-genomic and inter-genomic contexts. Indeed, the resolution of sexual conflict may be a key determinant of the long-term evolutionary potential of host-dependent reproductive strategies, counteracting the inherent instabilities arising from such systems. PMID:25355474

The Phylogenetic Signature Underlying ATP Synthase c-Ring Compliance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pandini, Alessandro; Kleinjung, Jens; Taylor, Willie R.

The proton-driven ATP synthase (F OF 1) is comprised of two rotary, stepping motors (F O and F 1) coupled by an elastic power transmission. The elastic compliance resides in the rotor module that includes the membrane-embedded FO c-ring. Proton transport by FO is firmly coupled to the rotation of the c-ring relative to other F O subunits (ab 2). It drives ATP synthesis. We used a computational method to investigate the contribution of the c-ring to the total elastic compliance. We performed principal component analysis of conformational ensembles built using distance constraints from the bovine mitochondrial c-ring x-ray structure.more » Angular rotary twist, the dominant ring motion, was estimated to show that the c-ring accounted in part for the measured compliance. Ring rotation was entrained to rotation of the external helix within each hairpin-shaped c-subunit in the ring. Ensembles of monomer and dimers extracted from complete c-rings showed that the coupling between collective ring and the individual subunit motions was independent of the size of the c-ring, which varies between organisms. Molecular determinants were identified by covariance analysis of residue coevolution and structural-alphabet-based local dynamics correlations. The residue coevolution gave a readout of subunit architecture. The dynamic couplings revealed that the hinge for both ring and subunit helix rotations was constructed from the proton-binding site and the adjacent glycine motif (IB-GGGG) in the midmembrane plane. IB-GGGG motifs were linked by long-range couplings across the ring, while intrasubunit couplings connected the motif to the conserved cytoplasmic loop and adjacent segments. The correlation with principal collective motions shows that the couplings underlie both ring rotary and bending motions. Noncontact couplings between IB-GGGG motifs matched the coevolution signal as well as contact couplings. The residue coevolution reflects the physiological importance of the dynamics that may link proton transfer to ring compliance.« less

Comparative Phylogenetic Studies on Schistosoma japonicum and Its Snail Intermediate Host Oncomelania hupensis: Origins, Dispersal and Coevolution

PubMed Central

Attwood, Stephen W.; Ibaraki, Motomu; Saitoh, Yasuhide; Nihei, Naoko; Janies, Daniel A.

2015-01-01

Background Schistosoma japonicum causes major public health problems in China and the Philippines; this parasite, which is transmitted by freshwater snails of the species Oncomelania hupensis, causes the disease intestinal schistosomiasis in humans and cattle. Researchers working on Schistosoma in Africa have described the relationship between the parasites and their snail intermediate hosts as coevolved or even as an evolutionary arms race. In the present study this hypothesis of coevolution is evaluated for S. japonicum and O. hupensis. The origins and radiation of the snails and the parasite across China, and the taxonomic validity of the sub-species of O. hupensis, are also assessed. Methodology/Principal Findings The findings provide no evidence for coevolution between S. japonicum and O. hupensis, and the phylogeographical analysis suggests a heterochronous radiation of the parasites and snails in response to different palaeogeographical and climatic triggers. The results are consistent with a hypothesis of East to West colonisation of China by Oncomelania with a re-invasion of Japan by O. hupensis from China. The Taiwan population of S. japonicum appears to be recently established in comparison with mainland Chinese populations. Conclusions/Significance The snail and parasite populations of the western mountain region of China (Yunnan and Sichuan) appear to have been isolated from Southeast Asian populations since the Pleistocene; this has implications for road and rail links being constructed in the region, which will breach biogeographical barriers between China and Southeast Asia. The results also have implications for the spread of S. japonicum. In the absence of coevolution, the parasite may more readily colonise new snail populations to which it is not locally adapted, or even new intermediate host species; this can facilitate its dispersal into new areas. Additional work is required to assess further the risk of spread of S. japonicum. PMID:26230619

Viral Diversity Threshold for Adaptive Immunity in Prokaryotes

PubMed Central

Weinberger, Ariel D.; Wolf, Yuri I.; Lobkovsky, Alexander E.; Gilmore, Michael S.; Koonin, Eugene V.

2012-01-01

ABSTRACT Bacteria and archaea face continual onslaughts of rapidly diversifying viruses and plasmids. Many prokaryotes maintain adaptive immune systems known as clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (Cas). CRISPR-Cas systems are genomic sensors that serially acquire viral and plasmid DNA fragments (spacers) that are utilized to target and cleave matching viral and plasmid DNA in subsequent genomic invasions, offering critical immunological memory. Only 50% of sequenced bacteria possess CRISPR-Cas immunity, in contrast to over 90% of sequenced archaea. To probe why half of bacteria lack CRISPR-Cas immunity, we combined comparative genomics and mathematical modeling. Analysis of hundreds of diverse prokaryotic genomes shows that CRISPR-Cas systems are substantially more prevalent in thermophiles than in mesophiles. With sequenced bacteria disproportionately mesophilic and sequenced archaea mostly thermophilic, the presence of CRISPR-Cas appears to depend more on environmental temperature than on bacterial-archaeal taxonomy. Mutation rates are typically severalfold higher in mesophilic prokaryotes than in thermophilic prokaryotes. To quantitatively test whether accelerated viral mutation leads microbes to lose CRISPR-Cas systems, we developed a stochastic model of virus-CRISPR coevolution. The model competes CRISPR-Cas-positive (CRISPR-Cas+) prokaryotes against CRISPR-Cas-negative (CRISPR-Cas−) prokaryotes, continually weighing the antiviral benefits conferred by CRISPR-Cas immunity against its fitness costs. Tracking this cost-benefit analysis across parameter space reveals viral mutation rate thresholds beyond which CRISPR-Cas cannot provide sufficient immunity and is purged from host populations. These results offer a simple, testable viral diversity hypothesis to explain why mesophilic bacteria disproportionately lack CRISPR-Cas immunity. More generally, fundamental limits on the adaptability of biological sensors (Lamarckian evolution) are predicted. PMID:23221803

An analysis of intergroup rivalry using Ising model and reinforcement learning

NASA Astrophysics Data System (ADS)

Zhao, Feng-Fei; Qin, Zheng; Shao, Zhuo

2014-01-01

Modeling of intergroup rivalry can help us better understand economic competitions, political elections and other similar activities. The result of intergroup rivalry depends on the co-evolution of individual behavior within one group and the impact from the rival group. In this paper, we model the rivalry behavior using Ising model. Different from other simulation studies using Ising model, the evolution rules of each individual in our model are not static, but have the ability to learn from historical experience using reinforcement learning technique, which makes the simulation more close to real human behavior. We studied the phase transition in intergroup rivalry and focused on the impact of the degree of social freedom, the personality of group members and the social experience of individuals. The results of computer simulation show that a society with a low degree of social freedom and highly educated, experienced individuals is more likely to be one-sided in intergroup rivalry.

Carbon-water Cycling in the Critical Zone: Understanding Ecosystem Process Variability Across Complex Terrain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barnard, Holly; Brooks, Paul

2016-06-16

One of the largest knowledge gaps in environmental science is the ability to understand and predict how ecosystems will respond to future climate variability. The links between vegetation, hydrology, and climate that control carbon sequestration in plant biomass and soils remain poorly understood. Soil respiration is the second largest carbon flux of terrestrial ecosystems, yet there is no consensus on how respiration will change as water availability and temperature co-vary. To address this knowledge gap, we use the variation in soil development and topography across an elevation and climate gradient on the Front Range of Colorado to conduct a naturalmore » experiment that enables us to examine the co-evolution of soil carbon, vegetation, hydrology, and climate in an accessible field laboratory. The goal of this project is to further our ability to combine plant water availability, carbon flux and storage, and topographically driven hydrometrics into a watershed scale predictive model of carbon balance. We hypothesize: (i) landscape structure and hydrology are important controls on soil respiration as a result of spatial variability in both physical and biological drivers: (ii) variation in rates of soil respiration during the growing season is due to corresponding shifts in belowground carbon inputs from vegetation; and (iii) aboveground carbon storage (biomass) and species composition are directly correlated with soil moisture and therefore, can be directly related to subsurface drainage patterns.« less

Integration of metagenomic and stable carbon isotope evidence reveals the extent and mechanisms of carbon dioxide fixation in high-temperature microbial communities

DOE PAGES

Jennings, Ryan de Montmollin; Moran, James J.; Jay, Zackary J.; ...

2017-02-03

Biological fixation of CO 2 is the primary mechanism of C reduction in natural systems, and provides a diverse suite of organic compounds utilized by chemoorganoheterotrophs. The extent and mechanisms of CO 2 fixation were evaluated across a comprehensive set of high-temperature, chemotrophic microbial communities in Yellowstone National Park by combining metagenomic and stable 13C isotope analyses. Fifteen geothermal sites representing three distinct habitat types (iron-oxide mats, anoxic sulfur sediments, and filamentous ‘streamer’ communities) were investigated. Genes of the 3-hydroxypropionate/4-hydroxybutyrate, dicarboxylate/4-hydroxybutyrate, and reverse tricarboxylic acid CO 2 fixation pathways were identified in assembled genome sequence corresponding to the predominant Crenarchaeotamore » and Aquificales observed across this habitat range. Stable 13C analyses of dissolved inorganic and organic C (DIC, DOC), and possible landscape C sources were used to interpret the 13C content of microbial community samples. Isotope mixing models showed that the minimum amounts of autotrophic C in microbial biomass were > 50 % in the majority of communities analyzed, but were also dependent on the amounts of heterotrophy and/or accumulation of landscape C. Furthermore, the significance of CO 2 as a C source in these communities provides a foundation for understanding metabolic linkages among autotrophs and heterotrophs, community assembly and succession, and the likely coevolution of deeply-branching thermophiles.« less

Evolutionary biology of plant defenses against herbivory and their predictive implications for endocrine disruptor susceptibility in vertebrates.

PubMed Central

Wynne-Edwards, K E

2001-01-01

Hormone disruption is a major, underappreciated component of the plant chemical arsenal, and the historical coevolution between hormone-disrupting plants and herbivores will have both increased the susceptibility of carnivores and diversified the sensitivities of herbivores to man-made endocrine disruptors. Here I review diverse evidence of the influence of plant secondary compounds on vertebrate reproduction, including human reproduction. Three of the testable hypotheses about the evolutionary responses of vertebrate herbivores to hormone-disrupting challenges from their diet are developed. Specifically, the hypotheses are that a) vertebrate herbivores will express steroid hormone receptors in the buccal cavity and/or the vomeronasal organ; b) absolute sex steroid concentrations will be lower in carnivores than in herbivores; and c) herbivore steroid receptors should be more diverse in their binding affinities than carnivore lineages. The argument developed in this review, if empirically validated by support for the specific hypotheses, suggests that a) carnivores will be more susceptible than herbivores to endocrine-disrupting compounds of anthropogenic origin entering their bodies, and b) diverse herbivore lineages will be variably susceptible to any given natural or synthetic contaminant. As screening methods for hormone-disrupting potential are compared and adopted, comparative endocrine physiology research is urgently needed to develop models that predict the broad applicability of those screening results in diverse vertebrate species. PMID:11401754

High school students' learning and perceptions of phylogenetics of flowering plants.

PubMed

Bokor, Julie R; Landis, Jacob B; Crippen, Kent J

2014-01-01

Basic phylogenetics and associated "tree thinking" are often minimized or excluded in formal school curricula. Informal settings provide an opportunity to extend the K-12 school curriculum, introducing learners to new ideas, piquing interest in science, and fostering scientific literacy. Similarly, university researchers participating in science, technology, engineering, and mathematics (STEM) outreach activities increase awareness of college and career options and highlight interdisciplinary fields of science research and augment the science curriculum. To aid in this effort, we designed a 6-h module in which students utilized 12 flowering plant species to generate morphological and molecular phylogenies using biological techniques and bioinformatics tools. The phylogenetics module was implemented with 83 high school students during a weeklong university STEM immersion program and aimed to increase student understanding of phylogenetics and coevolution of plants and pollinators. Student response reflected positive engagement and learning gains as evidenced through content assessments, program evaluation surveys, and program artifacts. We present the results of the first year of implementation and discuss modifications for future use in our immersion programs as well as in multiple course settings at the high school and undergraduate levels. © 2014 J. R. Bokor et al. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Genetic and linguistic coevolution in Northern Island Melanesia.

PubMed

Hunley, Keith; Dunn, Michael; Lindström, Eva; Reesink, Ger; Terrill, Angela; Healy, Meghan E; Koki, George; Friedlaender, Françoise R; Friedlaender, Jonathan S

2008-10-01

Recent studies have detailed a remarkable degree of genetic and linguistic diversity in Northern Island Melanesia. Here we utilize that diversity to examine two models of genetic and linguistic coevolution. The first model predicts that genetic and linguistic correspondences formed following population splits and isolation at the time of early range expansions into the region. The second is analogous to the genetic model of isolation by distance, and it predicts that genetic and linguistic correspondences formed through continuing genetic and linguistic exchange between neighboring populations. We tested the predictions of the two models by comparing observed and simulated patterns of genetic variation, genetic and linguistic trees, and matrices of genetic, linguistic, and geographic distances. The data consist of 751 autosomal microsatellites and 108 structural linguistic features collected from 33 Northern Island Melanesian populations. The results of the tests indicate that linguistic and genetic exchange have erased any evidence of a splitting and isolation process that might have occurred early in the settlement history of the region. The correlation patterns are also inconsistent with the predictions of the isolation by distance coevolutionary process in the larger Northern Island Melanesian region, but there is strong evidence for the process in the rugged interior of the largest island in the region (New Britain). There we found some of the strongest recorded correlations between genetic, linguistic, and geographic distances. We also found that, throughout the region, linguistic features have generally been less likely to diffuse across population boundaries than genes. The results from our study, based on exceptionally fine-grained data, show that local genetic and linguistic exchange are likely to obscure evidence of the early history of a region, and that language barriers do not particularly hinder genetic exchange. In contrast, global patterns may emphasize more ancient demographic events, including population splits associated with the early colonization of major world regions.

Genetic and Linguistic Coevolution in Northern Island Melanesia

PubMed Central

Hunley, Keith; Dunn, Michael; Lindström, Eva; Reesink, Ger; Terrill, Angela; Healy, Meghan E.; Koki, George; Friedlaender, Françoise R.; Friedlaender, Jonathan S.

2008-01-01

Recent studies have detailed a remarkable degree of genetic and linguistic diversity in Northern Island Melanesia. Here we utilize that diversity to examine two models of genetic and linguistic coevolution. The first model predicts that genetic and linguistic correspondences formed following population splits and isolation at the time of early range expansions into the region. The second is analogous to the genetic model of isolation by distance, and it predicts that genetic and linguistic correspondences formed through continuing genetic and linguistic exchange between neighboring populations. We tested the predictions of the two models by comparing observed and simulated patterns of genetic variation, genetic and linguistic trees, and matrices of genetic, linguistic, and geographic distances. The data consist of 751 autosomal microsatellites and 108 structural linguistic features collected from 33 Northern Island Melanesian populations. The results of the tests indicate that linguistic and genetic exchange have erased any evidence of a splitting and isolation process that might have occurred early in the settlement history of the region. The correlation patterns are also inconsistent with the predictions of the isolation by distance coevolutionary process in the larger Northern Island Melanesian region, but there is strong evidence for the process in the rugged interior of the largest island in the region (New Britain). There we found some of the strongest recorded correlations between genetic, linguistic, and geographic distances. We also found that, throughout the region, linguistic features have generally been less likely to diffuse across population boundaries than genes. The results from our study, based on exceptionally fine-grained data, show that local genetic and linguistic exchange are likely to obscure evidence of the early history of a region, and that language barriers do not particularly hinder genetic exchange. In contrast, global patterns may emphasize more ancient demographic events, including population splits associated with the early colonization of major world regions. PMID:18974871

Socio-hydrologic Modeling to Understand and Mediate the Competition for Water between Humans and Ecosystems: Murrumbidgee River Basin, Australia (Invited)

NASA Astrophysics Data System (ADS)

Sivapalan, M.

2013-12-01

Competition for water between humans and ecosystems is set to become a flash point in coming decades in all parts of the world. An entirely new and comprehensive quantitative framework is needed to establish a holistic understanding of that competition, thereby enabling development of effective mediation strategies. This paper presents a case study centered on the Murrumbidgee river basin in eastern Australia that illustrates the dynamics of the balance between water extraction and use for food production and efforts to mitigate and reverse consequent degradation of the riparian environment. Interactions between patterns of water management and climate driven hydrological variability within the prevailing socio-economic environment have contributed to the emergence of new whole system dynamics over the last 100 years. In particular, data analysis reveals a pendulum swing between an exclusive focus on agricultural development and food production in the initial stages of water resource development and its attendant socio-economic benefits, followed by the gradual realization of the adverse environmental impacts, efforts to mitigate these with the use of remedial measures, and ultimately concerted efforts and externally imposed solutions to restore environmental health and ecosystem services. A quasi-distributed coupled socio-hydrologic system model that explicitly includes the two-way coupling between human and hydrological systems, including evolution of human values/norms relating to water and the environment, is able to mimic broad features of this pendulum swing. The model consists of coupled nonlinear differential equations that include four state variables describing the co-evolution of storage capacity, irrigated area, human population, and ecosystem health. The model is used to generate insights into the dominant controls of the trajectory of co-evolution of the coupled human-water system, to serve as the theoretical framework for more detailed analysis of the system, and to generate organizing principles that may be transferable to other systems in different climatic and socio-economic settings.

Unbiased and targeted mass spectrometry for the HDL proteome.

PubMed

Singh, Sasha A; Aikawa, Masanori

2017-02-01

Mass spectrometry is an ever evolving technology that is equipped with a variety of tools for protein research. Some lipoprotein studies, especially those pertaining to HDL biology, have been exploiting the versatility of mass spectrometry to understand HDL function through its proteome. Despite the role of mass spectrometry in advancing research as a whole, however, the technology remains obscure to those without hands on experience, but still wishing to understand it. In this review, we walk the reader through the coevolution of common mass spectrometry workflows and HDL research, starting from the basic unbiased mass spectrometry methods used to profile the HDL proteome to the most recent targeted methods that have enabled an unprecedented view of HDL metabolism. Unbiased global proteomics have demonstrated that the HDL proteome is organized into subgroups across the HDL size fractions providing further evidence that HDL functional heterogeneity is in part governed by its varying protein constituents. Parallel reaction monitoring, a novel targeted mass spectrometry method, was used to monitor the metabolism of HDL apolipoproteins in humans and revealed that apolipoproteins contained within the same HDL size fraction exhibit diverse metabolic properties. Mass spectrometry provides a variety of tools and strategies to facilitate understanding, through its proteins, the complex biology of HDL.

Responses to olfactory signals reflect network structure of flower-visitor interactions.

PubMed

Junker, Robert R; Höcherl, Nicole; Blüthgen, Nico

2010-07-01

1. Network analyses provide insights into the diversity and complexity of ecological interactions and have motivated conclusions about community stability and co-evolution. However, biological traits and mechanisms such as chemical signals regulating the interactions between individual species--the microstructure of a network--are poorly understood. 2. We linked the responses of receivers (flower visitors) towards signals (flower scent) to the structure of a highly diverse natural flower-insect network. For each interaction, we define link temperature--a newly developed metric--as the deviation of the observed interaction strength from neutrality, assuming that animals randomly interact with flowers. 3. Link temperature was positively correlated to the specific visitors' responses to floral scents, experimentally examined in a mobile olfactometer. Thus, communication between plants and consumers via phytochemical signals reflects a significant part of the microstructure in a complex network. Negative as well as positive responses towards floral scents contributed to these results, where individual experience was important apart from innate behaviour. 4. Our results indicate that: (1) biological mechanisms have a profound impact on the microstructure of complex networks that underlies the outcome of aggregate statistics, and (2) floral scents act as a filter, promoting the visitation of some flower visitors, but also inhibiting the visitation of others.

Genetic variation for maternal effects on parasite susceptibility.

PubMed

Stjernman, M; Little, T J

2011-11-01

The expression of infectious disease is increasingly recognized to be impacted by maternal effects, where the environmental conditions experienced by mothers alter resistance to infection in offspring, independent of heritability. Here, we studied how maternal effects (high or low food availability to mothers) mediated the resistance of the crustacean Daphnia magna to its bacterial parasite Pasteuria ramosa. We sought to disentangle maternal effects from the effects of host genetic background by studying how maternal effects varied across 24 host genotypes sampled from a natural population. Under low-food conditions, females produced offspring that were relatively resistant, but this maternal effect varied strikingly between host genotypes, i.e. there were genotype by maternal environment interactions. As infection with P. ramosa causes a substantial reduction in host fecundity, this maternal effect had a large effect on host fitness. Maternal effects were also shown to impact parasite fitness, both because they prevented the establishment of the parasites and because even when parasites did establish in the offspring of poorly fed mothers, and they tended to grow more slowly. These effects indicate that food stress in the maternal generation can greatly influence parasite susceptibility and thus perhaps the evolution and coevolution of host-parasite interactions. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants.

PubMed

Hackenberg, Dieter; McKain, Michael R; Lee, Soon Goo; Roy Choudhury, Swarup; McCann, Tyler; Schreier, Spencer; Harkess, Alex; Pires, J Chris; Wong, Gane Ka-Shu; Jez, Joseph M; Kellogg, Elizabeth A; Pandey, Sona

2017-10-01

Signaling pathways regulated by heterotrimeric G-proteins exist in all eukaryotes. The regulator of G-protein signaling (RGS) proteins are key interactors and critical modulators of the Gα protein of the heterotrimer. However, while G-proteins are widespread in plants, RGS proteins have been reported to be missing from the entire monocot lineage, with two exceptions. A single amino acid substitution-based adaptive coevolution of the Gα:RGS proteins was proposed to enable the loss of RGS in monocots. We used a combination of evolutionary and biochemical analyses and homology modeling of the Gα and RGS proteins to address their expansion and its potential effects on the G-protein cycle in plants. Our results show that RGS proteins are widely distributed in the monocot lineage, despite their frequent loss. There is no support for the adaptive coevolution of the Gα:RGS protein pair based on single amino acid substitutions. RGS proteins interact with, and affect the activity of, Gα proteins from species with or without endogenous RGS. This cross-functional compatibility expands between the metazoan and plant kingdoms, illustrating striking conservation of their interaction interface. We propose that additional proteins or alternative mechanisms may exist which compensate for the loss of RGS in certain plant species. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Macroecological and macroevolutionary patterns of leaf herbivory across vascular plants.

PubMed

Turcotte, Martin M; Davies, T Jonathan; Thomsen, Christina J M; Johnson, Marc T J

2014-07-22

The consumption of plants by animals underlies important evolutionary and ecological processes in nature. Arthropod herbivory evolved approximately 415 Ma and the ensuing coevolution between plants and herbivores is credited with generating much of the macroscopic diversity on the Earth. In contemporary ecosystems, herbivory provides the major conduit of energy from primary producers to consumers. Here, we show that when averaged across all major lineages of vascular plants, herbivores consume 5.3% of the leaf tissue produced annually by plants, whereas previous estimates are up to 3.8× higher. This result suggests that for many plant species, leaf herbivory may play a smaller role in energy and nutrient flow than currently thought. Comparative analyses of a diverse global sample of 1058 species across 2085 populations reveal that models of stabilizing selection best describe rates of leaf consumption, and that rates vary substantially within and among major plant lineages. A key determinant of this variation is plant growth form, where woody plant species experience 64% higher leaf herbivory than non-woody plants. Higher leaf herbivory in woody species supports a key prediction of the plant apparency theory. Our study provides insight into how a long history of coevolution has shaped the ecological and evolutionary relationships between plants and herbivores. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Coevolution of adaptive technology, maladaptive culture and population size in a producer–scrounger game

PubMed Central

Lehmann, Laurent; Feldman, Marcus W.

2009-01-01

Technology (i.e. tools, methods of cultivation and domestication, systems of construction and appropriation, machines) has increased the vital rates of humans, and is one of the defining features of the transition from Malthusian ecological stagnation to a potentially perpetual rising population growth. Maladaptations, on the other hand, encompass behaviours, customs and practices that decrease the vital rates of individuals. Technology and maladaptations are part of the total stock of culture carried by the individuals in a population. Here, we develop a quantitative model for the coevolution of cumulative adaptive technology and maladaptive culture in a ‘producer–scrounger’ game, which can also usefully be interpreted as an ‘individual–social’ learner interaction. Producers (individual learners) are assumed to invent new adaptations and maladaptations by trial-and-error learning, insight or deduction, and they pay the cost of innovation. Scroungers (social learners) are assumed to copy or imitate (cultural transmission) both the adaptations and maladaptations generated by producers. We show that the coevolutionary dynamics of producers and scroungers in the presence of cultural transmission can have a variety of effects on population carrying capacity. From stable polymorphism, where scroungers bring an advantage to the population (increase in carrying capacity), to periodic cycling, where scroungers decrease carrying capacity, we find that selection-driven cultural innovation and transmission may send a population on the path of indefinite growth or to extinction. PMID:19692409

21CMMC with a 3D light-cone: the impact of the co-evolution approximation on the astrophysics of reionization and cosmic dawn

NASA Astrophysics Data System (ADS)

Greig, Bradley; Mesinger, Andrei

2018-07-01

We extend 21CMMC, a Monte Carlo Markov Chain sampler of 3D reionization simulations, to perform parameter estimation directly on 3D light-cones of the cosmic 21 cm signal. This brings theoretical analysis closer to the tomographic 21 cm observations achievable with next generation interferometers like the Hydrogen Epoch of Reionization Array and the Square Kilometre Array. Parameter recovery can therefore account for modes that evolve with redshift/frequency. Additionally, simulated data can be more easily corrupted to resemble real data. Using the light-cone version of 21CMMC, we quantify the biases in the recovered astrophysical parameters if we use the 21 cm power spectrum from the co-evolution approximation to fit a 3D light-cone mock observation. While ignoring the light-cone effect under most assumptions will not significantly bias the recovered astrophysical parameters, it can lead to an underestimation of the associated uncertainty. However, significant biases (˜few - 10σ) can occur if the 21 cm signal evolves rapidly (i.e. the epochs of reionization and heating overlap significantly), and (i) foreground removal is very efficient, allowing large physical scales (k ≲ 0.1 Mpc-1) to be used in the analysis or (ii) theoretical modelling is accurate to within ˜10 per cent in the power spectrum amplitude.

Coevolution of languages and genes on the island of Sumba, eastern Indonesia.

PubMed

Lansing, J Stephen; Cox, Murray P; Downey, Sean S; Gabler, Brandon M; Hallmark, Brian; Karafet, Tatiana M; Norquest, Peter; Schoenfelder, John W; Sudoyo, Herawati; Watkins, Joseph C; Hammer, Michael F

2007-10-09

Numerous studies indicate strong associations between languages and genes among human populations at the global scale, but all broader scale genetic and linguistic patterns must arise from processes originating at the community level. We examine linguistic and genetic variation in a contact zone on the eastern Indonesian island of Sumba, where Neolithic Austronesian farming communities settled and began interacting with aboriginal foraging societies approximately 3,500 years ago. Phylogenetic reconstruction based on a 200-word Swadesh list sampled from 29 localities supports the hypothesis that Sumbanese languages derive from a single ancestral Austronesian language. However, the proportion of cognates (words with a common origin) traceable to Proto-Austronesian (PAn) varies among language subgroups distributed across the island. Interestingly, a positive correlation was found between the percentage of Y chromosome lineages that derive from Austronesian (as opposed to aboriginal) ancestors and the retention of PAn cognates. We also find a striking correlation between the percentage of PAn cognates and geographic distance from the site where many Sumbanese believe their ancestors arrived on the island. These language-gene-geography correlations, unprecedented at such a fine scale, imply that historical patterns of social interaction between expanding farmers and resident hunter-gatherers largely explain community-level language evolution on Sumba. We propose a model to explain linguistic and demographic coevolution at fine spatial and temporal scales.

Inference, simulation, modeling, and analysis of complex networks, with special emphasis on complex networks in systems biology

NASA Astrophysics Data System (ADS)

Christensen, Claire Petra

Across diverse fields ranging from physics to biology, sociology, and economics, the technological advances of the past decade have engendered an unprecedented explosion of data on highly complex systems with thousands, if not millions of interacting components. These systems exist at many scales of size and complexity, and it is becoming ever-more apparent that they are, in fact, universal, arising in every field of study. Moreover, they share fundamental properties---chief among these, that the individual interactions of their constituent parts may be well-understood, but the characteristic behaviour produced by the confluence of these interactions---by these complex networks---is unpredictable; in a nutshell, the whole is more than the sum of its parts. There is, perhaps, no better illustration of this concept than the discoveries being made regarding complex networks in the biological sciences. In particular, though the sequencing of the human genome in 2003 was a remarkable feat, scientists understand that the "cellular-level blueprints" for the human being are cellular-level parts lists, but they say nothing (explicitly) about cellular-level processes. The challenge of modern molecular biology is to understand these processes in terms of the networks of parts---in terms of the interactions among proteins, enzymes, genes, and metabolites---as it is these processes that ultimately differentiate animate from inanimate, giving rise to life! It is the goal of systems biology---an umbrella field encapsulating everything from molecular biology to epidemiology in social systems---to understand processes in terms of fundamental networks of core biological parts, be they proteins or people. By virtue of the fact that there are literally countless complex systems, not to mention tools and techniques used to infer, simulate, analyze, and model these systems, it is impossible to give a truly comprehensive account of the history and study of complex systems. The author's own publications have contributed network inference, simulation, modeling, and analysis methods to the much larger body of work in systems biology, and indeed, in network science. The aim of this thesis is therefore twofold: to present this original work in the historical context of network science, but also to provide sufficient review and reference regarding complex systems (with an emphasis on complex networks in systems biology) and tools and techniques for their inference, simulation, analysis, and modeling, such that the reader will be comfortable in seeking out further information on the subject. The review-like Chapters 1, 2, and 4 are intended to convey the co-evolution of network science and the slow but noticeable breakdown of boundaries between disciplines in academia as research and comparison of diverse systems has brought to light the shared properties of these systems. It is the author's hope that theses chapters impart some sense of the remarkable and rapid progress in complex systems research that has led to this unprecedented academic synergy. Chapters 3 and 5 detail the author's original work in the context of complex systems research. Chapter 3 presents the methods and results of a two-stage modeling process that generates candidate gene-regulatory networks of the bacterium B.subtilis from experimentally obtained, yet mathematically underdetermined microchip array data. These networks are then analyzed from a graph theoretical perspective, and their biological viability is critiqued by comparing the networks' graph theoretical properties to those of other biological systems. The results of topological perturbation analyses revealing commonalities in behavior at multiple levels of complexity are also presented, and are shown to be an invaluable means by which to ascertain the level of complexity to which the network inference process is robust to noise. Chapter 5 outlines a learning algorithm for the development of a realistic, evolving social network (a city) into which a disease is introduced. The results of simulations in populations spanning two orders of magnitude are compared to prevaccine era measles data for England and Wales and demonstrate that the simulations are able to capture the quantitative and qualitative features of epidemics in populations as small as 10,000 people. The work presented in Chapter 5 validates the utility of network simulation in concurrently probing contact network dynamics and disease dynamics.

Assessing the potential for an ongoing arms race within and between the sexes: selection and heritable variation.

PubMed

Friberg, Urban; Lew, Timothy A; Byrne, Phillip G; Rice, William R

2005-07-01

In promiscuous species, sexual selection generates two opposing male traits: offense (acquiring new mates and supplanting stored sperm) and defense (enforcing fidelity on one's mates and preventing sperm displacement when this fails). Coevolution between these traits requires both additive genetic variation and associated natural selection. Previous work with Drosophila melanogaster found autosomal genetic variation for these traits among inbred lines from a mixture of populations, but only nonheritable genetic variation was found within a single outbred population. These results do not support ongoing antagonistic coevolution between offense and defense, nor between either of these male traits and female reproductive characters. Here we use a new method (hemiclonal analysis) to study genomewide genetic variation in a large outbred laboratory population of D. melanogaster. Hemiclonal analysis estimates the additive genetic variation among random, genomewide haplotypes taken from a large, outbred, locally adapted laboratory population and determines the direction of the selection gradient on this variation. In contrast to earlier studies, we found low but biologically significant heritable variation for defensive and offensive offspring production as well as all their components (P1, fidelity, P2, and remating). Genetic correlations between these traits were substantially different from those reported for inbred lines. A positive genetic correlation was found between defense and offense, demonstrating that some shared genes influence both traits. In addition to this common variation, evidence for unique genetic variation for each trait was also found, supporting an ongoing coevolutionary arms race between defense and offense. Reproductive conflict between males can strongly influence female fitness. Correspondingly, we found genetic variation in both defense and offense that affected female fitness. No evidence was found for intersexual conflict in the context of male defense, but we found substantial intersexual conflict in the context of male offensive sperm competitive ability. These results indicate that conflict between competing males also promotes an associated arms race between the sexes.

The Conundrum of Modern Art : Prestige-Driven Coevolutionary Aesthetics Trumps Evolutionary Aesthetics among Art Experts.

PubMed

Verpooten, Jan; Dewitte, Siegfried

2017-03-01

Two major mechanisms of aesthetic evolution have been suggested. One focuses on naturally selected preferences (Evolutionary Aesthetics), while the other describes a process of evaluative coevolution whereby preferences coevolve with signals. Signaling theory suggests that expertise moderates these mechanisms. In this article we set out to verify this hypothesis in the domain of art and use it to elucidate Western modern art's deviation from naturally selected preferences. We argue that this deviation is consistent with a Coevolutionary Aesthetics mechanism driven by prestige-biased social learning among art experts. In order to test this hypothesis, we conducted two studies in which we assessed the effects on lay and expert appreciation of both the biological relevance of the given artwork's depicted content, viz., facial beauty, and the prestige specific to the artwork's associated context (MoMA). We found that laypeople appreciate artworks based on their depictions of facial beauty, mediated by aesthetic pleasure, which is consistent with previous studies. In contrast, experts appreciate the artworks based on the prestige of the associated context, mediated by admiration for the artist. Moreover, experts appreciate artworks depicting neutral faces to a greater degree than artworks depicting attractive faces. These findings thus corroborate our contention that expertise moderates the Evolutionary and Coevolutionary Aesthetics mechanisms in the art domain. Furthermore, our findings provide initial support for our proposal that prestige-driven coevolution with expert evaluations plays a decisive role in modern art's deviation from naturally selected preferences. After discussing the limitations of our research as well as the relation that our results bear on cultural evolution theory, we provide a number of suggestions for further research into the potential functions of expert appreciation that deviates from naturally selected preferences, on the one hand, and expertise as a moderator of these mechanisms in other cultural domains, on the other.

Fast stochastic algorithm for simulating evolutionary population dynamics

NASA Astrophysics Data System (ADS)

Tsimring, Lev; Hasty, Jeff; Mather, William

2012-02-01

Evolution and co-evolution of ecological communities are stochastic processes often characterized by vastly different rates of reproduction and mutation and a coexistence of very large and very small sub-populations of co-evolving species. This creates serious difficulties for accurate statistical modeling of evolutionary dynamics. In this talk, we introduce a new exact algorithm for fast fully stochastic simulations of birth/death/mutation processes. It produces a significant speedup compared to the direct stochastic simulation algorithm in a typical case when the total population size is large and the mutation rates are much smaller than birth/death rates. We illustrate the performance of the algorithm on several representative examples: evolution on a smooth fitness landscape, NK model, and stochastic predator-prey system.

The common redstart as a suitable model to study cuckoo-host coevolution in a unique ecological context.

PubMed

Samaš, Peter; Rutila, Jarkko; Grim, Tomáš

2016-11-25

Co-evolutionary arms-races result in spatio-temporally dynamic relationships between interacting species, e.g., brood parasites and their avian hosts. However, majority of avian co-evolutionary studies are limited to "snap-shots" of a single breeding season in an open-nesting host. In a long-term study (11 breeding seasons), we explored a unique system between the brood parasitic common cuckoo (Cuculus canorus) and its host, the common redstart (Phoenicurus phoenicurus) which is exceptional among all cuckoo hosts due to being a cavity nester. Conditions in cavities are different from open nests, e.g., lower risks of predation, more favourable microclimate, increased risks of unsuccessful eviction of host offspring by the cuckoo nestling. Different conditions in cavities thus can be expected to shape parasite-host coevolution differently from what is typically studied in open nesting hosts. In our highly parasitised nest-box population (32.5%, n = 569 nests) only 35.7% of cuckoo eggs were laid into the nest cup and incubated by redstarts. Host nests shifted availability to later into the breeding season from 2006 to 2016 and cuckoos followed this trend by also shifting their timing of parasitism. Although previous studies revealed that redstarts selectively eject experimental non-mimetic eggs (desertion was not a specific response to foreign eggs), the hosts never ejected naturally-laid cuckoo eggs or cuckoo eggs cross-fostered into naturally non-parasitised nests. We solve the long-standing debate about the origin of cuckoo eggs found on the nest rim: we gained the first direct video-recording evidence that eggs found on the nest rim were mislaid by parasites and not ejected by hosts. Naturally-parasitised nests were deserted more often (18.6%) than control non-parasitized nests (5.6%) or nests artificially parasitised by us (1.4%). This suggests that the sight of the laying cuckoo female is the primary cue that triggers egg rejection (by desertion) in this host. Review of data from this and other study sites (10 populations, n = 853 experiments) demonstrates high variability in rejection rates and shows that populations facing higher parasitism rates reject parasitic eggs with higher frequencies. Surprisingly, cuckoo chicks either growing solitarily or with redstart chicks did not differ in their fledging success. We suggest that the redstart is an ideal model system to study the flexibility and limits of brood parasite-host co-evolution in an extreme ecological setting.

Human and Helicobacter pylori coevolution shapes the risk of gastric disease.

PubMed

Kodaman, Nuri; Pazos, Alvaro; Schneider, Barbara G; Piazuelo, M Blanca; Mera, Robertino; Sobota, Rafal S; Sicinschi, Liviu A; Shaffer, Carrie L; Romero-Gallo, Judith; de Sablet, Thibaut; Harder, Reed H; Bravo, Luis E; Peek, Richard M; Wilson, Keith T; Cover, Timothy L; Williams, Scott M; Correa, Pelayo

2014-01-28

Helicobacter pylori is the principal cause of gastric cancer, the second leading cause of cancer mortality worldwide. However, H. pylori prevalence generally does not predict cancer incidence. To determine whether coevolution between host and pathogen influences disease risk, we examined the association between the severity of gastric lesions and patterns of genomic variation in matched human and H. pylori samples. Patients were recruited from two geographically distinct Colombian populations with significantly different incidences of gastric cancer, but virtually identical prevalence of H. pylori infection. All H. pylori isolates contained the genetic signatures of multiple ancestries, with an ancestral African cluster predominating in a low-risk, coastal population and a European cluster in a high-risk, mountain population. The human ancestry of the biopsied individuals also varied with geography, with mostly African ancestry in the coastal region (58%), and mostly Amerindian ancestry in the mountain region (67%). The interaction between the host and pathogen ancestries completely accounted for the difference in the severity of gastric lesions in the two regions of Colombia. In particular, African H. pylori ancestry was relatively benign in humans of African ancestry but was deleterious in individuals with substantial Amerindian ancestry. Thus, coevolution likely modulated disease risk, and the disruption of coevolved human and H. pylori genomes can explain the high incidence of gastric disease in the mountain population.

Culture-gene coevolution of individualism-collectivism and the serotonin transporter gene.

PubMed

Chiao, Joan Y; Blizinsky, Katherine D

2010-02-22

Culture-gene coevolutionary theory posits that cultural values have evolved, are adaptive and influence the social and physical environments under which genetic selection operates. Here, we examined the association between cultural values of individualism-collectivism and allelic frequency of the serotonin transporter functional polymorphism (5-HTTLPR) as well as the role this culture-gene association may play in explaining global variability in prevalence of pathogens and affective disorders. We found evidence that collectivistic cultures were significantly more likely to comprise individuals carrying the short (S) allele of the 5-HTTLPR across 29 nations. Results further show that historical pathogen prevalence predicts cultural variability in individualism-collectivism owing to genetic selection of the S allele. Additionally, cultural values and frequency of S allele carriers negatively predict global prevalence of anxiety and mood disorder. Finally, mediation analyses further indicate that increased frequency of S allele carriers predicted decreased anxiety and mood disorder prevalence owing to increased collectivistic cultural values. Taken together, our findings suggest culture-gene coevolution between allelic frequency of 5-HTTLPR and cultural values of individualism-collectivism and support the notion that cultural values buffer genetically susceptible populations from increased prevalence of affective disorders. Implications of the current findings for understanding culture-gene coevolution of human brain and behaviour as well as how this coevolutionary process may contribute to global variation in pathogen prevalence and epidemiology of affective disorders, such as anxiety and depression, are discussed.

Co-Evolution.

ERIC Educational Resources Information Center

McGhee, Robert

2002-01-01

Discusses the role of techniques of DNA analysis in assessing the genetic relationships between various species. Focuses on wolf-dog evolution using DNA evidence and historical data about human/wolf-dog relationships. (DDR)

Modelling the co-evolution of indirect genetic effects and inherited variability.

PubMed

Marjanovic, Jovana; Mulder, Han A; Rönnegård, Lars; Bijma, Piter

2018-03-28

When individuals interact, their phenotypes may be affected not only by their own genes but also by genes in their social partners. This phenomenon is known as Indirect Genetic Effects (IGEs). In aquaculture species and some plants, however, competition not only affects trait levels of individuals, but also inflates variability of trait values among individuals. In the field of quantitative genetics, the variability of trait values has been studied as a quantitative trait in itself, and is often referred to as inherited variability. Such studies, however, consider only the genetic effect of the focal individual on trait variability and do not make a connection to competition. Although the observed phenotypic relationship between competition and variability suggests an underlying genetic relationship, the current quantitative genetic models of IGE and inherited variability do not allow for such a relationship. The lack of quantitative genetic models that connect IGEs to inherited variability limits our understanding of the potential of variability to respond to selection, both in nature and agriculture. Models of trait levels, for example, show that IGEs may considerably change heritable variation in trait values. Currently, we lack the tools to investigate whether this result extends to variability of trait values. Here we present a model that integrates IGEs and inherited variability. In this model, the target phenotype, say growth rate, is a function of the genetic and environmental effects of the focal individual and of the difference in trait value between the social partner and the focal individual, multiplied by a regression coefficient. The regression coefficient is a genetic trait, which is a measure of cooperation; a negative value indicates competition, a positive value cooperation, and an increasing value due to selection indicates the evolution of cooperation. In contrast to the existing quantitative genetic models, our model allows for co-evolution of IGEs and variability, as the regression coefficient can respond to selection. Our simulations show that the model results in increased variability of body weight with increasing competition. When competition decreases, i.e., cooperation evolves, variability becomes significantly smaller. Hence, our model facilitates quantitative genetic studies on the relationship between IGEs and inherited variability. Moreover, our findings suggest that we may have been overlooking an entire level of genetic variation in variability, the one due to IGEs.

Enemies with benefits: mutualistic interactions of viruses with lower eukaryotes.

PubMed

Jagdale, Shounak S; Joshi, Rakesh S

2018-04-01

Viruses represent some of the deadliest pathogens known to science. Recently they have been reported to have mutualistic interactions with their hosts, providing them direct or indirect benefits. The mutualism and symbiogenesis of such viruses with lower eukaryotic partners such as fungi, yeast, and insects have been reported but the full mechanism of interaction often remains an enigma. In many instances, these viral interactions provide resistance against several biotic and abiotic stresses, which could be the prime reason for the ecological success and positive selection of the hosts. These viruses modulate host metabolism and behavior, so both can obtain maximum benefits from the environment. They bring about micro- and macro-level changes in the hosts, benefiting their adaptation, reproduction, development, and survival. These virus-host interactions can be bilateral or tripartite with a variety of interacting partners. Exploration of these interactions can shed light on one of the well-coordinated biological phenomena of co-evolution and can be highly utilized for various applications in agriculture, fermentation and the pharmaceutical industries.

The Neomuran Revolution and Phagotrophic Origin of Eukaryotes and Cilia in the Light of Intracellular Coevolution and a Revised Tree of Life

PubMed Central

Cavalier-Smith, Thomas

2014-01-01

Three kinds of cells exist with increasingly complex membrane-protein targeting: Unibacteria (Archaebacteria, Posibacteria) with one cytoplasmic membrane (CM); Negibacteria with a two-membrane envelope (inner CM; outer membrane [OM]); eukaryotes with a plasma membrane and topologically distinct endomembranes and peroxisomes. I combine evidence from multigene trees, palaeontology, and cell biology to show that eukaryotes and archaebacteria are sisters, forming the clade neomura that evolved ∼1.2 Gy ago from a posibacterium, whose DNA segregation and cell division were destabilized by murein wall loss and rescued by the evolving novel neomuran endoskeleton, histones, cytokinesis, and glycoproteins. Phagotrophy then induced coevolving serial major changes making eukaryote cells, culminating in two dissimilar cilia via a novel gliding–fishing–swimming scenario. I transfer Chloroflexi to Posibacteria, root the universal tree between them and Heliobacteria, and argue that Negibacteria are a clade whose OM, evolving in a green posibacterium, was never lost. PMID:25183828

The neomuran revolution and phagotrophic origin of eukaryotes and cilia in the light of intracellular coevolution and a revised tree of life.

PubMed

Cavalier-Smith, Thomas

2014-09-02

Three kinds of cells exist with increasingly complex membrane-protein targeting: Unibacteria (Archaebacteria, Posibacteria) with one cytoplasmic membrane (CM); Negibacteria with a two-membrane envelope (inner CM; outer membrane [OM]); eukaryotes with a plasma membrane and topologically distinct endomembranes and peroxisomes. I combine evidence from multigene trees, palaeontology, and cell biology to show that eukaryotes and archaebacteria are sisters, forming the clade neomura that evolved ~1.2 Gy ago from a posibacterium, whose DNA segregation and cell division were destabilized by murein wall loss and rescued by the evolving novel neomuran endoskeleton, histones, cytokinesis, and glycoproteins. Phagotrophy then induced coevolving serial major changes making eukaryote cells, culminating in two dissimilar cilia via a novel gliding-fishing-swimming scenario. I transfer Chloroflexi to Posibacteria, root the universal tree between them and Heliobacteria, and argue that Negibacteria are a clade whose OM, evolving in a green posibacterium, was never lost. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Coevolutionary Free Lunches

NASA Technical Reports Server (NTRS)

Wolpert, David H.; Macready, William G.

2005-01-01

Recent work on the mathematical foundations of optimization has begun to uncover its rich structure. In particular, the "No Free Lunch" (NFL) theorems state that any two algorithms are equivalent when their performance is averaged across all possible problems. This highlights the need for exploiting problem-specific knowledge to achieve better than random performance. In this paper we present a general framework covering more search scenarios. In addition to the optimization scenarios addressed in the NFL results, this framework covers multi-armed bandit problems and evolution of multiple co-evolving players. As a particular instance of the latter, it covers "self-play" problems. In these problems the set of players work together to produce a champion, who then engages one or more antagonists in a subsequent multi-player game. In contrast to the traditional optimization case where the NFL results hold, we show that in self-play there are free lunches: in coevolution some algorithms have better performance than other algorithms, averaged across all possible problems. We consider the implications of these results to biology where there is no champion.

INTEGRATING PARASITES AND PATHOGENS INTO THE STUDY OF GEOGRAPHIC RANGE LIMITS.

PubMed

Bozick, Brooke A; Real, Leslie A

2015-12-01

The geographic distributions of all species are limited, and the determining factors that set these limits are of fundamental importance to the fields of ecology and evolutionary biology. Plant and animal ranges have been of primary concern, while those of parasites, which represent much of the Earth's biodiversity, have been neglected. Here, we review the determinants of the geographic ranges of parasites and pathogens, and explore how parasites provide novel systems with which to investigate the ecological and evolutionary processes governing host/parasite spatial distributions. Although there is significant overlap in the causative factors that determine range borders of parasites and free-living species, parasite distributions are additionally constrained by the geographic range and ecology of the host species' population, as well as by evolutionary factors that promote host-parasite coevolution. Recently, parasites have been used to infer population demographic and ecological information about their host organisms and we conclude that this strategy can be further exploited to understand geographic range limitations of both host and parasite populations.

Testing the Merger Paradigm: X-ray Observations of Radio-Selected Sub-Galactic-Scale Binary AGNs

NASA Astrophysics Data System (ADS)

Fu, Hai

2016-09-01

Interactions play an important role in galaxy evolution. Strong gas inflows are expected in the process of gas-rich mergers, which may fuel intense black hole accretion and star formation. Sub-galactic-scale binary/dual AGNs thus offer elegant laboratories to study the merger-driven co-evolution phase. However, previous samples of kpc-scale binaries are small and heterogeneous. We have identified a flux-limited sample of kpc-scale binary AGNs uniformly from a wide-area high-resolution radio survey conducted by the VLA. Here we propose Chandra X-ray characterization of a subset of four radio-confirmed binary AGNs at z 0.1. Our goal is to compare their X-ray properties with those of matched control samples to test the merger-driven co-evolution paradigm.

Testing for coevolutionary diversification: linking pattern with process.

PubMed

Althoff, David M; Segraves, Kari A; Johnson, Marc T J

2014-02-01

Coevolutionary diversification is cited as a major mechanism driving the evolution of diversity, particularly in plants and insects. However, tests of coevolutionary diversification have focused on elucidating macroevolutionary patterns rather than the processes giving rise to such patterns. Hence, there is weak evidence that coevolution promotes diversification. This is in part due to a lack of understanding about the mechanisms by which coevolution can cause speciation and the difficulty of integrating results across micro- and macroevolutionary scales. In this review, we highlight potential mechanisms of coevolutionary diversification, outline approaches to examine this process across temporal scales, and propose a set of minimal requirements for demonstrating coevolutionary diversification. Our aim is to stimulate research that tests more rigorously for coevolutionary diversification. Copyright © 2013 Elsevier Ltd. All rights reserved.

The influence of ignoring secondary structure on divergence time estimates from ribosomal RNA genes.

PubMed

Dohrmann, Martin

2014-02-01

Genes coding for ribosomal RNA molecules (rDNA) are among the most popular markers in molecular phylogenetics and evolution. However, coevolution of sites that code for pairing regions (stems) in the RNA secondary structure can make it challenging to obtain accurate results from such loci. While the influence of ignoring secondary structure on multiple sequence alignment and tree topology has been investigated in numerous studies, its effect on molecular divergence time estimates is still poorly known. Here, I investigate this issue in Bayesian Markov Chain Monte Carlo (BMCMC) and penalized likelihood (PL) frameworks, using empirical datasets from dragonflies (Odonata: Anisoptera) and glass sponges (Porifera: Hexactinellida). My results indicate that highly biased inferences under substitution models that ignore secondary structure only occur if maximum-likelihood estimates of branch lengths are used as input to PL dating, whereas in a BMCMC framework and in PL dating based on Bayesian consensus branch lengths, the effect is far less severe. I conclude that accounting for coevolution of paired sites in molecular dating studies is not as important as previously suggested, as long as the estimates are based on Bayesian consensus branch lengths instead of ML point estimates. This finding is especially relevant for studies where computational limitations do not allow the use of secondary-structure specific substitution models, or where accurate consensus structures cannot be predicted. I also found that the magnitude and direction (over- vs. underestimating node ages) of bias in age estimates when secondary structure is ignored was not distributed randomly across the nodes of the phylogenies, a phenomenon that requires further investigation. Copyright © 2013 Elsevier Inc. All rights reserved.

Multiscale Modeling of Human-Water Interactions: The Role of Time-Scales

NASA Astrophysics Data System (ADS)

Bloeschl, G.; Sivapalan, M.

2015-12-01

Much of the interest in hydrological modeling in the past decades revolved around resolving spatial variability. With the rapid changes brought about by human impacts on the hydrologic cycle, there is now an increasing need to refocus on time dependency. We present a co-evolutionary view of hydrologic systems, in which every part of the system including human systems, co-evolve, albeit at different rates. The resulting coupled human-nature system is framed as a dynamical system, characterized by interactions of fast and slow time scales and feedbacks between environmental and social processes. This gives rise to emergent phenomena such as the levee effect, adaptation to change and system collapse due to resource depletion. Changing human values play a key role in the emergence of these phenomena and should therefore be considered as internal to the system in a dynamic way. The co-evolutionary approach differs from the traditional view of water resource systems analysis as it allows for path dependence, multiple equilibria, lock-in situations and emergent phenomena. The approach may assist strategic water management for long time scales through facilitating stakeholder participation, exploring the possibility space of alternative futures, and helping to synthesise the observed dynamics of different case studies. Future research opportunities include the study of how changes in human values are connected to human-water interactions, historical analyses of trajectories of system co-evolution in individual places and comparative analyses of contrasting human-water systems in different climate and socio-economic settings. Reference Sivapalan, M. and G. Blöschl (2015) Time Scale Interactions and the Co-evolution of Humans and Water. Water Resour. Res., 51, in press.

Host shifts and evolutionary radiations of butterflies

PubMed Central

Fordyce, James A.

2010-01-01

Ehrlich and Raven proposed a model of coevolution where major host plant shifts of butterflies facilitate a burst of diversification driven by their arrival to a new adaptive zone. One prediction of this model is that reconstructions of historical diversification of butterflies should indicate an increase in diversification rate following major host shifts. Using reconstructed histories of 15 butterfly groups, I tested this prediction and found general agreement with Ehrlich and Raven's model. Butterfly lineages with an inferred major historical host shift showed evidence of diversification rate variation, with a significant acceleration following the host shift. Lineages without an inferred major host shift generally agreed with a constant-rate model of diversification. These results are consistent with the view that host plant associations have played a profound role in the evolutionary history of butterflies, and show that major shifts to chemically distinct plant groups leave a historical footprint that remains detectable today. PMID:20610430

Evolutionary disarmament in interspecific competition.

PubMed

Kisdi, E; Geritz, S A

2001-12-22

Competitive asymmetry, which is the advantage of having a larger body or stronger weaponry than a contestant, drives spectacular evolutionary arms races in intraspecific competition. Similar asymmetries are well documented in interspecific competition, yet they seldom lead to exaggerated traits. Here we demonstrate that two species with substantially different size may undergo parallel coevolution towards a smaller size under the same ecological conditions where a single species would exhibit an evolutionary arms race. We show that disarmament occurs for a wide range of parameters in an ecologically explicit model of competition for a single shared resource; disarmament also occurs in a simple Lotka-Volterra competition model. A key property of both models is the interplay between evolutionary dynamics and population density. The mechanism does not rely on very specific features of the model. Thus, evolutionary disarmament may be widespread and may help to explain the lack of interspecific arms races.

Evolutionary disarmament in interspecific competition.

PubMed Central

Kisdi, E.; Geritz, S. A.

2001-01-01

Competitive asymmetry, which is the advantage of having a larger body or stronger weaponry than a contestant, drives spectacular evolutionary arms races in intraspecific competition. Similar asymmetries are well documented in interspecific competition, yet they seldom lead to exaggerated traits. Here we demonstrate that two species with substantially different size may undergo parallel coevolution towards a smaller size under the same ecological conditions where a single species would exhibit an evolutionary arms race. We show that disarmament occurs for a wide range of parameters in an ecologically explicit model of competition for a single shared resource; disarmament also occurs in a simple Lotka-Volterra competition model. A key property of both models is the interplay between evolutionary dynamics and population density. The mechanism does not rely on very specific features of the model. Thus, evolutionary disarmament may be widespread and may help to explain the lack of interspecific arms races. PMID:11749715

Placement of attine ant-associated Pseudonocardia in a global Pseudonocardia phylogeny (Pseudonocardiaceae, Actinomycetales): a test of two symbiont-association models

PubMed Central

Mueller, Ulrich G.; Ishak, Heather; Lee, Jung C.; Sen, Ruchira; Gutell, Robin R.

2010-01-01

We reconstruct the phylogenetic relationships within the bacterial genus Pseudonocardia to evaluate two models explaining how and why Pseudonocardia bacteria colonize the microbial communities on the integument of fungus-gardening ant species (Attini, Formicidae). The traditional Coevolution-Codivergence model views the integument-colonizing Pseudonocardia as mutualistic microbes that are largely vertically transmitted between ant generations and that supply antibiotics that specifically suppress the garden pathogen Escovopsis. The more recent Acquisition model views Pseudonocardia as part of a larger integumental microbe community that frequently colonizes the ant integument from environmental sources (e.g., soil, plant material). Under this latter model, ant-associated Pseudonocardia may have diverse ecological roles on the ant integument (possibly ranging from pathogenic, to commensal, to mutualistic) and are not necessarily related to Escovopsis suppression. We test distinct predictions of these two models regarding the phylogenetic proximity of ant-associated and environmental Pseudonocardia. We amassed 16S-rRNA gene sequence information for 87 attine-associated and 238 environmental Pseudonocardia, aligned the sequences with the help of RNA secondary structure modeling, and reconstructed phylogenetic relationships using a maximum-likelihood approach. We present 16S-rRNA secondary structure models of representative Pseudonocardia species to improve sequence alignments and identify sequencing errors. Our phylogenetic analyses reveal close affinities and even identical sequence matches between environmental Pseudonocardia and ant-associated Pseudonocardia, as well as nesting of environmental Pseudonocardia in subgroups that were previously thought to be specialized to associate only with attine ants. The great majority of ant associated Pseudonocardia are closely related to autotrophic Pseudonocardia and are placed in a large subgroup of Pseudonocardia that is known essentially only from cultured isolates (rather than cloned 16S sequences). The preponderance of the known ant-associated Pseudonocardia in this latter clade of culturable lineages may not necessarily reflect abundance of these Pseudonocardia types on the ants, but isolation biases when screening for Pseudonocardia (e.g., preferential isolation of autotrophic Pseudonocardia with minimum-nutrient media). The accumulated phylogenetic patterns and the possibility of isolation biases in previous work further erode support for the traditional Coevolution-Codivergence model and calls for continued revision of our understanding how and why Pseudonocardia colonize the microbial communities on the integument of fungus-gardening ant species. PMID:20333466

Placement of attine ant-associated Pseudonocardia in a global Pseudonocardia phylogeny (Pseudonocardiaceae, Actinomycetales): a test of two symbiont-association models.

PubMed

Mueller, Ulrich G; Ishak, Heather; Lee, Jung C; Sen, Ruchira; Gutell, Robin R

2010-08-01

We reconstruct the phylogenetic relationships within the bacterial genus Pseudonocardia to evaluate two models explaining how and why Pseudonocardia bacteria colonize the microbial communities on the integument of fungus-gardening ant species (Attini, Formicidae). The traditional Coevolution-Codivergence model views the integument-colonizing Pseudonocardia as mutualistic microbes that are largely vertically transmitted between ant generations and that supply antibiotics that specifically suppress the garden pathogen Escovopsis. The more recent Acquisition model views Pseudonocardia as part of a larger integumental microbe community that frequently colonizes the ant integument from environmental sources (e.g., soil, plant material). Under this latter model, ant-associated Pseudonocardia may have diverse ecological roles on the ant integument (possibly ranging from pathogenic, to commensal, to mutualistic) and are not necessarily related to Escovopsis suppression. We test distinct predictions of these two models regarding the phylogenetic proximity of ant-associated and environmental Pseudonocardia. We amassed 16S-rRNA gene sequence information for 87 attine-associated and 238 environmental Pseudonocardia, aligned the sequences with the help of RNA secondary structure modeling, and reconstructed phylogenetic relationships using a maximum-likelihood approach. We present 16S-rRNA secondary structure models of representative Pseudonocardia species to improve sequence alignments and identify sequencing errors. Our phylogenetic analyses reveal close affinities and even identical sequence matches between environmental Pseudonocardia and ant-associated Pseudonocardia, as well as nesting of environmental Pseudonocardia in subgroups that were previously thought to be specialized to associate only with attine ants. The great majority of ant-associated Pseudonocardia are closely related to autotrophic Pseudonocardia and are placed in a large subgroup of Pseudonocardia that is known essentially only from cultured isolates (rather than cloned 16S sequences). The preponderance of the known ant-associated Pseudonocardia in this latter clade of culturable lineages may not necessarily reflect abundance of these Pseudonocardia types on the ants, but isolation biases when screening for Pseudonocardia (e.g., preferential isolation of autotrophic Pseudonocardia with minimum-nutrient media). The accumulated phylogenetic patterns and the possibility of isolation biases in previous work further erode support for the traditional Coevolution-Codivergence model and calls for continued revision of our understanding how and why Pseudonocardia colonize the microbial communities on the integument of fungus-gardening ant species.

Oxidative stress in cancer associated fibroblasts drives tumor-stroma co-evolution: A new paradigm for understanding tumor metabolism, the field effect and genomic instability in cancer cells.

PubMed

Martinez-Outschoorn, Ubaldo E; Balliet, Renee M; Rivadeneira, Dayana B; Chiavarina, Barbara; Pavlides, Stephanos; Wang, Chenguang; Whitaker-Menezes, Diana; Daumer, Kristin M; Lin, Zhao; Witkiewicz, Agnieszka K; Flomenberg, Neal; Howell, Anthony; Pestell, Richard G; Knudsen, Erik S; Sotgia, Federica; Lisanti, Michael P

2010-08-15

Loss of stromal fibroblast caveolin-1 (Cav-1) is a powerful single independent predictor of poor prognosis in human breast cancer patients, and is associated with early tumor recurrence, lymph node metastasis and tamoxifen-resistance. We developed a novel co-culture system to understand the mechanism(s) by which a loss of stromal fibroblast Cav-1 induces a "lethal tumor micro-environment." Here, we propose a new paradigm to explain the powerful prognostic value of stromal Cav-1. In this model, cancer cells induce oxidative stress in cancer-associated fibroblasts, which then acts as a "metabolic" and "mutagenic" motor to drive tumor-stroma co-evolution, DNA damage and aneuploidy in cancer cells. More specifically, we show that an acute loss of Cav-1 expression leads to mitochondrial dysfunction, oxidative stress and aerobic glycolysis in cancer associated fibroblasts. Also, we propose that defective mitochondria are removed from cancer-associated fibroblasts by autophagy/mitophagy that is induced by oxidative stress. As a consequence, cancer associated fibroblasts provide nutrients (such as lactate) to stimulate mitochondrial biogenesis and oxidative metabolism in adjacent cancer cells (the "Reverse Warburg Effect"). We provide evidence that oxidative stress in cancer-associated fibroblasts is sufficient to induce genomic instability in adjacent cancer cells, via a bystander effect, potentially increasing their aggressive behavior. Finally, we directly demonstrate that nitric oxide (NO) over-production, secondary to Cav-1 loss, is the root cause for mitochondrial dysfunction in cancer associated fibroblasts. In support of this notion, treatment with anti-oxidants (such as N-acetyl-cysteine, metformin and quercetin) or NO inhibitors (L-NAME) was sufficient to reverse many of the cancer-associated fibroblast phenotypes that we describe. Thus, cancer cells use "oxidative stress" in adjacent fibroblasts (i) as an "engine" to fuel their own survival via the stromal production of nutrients and (ii) to drive their own mutagenic evolution towards a more aggressive phenotype, by promoting genomic instability. We also present evidence that the "field effect" in cancer biology could also be related to the stromal production of ROS and NO species. eNOS-expressing fibroblasts have the ability to downregulate Cav-1 and induce mitochondrial dysfunction in adjacent fibroblasts that do not express eNOS. As such, the effects of stromal oxidative stress can be laterally propagated, amplified and are effectively "contagious"--spread from cell-to-cell like a virus--creating an "oncogenic/mutagenic" field promoting widespread DNA damage.

Coevolution between Hispaniolan crossbills and pine: does more time allow for greater phenotypic escalation at lower latitude?

PubMed

Parchman, Thomas L; Benkman, Craig W; Mezquida, Eduardo T

2007-09-01

Crossbills (Aves: Loxia) and several conifers have coevolved in predator-prey arms races over the last 10,000 years. However, the extent to which coevolutionary arms races have contributed to the adaptive radiation of crossbills or to any other adaptive radiation is largely unknown. Here we extend our previous studies of geographically structured coevolution by considering a crossbill-conifer interaction that has persisted for a much longer time period and involves a conifer with more variable annual seed production. We examined geographic variation in the cone and seed traits of two sister species of pines, Pinus occidentalis and P. cubensis, on the islands of Hispaniola and Cuba, respectively. We also compared the Hispaniolan crossbill (Loxia megaplaga) to its sister taxa the North American white-winged crossbill (Loxia leucoptera leucoptera). The Hispaniolan crossbill is endemic to Hispaniola whereas Cuba lacks crossbills. In addition and in contrast to previous studies, the variation in selection experienced by these pines due to crossbills is not confounded by the occurrence of selection by tree squirrels (Tamiasciurus and Sciurus). As predicted if P. occidentalis has evolved defenses in response to selection exerted by crossbills, cones of P. occidentalis have scales that are 53% thicker than those of P. cubensis. Cones of P. occidentalis, but not P. cubensis, also have well-developed spines, a known defense against vertebrate seed predators. Consistent with patterns of divergence seen in crossbills coevolving locally with other conifers, the Hispaniolan crossbill has evolved a bill that is 25% deeper than the white-winged crossbill. Together with phylogenetic analyses, our results suggest that predator-prey coevolution between Hispaniolan crossbills and P. occidentalis over approximately 600,000 years has caused substantial morphological evolution in both the crossbill and pine. This also indicates that cone crop fluctuations do not prevent crossbills and conifers from coevolving. Furthermore, because the traits at the phenotypic interface of the interaction apparently remain the same over at least several hundred thousand years, divergence as a result of coevolution is greater at lower latitude where crossbill-conifer interactions have been less interrupted by Pleistocene events.

Phylogenetically informed logic relationships improve detection of biological network organization

PubMed Central

2011-01-01

Background A "phylogenetic profile" refers to the presence or absence of a gene across a set of organisms, and it has been proven valuable for understanding gene functional relationships and network organization. Despite this success, few studies have attempted to search beyond just pairwise relationships among genes. Here we search for logic relationships involving three genes, and explore its potential application in gene network analyses. Results Taking advantage of a phylogenetic matrix constructed from the large orthologs database Roundup, we invented a method to create balanced profiles for individual triplets of genes that guarantee equal weight on the different phylogenetic scenarios of coevolution between genes. When we applied this idea to LAPP, the method to search for logic triplets of genes, the balanced profiles resulted in significant performance improvement and the discovery of hundreds of thousands more putative triplets than unadjusted profiles. We found that logic triplets detected biological network organization and identified key proteins and their functions, ranging from neighbouring proteins in local pathways, to well separated proteins in the whole pathway, and to the interactions among different pathways at the system level. Finally, our case study suggested that the directionality in a logic relationship and the profile of a triplet could disclose the connectivity between the triplet and surrounding networks. Conclusion Balanced profiles are superior to the raw profiles employed by traditional methods of phylogenetic profiling in searching for high order gene sets. Gene triplets can provide valuable information in detection of biological network organization and identification of key genes at different levels of cellular interaction. PMID:22172058

Early human communication helps in understanding language evolution.

PubMed

Lenti Boero, Daniela

2014-12-01

Building a theory on extant species, as Ackermann et al. do, is a useful contribution to the field of language evolution. Here, I add another living model that might be of interest: human language ontogeny in the first year of life. A better knowledge of this phase might help in understanding two more topics among the "several building blocks of a comprehensive theory of the evolution of spoken language" indicated in their conclusion by Ackermann et al., that is, the foundation of the co-evolution of linguistic motor skills with the auditory skills underlying speech perception, and the possible phylogenetic interactions of protospeech production with referential capabilities.

Modelling brain emergent behaviours through coevolution of neural agents.

PubMed

Maniadakis, Michail; Trahanias, Panos

2006-06-01

Recently, many research efforts focus on modelling partial brain areas with the long-term goal to support cognitive abilities of artificial organisms. Existing models usually suffer from heterogeneity, which constitutes their integration very difficult. The present work introduces a computational framework to address brain modelling tasks, emphasizing on the integrative performance of substructures. Moreover, implemented models are embedded in a robotic platform to support its behavioural capabilities. We follow an agent-based approach in the design of substructures to support the autonomy of partial brain structures. Agents are formulated to allow the emergence of a desired behaviour after a certain amount of interaction with the environment. An appropriate collaborative coevolutionary algorithm, able to emphasize both the speciality of brain areas and their cooperative performance, is employed to support design specification of agent structures. The effectiveness of the proposed approach is illustrated through the implementation of computational models for motor cortex and hippocampus, which are successfully tested on a simulated mobile robot.

ComplexContact: a web server for inter-protein contact prediction using deep learning.

PubMed

Zeng, Hong; Wang, Sheng; Zhou, Tianming; Zhao, Feifeng; Li, Xiufeng; Wu, Qing; Xu, Jinbo

2018-05-22

ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pair of protein sequences, ComplexContact first searches for their sequence homologs and builds two paired multiple sequence alignments (MSA), then it applies co-evolution analysis and a CASP-winning deep learning (DL) method to predict interfacial contacts from paired MSAs and visualizes the prediction as an image. The DL method was originally developed for intra-protein contact prediction and performed the best in CASP12. Our large-scale experimental test further shows that ComplexContact greatly outperforms pure co-evolution methods for inter-protein contact prediction, regardless of the species.

Cross-Resistance: A Consequence of Bi-partite Host-Parasite Coevolution

PubMed Central

Joop, Gerrit

2018-01-01

Host-parasite coevolution can influence interactions of the host and parasite with the wider ecological community. One way that this may manifest is in cross-resistance towards other parasites, which has been observed to occur in some host-parasite evolution experiments. In this paper, we test for cross-resistance towards Bacillus thuringiensis and Pseudomonas entomophila in the red flour beetle Tribolium castaneum, which was previously allowed to coevolve with the generalist entomopathogenic fungus Beauveria bassiana. We combine survival and gene expression assays upon infection to test for cross-resistance and underlying mechanisms. We show that larvae of T. castaneum that evolved with B. bassiana under coevolutionary conditions were positively cross-resistant to the bacterium B. thuringiensis, but not P. entomophila. Positive cross-resistance was mirrored at the gene expression level with markers that were representative of the oral route of infection being upregulated upon B. bassiana exposure. We find that positive cross-resistance towards B. thuringiensis evolved in T. castaneum as a consequence of its coevolutionary interactions with B. bassiana. This cross-resistance appears to be a consequence of resistance to oral toxicity. The fact that coevolution with B. bassiana results in resistance to B. thuringiensis, but not P. entomophila implies that B. thuringiensis and B. bassiana may share mechanisms of infection or toxicity not shared by P. entomophila. This supports previous suggestions that B. bassiana may possess Cry-like toxins, similar to those found in B. thuringiensis, which allow it to infect orally. PMID:29495405

Detecting Coevolution in Mammalian Sperm–Egg Fusion Proteins

PubMed Central

CLAW, KATRINA G.; GEORGE, RENEE D.; SWANSON, WILLIE J.

2018-01-01

SUMMARY Interactions between sperm and egg proteins can occur physically between gamete surface-binding proteins, and genetically between gamete proteins that work in complementary pathways in which they may not physically interact. Physically interacting sperm–egg proteins have been functionally identified in only a few species, and none have been verified within mammals. Candidate genes on both the sperm and egg surfaces exist, but gene deletion studies do not support functional interactions between these sperm–egg proteins; interacting sperm–egg proteins thus remain elusive. Cooperative gamete proteins undergo rapid evolution, and it is predicted that these sperm–egg proteins will also have correlated evolutionary rates due to compensatory changes on both the sperm and egg. To explore potential physical and genetic interactions in sperm–egg proteins, we sequenced four candidate genes from diverse primate species, and used regression and likelihood methods to test for signatures of coevolution between sperm–egg gene pairs. With both methods, we found that the egg protein CD9 coevolves with the sperm protein IZUMO1, suggesting a physical or genetic interaction occurs between them. With regression analysis, we found that CD9 and CRISP2 have correlated rates of evolution, and with likelihood analysis, that CD9 and CRISP1 have correlated rates. This suggests that the different tests may reflect different levels of interaction, be it physical or genetic. Coevolution tests thus provide an exploratory method for detecting potentially interacting sperm–egg protein pairs. PMID:24644026

Detecting coevolution in mammalian sperm-egg fusion proteins.

PubMed

Claw, Katrina G; George, Renee D; Swanson, Willie J

2014-06-01

Interactions between sperm and egg proteins can occur physically between gamete surface-binding proteins, and genetically between gamete proteins that work in complementary pathways in which they may not physically interact. Physically interacting sperm-egg proteins have been functionally identified in only a few species, and none have been verified within mammals. Candidate genes on both the sperm and egg surfaces exist, but gene deletion studies do not support functional interactions between these sperm-egg proteins; interacting sperm-egg proteins thus remain elusive. Cooperative gamete proteins undergo rapid evolution, and it is predicted that these sperm-egg proteins will also have correlated evolutionary rates due to compensatory changes on both the sperm and egg. To explore potential physical and genetic interactions in sperm-egg proteins, we sequenced four candidate genes from diverse primate species, and used regression and likelihood methods to test for signatures of coevolution between sperm-egg gene pairs. With both methods, we found that the egg protein CD9 coevolves with the sperm protein IZUMO1, suggesting a physical or genetic interaction occurs between them. With regression analysis, we found that CD9 and CRISP2 have correlated rates of evolution, and with likelihood analysis, that CD9 and CRISP1 have correlated rates. This suggests that the different tests may reflect different levels of interaction, be it physical or genetic. Coevolution tests thus provide an exploratory method for detecting potentially interacting sperm-egg protein pairs. © 2014 Wiley Periodicals, Inc.

Culture–gene coevolution of individualism–collectivism and the serotonin transporter gene

PubMed Central

Chiao, Joan Y.; Blizinsky, Katherine D.

2010-01-01

Culture–gene coevolutionary theory posits that cultural values have evolved, are adaptive and influence the social and physical environments under which genetic selection operates. Here, we examined the association between cultural values of individualism–collectivism and allelic frequency of the serotonin transporter functional polymorphism (5-HTTLPR) as well as the role this culture–gene association may play in explaining global variability in prevalence of pathogens and affective disorders. We found evidence that collectivistic cultures were significantly more likely to comprise individuals carrying the short (S) allele of the 5-HTTLPR across 29 nations. Results further show that historical pathogen prevalence predicts cultural variability in individualism–collectivism owing to genetic selection of the S allele. Additionally, cultural values and frequency of S allele carriers negatively predict global prevalence of anxiety and mood disorder. Finally, mediation analyses further indicate that increased frequency of S allele carriers predicted decreased anxiety and mood disorder prevalence owing to increased collectivistic cultural values. Taken together, our findings suggest culture–gene coevolution between allelic frequency of 5-HTTLPR and cultural values of individualism–collectivism and support the notion that cultural values buffer genetically susceptible populations from increased prevalence of affective disorders. Implications of the current findings for understanding culture–gene coevolution of human brain and behaviour as well as how this coevolutionary process may contribute to global variation in pathogen prevalence and epidemiology of affective disorders, such as anxiety and depression, are discussed. PMID:19864286

Watershed System Model: The Essentials to Model Complex Human-Nature System at the River Basin Scale

NASA Astrophysics Data System (ADS)

Li, Xin; Cheng, Guodong; Lin, Hui; Cai, Ximing; Fang, Miao; Ge, Yingchun; Hu, Xiaoli; Chen, Min; Li, Weiyue

2018-03-01

Watershed system models are urgently needed to understand complex watershed systems and to support integrated river basin management. Early watershed modeling efforts focused on the representation of hydrologic processes, while the next-generation watershed models should represent the coevolution of the water-land-air-plant-human nexus in a watershed and provide capability of decision-making support. We propose a new modeling framework and discuss the know-how approach to incorporate emerging knowledge into integrated models through data exchange interfaces. We argue that the modeling environment is a useful tool to enable effective model integration, as well as create domain-specific models of river basin systems. The grand challenges in developing next-generation watershed system models include but are not limited to providing an overarching framework for linking natural and social sciences, building a scientifically based decision support system, quantifying and controlling uncertainties, and taking advantage of new technologies and new findings in the various disciplines of watershed science. The eventual goal is to build transdisciplinary, scientifically sound, and scale-explicit watershed system models that are to be codesigned by multidisciplinary communities.

Coevolutionary diversification creates nested-modular structure in phage–bacteria interaction networks

PubMed Central

Beckett, Stephen J.; Williams, Hywel T. P.

2013-01-01

Phage and their bacterial hosts are the most diverse and abundant biological entities in the oceans, where their interactions have a major impact on marine ecology and ecosystem function. The structure of interaction networks for natural phage–bacteria communities offers insight into their coevolutionary origin. At small phylogenetic scales, observed communities typically show a nested structure, in which both hosts and phages can be ranked by their range of resistance and infectivity, respectively. A qualitatively different multi-scale structure is seen at larger phylogenetic scales; a natural assemblage sampled from the Atlantic Ocean displays large-scale modularity and local nestedness within each module. Here, we show that such ‘nested-modular’ interaction networks can be produced by a simple model of host–phage coevolution in which infection depends on genetic matching. Negative frequency-dependent selection causes diversification of hosts (to escape phages) and phages (to track their evolving hosts). This creates a diverse community of bacteria and phage, maintained by kill-the-winner ecological dynamics. When the resulting communities are visualized as bipartite networks of who infects whom, they show the nested-modular structure characteristic of the Atlantic sample. The statistical significance and strength of this observation varies depending on whether the interaction networks take into account the density of the interacting strains, with implications for interpretation of interaction networks constructed by different methods. Our results suggest that the apparently complex community structures associated with marine bacteria and phage may arise from relatively simple coevolutionary origins. PMID:24516719

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

PubMed Central

2011-01-01

Background Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. Results A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae) unigenes (median coverage of 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed. Conclusions The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives. This study represents a first step in the development of a community resource for further study of plant-insect co-evolution, anti-herbivore defense, floral developmental genetics, reproductive biology, chemical evolution, population genetics, and comparative genomics using milkweeds, and A. syriaca in particular, as ecological and evolutionary models. PMID:21542930

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing.

PubMed

Straub, Shannon C K; Fishbein, Mark; Livshultz, Tatyana; Foster, Zachary; Parks, Matthew; Weitemier, Kevin; Cronn, Richard C; Liston, Aaron

2011-05-04

Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae) unigenes (median coverage of 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed. The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives. This study represents a first step in the development of a community resource for further study of plant-insect co-evolution, anti-herbivore defense, floral developmental genetics, reproductive biology, chemical evolution, population genetics, and comparative genomics using milkweeds, and A. syriaca in particular, as ecological and evolutionary models.

Experimental viral evolution to specific host MHC genotypes reveals fitness and virulence trade-offs in alternative MHC types.

PubMed

Kubinak, Jason L; Ruff, James S; Hyzer, Cornelius Whitney; Slev, Patricia R; Potts, Wayne K

2012-02-28

The unprecedented genetic diversity found at vertebrate MHC (major histocompatibility complex) loci influences susceptibility to most infectious and autoimmune diseases. The evolutionary explanation for how these polymorphisms are maintained has been controversial. One leading explanation, antagonistic coevolution (also known as the Red Queen), postulates a never-ending molecular arms race where pathogens evolve to evade immune recognition by common MHC alleles, which in turn provides a selective advantage to hosts carrying rare MHC alleles. This cyclical process leads to negative frequency-dependent selection and promotes MHC diversity if two conditions are met: (i) pathogen adaptation must produce trade-offs that result in pathogen fitness being higher in familiar (i.e., host MHC genotype adapted to) vs. unfamiliar host MHC genotypes; and (ii) this adaptation must produce correlated patterns of virulence (i.e., disease severity). Here we test these fundamental assumptions using an experimental evolutionary approach (serial passage). We demonstrate rapid adaptation and virulence evolution of a mouse-specific retrovirus to its mammalian host across multiple MHC genotypes. Critically, this adaptive response results in trade-offs (i.e., antagonistic pleiotropy) between host MHC genotypes; both viral fitness and virulence is substantially higher in familiar versus unfamiliar MHC genotypes. These data are unique in experimentally confirming the requisite conditions of the antagonistic coevolution model of MHC evolution and providing quantification of fitness effects for pathogen and host. These data help explain the unprecedented diversity of MHC genes, including how disease-causing alleles are maintained.

Lessons from (co-)evolution in the docking of proteins and peptides for CAPRI Rounds 28-35.

PubMed

Yu, Jinchao; Andreani, Jessica; Ochsenbein, Françoise; Guerois, Raphaël

2017-03-01

Computational protein-protein docking is of great importance for understanding protein interactions at the structural level. Critical assessment of prediction of interactions (CAPRI) experiments provide the protein docking community with a unique opportunity to blindly test methods based on real-life cases and help accelerate methodology development. For CAPRI Rounds 28-35, we used an automatic docking pipeline integrating the coarse-grained co-evolution-based potential InterEvScore. This score was developed to exploit the information contained in the multiple sequence alignments of binding partners and selectively recognize co-evolved interfaces. Together with Zdock/Frodock for rigid-body docking, SOAP-PP for atomic potential and Rosetta applications for structural refinement, this pipeline reached high performance on a majority of targets. For protein-peptide docking and interfacial water position predictions, we also explored different means of taking evolutionary information into account. Overall, our group ranked 1 st by correctly predicting 10 targets, composed of 1 High, 7 Medium and 2 Acceptable predictions. Excellent and Outstanding levels of accuracy were reached for each of the two water prediction targets, respectively. Altogether, in 15 out of 18 targets in total, evolutionary information, either through co-evolution or conservation analyses, could provide key constraints to guide modeling towards the most likely assemblies. These results open promising perspectives regarding the way evolutionary information can be valuable to improve docking prediction accuracy. Proteins 2017; 85:378-390. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Long-Term and Short-Term Evolutionary Impacts of Transposable Elements on Drosophila

PubMed Central

Lee, Yuh Chwen G.; Langley, Charles H.

2012-01-01

Transposable elements (TEs) are considered to be genomic parasites and their interactions with their hosts have been likened to the coevolution between host and other nongenomic, horizontally transferred pathogens. TE families, however, are vertically inherited as integral segments of the nuclear genome. This transmission strategy has been suggested to weaken the selective benefits of host alleles repressing the transposition of specific TE variants. On the other hand, the elevated rates of TE transposition and high incidences of deleterious mutations observed during the rare cases of horizontal transfers of TE families between species could create at least a transient process analogous to the influence of horizontally transmitted pathogens. Here, we formally address this analogy, using empirical and theoretical analysis to specify the mechanism of how host–TE interactions may drive the evolution of host genes. We found that host TE-interacting genes actually have more pervasive evidence of adaptive evolution than immunity genes that interact with nongenomic pathogens in Drosophila. Yet, both our theoretical modeling and empirical observations comparing Drosophila melanogaster populations before and after the horizontal transfer of P elements, which invaded D. melanogaster early last century, demonstrated that horizontally transferred TEs have only a limited influence on host TE-interacting genes. We propose that the more prevalent and constant interaction with multiple vertically transmitted TE families may instead be the main force driving the fast evolution of TE-interacting genes, which is fundamentally different from the gene-for-gene interaction of host–pathogen coevolution. PMID:22997235

Are elicitins cryptograms in plant-Oomycete communications?

PubMed

Ponchet, M; Panabières, F; Milat M-L; Mikes, V; Montillet, J L; Suty, L; Triantaphylides, C; Tirilly, Y; Blein, J P

1999-12-01

Stimulation of plant natural defenses is an important challenge in phytoprotection prospects. In that context, elicitins, which are small proteins secreted by Phytophthora and Pythium species, have been shown to induce a hypersensitive-like reaction in tobacco plants. Moreover, these plants become resistant to their pathogens, and thus this interaction constitutes an excellent model to investigate the signaling pathways leading to plant resistance. However, most plants are not reactive to elicitins, although they possess the functional signaling pathways involved in tobacco responses to elicitin. The understanding of factors involved in this reactivity is needed to develop agronomic applications. In this review, it is proposed that elicitins could interact with regulating cell wall proteins before they reach the plasma membrane. Consequently, the plant reactivity or nonreactivity status could result from the equilibrium reached during this interaction. The possibility of overexpressing the elicitins directly from genomic DNA in Pichia pastoris allows site-directed mutagenesis experiments and structure/function studies. The recent discovery of the sterol carrier activity of elicitins brings a new insight on their molecular activity. This constitutes a crucial property, since the formation of a sterol-elicitin complex is required to trigger the biological responses of tobacco cells and plants. Only the elicitins loaded with a sterol are able to bind to their plasmalemma receptor, which is assumed to be an allosteric calcium channel. Moreover, Phytophthora and Pythium do not synthesize the sterols required for their growth and their fructification, and elicitins may act as shuttles trapping the sterols from the host plants. Sequence analysis of elicitin genes from several Phytophthora species sheds unexpected light on the phylogenetic relationships among the genus, and suggests that the expression of elicitins is under tight regulatory control. Finally, general involvement of these lipid transfer proteins in the biology of Pythiaceae, and in plant defense responses, is discussed. A possible scheme for the coevolution between Phytophthora and tobacco plants is approached.

Network Dynamics of Innovation Processes.

PubMed

Iacopini, Iacopo; Milojević, Staša; Latora, Vito

2018-01-26

We introduce a model for the emergence of innovations, in which cognitive processes are described as random walks on the network of links among ideas or concepts, and an innovation corresponds to the first visit of a node. The transition matrix of the random walk depends on the network weights, while in turn the weight of an edge is reinforced by the passage of a walker. The presence of the network naturally accounts for the mechanism of the "adjacent possible," and the model reproduces both the rate at which novelties emerge and the correlations among them observed empirically. We show this by using synthetic networks and by studying real data sets on the growth of knowledge in different scientific disciplines. Edge-reinforced random walks on complex topologies offer a new modeling framework for the dynamics of correlated novelties and are another example of coevolution of processes and networks.

Network Dynamics of Innovation Processes

NASA Astrophysics Data System (ADS)

Iacopini, Iacopo; Milojević, Staša; Latora, Vito

2018-01-01

We introduce a model for the emergence of innovations, in which cognitive processes are described as random walks on the network of links among ideas or concepts, and an innovation corresponds to the first visit of a node. The transition matrix of the random walk depends on the network weights, while in turn the weight of an edge is reinforced by the passage of a walker. The presence of the network naturally accounts for the mechanism of the "adjacent possible," and the model reproduces both the rate at which novelties emerge and the correlations among them observed empirically. We show this by using synthetic networks and by studying real data sets on the growth of knowledge in different scientific disciplines. Edge-reinforced random walks on complex topologies offer a new modeling framework for the dynamics of correlated novelties and are another example of coevolution of processes and networks.

Evolutionary fuzzy modeling human diagnostic decisions.

PubMed

Peña-Reyes, Carlos Andrés

2004-05-01

Fuzzy CoCo is a methodology, combining fuzzy logic and evolutionary computation, for constructing systems able to accurately predict the outcome of a human decision-making process, while providing an understandable explanation of the underlying reasoning. Fuzzy logic provides a formal framework for constructing systems exhibiting both good numeric performance (accuracy) and linguistic representation (interpretability). However, fuzzy modeling--meaning the construction of fuzzy systems--is an arduous task, demanding the identification of many parameters. To solve it, we use evolutionary computation techniques (specifically cooperative coevolution), which are widely used to search for adequate solutions in complex spaces. We have successfully applied the algorithm to model the decision processes involved in two breast cancer diagnostic problems, the WBCD problem and the Catalonia mammography interpretation problem, obtaining systems both of high performance and high interpretability. For the Catalonia problem, an evolved system was embedded within a Web-based tool-called COBRA-for aiding radiologists in mammography interpretation.

Cooperative Coevolution with Formula-Based Variable Grouping for Large-Scale Global Optimization.

PubMed

Wang, Yuping; Liu, Haiyan; Wei, Fei; Zong, Tingting; Li, Xiaodong

2017-08-09

For a large-scale global optimization (LSGO) problem, divide-and-conquer is usually considered an effective strategy to decompose the problem into smaller subproblems, each of which can then be solved individually. Among these decomposition methods, variable grouping is shown to be promising in recent years. Existing variable grouping methods usually assume the problem to be black-box (i.e., assuming that an analytical model of the objective function is unknown), and they attempt to learn appropriate variable grouping that would allow for a better decomposition of the problem. In such cases, these variable grouping methods do not make a direct use of the formula of the objective function. However, it can be argued that many real-world problems are white-box problems, that is, the formulas of objective functions are often known a priori. These formulas of the objective functions provide rich information which can then be used to design an effective variable group method. In this article, a formula-based grouping strategy (FBG) for white-box problems is first proposed. It groups variables directly via the formula of an objective function which usually consists of a finite number of operations (i.e., four arithmetic operations "[Formula: see text]", "[Formula: see text]", "[Formula: see text]", "[Formula: see text]" and composite operations of basic elementary functions). In FBG, the operations are classified into two classes: one resulting in nonseparable variables, and the other resulting in separable variables. In FBG, variables can be automatically grouped into a suitable number of non-interacting subcomponents, with variables in each subcomponent being interdependent. FBG can easily be applied to any white-box problem and can be integrated into a cooperative coevolution framework. Based on FBG, a novel cooperative coevolution algorithm with formula-based variable grouping (so-called CCF) is proposed in this article for decomposing a large-scale white-box problem into several smaller subproblems and optimizing them respectively. To further enhance the efficiency of CCF, a new local search scheme is designed to improve the solution quality. To verify the efficiency of CCF, experiments are conducted on the standard LSGO benchmark suites of CEC'2008, CEC'2010, CEC'2013, and a real-world problem. Our results suggest that the performance of CCF is very competitive when compared with those of the state-of-the-art LSGO algorithms.

Macroscopic description of complex adaptive networks coevolving with dynamic node states

NASA Astrophysics Data System (ADS)

Wiedermann, Marc; Donges, Jonathan F.; Heitzig, Jobst; Lucht, Wolfgang; Kurths, Jürgen

2015-05-01

In many real-world complex systems, the time evolution of the network's structure and the dynamic state of its nodes are closely entangled. Here we study opinion formation and imitation on an adaptive complex network which is dependent on the individual dynamic state of each node and vice versa to model the coevolution of renewable resources with the dynamics of harvesting agents on a social network. The adaptive voter model is coupled to a set of identical logistic growth models and we mainly find that, in such systems, the rate of interactions between nodes as well as the adaptive rewiring probability are crucial parameters for controlling the sustainability of the system's equilibrium state. We derive a macroscopic description of the system in terms of ordinary differential equations which provides a general framework to model and quantify the influence of single node dynamics on the macroscopic state of the network. The thus obtained framework is applicable to many fields of study, such as epidemic spreading, opinion formation, or socioecological modeling.

Macroscopic description of complex adaptive networks coevolving with dynamic node states.

PubMed

Wiedermann, Marc; Donges, Jonathan F; Heitzig, Jobst; Lucht, Wolfgang; Kurths, Jürgen

2015-05-01

In many real-world complex systems, the time evolution of the network's structure and the dynamic state of its nodes are closely entangled. Here we study opinion formation and imitation on an adaptive complex network which is dependent on the individual dynamic state of each node and vice versa to model the coevolution of renewable resources with the dynamics of harvesting agents on a social network. The adaptive voter model is coupled to a set of identical logistic growth models and we mainly find that, in such systems, the rate of interactions between nodes as well as the adaptive rewiring probability are crucial parameters for controlling the sustainability of the system's equilibrium state. We derive a macroscopic description of the system in terms of ordinary differential equations which provides a general framework to model and quantify the influence of single node dynamics on the macroscopic state of the network. The thus obtained framework is applicable to many fields of study, such as epidemic spreading, opinion formation, or socioecological modeling.

Socio-hydrologic Modeling to Understand and Mediate the Competition for Water between Humans and Ecosystems: Murrumbidgee River Basin, Australia

NASA Astrophysics Data System (ADS)

van Emmerik, Tim; Sivapalan, Murugesu; Li, Zheng; Pande, Saket; Savenije, Hubert

2014-05-01

Around the world the demand for water resources is growing in order to satisfy rapidly increasing human populations, leading to competition for water between humans and ecosystems. An entirely new and comprehensive quantitative framework is needed to establish a holistic understanding of that competition, thereby enabling development and evaluation of effective mediation strategies. We present a case study centered on the Murrumbidgee river basin in eastern Australia that illustrates the dynamics of the balance between water extraction and use for food production and efforts to mitigate and reverse consequent degradation of the riparian environment. Interactions between patterns of water resources management and climate driven hydrological variability within the prevailing socio-economic environment have contributed to the emergence of new whole system dynamics over the last 100 years. In particular, data analysis reveals a pendulum swing between an exclusive focus on agricultural development and food production in the initial stages of water resources development and its attendant socio-economic benefits, followed by the gradual realization of the adverse environmental impacts, efforts to mitigate these with the use of remedial measures, and ultimately concerted efforts and externally imposed solutions to restore environmental health and ecosystem services. A quasi-distributed coupled socio-hydrologic system model that explicitly includes the two-way coupling between human and hydrological systems, including evolution of human values/norms relating to water and the environment, is able to mimic broad features of this pendulum swing. The model consists of coupled nonlinear differential equations that include four state variables describing the co-evolution of storage capacity, irrigated area, human population, and ecosystem health, which are all connected by feedback mechanisms. The model is used to generate insights into the dominant controls of the trajectory of co-evolution of the coupled human-water system, to serve as the theoretical framework for more detailed analysis of the system, and to generate organizing principles that may be transferable to other systems in different climatic and socio-economic settings.

Aspiration-based coevolution of link weight promotes cooperation in the spatial prisoner's dilemma game

PubMed Central

Shen, Chen; Chu, Chen; Shi, Lei

2018-01-01

In this article, we propose an aspiration-based coevolution of link weight, and explore how this set-up affects the evolution of cooperation in the spatial prisoner's dilemma game. In particular, an individual will increase the weight of its link to its neighbours only if the payoff received via this interaction exceeds a pre-defined aspiration. Conversely, if the received payoff is below this aspiration, the link weight with the corresponding neighbour will decrease. Our results show that an appropriate aspiration level leads to a high-cooperation plateau, whereas too high or too low aspiration will impede the evolution of cooperation. We explain these findings with a comprehensive analysis of transition points and with a systematic analysis of typical configuration patterns. The presented results provide further theoretical insights with regards to the impact of different aspiration levels on cooperation in human societies. PMID:29892454

Aspiration-based coevolution of link weight promotes cooperation in the spatial prisoner's dilemma game

NASA Astrophysics Data System (ADS)

Shen, Chen; Chu, Chen; Shi, Lei; Perc, Matjaž; Wang, Zhen

2018-05-01

In this article, we propose an aspiration-based coevolution of link weight, and explore how this set-up affects the evolution of cooperation in the spatial prisoner's dilemma game. In particular, an individual will increase the weight of its link to its neighbours only if the payoff received via this interaction exceeds a pre-defined aspiration. Conversely, if the received payoff is below this aspiration, the link weight with the corresponding neighbour will decrease. Our results show that an appropriate aspiration level leads to a high-cooperation plateau, whereas too high or too low aspiration will impede the evolution of cooperation. We explain these findings with a comprehensive analysis of transition points and with a systematic analysis of typical configuration patterns. The presented results provide further theoretical insights with regards to the impact of different aspiration levels on cooperation in human societies.

Costly Advertising and the Evolution of Cooperation

PubMed Central

Brede, Markus

2013-01-01

In this paper, I investigate the co-evolution of fast and slow strategy spread and game strategies in populations of spatially distributed agents engaged in a one off evolutionary dilemma game. Agents are characterized by a pair of traits, a game strategy (cooperate or defect) and a binary ‘advertising’ strategy (advertise or don’t advertise). Advertising, which comes at a cost , allows investment into faster propagation of the agents’ traits to adjacent individuals. Importantly, game strategy and advertising strategy are subject to the same evolutionary mechanism. Via analytical reasoning and numerical simulations I demonstrate that a range of advertising costs exists, such that the prevalence of cooperation is significantly enhanced through co-evolution. Linking costly replication to the success of cooperators exposes a novel co-evolutionary mechanism that might contribute towards a better understanding of the origins of cooperation-supporting heterogeneity in agent populations. PMID:23861752

Effects of adaptive degrees of trust on coevolution of quantum strategies on scale-free networks.

PubMed

Li, Qiang; Chen, Minyou; Perc, Matjaž; Iqbal, Azhar; Abbott, Derek

2013-10-15

We study the impact of adaptive degrees of trust on the evolution of cooperation in the quantum prisoner's dilemma game. In addition to the strategies, links between players are also subject to evolution. Starting with a scale-free interaction network, players adjust trust towards their neighbors based on received payoffs. The latter governs the strategy adoption process, while trust governs the rewiring of links. As soon as the degree of trust towards a neighbor drops to zero, the link is rewired to another randomly chosen player within the network. We find that for small temptations to defect cooperators always dominate, while for intermediate and strong temptations a single quantum strategy is able to outperform all other strategies. In general, reciprocal trust remains within close relationships and favors the dominance of a single strategy. Due to coevolution, the power-law degree distributions transform to Poisson distributions.

Effects of adaptive degrees of trust on coevolution of quantum strategies on scale-free networks

NASA Astrophysics Data System (ADS)

Li, Qiang; Chen, Minyou; Perc, Matjaž; Iqbal, Azhar; Abbott, Derek

2013-10-01

We study the impact of adaptive degrees of trust on the evolution of cooperation in the quantum prisoner's dilemma game. In addition to the strategies, links between players are also subject to evolution. Starting with a scale-free interaction network, players adjust trust towards their neighbors based on received payoffs. The latter governs the strategy adoption process, while trust governs the rewiring of links. As soon as the degree of trust towards a neighbor drops to zero, the link is rewired to another randomly chosen player within the network. We find that for small temptations to defect cooperators always dominate, while for intermediate and strong temptations a single quantum strategy is able to outperform all other strategies. In general, reciprocal trust remains within close relationships and favors the dominance of a single strategy. Due to coevolution, the power-law degree distributions transform to Poisson distributions.

Costly advertising and the evolution of cooperation.

PubMed

Brede, Markus

2013-01-01

In this paper, I investigate the co-evolution of fast and slow strategy spread and game strategies in populations of spatially distributed agents engaged in a one off evolutionary dilemma game. Agents are characterized by a pair of traits, a game strategy (cooperate or defect) and a binary 'advertising' strategy (advertise or don't advertise). Advertising, which comes at a cost [Formula: see text], allows investment into faster propagation of the agents' traits to adjacent individuals. Importantly, game strategy and advertising strategy are subject to the same evolutionary mechanism. Via analytical reasoning and numerical simulations I demonstrate that a range of advertising costs exists, such that the prevalence of cooperation is significantly enhanced through co-evolution. Linking costly replication to the success of cooperators exposes a novel co-evolutionary mechanism that might contribute towards a better understanding of the origins of cooperation-supporting heterogeneity in agent populations.

Visual mimicry of host nestlings by cuckoos

PubMed Central

Langmore, Naomi E.; Stevens, Martin; Maurer, Golo; Heinsohn, Robert; Hall, Michelle L.; Peters, Anne; Kilner, Rebecca M.

2011-01-01

Coevolution between antagonistic species has produced instances of exquisite mimicry. Among brood-parasitic cuckoos, host defences have driven the evolution of mimetic eggs, but the evolutionary arms race was believed to be constrained from progressing to the chick stage, with cuckoo nestlings generally looking unlike host young. However, recent studies on bronze-cuckoos have confounded theoretical expectations by demonstrating cuckoo nestling rejection by hosts. Coevolutionary theory predicts reciprocal selection for visual mimicry of host young by cuckoos, although this has not been demonstrated previously. Here we show that, in the eyes of hosts, nestlings of three bronze-cuckoo species are striking visual mimics of the young of their morphologically diverse hosts, providing the first evidence that coevolution can select for visual mimicry of hosts in cuckoo chicks. Bronze-cuckoos resemble their own hosts more closely than other host species, but the accuracy of mimicry varies according to the diversity of hosts they exploit. PMID:21227972

Principles of cophylogenetic maps

NASA Astrophysics Data System (ADS)

Charleston, Michael A.

Cophylogeny is the study of the relationships between phylogenies of ecologically related groups (taxa, geographical areas, genes etc.), where one, the "host" phylogeny, is independent and the other, the "associate" phylogeny, is hypothesized to be dependent to some degree on the host. Given two such phylogenies our aim is to estimate the past associations between the host and associate taxa. This chapter describes cophylogeny and discusses some of its basic pri nciples. The necessary properties of any cophylogenetic method are described. Charleston [5] created a graph which contains all the potential solutions to a given cophylogenetic problem. The vertices of this graph are associations, either observed or hypothetical, between "host" and associated taxonomic units, and the arcs correspond to the associate phylogeny. A new and more general method of constructing the Jungle is presented, which will correctly account for reticulate host and/or parasite phylogenies. Keywords: cophylogeny, coevolution, gene tree/species tree, host/parasite coevolution, host switch, horizontal transfer, biogeography.

Are the metabolomic responses to folivory of closely related plant species linked to macroevolutionary and plant-folivore coevolutionary processes?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rivas-Ubach, Albert; Hódar, José A.; Sardans, Jordi

The debate whether the coevolution of plants and insects or macroevolutionary processes (phylogeny) is the main driver determining the arsenal of molecular defensive compounds of plants remains unresolved. Attacks by herbivorous insects affect not only the composition of defensive compounds in plants but the entire metabolome (the set of molecular metabolites), including defensive compounds. Metabolomes are the final products of genotypes and are directly affected by macroevolutionary processes, so closely related species should have similar metabolomic compositions and may respond in similar ways to attacks by folivores. We analyzed the elemental compositions and metabolomes of needles from Pinus pinaster, P.more » nigra and P. sylvestris to determine if these closely related Pinus species with different coevolutionary histories with the caterpillars of the processionary moth respond similarly to attacks by this lepidopteran. All pines had different metabolomes and metabolic responses to herbivorous attack. The metabolomic variation among the pine species and the responses to folivory reflected their macroevolutionary relationships, with P. pinaster having the most divergent metabolome. The concentrations of phenolic metabolites were generally not higher in the attacked trees, which had lower concentrations of terpenes, suggesting that herbivores avoid individuals with high concentrations of terpenes. Our results suggest that macroevolutionary history plays important roles in the metabolomic responses of these pine species to folivory, but plant-insect coevolution probably constrains those responses. Combinations of different evolutionary factors and trade-offs are likely responsible for the different responses of each species to folivory, which is not necessarily exclusively linked to plant-insect coevolution.« less

Phenotypic Mismatches Reveal Escape from Arms-Race Coevolution

PubMed Central

Hanifin, Charles T; Brodie, Edmund D; Brodie, Edmund D

2008-01-01

Because coevolution takes place across a broad scale of time and space, it is virtually impossible to understand its dynamics and trajectories by studying a single pair of interacting populations at one time. Comparing populations across a range of an interaction, especially for long-lived species, can provide insight into these features of coevolution by sampling across a diverse set of conditions and histories. We used measures of prey traits (tetrodotoxin toxicity in newts) and predator traits (tetrodotoxin resistance of snakes) to assess the degree of phenotypic mismatch across the range of their coevolutionary interaction. Geographic patterns of phenotypic exaggeration were similar in prey and predators, with most phenotypically elevated localities occurring along the central Oregon coast and central California. Contrary to expectations, however, these areas of elevated traits did not coincide with the most intense coevolutionary selection. Measures of functional trait mismatch revealed that over one-third of sampled localities were so mismatched that reciprocal selection could not occur given current trait distributions. Estimates of current locality-specific interaction selection gradients confirmed this interpretation. In every case of mismatch, predators were “ahead” of prey in the arms race; the converse escape of prey was never observed. The emergent pattern suggests a dynamic in which interacting species experience reciprocal selection that drives arms-race escalation of both prey and predator phenotypes at a subset of localities across the interaction. This coadaptation proceeds until the evolution of extreme phenotypes by predators, through genes of large effect, allows snakes to, at least temporarily, escape the arms race. PMID:18336073

Heavily Obscured AGN: An Ideal Laboratory To Study The Early Co-Evolution of Galaxies And Black Holes

NASA Astrophysics Data System (ADS)

Circosta, Chiara; Vignali, C.; Gilli, R.; Feltre, A.; Vito, F.

2016-10-01

Obscured AGN are a crucial ingredient to understand the full growth history of super massive black holes and the coevolution with their host galaxies, since they constitute the bulk of the BH accretion. In the distant Universe, many of them are hosted by submillimeter galaxies (SMGs), characterized by a high production of stars and a very fast consumption of gas. Therefore, the analysis of this class of objects is fundamental to investigate the role of the ISM in the early coevolution of galaxies and black holesWe collected a sample of six obscured X-ray selected AGN at z>2.5 in the CDF-S, detected in the far-IR/submm bands. We performed a multiwavelength analysis in order to characterize their physical properties, as well as those of their host galaxies (e.g. column density, accretion luminosity, stellar mass, SFR, dust and gas mass). I will present the results of the X-ray spectral analysis of these sources based on the 7Ms Chandra data - the deepest X-ray observation ever carried out on any field - along with their broad-band spectral energy distributions (SEDs), built up using the public UV to far-IR photometry from the CANDELS and Herschel catalogs. By comparing the column density associated with the ISM (estimated measuring the size of the system) with that obtained from the X-ray data, it is possible to understand whether the ISM in the host galaxy may be able to produce a substantial part of the observed nuclear obscuration.

Gene-culture coevolution in the age of genomics

PubMed Central

Richerson, Peter J.; Boyd, Robert; Henrich, Joseph

2010-01-01

The use of socially learned information (culture) is central to human adaptations. We investigate the hypothesis that the process of cultural evolution has played an active, leading role in the evolution of genes. Culture normally evolves more rapidly than genes, creating novel environments that expose genes to new selective pressures. Many human genes that have been shown to be under recent or current selection are changing as a result of new environments created by cultural innovations. Some changed in response to the development of agricultural subsistence systems in the Early and Middle Holocene. Alleles coding for adaptations to diets rich in plant starch (e.g., amylase copy number) and to epidemic diseases evolved as human populations expanded (e.g., sickle cell and G6PD deficiency alleles that provide protection against malaria). Large-scale scans using patterns of linkage disequilibrium to detect recent selection suggest that many more genes evolved in response to agriculture. Genetic change in response to the novel social environment of contemporary modern societies is also likely to be occurring. The functional effects of most of the alleles under selection during the last 10,000 years are currently unknown. Also unknown is the role of paleoenvironmental change in regulating the tempo of hominin evolution. Although the full extent of culture-driven gene-culture coevolution is thus far unknown for the deeper history of the human lineage, theory and some evidence suggest that such effects were profound. Genomic methods promise to have a major impact on our understanding of gene-culture coevolution over the span of hominin evolutionary history. PMID:20445092

From first galaxies to QSOs - feeding the baby monsters

NASA Astrophysics Data System (ADS)

Danese, L.; Shankar, F.; Granato, G. L.; Silva, L.; Bressan, A.; de Zotti, G.; Salucci, P.; Cirasuolo, M.

We present a physical model for the coevolution of massive spheroidal galaxies and active nuclei at their centers. Supernova heating is increasingly effective in slowing down the star formation and in driving gas outflows in smaller and smaller dark matter halos. Thus the more massive protogalaxies virializing at early times are the sites of faster star formation. The correspondingly higher radiation drag causes a faster angular momentum loss by the gas and induces a larger accretion rate onto the central black hole. In turn, the kinetic energy of the outflows powered by the active nuclei can unbind the residual gas in a time shorter for larger halos. The model accounts for a broad variety of dynamical, photometric and metallicity properties of early-type galaxies, for the MBH-σ relation and for the local supermassive black-hole mass function.

Culture and cooperation in a spatial public goods game

NASA Astrophysics Data System (ADS)

Stivala, Alex; Kashima, Yoshihisa; Kirley, Michael

2016-09-01

We study the coevolution of culture and cooperation by combining the Axelrod model of cultural dissemination with a spatial public goods game, incorporating both noise and social influence. Both participation and cooperation in public goods games are conditional on cultural similarity. We find that a larger "scope of cultural possibilities" in the model leads to the survival of cooperation, when noise is not present, and a higher probability of a multicultural state evolving, for low noise rates. High noise rates, however, lead to both rapid extinction of cooperation and collapse into cultural "anomie," in which stable cultural regions fail to form. These results suggest that cultural diversity can actually be beneficial for the evolution of cooperation, but that cultural information needs to be transmitted accurately in order to maintain both coherent cultural groups and cooperation.

Coevolution of dynamical states and interactions in dynamic networks

NASA Astrophysics Data System (ADS)

Zimmermann, Martín G.; Eguíluz, Víctor M.; San Miguel, Maxi

2004-06-01

We explore the coupled dynamics of the internal states of a set of interacting elements and the network of interactions among them. Interactions are modeled by a spatial game and the network of interaction links evolves adapting to the outcome of the game. As an example, we consider a model of cooperation in which the adaptation is shown to facilitate the formation of a hierarchical interaction network that sustains a highly cooperative stationary state. The resulting network has the characteristics of a small world network when a mechanism of local neighbor selection is introduced in the adaptive network dynamics. The highly connected nodes in the hierarchical structure of the network play a leading role in the stability of the network. Perturbations acting on the state of these special nodes trigger global avalanches leading to complete network reorganization.

In Vitro "Evolutionary Arms-Races" Between Hosts and Parasites in an Artificial RNA Replication System

NASA Astrophysics Data System (ADS)

Furubayashi, T.; Bansho, Y.; Motooka, D.; Nakamura, S.; Ichihashi, N.

2017-07-01

We performed coevolution of artificial RNA self-replicators and parasitic replicators in microdroplets. We observed evolutionary arms-races with oscillating population dynamics and faster evolution of self-replicators caused by parasitic replicators.

Kingian Co-Evolution of the Water and Mineral/Rock Components for Earth and Mars: Implications for Planetary Habitability (Invited)

NASA Astrophysics Data System (ADS)

Baker, V. R.

2013-12-01

Planetary habitability may fluctuate episodically against a background provided by the co-evolution of a planet's mineral/rock (geosphere) components and its water (hydrosphere) in relation to its position in a circumstellar system. The water/rock (geosphere/hydrosphere) co-evolution can be inferred from the geological histories of the terrestrial planets of the solar system, particularly from the very extensive understanding of Earth and Mars. Habitability and water/rock co-evolution have components that are tychistic (i.e., driven by chance) and anancastic (i.e., dynamically driven largely by deterministic forces). They also have a final, end-directed (i.e., teleomatic) aspect that operates in accordance with natural laws. This is a larger perspective on the idea of planetary habitability than is generally associated with an astronomical approach, and it incorporates additional insights from a geological perspective on the issue. The geological histories of Mars and Earth are punctuated with critical, short-term epochs of extreme change, which for Earth are known to be associated with major disruptions of its biosphere. These catastrophic epochs can be described as a type of non-Darwinian evolution that was envisioned by the geologist Clarence King. In an 1877 paper King proposed that accelerated evolutionary change occurs during sudden environmental disruptions. Such Kingian disruptions in mineral/rock and water evolution mark the planetary histories of Mars and Earth, including the early formation and condensation of a steam atmosphere, an impacting cataclysm at about 3.9 to 4 Ga, episodes of concentrated volcanism and tectonism, and associated rapid changes in the linked atmosphere and hydrosphere. These disruptions are closely tied to migrations of water between different planetary reservoirs, the nature of planetary accretion, the origin of a physically coupled atmosphere and ocean, the prospects for initiating plate tectonics, and punctuated greenhouse-to-icehouse climatic transitions. Recent discoveries from Mars missions reveal the extensive role of water in generating sedimentary rocks, active and relict glacial and periglacial features, aqueous weathering products (clay minerals and sulfates), alluvial fans and deltas, the extensive development of paleolakes, and even a probable, though transient ocean. The latter may have formed episodically, associated with episodes of intensive volcanism that disrupted a water-ice-rich permafrost, thereby transferring much of the hydrosphere f

The lack of foundation in the mechanism on which are based the physico-chemical theories for the origin of the genetic code is counterposed to the credible and natural mechanism suggested by the coevolution theory.

PubMed

Di Giulio, Massimo

2016-06-21

I analyze the mechanism on which are based the majority of theories that put to the center of the origin of the genetic code the physico-chemical properties of amino acids. As this mechanism is based on excessive mutational steps, I conclude that it could not have been operative or if operative it would not have allowed a full realization of predictions of these theories, because this mechanism contained, evidently, a high indeterminacy. I make that disapproving the four-column theory of the origin of the genetic code (Higgs, 2009) and reply to the criticism that was directed towards the coevolution theory of the origin of the genetic code. In this context, I suggest a new hypothesis that clarifies the mechanism by which the domains of codons of the precursor amino acids would have evolved, as predicted by the coevolution theory. This mechanism would have used particular elongation factors that would have constrained the evolution of all amino acids belonging to a given biosynthetic family to the progenitor pre-tRNA, that for first recognized, the first codons that evolved in a certain codon domain of a determined precursor amino acid. This happened because the elongation factors recognized two characteristics of the progenitor pre-tRNAs of precursor amino acids, which prevented the elongation factors from recognizing the pre-tRNAs belonging to biosynthetic families of different precursor amino acids. Finally, I analyze by means of Fisher's exact test, the distribution, within the genetic code, of the biosynthetic classes of amino acids and the ones of polarity values of amino acids. This analysis would seem to support the biosynthetic classes of amino acids over the ones of polarity values, as the main factor that led to the structuring of the genetic code, with the physico-chemical properties of amino acids playing only a subsidiary role in this evolution. As a whole, the full analysis brings to the conclusion that the coevolution theory of the origin of the genetic code would be a theory highly corroborated. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mitigating amphibian disease: strategies to maintain wild populations and control chytridiomycosis

USGS Publications Warehouse

Woodhams, Douglas C.; Bosch, Jaime; Briggs, Cheryl J.; Cashins, Scott; Davis, Leyla R.; Lauer, Antje; Muths, Erin L.; Puschendorf, Robert; Schmidt, Benedikt R.; Sheafor, Brandon; Voyles, Jamie

2011-01-01

Because sustainable conservation of amphibians in nature is dependent on long-term population persistence and co-evolution with potentially lethal pathogens, we suggest that disease mitigation not focus exclusively on the elimination or containment of the pathogen, or on the captive breeding of amphibian hosts. Rather, successful disease mitigation must be context specific with epidemiologically informed strategies to manage already infected populations by decreasing pathogenicity and host susceptibility. We propose population level treatments based on three steps: first, identify mechanisms of disease suppression; second, parameterize epizootiological models of disease and population dynamics for testing under semi-natural conditions; and third, begin a process of adaptive management in field trials with natural populations.

Sapronosis: a distinctive type of infectious agent

USGS Publications Warehouse

Kuris, Armand M.; Lafferty, Kevin D.; Sokolow, Susanne H.

2014-01-01

Sapronotic disease agents have evolutionary and epidemiological properties unlike other infectious organisms. Their essential saprophagic existence prevents coevolution, and no host–parasite virulence trade-off can evolve. However, the host may evolve defenses. Models of pathogens show that sapronoses, lacking a threshold of transmission, cannot regulate host populations, although they can reduce host abundance and even extirpate their hosts. Immunocompromised hosts are relatively susceptible to sapronoses. Some particularly important sapronoses, such as cholera and anthrax, can sustain an epidemic in a host population. However, these microbes ultimately persist as saprophages. One-third of human infectious disease agents are sapronotic, including nearly all fungal diseases. Recognition that an infectious disease is sapronotic illuminates a need for effective environmental control strategies.

A Simulation of Cooperation and Competition in Insurgent Networks

NASA Astrophysics Data System (ADS)

Gabbay, Michael

2014-03-01

Insurgencies are often characterized by multiple groups who share a common foe in the national government but have independent organizations which may differ with respect to social identities, ideologies, strategies, and their use of violence. These groups may cooperate in various ways such as conducting joint attacks, pooling resources, and establishing formal alliances or mergers. However, they may also compete with each other over popular support, recruitment of fighters, funding, allies, and ultimately military dominance. A network coevolution model of insurgent factional dynamics is presented which accounts for factors driving cooperation and competition. The model is formulated as a system of coupled ODEs which evolves network ties between insurgent groups along with group policies concerning the targets of violence. Simulation results are presented showing sharp transitions in network structure as model parameters are varied. Connections are drawn between the model results and empirical data from the Iraqi insurgency. This work was supported by the Office of Naval Research under grant N00014-13-1-0381.

The Impact of Heterogeneity and Awareness in Modeling Epidemic Spreading on Multiplex Networks

PubMed Central

Scatà, Marialisa; Di Stefano, Alessandro; Liò, Pietro; La Corte, Aurelio

2016-01-01

In the real world, dynamic processes involving human beings are not disjoint. To capture the real complexity of such dynamics, we propose a novel model of the coevolution of epidemic and awareness spreading processes on a multiplex network, also introducing a preventive isolation strategy. Our aim is to evaluate and quantify the joint impact of heterogeneity and awareness, under different socioeconomic conditions. Considering, as case study, an emerging public health threat, Zika virus, we introduce a data-driven analysis by exploiting multiple sources and different types of data, ranging from Big Five personality traits to Google Trends, related to different world countries where there is an ongoing epidemic outbreak. Our findings demonstrate how the proposed model allows delaying the epidemic outbreak and increasing the resilience of nodes, especially under critical economic conditions. Simulation results, using data-driven approach on Zika virus, which has a growing scientific research interest, are coherent with the proposed analytic model. PMID:27848978

A virocentric perspective on the evolution of life

PubMed Central

Koonin, Eugene V.; Dolja, Valerian V.

2015-01-01

Viruses and/or virus-like selfish elements are associated with all cellular life forms and are the most abundant biological entities on Earth, with the number of virus particles in many environments exceeding the number of cells by one to two orders of magnitude. The genetic diversity of viruses is commensurately enormous and might substantially exceed the diversity of cellular organisms. Unlike cellular organisms with their uniform replication-expression scheme, viruses possess either RNA or DNA genomes and exploit all conceivable replication-expression strategies. Although viruses extensively exchange genes with their hosts, there exists a set of viral hallmark genes that are shared by extremely diverse groups of viruses to the exclusion of cellular life forms. Coevolution of viruses and host defense systems is a key aspect in the evolution of both viruses and cells, and viral genes are often recruited for cellular functions. Together with the fundamental inevitability of the emergence of genomic parasites in any evolving replicator system, these multiple lines of evidence reveal the central role of viruses in the entire evolution of life. PMID:23850169

[A review of the role and function of microbes in coral reef ecosystem].

PubMed

Zhou, Jin; Jin, Hui; Cai, Zhong-Hua

2014-03-01

Coral reef is consisted with several kinds of reef-associated organisms, including coral, fish, benthos, algae and microbes, which is an important marine ecosystem. Coral reef lives in the oligotrophic environment, has very highly primary productivity and net productivity, and is called "tropical rain forest in ocean". In corals, diverse microorganisms exert a significant influence on biogeochemical and ecological processes, including food webs, organism life cycles, and nutrient cycling. With the development of molecular biology, the role of microorganisms in a coral system is becoming more outstanding. In this article, we reviewed current understanding on 1) the onset of coral-bacterial associations; 2) the characteristics of microbes in coral (specificity, plasticity and co-evolution) ; 3) the role and signal regulation of microbes in the health and disease of coral; and 4) the response mechanism of microbes for global climatic change and consequent effects, such as temperature rise, ocean acidification and eutrophication. The aims of this article were to summarize the latest theories and achievements, clear the mechanism of microbial ecology in coral reefs and provide a theoretical reference for better protection and maintaining the coral's biodiversity.

Coevolutionary Free Lunches

NASA Technical Reports Server (NTRS)

Wolpert, David H.; Macready, William G.

2005-01-01

Recent work on the foundations of optimization has begun to uncover its underlying rich structure. In particular, the "No Free Lunch" (NFL) theorems [WM97] state that any two algorithms are equivalent when their performance is averaged across all possible problems. This highlights the need for exploiting problem-specific knowledge to achieve better than random performance. In this paper we present a general framework covering most search scenarios. In addition to the optimization scenarios addressed in the NFL results, this framework covers multi-armed bandit problems and evolution of multiple co-evolving agents. As a particular instance of the latter, it covers "self-play" problems. In these problems the agents work together to produce a champion, who then engages one or more antagonists in a subsequent multi-player game In contrast to the traditional optimization case where the NFL results hold, we show that in self-play there are free lunches: in coevolution some algorithms have better performance than other algorithms, averaged across all possible problems. However in the typical coevolutionary scenarios encountered in biology, where there is no champion, NFL still holds.

Evolutionary emergence and maintenance of horizontally transmitted mutualism that do not rely on the supply of standing variation in symbiont quality.

PubMed

Uchiumi, Y; Ohtsuki, H; Sasaki, A

2017-12-01

Mutualism based on reciprocal exchange of costly services must avoid exploitation by 'free-rides'. Accordingly, hosts discriminate against free-riding symbionts in many mutualistic relationships. However, as the selective advantage of discriminators comes from the presence of variability in symbiont quality that they eliminate, discrimination and thus mutualism have been considered to be maintained with exogenous supply of free-riders. In this study, we tried to resolve the 'paradoxical' co-evolution of discrimination by hosts and cooperation by symbionts, by comparing two different types of discrimination: 'one-shot' discrimination, where a host does not reacquire new symbionts after evicting free-riders, and 'resampling' discrimination, where a host does from the environment. Our study shows that this apparently minor difference in discrimination types leads to qualitatively different evolutionary outcomes. First, although it has been usually considered that the benefit of discriminators is derived from the variability of symbiont quality, the benefit of a certain type of discriminators (e.g. one-shot discrimination) is proportional to the frequency of free-riders, which is in stark contrast to the case of resampling discrimination. As a result, one-shot discriminators can invade the free-rider/nondiscriminator population, even if standing variation for symbiont quality is absent. Second, our one-shot discriminators can also be maintained without exogenous supply of free-riders and hence is free from the paradox of discrimination. Therefore, our result indicates that the paradox is not a common feature of evolution of discrimination but is a problem of specific types of discrimination. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Beyond topology: coevolution of structure and flux in metabolic networks.

PubMed

Morrison, E S; Badyaev, A V

2017-10-01

Interactions between the structure of a metabolic network and its functional properties underlie its evolutionary diversification, but the mechanism by which such interactions arise remains elusive. Particularly unclear is whether metabolic fluxes that determine the concentrations of compounds produced by a metabolic network, are causally linked to a network's structure or emerge independently of it. A direct empirical study of populations where both structural and functional properties vary among individuals' metabolic networks is required to establish whether changes in structure affect the distribution of metabolic flux. In a population of house finches (Haemorhous mexicanus), we reconstructed full carotenoid metabolic networks for 442 individuals and uncovered 11 structural variants of this network with different compounds and reactions. We examined the consequences of this structural diversity for the concentrations of plumage-bound carotenoids produced by flux in these networks. We found that concentrations of metabolically derived, but not dietary carotenoids, depended on network structure. Flux was partitioned similarly among compounds in individuals of the same network structure: within each network, compound concentrations were closely correlated. The highest among-individual variation in flux occurred in networks with the strongest among-compound correlations, suggesting that changes in the magnitude, but not the distribution of flux, underlie individual differences in compound concentrations on a static network structure. These findings indicate that the distribution of flux in carotenoid metabolism closely follows network structure. Thus, evolutionary diversification and local adaptations in carotenoid metabolism may depend more on the gain or loss of enzymatic reactions than on changes in flux within a network structure. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Lineage-specific co-evolution of the Egf receptor/ligand signaling system.

PubMed

Laisney, Juliette A G C; Braasch, Ingo; Walter, Ronald B; Meierjohann, Svenja; Schartl, Manfred

2010-01-27

The epidermal growth factor receptor (Egfr) with its numerous ligands has fundamental roles in development, cell differentiation and physiology. Dysfunction of the receptor-ligand system contributes to many human malignancies. Consistent with such various tasks, the Egfr gene family has expanded during vertebrate evolution as a consequence of several rounds of whole genome duplication. Of particular interest is the effect of the fish-specific whole genome duplication (FSGD) on the ligand-receptor system, as it has supplied this largest group of vertebrates with additional opportunities for sub- and/or neofunctionalization in this signaling system. We identified the predicted components of the Egf receptor-ligand signaling system in teleost fishes (medaka, platyfish, stickleback, pufferfishes and zebrafish). We found two duplicated egfr genes, egfra and egfrb, in all available teleost genomes. Surprisingly only one copy for each of the seven Egfr ligands could be identified in most fishes, with zebrafish hbegf being the only exception. Special focus was put on medaka, for which we more closely investigated all Egf receptors and Egfr ligands. The different expression patterns of egfra, egfrb and their ligands in medaka tissues and embryo stages suggest differences in role and function. Preferential co-expression of different subsets of Egfr ligands corroborates the possible subfunctionalization and specialization of the two receptors in adult tissues. Bioinformatic analyses of the ligand-receptor interface between Egfr and its ligands show a very weak evolutionary conservation within this region. Using in vitro analyses of medaka Egfra, we could show that this receptor is only activated by medaka ligands, but not by human EGF. Altogether, our data suggest a lineage-specific Egfr/Egfr ligand co-evolution. Our data indicate that medaka Egfr signaling occurs via its two copies, Egfra and Egfrb, each of them being preferentially coexpressed with different subsets of Egfr ligands. This fish-specific occurrence of Egf receptor specialization offers unique opportunities to study the functions of different Egf receptor-ligand combinations and their biological outputs in vertebrates. Furthermore, our results strongly support the use of homologous ligands in future studies, as sufficient cross-specificity is very unlikely for this ligand/receptor system.

Lineage-specific co-evolution of the Egf receptor/ligand signaling system

PubMed Central

2010-01-01

Background The epidermal growth factor receptor (Egfr) with its numerous ligands has fundamental roles in development, cell differentiation and physiology. Dysfunction of the receptor-ligand system contributes to many human malignancies. Consistent with such various tasks, the Egfr gene family has expanded during vertebrate evolution as a consequence of several rounds of whole genome duplication. Of particular interest is the effect of the fish-specific whole genome duplication (FSGD) on the ligand-receptor system, as it has supplied this largest group of vertebrates with additional opportunities for sub- and/or neofunctionalization in this signaling system. Results We identified the predicted components of the Egf receptor-ligand signaling system in teleost fishes (medaka, platyfish, stickleback, pufferfishes and zebrafish). We found two duplicated egfr genes, egfra and egfrb, in all available teleost genomes. Surprisingly only one copy for each of the seven Egfr ligands could be identified in most fishes, with zebrafish hbegf being the only exception. Special focus was put on medaka, for which we more closely investigated all Egf receptors and Egfr ligands. The different expression patterns of egfra, egfrb and their ligands in medaka tissues and embryo stages suggest differences in role and function. Preferential co-expression of different subsets of Egfr ligands corroborates the possible subfunctionalization and specialization of the two receptors in adult tissues. Bioinformatic analyses of the ligand-receptor interface between Egfr and its ligands show a very weak evolutionary conservation within this region. Using in vitro analyses of medaka Egfra, we could show that this receptor is only activated by medaka ligands, but not by human EGF. Altogether, our data suggest a lineage-specific Egfr/Egfr ligand co-evolution. Conclusions Our data indicate that medaka Egfr signaling occurs via its two copies, Egfra and Egfrb, each of them being preferentially coexpressed with different subsets of Egfr ligands. This fish-specific occurrence of Egf receptor specialization offers unique opportunities to study the functions of different Egf receptor-ligand combinations and their biological outputs in vertebrates. Furthermore, our results strongly support the use of homologous ligands in future studies, as sufficient cross-specificity is very unlikely for this ligand/receptor system. PMID:20105326

Beta and Gamma Human Herpesviruses: Agonistic and Antagonistic Interactions with the Host Immune System

PubMed Central

Cruz-Muñoz, Mario E.; Fuentes-Pananá, Ezequiel M.

2018-01-01

Viruses are the most abundant and diverse biological entities in the planet. Historically, our main interest in viruses has focused on their pathogenic role, recognized by pandemics that have decimated the world population. However, viral infections have also played a major role in the evolution of cellular organisms, both through interchanging of genes with novel functions and shaping the immune system. Examples abound of infections that seriously compromise the host integrity, but evidence of plant and insect viruses mutualistic relationships have recently surfaced in which infected hosts are better suited for survival, arguing that virus-host interactions are initially parasitic but become mutualistic over years of co-evolution. A similar mutual help scenario has emerged with commensal gut bacteria. EBV is a herpesvirus that shares more than a hundred million years of co-evolution with humans, today successfully infecting close to 100% of the adult world population. Infection is usually acquired early in childhood persisting for the host lifetime mostly without apparent clinical symptoms. Disturbance of this homeostasis is rare and results in several diseases, of which the best understood are infectious mononucleosis and several EBV-associated cancers. Less understood are recently found inborn errors of the immune system that result in primary immunodeficiencies with an increased predisposition almost exclusive to EBV-associated diseases. Puzzling to these scenarios of broken homeostasis is the co-existence of immunosuppression, inflammation, autoimmunity and cancer. Homologous to EBV, HCMV, HHV-6 and HHV-7 are herpesviruses that also latently infect most individuals. Several lines of evidence support a mutualistic equilibrium between HCMV/EBV and hosts, that when altered trigger diseases in which the immune system plays a critical role. Interestingly, these beta and gamma herpesviruses persistently infect all immune lineages and early precursor cells. In this review, we will discuss the evidence of the benefits that infection of immune cells with these herpesviruses brings to the host. Also, the circumstances in which this positive relationship is broken, predisposing the host to diseases characterized by an abnormal function of the host immune system. PMID:29354096

Adaptive Evolution and Divergence of SERPINB3: A Young Duplicate in Great Apes

PubMed Central

Gomes, Sílvia; Marques, Patrícia I.; Matthiesen, Rune; Seixas, Susana

2014-01-01

A series of duplication events led to an expansion of clade B Serine Protease Inhibitors (SERPIN), currently displaying a large repertoire of functions in vertebrates. Accordingly, the recent duplicates SERPINB3 and B4 located in human 18q21.3 SERPIN cluster control the activity of different cysteine and serine proteases, respectively. Here, we aim to assess SERPINB3 and B4 coevolution with their target proteases in order to understand the evolutionary forces shaping the accelerated divergence of these duplicates. Phylogenetic analysis of primate sequences placed the duplication event in a Hominoidae ancestor (∼30 Mya) and the emergence of SERPINB3 in Homininae (∼9 Mya). We detected evidence of strong positive selection throughout SERPINB4/B3 primate tree and target proteases, cathepsin L2 (CTSL2) and G (CTSG) and chymase (CMA1). Specifically, in the Homininae clade a perfect match was observed between the adaptive evolution of SERPINB3 and cathepsin S (CTSS) and most of sites under positive selection were located at the inhibitor/protease interface. Altogether our results seem to favour a coevolution hypothesis for SERPINB3, CTSS and CTSL2 and for SERPINB4 and CTSG and CMA1. A scenario of an accelerated evolution driven by host-pathogen interactions is also possible since SERPINB3/B4 are potent inhibitors of exogenous proteases, released by infectious agents. Finally, similar patterns of expression and the sharing of many regulatory motifs suggest neofunctionalization as the best fitted model of the functional divergence of SERPINB3 and B4 duplicates. PMID:25133778

Origins of altruism diversity II: Runaway co-evolution of altruistic strategies via “reciprocal niche construction”

PubMed Central

Van Dyken, J. David; Wade, Michael J.

2012-01-01

Understanding the evolution of altruism requires knowledge of both its constraints and its drivers. Here we show that, paradoxically, ecological constraints on altruism may ultimately be its strongest driver. We construct a two-trait, co-evolutionary adaptive dynamics model of social evolution in a genetically structured population with local resource competition. The intensity of local resource competition, which influences the direction and strength of social selection and which is typically treated as a static parameter, is here allowed to be an evolvable trait. Evolution of survival/fecundity altruism, which requires weak local competition, increases local competition as it evolves, creating negative environmental feedback that ultimately inhibits its further evolutionary advance. Alternatively, evolution of resource-based altruism, which requires strong local competition, weakens local competition as it evolves, also ultimately causing its own evolution to stall. When evolving independently, these altruistic strategies are intrinsically self-limiting. However, the co-existence of these two altruism types transforms the negative eco-evolutionary feedback generated by each strategy on itself into positive feedback on the other, allowing the presence of one trait to drive the evolution of the other. We call this feedback conversion “reciprocal niche construction”. In the absence of constraints, this process leads to runaway co-evolution of altruism types. We discuss applications to the origins and evolution of eusociality, division of labor, the inordinate ecological success of eusocial species, and the interaction between technology and demography in human evolution. Our theory suggests that the evolution of extreme sociality may often be an autocatalytic process. PMID:22834748

The coevolutionary dynamics of obligate ant social parasite systems--between prudence and antagonism.

PubMed

Brandt, Miriam; Foitzik, Susanne; Fischer-Blass, Birgit; Heinze, Jürgen

2005-05-01

In this synthesis we apply coevolutionary models to the interactions between socially parasitic ants and their hosts. Obligate social parasite systems are ideal models for coevolution, because the close phylogenetic relationship between these parasites and their hosts results in similar evolutionary potentials, thus making mutual adaptations in a stepwise fashion especially likely to occur. The evolutionary dynamics of host-parasite interactions are influenced by a number of parameters, for example the parasite's transmission mode and rate, the genetic structure of host and parasite populations, the antagonists' migration rates, and the degree of mutual specialisation. For the three types of obligate ant social parasites, queen-tolerant and queen-intolerant inquilines and slavemakers, several of these parameters, and thus the evolutionary trajectory, are likely to differ. Because of the fundamental differences in lifestyle between these social parasite systems, coevolution should further select for different traits in the parasites and their hosts. Queen-tolerant inquilines are true parasites that exert a low selection pressure on their host, because of their rarity and the fact that they do not conduct slave raids to replenish their labour force. Due to their high degree of specialisation and the potential for vertical transmission, coevolutionary theory would predict interactions between these workerless parasites and their hosts to become even more benign over time. Queen-intolerant inquilines that kill the host queen during colony take-over are best described as parasitoids, and their reproductive success is limited by the existing worker force of the invaded host nest. These parasites should therefore evolve strategies to best exploit this fixed resource. Slavemaking ants, by contrast, act as parasites only during colony foundation, while their frequent slave raids follow a predator prey dynamic. They often exploit a number of host species at a given site, and theory predicts that their associations are best described in terms of a highly antagonistic coevolutionary arms race.

Positive selection on human gamete-recognition genes

PubMed Central

Stover, Daryn A.; Guerra, Vanessa; Mozaffari, Sahar V.; Ober, Carole; Mugal, Carina F.; Kaj, Ingemar

2018-01-01

Coevolution of genes that encode interacting proteins expressed on the surfaces of sperm and eggs can lead to variation in reproductive compatibility between mates and reproductive isolation between members of different species. Previous studies in mice and other mammals have focused in particular on evidence for positive or diversifying selection that shapes the evolution of genes that encode sperm-binding proteins expressed in the egg coat or zona pellucida (ZP). By fitting phylogenetic models of codon evolution to data from the 1000 Genomes Project, we identified candidate sites evolving under diversifying selection in the human genes ZP3 and ZP2. We also identified one candidate site under positive selection in C4BPA, which encodes a repetitive protein similar to the mouse protein ZP3R that is expressed in the sperm head and binds to the ZP at fertilization. Results from several additional analyses that applied population genetic models to the same data were consistent with the hypothesis of selection on those candidate sites leading to coevolution of sperm- and egg-expressed genes. By contrast, we found no candidate sites under selection in a fourth gene (ZP1) that encodes an egg coat structural protein not directly involved in sperm binding. Finally, we found that two of the candidate sites (in C4BPA and ZP2) were correlated with variation in family size and birth rate among Hutterite couples, and those two candidate sites were also in linkage disequilibrium in the same Hutterite study population. All of these lines of evidence are consistent with predictions from a previously proposed hypothesis of balancing selection on epistatic interactions between C4BPA and ZP3 at fertilization that lead to the evolution of co-adapted allele pairs. Such patterns also suggest specific molecular traits that may be associated with both natural reproductive variation and clinical infertility. PMID:29340252

Protein 3D Structure Computed from Evolutionary Sequence Variation

PubMed Central

Sheridan, Robert; Hopf, Thomas A.; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

2011-01-01

The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing. In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy. We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues., including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7–4.8 Å Cα-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein structures, new strategies in protein and drug design, and the identification of functional genetic variants in normal and disease genomes. PMID:22163331

Design, synthesis and evaluation of a potent substrate analog inhibitor identified by scanning Ala/Phe mutagenesis, mimicking substrate co-evolution, against multidrug-resistant HIV-1 protease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yedidi, Ravikiran S.; Muhuhi, Joseck M.; Liu, Zhigang

Highlights: •Inhibitors against MDR HIV-1 protease were designed, synthesized and evaluated. •Lead peptide (6a) showed potent inhibition (IC{sub 50}: 4.4 nM) of MDR HIV-1 protease. •(6a) Showed favorable binding isotherms against NL4-3 and MDR proteases. •(6a) Induced perturbations in the {sup 15}N-HSQC spectrum of MDR HIV-1 protease. •Molecular modeling suggested that (6a) may induce total flap closure inMDR protease. -- Abstract: Multidrug-resistant (MDR) clinical isolate-769, human immunodeficiency virus type-1 (HIV-1) protease (PDB ID: (1TW7)), was shown to exhibit wide-open flaps and an expanded active site cavity, causing loss of contacts with protease inhibitors. In the current study, the expanded activemore » site cavity of MDR769 HIV-1 protease was screened with a series of peptide-inhibitors that were designed to mimic the natural substrate cleavage site, capsid/p2. Scanning Ala/Phe chemical mutagenesis approach was incorporated into the design of the peptide series to mimic the substrate co-evolution. Among the peptides synthesized and evaluated, a lead peptide (6a) with potent activity (IC{sub 50}: 4.4 nM) was identified against the MDR769 HIV-1 protease. Isothermal titration calorimetry data showed favorable binding profile for 6aagainst both wild type and MDR769 HIV-1 protease variants. Nuclear magnetic resonance spectrum of {sup 15}N-labeled MDR769 HIV-1 protease in complex with 6a showed some major perturbations in chemical shift, supporting the peptide induced conformational changes in protease. Modeling analysis revealed multiple contacts between 6a and MDR769 HIV-1 protease. The lead peptide-inhibitor, 6a, with high potency and good binding profile can be used as the basis for developing potent small molecule inhibitors against MDR variants of HIV.« less

Food fight: sexual conflict over free amino acids in the nuptial gifts of male decorated crickets.

PubMed

Gershman, S N; Hunt, J; Sakaluk, S K

2013-04-01

In decorated crickets, Gryllodes sigillatus, the spermatophore that a male transfers at mating includes a gelatinous spermatophylax that the female consumes, delaying her removal of the sperm-filled ampulla. Male fertilization success increases with the length of time females spend feeding on the spermatophylax, while females may benefit by prematurely discarding the spermatophylaxes of undesirable males. This sexual conflict should favour males that produce increasingly appealing spermatophylaxes, and females that resist this manipulation. To determine the genetic basis of female spermatophylax feeding behaviour, we fed spermatophylaxes to females of nine inbred lines and found that female genotype had a major influence on spermatophylax feeding duration. The amino acid composition of the spermatophylax was also significantly heritable. There was a positive genetic correlation between spermatophylax feeding duration and the gustatory appeal of the spermatophylax. This correlation suggests that genes expressed in males that produce more manipulative spermatophylaxes are positively linked to genes expressed in females that make them more vulnerable to manipulation. Outbred females spent less time feeding on spermatophylaxes than inbred females, and thus showed greater resistance to male manipulation. Further, in a nonspermatophylax producing cricket (Acheta domesticus), females were significantly more prone to feeding on spermatophylaxes than outbred female Gryllodes. Collectively, these results suggest a history of sexually antagonistic coevolution over the consumption of nuptial food gifts. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Radiolarians decreased silicification as an evolutionary response to reduced Cenozoic ocean silica availability.

PubMed

Lazarus, David B; Kotrc, Benjamin; Wulf, Gerwin; Schmidt, Daniela N

2009-06-09

It has been hypothesized that increased water column stratification has been an abiotic "universal driver" affecting average cell size in Cenozoic marine plankton. Gradually decreasing Cenozoic radiolarian shell weight, by contrast, suggests that competition for dissolved silica, a shared nutrient, resulted in biologic coevolution between radiolaria and marine diatoms, which expanded dramatically in the Cenozoic. We present data on the 2 components of shell weight change--size and silicification--of Cenozoic radiolarians. In low latitudes, increasing Cenozoic export of silica to deep waters by diatoms and decreasing nutrient upwelling from increased water column stratification have created modern silica-poor surface waters. Here, radiolarian silicification decreases significantly (r = 0.91, P < 0.001), from approximately 0.18 (shell volume fraction) in the basal Cenozoic to modern values of approximately 0.06. A third of the total change occurred rapidly at 35 Ma, in correlation to major increases in water column stratification and abundance of diatoms. In high southern latitudes, Southern Ocean circulation, present since the late Eocene, maintains significant surface water silica availability. Here, radiolarian silicification decreased insignificantly (r = 0.58, P = 0.1), from approximately 0.13 at 35 Ma to 0.11 today. Trends in shell size in both time series are statistically insignificant and are not correlated with each other. We conclude that there is no universal driver changing cell size in Cenozoic marine plankton. Furthermore, biologic and physical factors have, in concert, by reducing silica availability in surface waters, forced macroevolutionary changes in Cenozoic low-latitude radiolarians.

How Did the Spider Cross the River? Behavioral Adaptations for River-Bridging Webs in Caerostris darwini (Araneae: Araneidae)

PubMed Central

Gregorič, Matjaž; Agnarsson, Ingi; Blackledge, Todd A.; Kuntner, Matjaž

2011-01-01

Background Interspecific coevolution is well described, but we know significantly less about how multiple traits coevolve within a species, particularly between behavioral traits and biomechanical properties of animals' “extended phenotypes”. In orb weaving spiders, coevolution of spider behavior with ecological and physical traits of their webs is expected. Darwin's bark spider (Caerostris darwini) bridges large water bodies, building the largest known orb webs utilizing the toughest known silk. Here, we examine C. darwini web building behaviors to establish how bridge lines are formed over water. We also test the prediction that this spider's unique web ecology and architecture coevolved with new web building behaviors. Methodology We observed C. darwini in its natural habitat and filmed web building. We observed 90 web building events, and compared web building behaviors to other species of orb web spiders. Conclusions Caerostris darwini uses a unique set of behaviors, some unknown in other spiders, to construct its enormous webs. First, the spiders release unusually large amounts of bridging silk into the air, which is then carried downwind, across the water body, establishing bridge lines. Second, the spiders perform almost no web site exploration. Third, they construct the orb capture area below the initial bridge line. In contrast to all known orb-weavers, the web hub is therefore not part of the initial bridge line but is instead built de novo. Fourth, the orb contains two types of radial threads, with those in the upper half of the web doubled. These unique behaviors result in a giant, yet rather simplified web. Our results continue to build evidence for the coevolution of behavioral (web building), ecological (web microhabitat) and biomaterial (silk biomechanics) traits that combined allow C. darwini to occupy a unique niche among spiders. PMID:22046378

Co-evolving Physical and Biological Organization in Step-pool Channels: Experiments from a Restoration Reach on Wildcat Creek, California

NASA Astrophysics Data System (ADS)

Chin, A.; O'Dowd, A. P.; Mendez, P. K.; Velasco, K. Z.; Leventhal, R. D.; Storesund, R.; Laurencio, L. R.

2014-12-01

Step-pools are important features in fluvial systems. Through energy dissipation, step-pools provide stability in high-energy environments that otherwise may erode and degrade. Although research has focused on geomorphological aspects of step-pool channels, the ecological significance of step-pool streams is increasingly recognized. Step-pool streams often contain higher density and diversity of benthic macroinvertebrates and are critical habitats for organisms such as salmonids and tailed frogs. Step-pools are therefore increasingly used to restore eroding channels and improve ecological conditions. This paper addresses a restoration reach of Wildcat Creek in Berkeley, California that featured an installation of step-pools in 2012. The design framework recognized step-pool formation as a self-organizing process that produces a rhythmic morphology. After placing step particles at locations where step-pools are expected to form according to hydraulic theory, the self-organizing approach allowed fluvial processes to refine the rocks into adjusted sequences over time. In addition, a 30-meter "experimental" reach was created to explore the co-evolution of geomorphological and ecological characteristics. After constructing a plane bed channel, boulders and cobbles piled at the upstream end allowed natural flows to mobilize and sort them into step-pool sequences. Ground surveys and LiDAR recorded the development of step-pool sequences over several seasons. Concurrent sampling of benthic macroinvertebrates documented the formation of biological communities in conjunction with habitat. Biological sampling in an upstream reference reach provided a comparison with the restored reach over time. Results to date show an emergent step-pool channel with steps that segment the plane bed into initial step and pool habitats. Biological communities are beginning to form, showing more distinction among habitat types during some seasons, although they do not yet approach reference values at this stage of development. Research over longer timeframes is needed to reveal how biological and physical characteristics may co-organize toward an equilibrium landscape. Such integrated understanding will assist development of innovative restoration designs.

The Compton-thick Growth of Supermassive Black Holes constrained

NASA Astrophysics Data System (ADS)

Buchner, Johannes; Georgakakis, Antonis; Nandra, Kirpal; Brightman, Murray; Menzel, Marie-Luise; Liu, Zhu; Hsu, Li-Ting; Salvato, Mara; Rangel, Cyprian; Aird, James

2017-08-01

A heavily obscured growth phase of supermassive black holes (SMBH) is thought to be important in the co-evolution with galaxies. X-rays provide a clean and efficient selection of unobscured and obscured AGN. Recent work with deeper observations and improved analysis methodology allowed us to extend constraints to Compton-thick number densities. We present the first luminosity function of Compton-thick AGN at z=0.5-4 and constrain the overall mass density locked into black holes over cosmic time, a fundamental constraint for cosmological simulations. Recent studies including ours find that the obscuration is redshift and luminosity-dependent in a complex way, which rules out entire sets of obscurer models. A new paradigm, the radiation-lifted torus model, is proposed, in which the obscurer is Eddington-rate dependent and accretion creates and displaces torus clouds. We place observational limits on the behaviour of this mechanism.

The Compton-thick Growth of Supermassive Black Holes constrained

NASA Astrophysics Data System (ADS)

Buchner, J.; Georgakakis, A.; Nandra, K.

2017-10-01

A heavily obscured growth phase of supermassive black holes (SMBH) is thought to be important in the co-evolution with galaxies. X-rays provide a clean and efficient selection of unobscured and obscured AGN. Recent work with deeper observations and improved analysis methodology allowed us to extend constraints to Compton-thick number densities. We present the first luminosity function of Compton-thick AGN at z=0.5-4 and constrain the overall mass density locked into black holes over cosmic time, a fundamental constraint for cosmological simulations. Recent studies including ours find that the obscuration is redshift and luminosity-dependent in a complex way, which rules out entire sets of obscurer models. A new paradigm, the radiation-lifted torus model, is proposed, in which the obscurer is Eddington-rate dependent and accretion creates and displaces torus clouds. We place observational limits on the behaviour of this mechanism.

Three-dimensional co-culture models to study prostate cancer growth, progression, and metastasis to bone.

PubMed

Wang, Ruoxiang; Xu, Jianchun; Juliette, Lisa; Castilleja, Agapito; Love, John; Sung, Shian-Ying; Zhau, Haiyen E; Goodwin, Thomas J; Chung, Leland W K

2005-10-01

Cancer-stromal interaction results in the co-evolution of both the cancer cells and the surrounding host stromal cells. As a consequence of this interaction, cancer cells acquire increased malignant potential and stromal cells become more inductive. In this review we suggest that cancer-stromal interaction can best be investigated by three-dimensional (3D) co-culture models with the results validated by clinical specimens. We showed that 3D culture promoted bone formation in vitro, and explored for the first time, with the help of the astronauts of the Space Shuttle Columbia, the co-culture of human prostate cancer and bone cells to further understand the interactions between these cells. Continued exploration of cancer growth under 3D conditions will rapidly lead to new discoveries and ultimately to improvements in the treatment of men with hormonal refractory prostate cancer.

The powdery mildews: a review of the world's most familiar (yet poorly known) plant pathogens.

PubMed

Glawe, Dean A

2008-01-01

The past decade has seen fundamental changes in our understanding of powdery mildews (Erysiphales). Research on molecular phylogeny demonstrated that Erysiphales are Leotiomycetes (inoperculate discomycetes) rather than Pyrenomycetes or Plectomycetes. Life cycles are surprisingly variable, including both sexual and asexual states, or only sexual states, or only asexual states. At least one species produces dematiaceous conidia. Analyses of rDNA sequences indicate that major lineages are more closely correlated with anamorphic features such as conidial ontogeny and morphology than with teleomorph features. Development of molecular clock models is enabling researchers to reconstruct patterns of coevolution and host-jumping, as well as ancient migration patterns. Geographic distributions of some species appear to be increasing rapidly but little is known about species diversity in many large areas, including North America. Powdery mildews may already be responding to climate change, suggesting they may be useful models for studying effects of climate change on plant diseases.

Summary of FY17 ParaChoice Accomplishments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Levinson, Rebecca Sobel; West, Todd H.

As part of analysis support for FCTO, Sandia assesses the factors that influence the future of FCEVs and Hydrogen in the US vehicle fleet. Using ParaChoice, we model competition between FCEVs, conventional vehicles, and other alternative vehicle technologies in order to understand the drivers and sensitivities of adoption of FCEVs. ParaChoice leverages existing tools such as Autonomie (Moawad et al., 2016), AEO (U.S. Energy Information Administration, 2016), and the Macro System Model (Ruth et al., 2009) in order to synthesize a complete picture of the co-evolution of vehicle technology development, energy price evolution, and hydrogen production and pricing, with consumermore » demand for vehicles and fuel. We then assess impacts of FCEV market penetration and hydrogen use on green- house gas (GHG) emissions and petroleum consumption, providing context for the role of policy, technology development, infrastructure, and consumer behavior on the vehicle and fuel mix through parametric and sensitivity analyses.« less

Correlated evolution in parental care in females but not males in response to selection on paternity assurance behaviour.

PubMed

Head, Megan L; Hinde, Camilla A; Moore, Allen J; Royle, Nick J

2014-07-01

According to classical parental care theory males are expected to provide less parental care when offspring in a brood are less likely to be their own, but empirical evidence in support of this relationship is equivocal. Recent work predicts that social interactions between the sexes can modify co-evolution between traits involved in mating and parental care as a result of costs associated with these social interactions (i.e. sexual conflict). In burying beetles (Nicrophorus vespilloides), we use artificial selection on a paternity assurance trait, and crosses within and between selection lines, to show that selection acting on females, not males, can drive the co-evolution of paternity assurance traits and parental care. Males do not care more in response to selection on mating rate. Instead, patterns of parental care change as an indirect response to costs of mating for females. © 2014 The Authors. Ecology Letters published by John Wiley & Sons Ltd and CNRS.

Ant Species Differences Determined by Epistasis between Brood and Worker Genomes

PubMed Central

Linksvayer, Timothy A.

2007-01-01

Epistasis arising from physiological interactions between gene products often contributes to species differences, particularly those involved in reproductive isolation. In social organisms, phenotypes are influenced by the genotypes of multiple interacting individuals. In theory, social interactions can give rise to an additional type of epistasis between the genomes of social partners that can contribute to species differences. Using a full-factorial cross-fostering design with three species of closely related Temnothorax ants, I found that adult worker size was determined by an interaction between the genotypes of developing brood and care-giving workers, i.e. intergenomic epistasis. Such intergenomic social epistasis provides a strong signature of coevolution between social partners. These results demonstrate that just as physiologically interacting genes coevolve, diverge, and contribute to species differences, so do socially interacting genes. Coevolution and conflict between social partners, especially relatives such as parents and offspring, has long been recognized as having widespread evolutionary effects. This coevolutionary process may often result in coevolved socially-interacting gene complexes that contribute to species differences. PMID:17912371

Novel paramyxoviruses in Australian flying-fox populations support host-virus co-evolution.

PubMed

Vidgen, Miranda E; de Jong, Carol; Rose, Karrie; Hall, Jane; Field, Hume E; Smith, Craig S

2015-07-01

Understanding the diversity of henipaviruses and related viruses is important in determining the viral ecology within flying-fox populations and assessing the potential threat posed by these agents. This study sought to identify the abundance and diversity of previously unknown paramyxoviruses (UPVs) in Australian flying-fox species (Pteropus alecto, Pteropus scapulatus, Pteropus poliocephalus and Pteropus conspicillatus) and in the Christmas Island species Pteropus melanotus natalis. Using a degenerative reverse transcription-PCR specific for the L gene of known species of the genus Henipavirus and two closely related paramyxovirus genera Respirovirus and Morbillivirus, we identified an abundance and diversity of previously UPVs, with a representative 31 UPVs clustering in eight distinct groups (100 UPVs/495 samples). No new henipaviruses were identified. The findings were consistent with a hypothesis of co-evolution of paramyxoviruses and their flying-fox hosts. Quantification of the degree of co-speciation between host and virus (beyond the scope of this study) would strengthen this hypothesis.

Long-legged bees make adaptive leaps: linking adaptation to coevolution in a plant-pollinator network.

PubMed

Pauw, Anton; Kahnt, Belinda; Kuhlmann, Michael; Michez, Denis; Montgomery, Graham A; Murray, Elizabeth; Danforth, Bryan N

2017-09-13

Adaptation is evolution in response to natural selection. Hence, an adaptation is expected to originate simultaneously with the acquisition of a particular selective environment. Here we test whether long legs evolve in oil-collecting Rediviva bees when they come under selection by long-spurred, oil-secreting flowers. To quantify the selective environment, we drew a large network of the interactions between Rediviva species and oil-secreting plant species. The selective environment of each bee species was summarized as the average spur length of the interacting plant species weighted by interaction frequency. Using phylogenetically independent contrasts, we calculated divergence in selective environment and evolutionary divergence in leg length between sister species (and sister clades) of Rediviva We found that change in the selective environment explained 80% of evolutionary change in leg length, with change in body size contributing an additional 6% of uniquely explained variance. The result is one of four proposed steps in testing for plant-pollinator coevolution. © 2017 The Author(s).