Lunar base launch and landing facility conceptual design, 2nd edition

NASA Technical Reports Server (NTRS)

1988-01-01

This report documents the Lunar Base Launch and Landing Facility Conceptual Design study. The purpose of this study was to examine the requirements for launch and landing facilities for early lunar bases and to prepare conceptual designs for some of these facilities. The emphasis of this study is on the facilities needed from the first manned landing until permanent occupancy. Surface characteristics and flight vehicle interactions are described, and various facility operations are related. Specific recommendations for equipment, facilities, and evolutionary planning are made, and effects of different aspects of lunar development scenarios on facilities and operations are detailed. Finally, for a given scenario, a specific conceptual design is developed and presented.

Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae) on the Canary Islands.

PubMed

Sun, Ye; Vargas-Mendoza, Carlos F

2017-01-01

Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat). The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote) and western islands (EI Hierro, La Palma, La Gomera, Tenerife), this west-east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.

Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae) on the Canary Islands

PubMed Central

Sun, Ye; Vargas-Mendoza, Carlos F.

2017-01-01

Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat). The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote) and western islands (EI Hierro, La Palma, La Gomera, Tenerife), this west–east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago. PMID:28713419

Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes

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

Mueller, Rachel Lockridge; Macey, J. Robert; Jaekel, Martin

2004-08-01

The evolutionary history of the largest salamander family (Plethodontidae) is characterized by extreme morphological homoplasy. Analysis of the mechanisms generating such homoplasy requires an independent, molecular phylogeny. To this end, we sequenced 24 complete mitochondrial genomes (22 plethodontids and two outgroup taxa), added data for three species from GenBank, and performed partitioned and unpartitioned Bayesian, ML, and MP phylogenetic analyses. We explored four dataset partitioning strategies to account for evolutionary process heterogeneity among genes and codon positions, all of which yielded increased model likelihoods and decreased numbers of supported nodes in the topologies (PP > 0.95) relative to the unpartitionedmore » analysis. Our phylogenetic analyses yielded congruent trees that contrast with the traditional morphology-based taxonomy; the monophyly of three out of four major groups is rejected. Reanalysis of current hypotheses in light of these new evolutionary relationships suggests that (1) a larval life history stage re-evolved from a direct-developing ancestor multiple times, (2) there is no phylogenetic support for the ''Out of Appalachia'' hypothesis of plethodontid origins, and (3) novel scenarios must be reconstructed for the convergent evolution of projectile tongues, reduction in toe number, and specialization for defensive tail loss. Some of these novel scenarios imply morphological transformation series that proceed in the opposite direction than was previously thought. In addition, they suggest surprising evolutionary lability in traits previously interpreted to be conservative.« less

Lunar and Mars missions - Challenges for advanced life support

NASA Technical Reports Server (NTRS)

Duke, Michael B.

1988-01-01

The development of a suite of scenarios is a prerequisite to the studies that will enable an informed decision by the United States on a program to meet the recently announced space policy goal to expand human presence beyond earth orbit. NASA's Office of Exploration is currently studying a range of initiative options that would extend the sphere of human activity in space to Mars and include permanent bases or outposts on the moon and on Mars. This paper describes the evolutionary lunar base and the Mars expedition scenarios in some detail so that an evaluation can be made from the point of view of human support and opportunities. Alternative approaches in the development of lunar outposts are outlined along with Mars expeditionary scenarios. Human environmental issues are discussed, including: closed loop life support systems; EVA systems; mobility systems; and medical support, physiological deconditioning, and psychological effects associated with long-duration missions.

Deuterium and 15N fractionation in N2H+ during the formation of a Sun-like star

NASA Astrophysics Data System (ADS)

De Simone, M.; Fontani, F.; Codella, C.; Ceccarelli, C.; Lefloch, B.; Bachiller, R.; López-Sepulcre, A.; Caux, E.; Vastel, C.; Soldateschi, J.

2018-05-01

Although chemical models predict that the deuterium fractionation in N2H+ is a good evolutionary tracer in the star formation process, the fractionation of nitrogen is still a poorly understood process. Recent models have questioned the similar evolutionary trend expected for the two fractionation mechanisms in N2H+, based on a classical scenario in which ion-neutral reactions occurring in cold gas should have caused an enhancement of the abundance of N2D+, 15NNH+, and N15NH+. In the framework of the ASAI IRAM-30m large program, we have investigated the fractionation of deuterium and 15N in N2H+ in the best known representatives of the different evolutionary stages of the Sun-like star formation process. The goal is to ultimately confirm (or deny) the classical `ion-neutral reactions' scenario that predicts a similar trend for D and 15N fractionation. We do not find any evolutionary trend of the 14N/15N ratio from both the 15NNH+ and N15NH+ isotopologues. Therefore, our findings confirm that, during the formation of a Sun-like star, the core evolution is irrelevant in the fractionation of 15N. The independence of the 14N/15N ratio with time, found also in high-mass star-forming cores, indicates that the enrichment in 15N revealed in comets and protoplanetary discs is unlikely to happen at core scales. Nevertheless, we have firmly confirmed the evolutionary trend expected for the H/D ratio, with the N2H+/N2D+ ratio decreasing before the pre-stellar core phase, and increasing monotonically during the protostellar phase. We have also confirmed clearly that the two fractionation mechanisms are not related.

Communications system evolutionary scenarios for Martian SEI support

NASA Technical Reports Server (NTRS)

Kwong, Paulman W.; Bruno, Ronald C.

1992-01-01

In the Space Exploration Initiative (SEI) mission scenarios, expanding human presence is the primary driver for high data rate Mars-Earth communications. To support an expanding human presence, the data rate requirement will be gradual, following the phased implementation over time of the evolving SEI mission. Similarly, the growth and evolution of the space communications infrastructure to serve this requirement will also be gradual to efficiently exploit the useful life of the installed communications infrastructure and to ensure backward compatibility with long-term users. In work conducted over the past year, a number of alternatives for supporting high data rate Mars-Earth communications have been analyzed with respect to their compatibility with gradual evolution of the space communications infrastructure. The alternatives include RF, millimeter wave (MMW), and optical implementations, and incorporate both surface and space-based relay terminals in the Mars and Earth regions. Each alternative is evaluated with respect to its ability to efficiently meet a projected growth in data rate over time, its technology readiness, and its capability to satisfy the key conditions and constraints imposed by evolutionary transition. As a result of this analysis, a set of attractive alternative communications architectures have been identified and described, and a road map is developed that illustrates the most rational and beneficial evolutionary paths for the communications infrastructure.

Orbital Debris Modeling

NASA Technical Reports Server (NTRS)

Liou, J. C.

2012-01-01

Presentation outlne: (1) The NASA Orbital Debris (OD) Engineering Model -- A mathematical model capable of predicting OD impact risks for the ISS and other critical space assets (2) The NASA OD Evolutionary Model -- A physical model capable of predicting future debris environment based on user-specified scenarios (3) The NASA Standard Satellite Breakup Model -- A model describing the outcome of a satellite breakup (explosion or collision)

Space station needs, attributes and architectural options. Volume 1: Executive summary NASA

NASA Technical Reports Server (NTRS)

1983-01-01

The uses alignment plan was implemented. The existing data bank was used to define a large number of station requirements. Ten to 20 valid mission scenarios were developed. Architectural options as they are influenced by communications operations, subsystem evolvability, and required technology growth are defined. Costing of evolutionary concepts, alternative approaches, and options, was based on minimum design details.

Multi-objective evolutionary algorithms for fuzzy classification in survival prediction.

PubMed

Jiménez, Fernando; Sánchez, Gracia; Juárez, José M

2014-03-01

This paper presents a novel rule-based fuzzy classification methodology for survival/mortality prediction in severe burnt patients. Due to the ethical aspects involved in this medical scenario, physicians tend not to accept a computer-based evaluation unless they understand why and how such a recommendation is given. Therefore, any fuzzy classifier model must be both accurate and interpretable. The proposed methodology is a three-step process: (1) multi-objective constrained optimization of a patient's data set, using Pareto-based elitist multi-objective evolutionary algorithms to maximize accuracy and minimize the complexity (number of rules) of classifiers, subject to interpretability constraints; this step produces a set of alternative (Pareto) classifiers; (2) linguistic labeling, which assigns a linguistic label to each fuzzy set of the classifiers; this step is essential to the interpretability of the classifiers; (3) decision making, whereby a classifier is chosen, if it is satisfactory, according to the preferences of the decision maker. If no classifier is satisfactory for the decision maker, the process starts again in step (1) with a different input parameter set. The performance of three multi-objective evolutionary algorithms, niched pre-selection multi-objective algorithm, elitist Pareto-based multi-objective evolutionary algorithm for diversity reinforcement (ENORA) and the non-dominated sorting genetic algorithm (NSGA-II), was tested using a patient's data set from an intensive care burn unit and a standard machine learning data set from an standard machine learning repository. The results are compared using the hypervolume multi-objective metric. Besides, the results have been compared with other non-evolutionary techniques and validated with a multi-objective cross-validation technique. Our proposal improves the classification rate obtained by other non-evolutionary techniques (decision trees, artificial neural networks, Naive Bayes, and case-based reasoning) obtaining with ENORA a classification rate of 0.9298, specificity of 0.9385, and sensitivity of 0.9364, with 14.2 interpretable fuzzy rules on average. Our proposal improves the accuracy and interpretability of the classifiers, compared with other non-evolutionary techniques. We also conclude that ENORA outperforms niched pre-selection and NSGA-II algorithms. Moreover, given that our multi-objective evolutionary methodology is non-combinational based on real parameter optimization, the time cost is significantly reduced compared with other evolutionary approaches existing in literature based on combinational optimization. Copyright © 2014 Elsevier B.V. All rights reserved.

Health care professional workstation: software system construction using DSSA scenario-based engineering process.

PubMed

Hufnagel, S; Harbison, K; Silva, J; Mettala, E

1994-01-01

This paper describes a new method for the evolutionary determination of user requirements and system specifications called scenario-based engineering process (SEP). Health care professional workstations are critical components of large scale health care system architectures. We suggest that domain-specific software architectures (DSSAs) be used to specify standard interfaces and protocols for reusable software components throughout those architectures, including workstations. We encourage the use of engineering principles and abstraction mechanisms. Engineering principles are flexible guidelines, adaptable to particular situations. Abstraction mechanisms are simplifications for management of complexity. We recommend object-oriented design principles, graphical structural specifications, and formal components' behavioral specifications. We give an ambulatory care scenario and associated models to demonstrate SEP. The scenario uses health care terminology and gives patients' and health care providers' system views. Our goal is to have a threefold benefit. (i) Scenario view abstractions provide consistent interdisciplinary communications. (ii) Hierarchical object-oriented structures provide useful abstractions for reuse, understandability, and long term evolution. (iii) SEP and health care DSSA integration into computer aided software engineering (CASE) environments. These environments should support rapid construction and certification of individualized systems, from reuse libraries.

Using genomics to characterize evolutionary potential for conservation of wild populations

PubMed Central

Harrisson, Katherine A; Pavlova, Alexandra; Telonis-Scott, Marina; Sunnucks, Paul

2014-01-01

Genomics promises exciting advances towards the important conservation goal of maximizing evolutionary potential, notwithstanding associated challenges. Here, we explore some of the complexity of adaptation genetics and discuss the strengths and limitations of genomics as a tool for characterizing evolutionary potential in the context of conservation management. Many traits are polygenic and can be strongly influenced by minor differences in regulatory networks and by epigenetic variation not visible in DNA sequence. Much of this critical complexity is difficult to detect using methods commonly used to identify adaptive variation, and this needs appropriate consideration when planning genomic screens, and when basing management decisions on genomic data. When the genomic basis of adaptation and future threats are well understood, it may be appropriate to focus management on particular adaptive traits. For more typical conservations scenarios, we argue that screening genome-wide variation should be a sensible approach that may provide a generalized measure of evolutionary potential that accounts for the contributions of small-effect loci and cryptic variation and is robust to uncertainty about future change and required adaptive response(s). The best conservation outcomes should be achieved when genomic estimates of evolutionary potential are used within an adaptive management framework. PMID:25553064

Reconciling the evolutionary origin of bread wheat (Triticum aestivum).

PubMed

El Baidouri, Moaine; Murat, Florent; Veyssiere, Maeva; Molinier, Mélanie; Flores, Raphael; Burlot, Laura; Alaux, Michael; Quesneville, Hadi; Pont, Caroline; Salse, Jérôme

2017-02-01

The origin of bread wheat (Triticum aestivum; AABBDD) has been a subject of controversy and of intense debate in the scientific community over the last few decades. In 2015, three articles published in New Phytologist discussed the origin of hexaploid bread wheat (AABBDD) from the diploid progenitors Triticum urartu (AA), a relative of Aegilops speltoides (BB) and Triticum tauschii (DD). Access to new genomic resources since 2013 has offered the opportunity to gain novel insights into the paleohistory of modern bread wheat, allowing characterization of its origin from its diploid progenitors at unprecedented resolution. We propose a reconciled evolutionary scenario for the modern bread wheat genome based on the complementary investigation of transposable element and mutation dynamics between diploid, tetraploid and hexaploid wheat. In this scenario, the structural asymmetry observed between the A, B and D subgenomes in hexaploid bread wheat derives from the cumulative effect of diploid progenitor divergence, the hybrid origin of the D subgenome, and subgenome partitioning following the polyploidization events. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Deontic Reasoning with Emotional Content: Evolutionary Psychology or Decision Theory?

ERIC Educational Resources Information Center

Perham, Nick; Oaksford, Mike

2005-01-01

Three experiments investigated the contrasting predictions of the evolutionary and decision-theoretic approaches to deontic reasoning. Two experiments embedded a hazard management (HM) rule in a social contract scenario that should lead to competition between innate modules. A 3rd experiment used a pure HM task. Threatening material was also…

WR and LBV stars

NASA Astrophysics Data System (ADS)

Kochiashvili, Nino; Beradze, Sophie; Kochiashvili, Ia; Natsvlishvili, Rezo; Vardosanidze, Manana

Evolutionary scenarios of massive stars were revised in recent decades, after finding "unusual", blue progenitor of SN 1987A and after detecting the more massive stars than the accepted 120 M ⊙ maximum limit of stellar masses. A very important relation exists between WR and LBV stars. They represent the earlier, pre-SN evolutionary states of massive stars. WR and LBV stars and "classic" evolutionary scheme of the relation between the different type massive stars are discussed in this article. There also exist the newest evolutionary scenarios for low metallicity massive stars, which give us a different picture of their post main-sequence evolution. There is a rather good tradition of observations and investigations of massive stars at Abastumani Astrophysical Observatory. The authors discuss the new findings on the fate of P Cygni, the LBV star. These results on the reddening of the star and about its next possible outburst in the near future were obtained on the basis of UBV long-term electrophotometric observations of P Cygni by Eugene Kharadze and Nino Magalashvili. The observations were held in 1951-1983 at Abastumani Observatory using 33-cm and 48-cm reflectors.

Wolf-Rayet stars, black holes and the first detected gravitational wave source

NASA Astrophysics Data System (ADS)

Bogomazov, A. I.; Cherepashchuk, A. M.; Lipunov, V. M.; Tutukov, A. V.

2018-01-01

The recently discovered burst of gravitational waves GW150914 provides a good new chance to verify the current view on the evolution of close binary stars. Modern population synthesis codes help to study this evolution from two main sequence stars up to the formation of two final remnant degenerate dwarfs, neutron stars or black holes (Masevich and Tutukov, 1988). To study the evolution of the GW150914 predecessor we use the ;Scenario Machine; code presented by Lipunov et al. (1996). The scenario modeling conducted in this study allowed to describe the evolution of systems for which the final stage is a massive BH+BH merger. We find that the initial mass of the primary component can be 100÷140M⊙ and the initial separation of the components can be 50÷350R⊙. Our calculations show the plausibility of modern evolutionary scenarios for binary stars and the population synthesis modeling based on it.

Kramers problem in evolutionary strategies

NASA Astrophysics Data System (ADS)

Dunkel, J.; Ebeling, W.; Schimansky-Geier, L.; Hänggi, P.

2003-06-01

We calculate the escape rates of different dynamical processes for the case of a one-dimensional symmetric double-well potential. In particular, we compare the escape rates of a Smoluchowski process, i.e., a corresponding overdamped Brownian motion dynamics in a metastable potential landscape, with the escape rates obtained for a biologically motivated model known as the Fisher-Eigen process. The main difference between the two models is that the dynamics of the Smoluchowski process is determined by local quantities, whereas the Fisher-Eigen process is based on a global coupling (nonlocal interaction). If considered in the context of numerical optimization algorithms, both processes can be interpreted as archetypes of physically or biologically inspired evolutionary strategies. In this sense, the results discussed in this work are utile in order to evaluate the efficiency of such strategies with regard to the problem of surmounting various barriers. We find that a combination of both scenarios, starting with the Fisher-Eigen strategy, provides a most effective evolutionary strategy.

Hyper-heuristic Evolution of Dispatching Rules: A Comparison of Rule Representations.

PubMed

Branke, Jürgen; Hildebrandt, Torsten; Scholz-Reiter, Bernd

2015-01-01

Dispatching rules are frequently used for real-time, online scheduling in complex manufacturing systems. Design of such rules is usually done by experts in a time consuming trial-and-error process. Recently, evolutionary algorithms have been proposed to automate the design process. There are several possibilities to represent rules for this hyper-heuristic search. Because the representation determines the search neighborhood and the complexity of the rules that can be evolved, a suitable choice of representation is key for a successful evolutionary algorithm. In this paper we empirically compare three different representations, both numeric and symbolic, for automated rule design: A linear combination of attributes, a representation based on artificial neural networks, and a tree representation. Using appropriate evolutionary algorithms (CMA-ES for the neural network and linear representations, genetic programming for the tree representation), we empirically investigate the suitability of each representation in a dynamic stochastic job shop scenario. We also examine the robustness of the evolved dispatching rules against variations in the underlying job shop scenario, and visualize what the rules do, in order to get an intuitive understanding of their inner workings. Results indicate that the tree representation using an improved version of genetic programming gives the best results if many candidate rules can be evaluated, closely followed by the neural network representation that already leads to good results for small to moderate computational budgets. The linear representation is found to be competitive only for extremely small computational budgets.

New Insight into the Colonization Processes of Common Voles: Inferences from Molecular and Fossil Evidence

PubMed Central

Tougard, Christelle; Renvoisé, Elodie; Petitjean, Amélie; Quéré, Jean-Pierre

2008-01-01

Elucidating the colonization processes associated with Quaternary climatic cycles is important in order to understand the distribution of biodiversity and the evolutionary potential of temperate plant and animal species. In Europe, general evolutionary scenarios have been defined from genetic evidence. Recently, these scenarios have been challenged with genetic as well as fossil data. The origins of the modern distributions of most temperate plant and animal species could predate the Last Glacial Maximum. The glacial survival of such populations may have occurred in either southern (Mediterranean regions) and/or northern (Carpathians) refugia. Here, a phylogeographic analysis of a widespread European small mammal (Microtus arvalis) is conducted with a multidisciplinary approach. Genetic, fossil and ecological traits are used to assess the evolutionary history of this vole. Regardless of whether the European distribution of the five previously identified evolutionary lineages is corroborated, this combined analysis brings to light several colonization processes of M. arvalis. The species' dispersal was relatively gradual with glacial survival in small favourable habitats in Western Europe (from Germany to Spain) while in the rest of Europe, because of periglacial conditions, dispersal was less regular with bottleneck events followed by postglacial expansions. Our study demonstrates that the evolutionary history of European temperate small mammals is indeed much more complex than previously suggested. Species can experience heterogeneous evolutionary histories over their geographic range. Multidisciplinary approaches should therefore be preferentially chosen in prospective studies, the better to understand the impact of climatic change on past and present biodiversity. PMID:18958287

Local Nash equilibrium in social networks.

PubMed

Zhang, Yichao; Aziz-Alaoui, M A; Bertelle, Cyrille; Guan, Jihong

2014-08-29

Nash equilibrium is widely present in various social disputes. As of now, in structured static populations, such as social networks, regular, and random graphs, the discussions on Nash equilibrium are quite limited. In a relatively stable static gaming network, a rational individual has to comprehensively consider all his/her opponents' strategies before they adopt a unified strategy. In this scenario, a new strategy equilibrium emerges in the system. We define this equilibrium as a local Nash equilibrium. In this paper, we present an explicit definition of the local Nash equilibrium for the two-strategy games in structured populations. Based on the definition, we investigate the condition that a system reaches the evolutionary stable state when the individuals play the Prisoner's dilemma and snow-drift game. The local Nash equilibrium provides a way to judge whether a gaming structured population reaches the evolutionary stable state on one hand. On the other hand, it can be used to predict whether cooperators can survive in a system long before the system reaches its evolutionary stable state for the Prisoner's dilemma game. Our work therefore provides a theoretical framework for understanding the evolutionary stable state in the gaming populations with static structures.

Local Nash Equilibrium in Social Networks

PubMed Central

Zhang, Yichao; Aziz-Alaoui, M. A.; Bertelle, Cyrille; Guan, Jihong

2014-01-01

Nash equilibrium is widely present in various social disputes. As of now, in structured static populations, such as social networks, regular, and random graphs, the discussions on Nash equilibrium are quite limited. In a relatively stable static gaming network, a rational individual has to comprehensively consider all his/her opponents' strategies before they adopt a unified strategy. In this scenario, a new strategy equilibrium emerges in the system. We define this equilibrium as a local Nash equilibrium. In this paper, we present an explicit definition of the local Nash equilibrium for the two-strategy games in structured populations. Based on the definition, we investigate the condition that a system reaches the evolutionary stable state when the individuals play the Prisoner's dilemma and snow-drift game. The local Nash equilibrium provides a way to judge whether a gaming structured population reaches the evolutionary stable state on one hand. On the other hand, it can be used to predict whether cooperators can survive in a system long before the system reaches its evolutionary stable state for the Prisoner's dilemma game. Our work therefore provides a theoretical framework for understanding the evolutionary stable state in the gaming populations with static structures. PMID:25169150

Local Nash Equilibrium in Social Networks

NASA Astrophysics Data System (ADS)

Zhang, Yichao; Aziz-Alaoui, M. A.; Bertelle, Cyrille; Guan, Jihong

2014-08-01

Nash equilibrium is widely present in various social disputes. As of now, in structured static populations, such as social networks, regular, and random graphs, the discussions on Nash equilibrium are quite limited. In a relatively stable static gaming network, a rational individual has to comprehensively consider all his/her opponents' strategies before they adopt a unified strategy. In this scenario, a new strategy equilibrium emerges in the system. We define this equilibrium as a local Nash equilibrium. In this paper, we present an explicit definition of the local Nash equilibrium for the two-strategy games in structured populations. Based on the definition, we investigate the condition that a system reaches the evolutionary stable state when the individuals play the Prisoner's dilemma and snow-drift game. The local Nash equilibrium provides a way to judge whether a gaming structured population reaches the evolutionary stable state on one hand. On the other hand, it can be used to predict whether cooperators can survive in a system long before the system reaches its evolutionary stable state for the Prisoner's dilemma game. Our work therefore provides a theoretical framework for understanding the evolutionary stable state in the gaming populations with static structures.

Star formation history: Modeling of visual binaries

NASA Astrophysics Data System (ADS)

Gebrehiwot, Y. M.; Tessema, S. B.; Malkov, O. Yu.; Kovaleva, D. A.; Sytov, A. Yu.; Tutukov, A. V.

2018-05-01

Most stars form in binary or multiple systems. Their evolution is defined by masses of components, orbital separation and eccentricity. In order to understand star formation and evolutionary processes, it is vital to find distributions of physical parameters of binaries. We have carried out Monte Carlo simulations in which we simulate different pairing scenarios: random pairing, primary-constrained pairing, split-core pairing, and total and primary pairing in order to get distributions of binaries over physical parameters at birth. Next, for comparison with observations, we account for stellar evolution and selection effects. Brightness, radius, temperature, and other parameters of components are assigned or calculated according to approximate relations for stars in different evolutionary stages (main-sequence stars, red giants, white dwarfs, relativistic objects). Evolutionary stage is defined as a function of system age and component masses. We compare our results with the observed IMF, binarity rate, and binary mass-ratio distributions for field visual binaries to find initial distributions and pairing scenarios that produce observed distributions.

Woese on the received view of evolution.

PubMed

Sarkar, Sahotra

2014-01-01

As part of his attempt to reconstruct the earliest phase of the evolution of life on Earth, Woese produced a compelling critique of the received view of evolution from the 20th century. This paper explicitly articulates two related features of that critique that are fundamental but the first of which has not been sufficiently clearly recognized in the context of evolutionary theorizing: (1) according to Woese's scenario of communal evolution during life's earliest phase (roughly, the first billion years of life on Earth), well-defined biological individuals (and, thus, individual lineages) did not exist; and (2) during that phase, evolutionary change took place through ubiquitous horizontal gene transfer (HGT) rather than through vertical transmission of features (including genes) and the combinatorics of HGT was the dominant mechanism of evolutionary change. Both factors present serious challenges to the received view of evolution and that framework would have to be radically altered to incorporate these factors. The extent to which this will be necessary will depend on whether Woese's scenario of collective early evolution is correct.

The dynamic evolutionary history of the bananaquit (Coereba flaveola) in the Caribbean revealed by a multigene analysis

PubMed Central

2008-01-01

Background The bananaquit (Coereba flaveola) is a small nectivorous and frugivorous emberizine bird (order Passeriformes) that is an abundant resident throughout the Caribbean region. We used multi-gene analyses to investigate the evolutionary history of this species throughout its distribution in the West Indies and in South and Middle America. We sequenced six mitochondrial genes (3744 base pairs) and three nuclear genes (2049 base pairs) for forty-four bananaquits and three outgroup species. We infer the ancestral area of the present-day bananaquit populations, report on the species' phylogenetic, biogeographic and evolutionary history, and propose scenarios for its diversification and range expansion. Results Phylogenetic concordance between mitochondrial and nuclear genes at the base of the bananaquit phylogeny supported a West Indian origin for continental populations. Multi-gene analysis showing genetic remnants of successive colonization events in the Lesser Antilles reinforced earlier research demonstrating that bananaquits alternate periods of invasiveness and colonization with biogeographic quiescence. Although nuclear genes provided insufficient information at the tips of the tree to further evaluate relationships of closely allied but strongly supported mitochondrial DNA clades, the discrepancy between mitochondrial and nuclear data in the population of Dominican Republic suggested that the mitochondrial genome was recently acquired by introgression from Jamaica. Conclusion This study represents one of the most complete phylogeographic analyses of its kind and reveals three patterns that are not commonly appreciated in birds: (1) island to mainland colonization, (2) multiple expansion phases, and (3) mitochondrial genome replacement. The detail revealed by this analysis will guide evolutionary analyses of populations in archipelagos such as the West Indies, which include islands varying in size, age, and geological history. Our results suggest that multi-gene phylogenies will permit improved comparative analysis of the evolutionary histories of different lineages in the same geographical setting, which provide replicated "natural experiments" for testing evolutionary hypotheses. PMID:18718030

Promotion of cooperation induced by discriminators in the spatial multi-player donor-recipient game

NASA Astrophysics Data System (ADS)

Cui, Guang-Hai; Wang, Zhen; Ren, Jian-Kang; Lu, Kun; Li, Ming-Chu

2016-11-01

Although the two-player donor-recipient game has been used extensively in studying cooperation in social dilemmas, the scenario in which a donor can simultaneously donate resources to multiple recipients is also common in human societies, economic systems, and social networks. This paper formulates a model of the multi-player donor-recipient game considering a multi-recipient scenario. The promotion of cooperation is also studied by introducing a discriminative cooperation strategy into the game, which donates resources to recipients in proportion to their previous donations with a cost for the collection of information. The evolutionary dynamics of individual strategies are explored in homogeneous and heterogeneous scenarios by leveraging spatial evolutionary game theory. The results show that in a homogeneous scenario, defectors can dominate the network at the equilibrium state only when the cost-to-benefit ratio (R) of donated resources is large. In a heterogeneous scenario, three strategies can coexist all the time within the range of R that was studied, and the promotion of cooperation is more effective when the values of R are smaller. Results from a single node evolution and the formation of local patterns of interaction are provided, and it is analytically shown that discriminators can maintain fairness in resource donation and guarantee long-term cooperation when R is not too large.

An evolutionary communications scenario for Mars exploration

NASA Technical Reports Server (NTRS)

Stevenson, Steven M.

1987-01-01

As Mars exploration grows in complexity with time, the corresponding communication needs will grow in variety and complexity also. From initial Earth/Mars links, further needs will arise for complete surface connectivity for the provision of navigation, position location, and voice, data, and video communications services among multiple Mars bases and remote exploration sites. This paper addresses the likely required communication functions over the first few decades of Martian exploration and postulates systems for providing these services. Required technologies are identified and development requirements indicated.

Satellite Power Systems (SPS) concept definition study (Exhibit D). Volume 5: Systems engineering/integration research and technology

NASA Technical Reports Server (NTRS)

Hanley, G. M.

1981-01-01

Guidelines and ground rules followed in the development of requirements for the SPS are presented. Development planning objectives are specified in each of these areas, and evolutionary SPS program scenarios are described for the various concepts studied during the past one year contract. Program descriptions are presented as planning packages of technical tasks, and schedule phasing. Each package identifies the ground based technology effort that will facilitate SPS definitions, designs, development, and operations.

Adaptive Memory: Is There a Reproduction-Processing Effect?

PubMed

Seitz, Benjamin M; Polack, Cody W; Miller, Ralph R

2017-12-14

Like all biological systems, human memory is likely to have been influenced by evolutionary processes, and its abilities have been subjected to selective mechanisms. Consequently, human memory should be primed to better remember information relevant to one's evolutionary fitness. Supporting this view, participants asked to rate words based on their relevance to an imaginary survival situation better recall those words (even the words rated low in relevancy) than the same words rated with respect to non-survival situations. This mnemonic advantage is called the "survival-processing effect," and presumably it was selected for because it contributed to evolutionary fitness. The same reasoning suggests that there should be an advantage for recall of information that has been rated for relevancy to reproduction and/or mate seeking, although little evidence has existed to assess this proposition. We used an experimental design similar to that in the original survival-processing effect study (Nairne, Thompson, & Pandeirada, 2007) and across 3 experiments tested several newly designed scenarios to determine whether a reproduction-processing effect could be found in an ancestral environment, a modern mating environment, and an ancestral environment in which the emphasis was on raising offspring as opposed to finding a mate. Our results replicated the survival-processing effect but provided no evidence of a reproduction-processing effect when the scenario emphasized finding a mate. However, when rating items on their relevancy to raising one's offspring in an ancestral environment, a mnemonic advantage comparable to that of the survival-processing effect was found. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Conceptual models of the evolution of transgressive dune field systems

NASA Astrophysics Data System (ADS)

A. Hesp, Patrick

2013-10-01

This paper examines the evolutionary paths of some transgressive dune fields that have formed on different coasts of the world, and presents some initial conceptual models of system dynamics for transgressive dune sheets and dune fields. Various evolutionary pathways are conceptualized based on a visual examination of dune fields from around the world. On coasts with high sediment supply, dune sheets and dune fields tend to accumulate as large scale barrier systems with little colonization of vegetation in arid-hyper to arid climate regimes, and as multiple, active discrete phases of dune field and deflation plain couplets in temperate to tropical environments. Active dune fields tend to be singular entities on coasts with low to moderate sediment supply. Landscape complexity and vegetation richness and diversity increases as dune fields evolve from simple active sheets and dunes to single and multiple deflation plains and basins, precipitation ridges, nebkha fields and a host of other dune types associated with vegetation (e.g. trailing ridges, slacks, remnant knobs, gegenwalle ridges and dune track ridges, ‘tree islands' and ‘bush pockets'). Three principal scenarios of transgressive dune sheet and dune field development are discussed, including dune sheets or dune fields evolving directly from the backshore, development following foredune and/or dune field erosion, and development from the breakdown or merging of parabolic dunes. Various stages of evolution are outlined for each scenario. Knowledge of evolutionary patterns and stages in coastal dune fields is very limited and caution is urged in attempts to reverse, change and/or modify dune fields to ‘restore' some perceived loss of ecosystem or dune functioning.

Conceptual models of the evolution of transgressive dune field systems

NASA Astrophysics Data System (ADS)

Hesp, Patrick A.

2013-10-01

This paper examines the evolutionary paths of some transgressive dune fields that have formed on different coasts of the world, and presents some initial conceptual models of system dynamics for transgressive dune sheets and dune fields. Various evolutionary pathways are conceptualized based on a visual examination of dune fields from around the world. On coasts with high sediment supply, dune sheets and dune fields tend to accumulate as large scale barrier systems with little colonization of vegetation in arid-hyper to arid climate regimes, and as multiple, active discrete phases of dune field and deflation plain couplets in temperate to tropical environments. Active dune fields tend to be singular entities on coasts with low to moderate sediment supply. Landscape complexity and vegetation richness and diversity increases as dune fields evolve from simple active sheets and dunes to single and multiple deflation plains and basins, precipitation ridges, nebkha fields and a host of other dune types associated with vegetation (e.g. trailing ridges, slacks, remnant knobs, gegenwalle ridges and dune track ridges, 'tree islands' and 'bush pockets'). Three principal scenarios of transgressive dune sheet and dune field development are discussed, including dune sheets or dune fields evolving directly from the backshore, development following foredune and/or dune field erosion, and development from the breakdown or merging of parabolic dunes. Various stages of evolution are outlined for each scenario. Knowledge of evolutionary patterns and stages in coastal dune fields is very limited and caution is urged in attempts to reverse, change and/or modify dune fields to 'restore' some perceived loss of ecosystem or dune functioning.

Trends in the sand: Directional evolution in the shell shape of recessing scallops (Bivalvia: Pectinidae).

PubMed

Sherratt, Emma; Alejandrino, Alvin; Kraemer, Andrew C; Serb, Jeanne M; Adams, Dean C

2016-09-01

Directional evolution is one of the most compelling evolutionary patterns observed in macroevolution. Yet, despite its importance, detecting such trends in multivariate data remains a challenge. In this study, we evaluate multivariate evolution of shell shape in 93 bivalved scallop species, combining geometric morphometrics and phylogenetic comparative methods. Phylomorphospace visualization described the history of morphological diversification in the group; revealing that taxa with a recessing life habit were the most distinctive in shell shape, and appeared to display a directional trend. To evaluate this hypothesis empirically, we extended existing methods by characterizing the mean directional evolution in phylomorphospace for recessing scallops. We then compared this pattern to what was expected under several alternative evolutionary scenarios using phylogenetic simulations. The observed pattern did not fall within the distribution obtained under multivariate Brownian motion, enabling us to reject this evolutionary scenario. By contrast, the observed pattern was more similar to, and fell within, the distribution obtained from simulations using Brownian motion combined with a directional trend. Thus, the observed data are consistent with a pattern of directional evolution for this lineage of recessing scallops. We discuss this putative directional evolutionary trend in terms of its potential adaptive role in exploiting novel habitats. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Evolution of sparsity and modularity in a model of protein allostery

NASA Astrophysics Data System (ADS)

Hemery, Mathieu; Rivoire, Olivier

2015-04-01

The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary constraints may take is important to interpret the information in protein sequences. To study this problem, we introduce a simple but physical model of protein evolution where selection targets allostery, the functional coupling of distal sites on protein surfaces. This model shows how the geometrical organization of couplings between amino acids within a protein structure can depend crucially on its evolutionary history. In particular, two scenarios are found to generate a spatial concentration of functional constraints: high mutation rates and fluctuating selective pressures. This second scenario offers a plausible explanation for the high tolerance of natural proteins to mutations and for the spatial organization of their least tolerant amino acids, as revealed by sequence analysis and mutagenesis experiments. It also implies a faculty to adapt to new selective pressures that is consistent with observations. The model illustrates how several independent functional modules may emerge within the same protein structure, depending on the nature of past environmental fluctuations. Our model thus relates the evolutionary history of proteins to the geometry of their functional constraints, with implications for decoding and engineering protein sequences.

Testing inferences in developmental evolution: the forensic evidence principle.

PubMed

Larsson, Hans C E; Wagner, Günter P

2012-09-01

Developmental evolution (DE) examines the influence of developmental mechanisms on biological evolution. Here we consider the question: "what is the evidence that allows us to decide whether a certain developmental scenario for an evolutionary change is in fact "correct" or at least falsifiable?" We argue that the comparative method linked with what we call the "forensic evidence principle" (FEP) is sufficient to conduct rigorous tests of DE scenarios. The FEP states that different genetically mediated developmental causes of an evolutionary transformation will leave different signatures in the development of the derived character. Although similar inference rules have been used in practically every empirical science, we expand this approach here in two ways: (1) we justify the validity of this principle with reference to a well-known result from mathematical physics, known as the symmetry principle, and (2) propose a specific form of the FEP for DE: given two or more developmental explanations for a certain evolutionary event, say an evolutionary novelty, then the evidence discriminating between these hypotheses will be found in the most proximal internal drivers of the derived character. Hence, a detailed description of the ancestral and derived states, and their most proximal developmental drivers are necessary to discriminate between various evolutionary developmental hypotheses. We discuss how this stepwise order of testing is necessary, establishes a formal test, and how skipping this order of examination may violate a more accurate examination of DE. We illustrate the approach with an example from avian digit evolution. © 2012 Wiley Periodicals, Inc.

Assessment of Masonry Buildings Subjected to Landslide-Induced Settlements: From Load Path Method to Evolutionary Optimization Method

NASA Astrophysics Data System (ADS)

Palmisano, Fabrizio; Elia, Angelo

2017-10-01

One of the main difficulties, when dealing with landslide structural vulnerability, is the diagnosis of the causes of crack patterns. This is also due to the excessive complexity of models based on classical structural mechanics that makes them inappropriate especially when there is the necessity to perform a rapid vulnerability assessment at the territorial scale. This is why, a new approach, based on a ‘simple model’ (i.e. the Load Path Method, LPM), has been proposed by Palmisano and Elia for the interpretation of the behaviour of masonry buildings subjected to landslide-induced settlements. However, the LPM is very useful for rapidly finding the 'most plausible solution' instead of the exact solution. To find the solution, optimization algorithms are necessary. In this scenario, this article aims to show how the Bidirectional Evolutionary Structural Optimization method by Huang and Xie, can be very useful to optimize the strut-and-tie models obtained by using the Load Path Method.

Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages

PubMed Central

Fukasawa, Yoshinori; Oda, Toshiyuki; Tomii, Kentaro

2017-01-01

Abstract Protein transport systems are fundamentally important for maintaining mitochondrial function. Nevertheless, mitochondrial protein translocases such as the kinetoplastid ATOM complex have recently been shown to vary in eukaryotic lineages. Various evolutionary hypotheses have been formulated to explain this diversity. To resolve any contradiction, estimating the primitive state and clarifying changes from that state are necessary. Here, we present more likely primitive models of mitochondrial translocases, specifically the translocase of the outer membrane (TOM) and translocase of the inner membrane (TIM) complexes, using scrutinized phylogenetic profiles. We then analyzed the translocases’ evolution in eukaryotic lineages. Based on those results, we propose a novel evolutionary scenario for diversification of the mitochondrial transport system. Our results indicate that presequence transport machinery was mostly established in the last eukaryotic common ancestor, and that primitive translocases already had a pathway for transporting presequence-containing proteins. Moreover, secondary changes including convergent and migrational gains of a presequence receptor in TOM and TIM complexes, respectively, likely resulted from constrained evolution. The nature of a targeting signal can constrain alteration to the protein transport complex. PMID:28369657

The 25 kW power module evolution study. Part 3: Conceptual designs for power module evolution. Volume 1: Power module evolution

NASA Technical Reports Server (NTRS)

1979-01-01

Candidate power module confugurations which will directly support an evolutionary scenario allowing growth from 25 kW to 100 kW are described. The growth rationale is structured to support a nominal scenario for sortie mission support to the POrbiter and to free-flying payloads during the 1983 to 1990 era.

An Analysis on a Negotiation Model Based on Multiagent Systems with Symbiotic Learning and Evolution

NASA Astrophysics Data System (ADS)

Hossain, Md. Tofazzal

This study explores an evolutionary analysis on a negotiation model based on Masbiole (Multiagent Systems with Symbiotic Learning and Evolution) which has been proposed as a new methodology of Multiagent Systems (MAS) based on symbiosis in the ecosystem. In Masbiole, agents evolve in consideration of not only their own benefits and losses, but also the benefits and losses of opponent agents. To aid effective application of Masbiole, we develop a competitive negotiation model where rigorous and advanced intelligent decision-making mechanisms are required for agents to achieve solutions. A Negotiation Protocol is devised aiming at developing a set of rules for agents' behavior during evolution. Simulations use a newly developed evolutionary computing technique, called Genetic Network Programming (GNP) which has the directed graph-type gene structure that can develop and design the required intelligent mechanisms for agents. In a typical scenario, competitive negotiation solutions are reached by concessions that are usually predetermined in the conventional MAS. In this model, however, not only concession is determined automatically by symbiotic evolution (making the system intelligent, automated, and efficient) but the solution also achieves Pareto optimal automatically.

Investigating the timing of origin and evolutionary processes shaping regional species diversity: Insights from simulated data and neotropical butterfly diversification rates.

PubMed

Matos-Maraví, Pável

2016-07-01

Different diversification scenarios have been proposed to explain the origin of extant biodiversity. However, most existing meta-analyses of time-calibrated phylogenies rely on approaches that do not quantitatively test alternative diversification processes. Here, I highlight the shortcomings of using species divergence ranks, which is a method widely used in meta-analyses. Divergence ranks consist of categorizing cladogenetic events to certain periods of time, typically to either Pleistocene or to pre-Pleistocene ages. This approach has been claimed to shed light on the origin of most extant species and the timing and dynamics of diversification in any biogeographical region. However, interpretations drawn from such method often confound two fundamental questions in macroevolutionary studies, tempo (timing of evolutionary rate shifts) and mode ("how" and "why" of speciation). By using simulated phylogenies under four diversification scenarios, constant-rate, diversity-dependence, high extinction, and high speciation rates in the Pleistocene, I showed that interpretations based on species divergence ranks might have been seriously misleading. Future meta-analyses of dated phylogenies need to be aware of the impacts of incomplete taxonomic sampling, tree topology, and divergence time uncertainties, as well as they might be benefited by including quantitative tests of alternative diversification models that acknowledge extinction and diversity dependence. © 2016 The Author(s).

Genetic structure and demographic history of the endangered and endemic schizothoracine fish Gymnodiptychus pachycheilus in Qinghai-Tibetan Plateau.

PubMed

Su, Junhu; Ji, Weihong; Wei, Yanming; Zhang, Yanping; Gleeson, Dianne M; Lou, Zhongyu; Ren, Jing

2014-08-01

The endangered schizothoracine fish Gymnodiptychus pachycheilus is endemic to the Qinghai-Tibetan Plateau (QTP), but very little genetic information is available for this species. Here, we accessed the current genetic divergence of G. pachycheilus population to evaluate their distributions modulated by contemporary and historical processes. Population structure and demographic history were assessed by analyzing 1811-base pairs of mitochondrial DNA from 61 individuals across a large proportion of its geographic range. Our results revealed low nucleotide diversity, suggesting severe historical bottleneck events. Analyses of molecular variance and the conventional population statistic FST (0.0435, P = 0.0215) confirmed weak genetic structure. The monophyly of G. pachycheilus was statistically well-supported, while two divergent evolutionary clusters were identified by phylogenetic analyses, suggesting a microgeographic population structure. The consistent scenario of recent population expansion of two clusters was identified based on several complementary analyses of demographic history (0.096 Ma and 0.15 Ma). This genetic divergence and evolutionary process are likely to have resulted from a series of drainage arrangements triggered by the historical tectonic events of the region. The results obtained here provide the first insights into the evolutionary history and genetic status of this little-known fish.

Phylogenetic estimates of diversification rate are affected by molecular rate variation.

PubMed

Duchêne, D A; Hua, X; Bromham, L

2017-10-01

Molecular phylogenies are increasingly being used to investigate the patterns and mechanisms of macroevolution. In particular, node heights in a phylogeny can be used to detect changes in rates of diversification over time. Such analyses rest on the assumption that node heights in a phylogeny represent the timing of diversification events, which in turn rests on the assumption that evolutionary time can be accurately predicted from DNA sequence divergence. But there are many influences on the rate of molecular evolution, which might also influence node heights in molecular phylogenies, and thus affect estimates of diversification rate. In particular, a growing number of studies have revealed an association between the net diversification rate estimated from phylogenies and the rate of molecular evolution. Such an association might, by influencing the relative position of node heights, systematically bias estimates of diversification time. We simulated the evolution of DNA sequences under several scenarios where rates of diversification and molecular evolution vary through time, including models where diversification and molecular evolutionary rates are linked. We show that commonly used methods, including metric-based, likelihood and Bayesian approaches, can have a low power to identify changes in diversification rate when molecular substitution rates vary. Furthermore, the association between the rates of speciation and molecular evolution rate can cause the signature of a slowdown or speedup in speciation rates to be lost or misidentified. These results suggest that the multiple sources of variation in molecular evolutionary rates need to be considered when inferring macroevolutionary processes from phylogenies. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Integrating evolutionary game theory into an agent-based model of ductal carcinoma in situ: Role of gap junctions in cancer progression.

PubMed

Malekian, Negin; Habibi, Jafar; Zangooei, Mohammad Hossein; Aghakhani, Hojjat

2016-11-01

There are many cells with various phenotypic behaviors in cancer interacting with each other. For example, an apoptotic cell may induce apoptosis in adjacent cells. A living cell can also protect cells from undergoing apoptosis and necrosis. These survival and death signals are propagated through interaction pathways between adjacent cells called gap junctions. The function of these signals depends on the cellular context of the cell receiving them. For instance, a receiver cell experiencing a low level of oxygen may interpret a received survival signal as an apoptosis signal. In this study, we examine the effect of these signals on tumor growth. We make an evolutionary game theory component in order to model the signal propagation through gap junctions. The game payoffs are defined as a function of cellular context. Then, the game theory component is integrated into an agent-based model of tumor growth. After that, the integrated model is applied to ductal carcinoma in situ, a type of early stage breast cancer. Different scenarios are explored to observe the impact of the gap junction communication and parameters of the game theory component on cancer progression. We compare these scenarios by using the Wilcoxon signed-rank test. The Wilcoxon signed-rank test succeeds in proving a significant difference between the tumor growth of the model before and after considering the gap junction communication. The Wilcoxon signed-rank test also proves that the tumor growth significantly depends on the oxygen threshold of turning survival signals into apoptosis. In this study, the gap junction communication is modeled by using evolutionary game theory to illustrate its role at early stage cancers such as ductal carcinoma in situ. This work indicates that the gap junction communication and the oxygen threshold of turning survival signals into apoptosis can notably affect cancer progression. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Adaptive Memory: Evaluating Alternative Forms of Fitness-Relevant Processing in the Survival Processing Paradigm

PubMed Central

Sandry, Joshua; Trafimow, David; Marks, Michael J.; Rice, Stephen

2013-01-01

Memory may have evolved to preserve information processed in terms of its fitness-relevance. Based on the assumption that the human mind comprises different fitness-relevant adaptive mechanisms contributing to survival and reproductive success, we compared alternative fitness-relevant processing scenarios with survival processing. Participants rated words for relevancy to fitness-relevant and control conditions followed by a delay and surprise recall test (Experiment 1a). Participants recalled more words processed for their relevance to a survival situation. We replicated these findings in an online study (Experiment 2) and a study using revised fitness-relevant scenarios (Experiment 3). Across all experiments, we did not find a mnemonic benefit for alternative fitness-relevant processing scenarios, questioning assumptions associated with an evolutionary account of remembering. Based on these results, fitness-relevance seems to be too wide-ranging of a construct to account for the memory findings associated with survival processing. We propose that memory may be hierarchically sensitive to fitness-relevant processing instructions. We encourage future researchers to investigate the underlying mechanisms responsible for survival processing effects and work toward developing a taxonomy of adaptive memory. PMID:23585858

Bio-inspired algorithms applied to molecular docking simulations.

PubMed

Heberlé, G; de Azevedo, W F

2011-01-01

Nature as a source of inspiration has been shown to have a great beneficial impact on the development of new computational methodologies. In this scenario, analyses of the interactions between a protein target and a ligand can be simulated by biologically inspired algorithms (BIAs). These algorithms mimic biological systems to create new paradigms for computation, such as neural networks, evolutionary computing, and swarm intelligence. This review provides a description of the main concepts behind BIAs applied to molecular docking simulations. Special attention is devoted to evolutionary algorithms, guided-directed evolutionary algorithms, and Lamarckian genetic algorithms. Recent applications of these methodologies to protein targets identified in the Mycobacterium tuberculosis genome are described.

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

PubMed Central

Brosius, Jürgen

2014-01-01

Currently, the best scenario for earliest forms of life is based on RNA molecules as they have the proven ability to catalyze enzymatic reactions and harbor genetic information. Evolutionary principles valid today become apparent in such models already. Furthermore, many features of eukaryotic genome architecture might have their origins in an RNA or RNA/protein (RNP) world, including the onset of a further transition, when DNA replaced RNA as the genetic bookkeeper of the cell. Chromosome maintenance, splicing, and regulatory function via RNA may be deeply rooted in the RNA/RNP worlds. Mostly in eukaryotes, conversion from RNA to DNA is still ongoing, which greatly impacts the plasticity of extant genomes. Raw material for novel genes encoding protein or RNA, or parts of genes including regulatory elements that selection can act on, continues to enter the evolutionary lottery. PMID:25081515

A multilocus approach to assessing co-evolutionary relationships between Steinernema spp. (Nematoda: Steinernematidae) and their bacterial symbionts Xenorhabdus spp. (gamma-Proteobacteria: Enterobacteriaceae).

PubMed

Lee, Ming-Min; Stock, S Patricia

2010-09-01

Nematodes of the genus Steinernema Travassos, 1927 (Nematoda: Steinernematidae) and their associated bacteria, Xenorhabdus spp. (gamma-Proteobacteria), are an emergent model of terrestrial animal-microbe symbiosis. Interest in this association initially arose out of their potential as biocontrol agents against insect pests, but, despite advances in their field application and the growing popularity of this model system, relatively little has been published to uncover the evolutionary facets of this beneficial partnership. This study adds to the body of knowledge regarding nematode-bacteria symbiosis by proposing a possible scenario for their historical association in the form of a cophylogenetic hypothesis. Topological and likelihood based testing methods were employed to reconstruct a history of association between 30 host-symbiont pairs and to gauge the level of similarity between their inferred phylogenetic patterns.

The evolution of respiratory O2/NO reductases: an out-of-the-phylogenetic-box perspective

PubMed Central

Ducluzeau, Anne-Lise; Schoepp-Cothenet, Barbara; van Lis, Robert; Baymann, Frauke; Russell, Michael J.; Nitschke, Wolfgang

2014-01-01

Complex life on our planet crucially depends on strong redox disequilibria afforded by the almost ubiquitous presence of highly oxidizing molecular oxygen. However, the history of O2-levels in the atmosphere is complex and prior to the Great Oxidation Event some 2.3 billion years ago, the amount of O2 in the biosphere is considered to have been extremely low as compared with present-day values. Therefore the evolutionary histories of life and of O2-levels are likely intricately intertwined. The obvious biological proxy for inferring the impact of changing O2-levels on life is the evolutionary history of the enzyme allowing organisms to tap into the redox power of molecular oxygen, i.e. the bioenergetic O2 reductases, alias the cytochrome and quinol oxidases. Consequently, molecular phylogenies reconstructed for this enzyme superfamily have been exploited over the last two decades in attempts to elucidate the interlocking between O2 levels in the environment and the evolution of respiratory bioenergetic processes. Although based on strictly identical datasets, these phylogenetic approaches have led to diametrically opposite scenarios with respect to the history of both the enzyme superfamily and molecular oxygen on the Earth. In an effort to overcome the deadlock of molecular phylogeny, we here review presently available structural, functional, palaeogeochemical and thermodynamic information pertinent to the evolution of the superfamily (which notably also encompasses the subfamily of nitric oxide reductases). The scenario which, in our eyes, most closely fits the ensemble of these non-phylogenetic data, sees the low O2-affinity SoxM- (or A-) type enzymes as the most recent evolutionary innovation and the high-affinity O2 reductases (SoxB or B and cbb3 or C) as arising independently from NO-reducing precursor enzymes. PMID:24968694

Contrasting introduction scenarios among continents in the worldwide invasion of the banana fungal pathogen Mycosphaerella fijiensis.

PubMed

Robert, S; Ravigne, V; Zapater, M-F; Abadie, C; Carlier, J

2012-03-01

Reconstructing and characterizing introduction routes is a key step towards understanding the ecological and evolutionary factors underlying successful invasions and disease emergence. Here, we aimed to decipher scenarios of introduction and stochastic demographic events associated with the global spread of an emerging disease of bananas caused by the destructive fungal pathogen Mycosphaerella fijiensis. We analysed the worldwide population structure of this fungus using 21 microsatellites and 8 sequence-based markers on 735 individuals from 37 countries. Our analyses designated South-East Asia as the source of the global invasion and supported the location of the centre of origin of M. fijiensis within this area. We confirmed the occurrence of bottlenecks upon introduction into other continents followed by widespread founder events within continents. Furthermore, this study suggested contrasting introduction scenarios of the pathogen between the African and American continents. While potential signatures of admixture resulting from multiple introductions were detected in America, all the African samples examined seem to descend from a single successful founder event. In combination with historical information, our study reveals an original and unprecedented global scenario of invasion for this recently emerging disease caused by a wind-dispersed pathogen. © 2012 Blackwell Publishing Ltd.

Semantic wireless localization of WiFi terminals in smart buildings

NASA Astrophysics Data System (ADS)

Ahmadi, H.; Polo, A.; Moriyama, T.; Salucci, M.; Viani, F.

2016-06-01

The wireless localization of mobile terminals in indoor scenarios by means of a semantic interpretation of the environment is addressed in this work. A training-less approach based on the real-time calibration of a simple path loss model is proposed which combines (i) the received signal strength information measured by the wireless terminal and (ii) the topological features of the localization domain. A customized evolutionary optimization technique has been designed to estimate the optimal target position that fits the complex wireless indoor propagation and the semantic target-environment relation, as well. The proposed approach is experimentally validated in a real building area where the available WiFi network is opportunistically exploited for data collection. The presented results point out a reduction of the localization error obtained with the introduction of a very simple semantic interpretation of the considered scenario.

On the Plausibility of Pseudosugar Formation in Cometary Ices and Oxygen-rich Tholins

NASA Astrophysics Data System (ADS)

Lavado, Nieves; Ávalos, Martín; Babiano, Reyes; Cintas, Pedro; Light, Mark E.; Jiménez, José Luis; Palacios, Juan C.

2016-03-01

We revisit herein the formation and structure of dihydroxy dioxanes, which can be obtained from prebiotically available precursors and can be regarded as primeval sugar surrogates. Previous studies dealing with the heterogeneous composition of interstellar bodies point to the existence of significant amounts of small polyalcohols along with oxygen-containing oligomers. Even though such derivatives did not give rise to nucleosides and oligonucleotides, nor they were incorporated into subsequent metabolic routes, molecular chimeras based on sugar-like species could be opportunistic scaffolds in pre-evolutionary scenarios. We could figure out that pseudosugars, assembled by hemiacetalic bonds from available precursors in both interstellar and terrestrial scenarios, were presumably more abundant than thought. Moreover, these species share some key features with naturally-occurring sugar rings, such as anomeric preferences, coordinating ability, and the prevalent occurrence of racemic compounds.

Improved Maximum Parsimony Models for Phylogenetic Networks.

PubMed

Van Iersel, Leo; Jones, Mark; Scornavacca, Celine

2018-05-01

Phylogenetic networks are well suited to represent evolutionary histories comprising reticulate evolution. Several methods aiming at reconstructing explicit phylogenetic networks have been developed in the last two decades. In this article, we propose a new definition of maximum parsimony for phylogenetic networks that permits to model biological scenarios that cannot be modeled by the definitions currently present in the literature (namely, the "hardwired" and "softwired" parsimony). Building on this new definition, we provide several algorithmic results that lay the foundations for new parsimony-based methods for phylogenetic network reconstruction.

Intelligence with representation.

PubMed

Steels, Luc

2003-10-15

Behaviour-based robotics has always been inspired by earlier cybernetics work such as that of W. Grey Walter. It emphasizes that intelligence can be achieved without the kinds of representations common in symbolic AI systems. The paper argues that such representations might indeed not be needed for many aspects of sensory-motor intelligence but become a crucial issue when bootstrapping to higher levels of cognition. It proposes a scenario in the form of evolutionary language games by which embodied agents develop situated grounded representations adapted to their needs and the conventions emerging in the population.

Evolutionary lability of a complex life cycle in the aphid genus Brachycaudus.

PubMed

Emmanuelle, Jousselin; Gwenaelle, Genson; Armelle, Coeur d'acier

2010-09-28

Most aphid species complete their life cycle on the same set of host-plant species, but some (heteroecious species) alternate between different hosts, migrating from primary (woody) to secondary (herbaceous) host plants. The evolutionary processes behind the evolution of this complex life cycle have often been debated. One widely accepted scenario is that heteroecy evolved from monoecy on woody host plants. Several shifts towards monoecy on herbaceous plants have subsequently occurred and resulted in the radiation of aphids. Host alternation would have persisted in some cases due to developmental constraints preventing aphids from shifting their entire life cycle to herbaceous hosts (which are thought to be more favourable). According to this scenario, if aphids lose their primary host during evolution they should not regain it. The genus Brachycaudus includes species with all the types of life cycle (monoecy on woody plants, heteroecy, monoecy on herbs). We used this genus to test hypotheses concerning the evolution of life cycles in aphids. Phylogenetic investigation and character reconstruction suggest that life cycle is evolutionary labile in the genus. Though ancestral character states can be ambiguous depending on optimization methods, all analyses suggest that transitions from monoecy on herbs towards heteroecy have occurred several times. Transitions from heteroecy towards monoecy, are also likely. There have been many shifts in feeding behaviour but we found no significant correlation between life cycle changes and changes in diet. The transitions from monoecy on herbs towards heteroecy observed in this study go against a widely accepted evolutionary scenario: aphids in the genus Brachycaudus seem to be able to recapture their supposedly ancestral woody host. This suggests that the determinants of host alternation are probably not as complicated as previously thought. Definitive proofs of the lability of life cycle in Brachycaudus will necessitate investigation of these determinants. Life cycle changes, whether corresponding to the loss or acquisition of a primary host, necessarily promote speciation, by inducing shifts of the reproductive phase on different plants. We suggest that the evolutionary lability of life cycle may have driven speciation events in the Brachycaudus genus.

Inferring the mode of origin of polyploid species from next-generation sequence data.

PubMed

Roux, Camille; Pannell, John R

2015-03-01

Many eukaryote organisms are polyploid. However, despite their importance, evolutionary inference of polyploid origins and modes of inheritance has been limited by a need for analyses of allele segregation at multiple loci using crosses. The increasing availability of sequence data for nonmodel species now allows the application of established approaches for the analysis of genomic data in polyploids. Here, we ask whether approximate Bayesian computation (ABC), applied to realistic traditional and next-generation sequence data, allows correct inference of the evolutionary and demographic history of polyploids. Using simulations, we evaluate the robustness of evolutionary inference by ABC for tetraploid species as a function of the number of individuals and loci sampled, and the presence or absence of an outgroup. We find that ABC adequately retrieves the recent evolutionary history of polyploid species on the basis of both old and new sequencing technologies. The application of ABC to sequence data from diploid and polyploid species of the plant genus Capsella confirms its utility. Our analysis strongly supports an allopolyploid origin of C. bursa-pastoris about 80 000 years ago. This conclusion runs contrary to previous findings based on the same data set but using an alternative approach and is in agreement with recent findings based on whole-genome sequencing. Our results indicate that ABC is a promising and powerful method for revealing the evolution of polyploid species, without the need to attribute alleles to a homeologous chromosome pair. The approach can readily be extended to more complex scenarios involving higher ploidy levels. © 2015 John Wiley & Sons Ltd.

Novel hybrid linear stochastic with non-linear extreme learning machine methods for forecasting monthly rainfall a tropical climate.

PubMed

Zeynoddin, Mohammad; Bonakdari, Hossein; Azari, Arash; Ebtehaj, Isa; Gharabaghi, Bahram; Riahi Madavar, Hossein

2018-09-15

A novel hybrid approach is presented that can more accurately predict monthly rainfall in a tropical climate by integrating a linear stochastic model with a powerful non-linear extreme learning machine method. This new hybrid method was then evaluated by considering four general scenarios. In the first scenario, the modeling process is initiated without preprocessing input data as a base case. While in other three scenarios, the one-step and two-step procedures are utilized to make the model predictions more precise. The mentioned scenarios are based on a combination of stationarization techniques (i.e., differencing, seasonal and non-seasonal standardization and spectral analysis), and normality transforms (i.e., Box-Cox, John and Draper, Yeo and Johnson, Johnson, Box-Cox-Mod, log, log standard, and Manly). In scenario 2, which is a one-step scenario, the stationarization methods are employed as preprocessing approaches. In scenario 3 and 4, different combinations of normality transform, and stationarization methods are considered as preprocessing techniques. In total, 61 sub-scenarios are evaluated resulting 11013 models (10785 linear methods, 4 nonlinear models, and 224 hybrid models are evaluated). The uncertainty of the linear, nonlinear and hybrid models are examined by Monte Carlo technique. The best preprocessing technique is the utilization of Johnson normality transform and seasonal standardization (respectively) (R 2  = 0.99; RMSE = 0.6; MAE = 0.38; RMSRE = 0.1, MARE = 0.06, UI = 0.03 &UII = 0.05). The results of uncertainty analysis indicated the good performance of proposed technique (d-factor = 0.27; 95PPU = 83.57). Moreover, the results of the proposed methodology in this study were compared with an evolutionary hybrid of adaptive neuro fuzzy inference system (ANFIS) with firefly algorithm (ANFIS-FFA) demonstrating that the new hybrid methods outperformed ANFIS-FFA method. Copyright © 2018 Elsevier Ltd. All rights reserved.

Comparison of the genetic algorithm and incremental optimisation routines for a Bayesian inverse modelling based network design

NASA Astrophysics Data System (ADS)

Nickless, A.; Rayner, P. J.; Erni, B.; Scholes, R. J.

2018-05-01

The design of an optimal network of atmospheric monitoring stations for the observation of carbon dioxide (CO2) concentrations can be obtained by applying an optimisation algorithm to a cost function based on minimising posterior uncertainty in the CO2 fluxes obtained from a Bayesian inverse modelling solution. Two candidate optimisation methods assessed were the evolutionary algorithm: the genetic algorithm (GA), and the deterministic algorithm: the incremental optimisation (IO) routine. This paper assessed the ability of the IO routine in comparison to the more computationally demanding GA routine to optimise the placement of a five-member network of CO2 monitoring sites located in South Africa. The comparison considered the reduction in uncertainty of the overall flux estimate, the spatial similarity of solutions, and computational requirements. Although the IO routine failed to find the solution with the global maximum uncertainty reduction, the resulting solution had only fractionally lower uncertainty reduction compared with the GA, and at only a quarter of the computational resources used by the lowest specified GA algorithm. The GA solution set showed more inconsistency if the number of iterations or population size was small, and more so for a complex prior flux covariance matrix. If the GA completed with a sub-optimal solution, these solutions were similar in fitness to the best available solution. Two additional scenarios were considered, with the objective of creating circumstances where the GA may outperform the IO. The first scenario considered an established network, where the optimisation was required to add an additional five stations to an existing five-member network. In the second scenario the optimisation was based only on the uncertainty reduction within a subregion of the domain. The GA was able to find a better solution than the IO under both scenarios, but with only a marginal improvement in the uncertainty reduction. These results suggest that the best use of resources for the network design problem would be spent in improvement of the prior estimates of the flux uncertainties rather than investing these resources in running a complex evolutionary optimisation algorithm. The authors recommend that, if time and computational resources allow, that multiple optimisation techniques should be used as a part of a comprehensive suite of sensitivity tests when performing such an optimisation exercise. This will provide a selection of best solutions which could be ranked based on their utility and practicality.

Malagasy bats shelter a considerable genetic diversity of pathogenic Leptospira suggesting notable host-specificity patterns.

PubMed

Gomard, Yann; Dietrich, Muriel; Wieseke, Nicolas; Ramasindrazana, Beza; Lagadec, Erwan; Goodman, Steven M; Dellagi, Koussay; Tortosa, Pablo

2016-04-01

Pathogenic Leptospira are the causative agents of leptospirosis, a disease of global concern with major impact in tropical regions. Despite the importance of this zoonosis for human health, the evolutionary and ecological drivers shaping bacterial communities in host reservoirs remain poorly investigated. Here, we describe Leptospira communities hosted by Malagasy bats, composed of mostly endemic species, in order to characterize host-pathogen associations and investigate their evolutionary histories. We screened 947 individual bats (representing 31 species, 18 genera and seven families) for Leptospira infection and subsequently genotyped positive samples using three different bacterial loci. Molecular identification showed that these Leptospira are notably diverse and include several distinct lineages mostly belonging to Leptospira borgpetersenii and L. kirschneri. The exploration of the most probable host-pathogen evolutionary scenarios suggests that bacterial genetic diversity results from a combination of events related to the ecology and the evolutionary history of their hosts. Importantly, based on the data set presented herein, the notable host-specificity we have uncovered, together with a lack of geographical structuration of bacterial genetic diversity, indicates that the Leptospira community at a given site depends on the co-occurring bat species assemblage. The implications of such tight host-specificity on the epidemiology of leptospirosis are discussed. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages.

PubMed

Fukasawa, Yoshinori; Oda, Toshiyuki; Tomii, Kentaro; Imai, Kenichiro

2017-07-01

Protein transport systems are fundamentally important for maintaining mitochondrial function. Nevertheless, mitochondrial protein translocases such as the kinetoplastid ATOM complex have recently been shown to vary in eukaryotic lineages. Various evolutionary hypotheses have been formulated to explain this diversity. To resolve any contradiction, estimating the primitive state and clarifying changes from that state are necessary. Here, we present more likely primitive models of mitochondrial translocases, specifically the translocase of the outer membrane (TOM) and translocase of the inner membrane (TIM) complexes, using scrutinized phylogenetic profiles. We then analyzed the translocases' evolution in eukaryotic lineages. Based on those results, we propose a novel evolutionary scenario for diversification of the mitochondrial transport system. Our results indicate that presequence transport machinery was mostly established in the last eukaryotic common ancestor, and that primitive translocases already had a pathway for transporting presequence-containing proteins. Moreover, secondary changes including convergent and migrational gains of a presequence receptor in TOM and TIM complexes, respectively, likely resulted from constrained evolution. The nature of a targeting signal can constrain alteration to the protein transport complex. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Egg clutch patterning in Lestes virens (Odonata, Lestidae) with evolutionary emphasis on endophytic oviposition in lestid dragonflies.

PubMed

Matushkina, Natalia A; Buy, Denis; Lambret, Philippe

2016-12-01

Egg deposition within plants is one of the most widely distributed and ancient behaviors in Odonata. The resulting clutch consists of eggs placed in peculiar pattern that can be a characteristic for certain groups of Odonata. Despite their importance for paleontological and evolutionary research, data on egg-clutch positioning are missing or insufficient for most species. Here, patterning of egg clutches in Lestes virens was measured and described in detail for the first time. The female usually produces a linear row of single eggs directed at an angle rightward or leftward to the longitudinal axis of plant substrate. Less often eggs are arranged in egg-sets consisting of up to 4 eggs. Apparently, the female insect follows the rigid behavior stereotypes during oviposition and is unable to easily switch to the alternate stereotypical behavior of single egg deposition or production of multiegg sets. Based on a literature review and original data, egg clutch patterning of European Lestidae is overlaid on preexisting phylogenies. The resulting evolutionary scenario of egg-clutch patterning can be considered in the framework of egg-laying behavior in Lestidae. © 2015 Institute of Zoology, Chinese Academy of Sciences.

Evolutionary Divergence in Brain Size between Migratory and Resident Birds

PubMed Central

Sol, Daniel; Garcia, Núria; Iwaniuk, Andrew; Davis, Katie; Meade, Andrew; Boyle, W. Alice; Székely, Tamás

2010-01-01

Despite important recent progress in our understanding of brain evolution, controversy remains regarding the evolutionary forces that have driven its enormous diversification in size. Here, we report that in passerine birds, migratory species tend to have brains that are substantially smaller (relative to body size) than those of resident species, confirming and generalizing previous studies. Phylogenetic reconstructions based on Bayesian Markov chain methods suggest an evolutionary scenario in which some large brained tropical passerines that invaded more seasonal regions evolved migratory behavior and migration itself selected for smaller brain size. Selection for smaller brains in migratory birds may arise from the energetic and developmental costs associated with a highly mobile life cycle, a possibility that is supported by a path analysis. Nevertheless, an important fraction (over 68%) of the correlation between brain mass and migratory distance comes from a direct effect of migration on brain size, perhaps reflecting costs associated with cognitive functions that have become less necessary in migratory species. Overall, our results highlight the importance of retrospective analyses in identifying selective pressures that have shaped brain evolution, and indicate that when it comes to the brain, larger is not always better. PMID:20224776

Acceptance of evolutionary explanations as they are applied to plants, animals, and humans

NASA Astrophysics Data System (ADS)

Thanukos, Anastasia

In four investigations using Likert-scale questionnaires and think-aloud protocols with 173 university students in total, the willingness to accept evolutionary explanations regarding plant, animal, and human characteristics was examined. Participants were presented with evolutionary explanations for features and behaviors and were asked to rate how much they agreed with evolution as an explanation for each scenario. Some were also asked to explain their reasoning in think-aloud protocols or to discuss item ratings with one another. Overall, participants thought evolutionary explanations appropriate, with median ratings in the upper quarter of the rating scale. They were slightly more willing to ascribe evolutionary explanations to plant than to human phenomena; however, this general effect was mediated by more specific aspects of the evolutionary scenarios in question. Participants who were generally negative regarding evolution were particularly negative towards human evolution. Those who were positive or neutral towards evolution in general were more willing to accept human evolution, but were more likely to use evolution to explain similarities between humans and other species than to explain particular human adaptations. For example, they were more likely to agree that evolution is responsible for the DNA similarities between humans and chimpanzees than that evolution is responsible for human behavioral characteristics, such as the fight or flight response. Think-aloud protocols suggest that, while people are more familiar with human evolutionary relationships than plant evolutionary relationships, they may be less likely to see human characteristics as adaptively valuable. One plausible explanation for these patterns is that an evolutionary explanation is judged jointly by its availability in an individual's memory and its plausibility (i.e., its congruence with the individual's worldview). Popular media coverage, with its focus on controversy and litigation, makes it likely that awareness of human evolution is high, compared with plant evolution (which may not even "enter the radar screen" when most people think of evolution). Some aspects of human evolution, such as the basic relationship between all primates, may have become so pedestrian that they do not threaten many individuals' worldviews. However, even for those positively disposed towards evolution, extending the ramifications of human evolution by suggesting that evolution shapes our behaviors and physical traits may pose a threat to their sense of personal agency. This threat is not associated with plant evolution.

Derived heuristics-based consistent optimization of material flow in a gold processing plant

NASA Astrophysics Data System (ADS)

Myburgh, Christie; Deb, Kalyanmoy

2018-01-01

Material flow in a chemical processing plant often follows complicated control laws and involves plant capacity constraints. Importantly, the process involves discrete scenarios which when modelled in a programming format involves if-then-else statements. Therefore, a formulation of an optimization problem of such processes becomes complicated with nonlinear and non-differentiable objective and constraint functions. In handling such problems using classical point-based approaches, users often have to resort to modifications and indirect ways of representing the problem to suit the restrictions associated with classical methods. In a particular gold processing plant optimization problem, these facts are demonstrated by showing results from MATLAB®'s well-known fmincon routine. Thereafter, a customized evolutionary optimization procedure which is capable of handling all complexities offered by the problem is developed. Although the evolutionary approach produced results with comparatively less variance over multiple runs, the performance has been enhanced by introducing derived heuristics associated with the problem. In this article, the development and usage of derived heuristics in a practical problem are presented and their importance in a quick convergence of the overall algorithm is demonstrated.

Phylogenetic Analysis of Thecosomata Blainville, 1824 (Holoplanktonic Opisthobranchia) Using Morphological and Molecular Data

PubMed Central

Corse, Emmanuel; Rampal, Jeannine; Cuoc, Corinne; Pech, Nicolas

2013-01-01

Thecosomata is a marine zooplankton group, which played an important role in the carbonate cycle in oceans due to their shell composition. So far, there is important discrepancy between the previous morphological-based taxonomies, and subsequently the evolutionary history of Thecosomata. In this study, the remarkable planktonic sampling of TARA Oceans expedition associated with a set of various other missions allowed us to assess the phylogenetic relationships of Thecosomata using morphological and molecular data (28 S and COI genes). The two gene trees showed incongruities (e.g. Hyalocylis, Cavolinia), and high congruence between morphological and 28S trees (e.g. monophyly of Euthecosomata). The monophyly of straight shell species led us to reviving the Orthoconcha, and the split of Limacinidae led us to the revival of Embolus inflata replacing Limacina inflata. The results also jeopardized the Euthecosomata families that are based on plesiomorphic character state as in the case for Creseidae which was not a monophyletic group. Divergence times were also estimated, and suggested that the evolutionary history of Thecosomata was characterized by four major diversifying events. By bringing the knowledge of palaeontology, we propose a new evolutionary scenario for which macro-evolution implying morphological innovations were rhythmed by climatic changes and associated species turn-over that spread from the Eocene to Miocene, and were shaped principally by predation and shell buoyancy. PMID:23593138

“Candidatus Midichloriaceae” fam. nov. (Rickettsiales), an Ecologically Widespread Clade of Intracellular Alphaproteobacteria

PubMed Central

Montagna, Matteo; Sassera, Davide; Epis, Sara; Bazzocchi, Chiara; Vannini, Claudia; Lo, Nathan; Sacchi, Luciano; Fukatsu, Takema; Petroni, Giulio

2013-01-01

“Candidatus Midichloria mitochondrii” is an intramitochondrial bacterium of the order Rickettsiales associated with the sheep tick Ixodes ricinus. Bacteria phylogenetically related to “Ca. Midichloria mitochondrii” (midichloria and like organisms [MALOs]) have been shown to be associated with a wide range of hosts, from amoebae to a variety of animals, including humans. Despite numerous studies focused on specific members of the MALO group, no comprehensive phylogenetic and statistical analyses have so far been performed on the group as a whole. Here, we present a multidisciplinary investigation based on 16S rRNA gene sequences using both phylogenetic and statistical methods, thereby analyzing MALOs in the overall framework of the Rickettsiales. This study revealed that (i) MALOs form a monophyletic group; (ii) the MALO group is structured into distinct subgroups, verifying current genera as significant evolutionary units and identifying several subclades that could represent novel genera; (iii) the MALO group ranks at the level of described Rickettsiales families, leading to the proposal of the novel family “Candidatus Midichloriaceae.” In addition, based on the phylogenetic trees generated, we present an evolutionary scenario to interpret the distribution and life history transitions of these microorganisms associated with highly divergent eukaryotic hosts: we suggest that aquatic/environmental protista have acted as evolutionary reservoirs for members of this novel family, from which one or more lineages with the capacity of infecting metazoa have evolved. PMID:23503305

Evolutionary responses to climate change in parasitic systems.

PubMed

Chaianunporn, Thotsapol; Hovestadt, Thomas

2015-08-01

Species may respond to climate change in many ecological and evolutionary ways. In this simulation study, we focus on the concurrent evolution of three traits in response to climate change, namely dispersal probability, temperature tolerance (or niche width), and temperature preference (optimal habitat). More specifically, we consider evolutionary responses in host species involved in different types of interaction, that is parasitism or commensalism, and for low or high costs of a temperature tolerance-fertility trade-off (cost of generalization). We find that host species potentially evolve all three traits simultaneously in response to increasing temperature but that the evolutionary response interacts and may be compensatory depending on the conditions. The evolutionary adjustment of temperature preference is slower in the parasitism than in commensalism scenario. Parasitism, in turn, selects for higher temperature tolerance and increased dispersal. High costs for temperature tolerance (i.e. generalization) restrict evolution of tolerance and thus lead to a faster response in temperature preference than that observed under low costs. These results emphasize the possible role of biotic interactions and the importance of 'multidimensional' evolutionary responses to climate change. © 2015 John Wiley & Sons Ltd.

The Evolution of Massive Stars: a Selection of Facts and Questions

NASA Astrophysics Data System (ADS)

Vanbeveren, D.

In the present paper we discuss a selection of facts and questions related to observations and evolutionary calculations of massive single stars and massive stars in interacting binaries. We focus on the surface chemical abundances, the role of stellar winds, the early Be-stars, the high mass X-ray binaries and the effects of rotation on stellar evolution. Finally, we present an unconventionally formed object scenario (UFO-scenario) of WR binaries in dense stellar environments.

Predicting loss of evolutionary history: Where are we?

PubMed

Veron, Simon; Davies, T Jonathan; Cadotte, Marc W; Clergeau, Philippe; Pavoine, Sandrine

2017-02-01

The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic groups and test the assumption that preserving ED and PD also protects rare species and ecosystem services. Such research will be useful to inform and guide the conservation of Earth's biodiversity and the services it provides. © 2015 Cambridge Philosophical Society.

On black widow evolutionary scenarios for binary neutron stars

NASA Technical Reports Server (NTRS)

Eichler, David; Levinson, Amir

1988-01-01

The scenario whereby the pulsar 1957 + 20 ablates its companion by soft gamma-ray synchrotron emission (Ruderman et al., 1988) is critically examined, with particular regard to how the outflowing material, beginning at photospheric temperatures, is heated through the cooling barrier to coronal temperatures. Assuming the conductivity to be at most the Spitzer value, this consideration is found to constrain the mass flux more than two orders of magnitude more severely than merely considering cooling near the sonic point. This would imply that the ablation scenario fails by a large margin, even if the emission from the pulsar is beamed along the orbital plane.

A systematic mapping study of process mining

NASA Astrophysics Data System (ADS)

Maita, Ana Rocío Cárdenas; Martins, Lucas Corrêa; López Paz, Carlos Ramón; Rafferty, Laura; Hung, Patrick C. K.; Peres, Sarajane Marques; Fantinato, Marcelo

2018-05-01

This study systematically assesses the process mining scenario from 2005 to 2014. The analysis of 705 papers evidenced 'discovery' (71%) as the main type of process mining addressed and 'categorical prediction' (25%) as the main mining task solved. The most applied traditional technique is the 'graph structure-based' ones (38%). Specifically concerning computational intelligence and machine learning techniques, we concluded that little relevance has been given to them. The most applied are 'evolutionary computation' (9%) and 'decision tree' (6%), respectively. Process mining challenges, such as balancing among robustness, simplicity, accuracy and generalization, could benefit from a larger use of such techniques.

Tempo and mode of evolution in the tangled nature model.

PubMed

Jones, Dominic; Jensen, Henrik Jeldtoft; Sibani, Paolo

2010-09-01

The fossil record has been interpreted as exhibiting a gradual decrease in the extinction rate. We use the individual based Tangled Nature model of evolutionary ecology to study the mechanisms behind this kind of nonstationary macrodynamics. We demonstrate that the long time aging in the system (manifested as a slowing down of the rate of large jumps, or quakes, that the system undergoes) is related to decreasing fluctuations in the offspring probability. The scenario is reminiscent of relaxation in a quenched spin glass but purely dynamical in nature since no energy barriers can be defined.

Deontic reasoning with emotional content: evolutionary psychology or decision theory?

PubMed

Perham, Nick; Oaksford, Mike

2005-09-10

Three experiments investigated the contrasting predictions of the evolutionary and decision-theoretic approaches to deontic reasoning. Two experiments embedded a hazard management (HM) rule in a social contract scenario that should lead to competition between innate modules. A 3rd experiment used a pure HM task. Threatening material was also introduced into the antecedent, p, of a deontic rule, if p then must q. According to the evolutionary approach, more HM responses (Cosmides & Tooby, 2000) are predicted when p is threatening, whereas decision theory predicts fewer. All 3 experiments were consistent with decision theory. Other theories are discussed, and it is concluded that they cannot account for the behavior observed in these experiments. 2005 Lawrence Erlbaum Associates, Inc.

College students' use of science content during socioscientific issues negotiation: Impact of evolution understanding and acceptance

NASA Astrophysics Data System (ADS)

Fowler, Samantha R.

The purpose of this study was to explore the evolution science content used during college students' negotiation of biology-based socioscientific issues (SSI) and examine how it related to students' conceptual understanding and acceptance of biological evolution. Specific research questions were, (1a) what specific evolutionary science content do college students evoke during SSI negotiation, (1b) what is the depth of the evolutionary science content reflected in college students. SSI negotiation, and (2) what is the nature of the interaction between evolution understanding and evolution acceptance as they relate to depth of use of evolution content during SSI negotiation? The Socioscientific Issues Questionnaire (SSI-Q) was developed using inductive data analysis to examine science content use and to develop a rubric for measuring depth of evolutionary science content use during SSI negotiation. Sixty upper level undergraduate biology and non-biology majors completed the SSI-Q and also the Conceptual Inventory of Natural Selection (CINS: Anderson, Fisher, & Norman, 2002) to measure evolution understanding and the Measure of Acceptance of the Theory of Evolution (MATE: Rutledge & Warden, 1999) to measure evolution acceptance. A multiple regression analysis tested for interaction effects between the predictor variables, evolution understanding and evolution acceptance. Results indicate that college students primarily use science concepts related to evolution to negotiate biology-based SSI: variation in a population, inheritance of traits, differential success, and change through time. The hypothesis that the extent of one's acceptance of evolution is a mitigating factor in how evolution content is evoked during SSI negotiation was supported by the data. This was seen in that evolution was the predominant science content used by participants for each of the three SSI scenarios used in this study and used consistently throughout the three SSI scenarios. In addition to its potential to assess aspects of argumentation, a modification of the SSI-Q could be used for further study about students' misconceptions about evolution or scientific literacy, if it is defined as one's tendency to utilize science content during a decision-making process within an SSI context.

Evolutionary games in the multiverse.

PubMed

Gokhale, Chaitanya S; Traulsen, Arne

2010-03-23

Evolutionary game dynamics of two players with two strategies has been studied in great detail. These games have been used to model many biologically relevant scenarios, ranging from social dilemmas in mammals to microbial diversity. Some of these games may, in fact, take place between a number of individuals and not just between two. Here we address one-shot games with multiple players. As long as we have only two strategies, many results from two-player games can be generalized to multiple players. For games with multiple players and more than two strategies, we show that statements derived for pairwise interactions no longer hold. For two-player games with any number of strategies there can be at most one isolated internal equilibrium. For any number of players with any number of strategies , there can be at most isolated internal equilibria. Multiplayer games show a great dynamical complexity that cannot be captured based on pairwise interactions. Our results hold for any game and can easily be applied to specific cases, such as public goods games or multiplayer stag hunts.

Biodiversity scenarios neglect future land-use changes.

PubMed

Titeux, Nicolas; Henle, Klaus; Mihoub, Jean-Baptiste; Regos, Adrián; Geijzendorffer, Ilse R; Cramer, Wolfgang; Verburg, Peter H; Brotons, Lluís

2016-07-01

Efficient management of biodiversity requires a forward-looking approach based on scenarios that explore biodiversity changes under future environmental conditions. A number of ecological models have been proposed over the last decades to develop these biodiversity scenarios. Novel modelling approaches with strong theoretical foundation now offer the possibility to integrate key ecological and evolutionary processes that shape species distribution and community structure. Although biodiversity is affected by multiple threats, most studies addressing the effects of future environmental changes on biodiversity focus on a single threat only. We examined the studies published during the last 25 years that developed scenarios to predict future biodiversity changes based on climate, land-use and land-cover change projections. We found that biodiversity scenarios mostly focus on the future impacts of climate change and largely neglect changes in land use and land cover. The emphasis on climate change impacts has increased over time and has now reached a maximum. Yet, the direct destruction and degradation of habitats through land-use and land-cover changes are among the most significant and immediate threats to biodiversity. We argue that the current state of integration between ecological and land system sciences is leading to biased estimation of actual risks and therefore constrains the implementation of forward-looking policy responses to biodiversity decline. We suggest research directions at the crossroads between ecological and environmental sciences to face the challenge of developing interoperable and plausible projections of future environmental changes and to anticipate the full range of their potential impacts on biodiversity. An intergovernmental platform is needed to stimulate such collaborative research efforts and to emphasize the societal and political relevance of taking up this challenge. © 2016 John Wiley & Sons Ltd.

Photosynthesis: what color was its origin?

PubMed Central

Xiong, Jin

2006-01-01

Recent studies using geological and molecular phylogenetic evidence suggest several alternative evolutionary scenarios for the origin of photosynthesis. The earliest photosynthetic group is variously thought to be heliobacteria, proteobacteria or a precursor of cyanobacteria, organisms whose photosynthetic pigments make them different colors. PMID:17210067

An investigation of the evolutionary origin of reciprocal communication using simulated autonomous agents.

PubMed

Tuci, Elio

2009-09-01

How does communication originates in a population of originally non-communicating individuals? Providing an answer to this question from a neo-Darwinian epistemological perspective is not a trivial task. The reason is that, for non-communicating agents, the capabilities of emitting signals and responding to them are both adaptively neutral traits if they are not simultaneously present. Research studies based on rather general and theoretically oriented evolutionary simulation models have, so far, demonstrated that at least two different processes can account for the origin of communication. On the one hand, communicative behaviour may first evolve in a non-communicative context and only subsequently acquire its adaptive function.On the other hand, communication may originate thanks to cognitive constraints; that is, communication may originate thanks to the existence of neural substrates that are common to the signalling and categorising capabilities. This article provides a proof-of-concept demonstration of the origin of communication in a novel-simulated scenario in which groups of two homogeneous (i.e. genetically identical) agents exploit reciprocal communication to develop common perceptual categories nd to perform a collective task. In particular, in circumstances in which communication is evolutionarily advantageous, simulated agents evolve from scratch social behaviour through acoustic interactions.We look into the phylogeny of successful communication protocol, and we describe the evolutionary phenomena that, in early evolutionary stages, paved the way for the subsequent development of reciprocal communication, categorisation capabilities and successful cooperative strategies.

An Evolutionary-Based Framework for Analyzing Mold and Dampness-Associated Symptoms in DMHS

PubMed Central

Daschner, Alvaro

2017-01-01

Among potential environmental harmful factors, fungi deserve special consideration. Their intrinsic ability to actively germinate or infect host tissues might determine a prominent trigger in host defense mechanisms. With the appearance of fungi in evolutionary history, other organisms had to evolve strategies to recognize and cope with them. Existing controversies around dampness and mold hypersensitivity syndrome (DMHS) can be due to the great variability of clinical symptoms but also of possible eliciting factors associated with mold and dampness. An hypothesis is presented, where an evolutionary analysis of the different response patterns seen in DMHS is able to explain the existing variability of disease patterns. Classical interpretation of immune responses and symptoms are addressed within the field of pathophysiology. The presented evolutionary analysis seeks for the ultimate causes of the vast array of symptoms in DMHS. Symptoms can be interpreted as induced by direct (toxic) actions of spores, mycotoxins, or other fungal metabolites, or on the other side by the host-initiated response, which aims to counterbalance and fight off potentially deleterious effects or fungal infection. Further, individual susceptibility of immune reactions can confer an exaggerated response, and magnified symptoms are then explained in terms of immunopathology. IgE-mediated allergy fits well in this scenario, where individuals with an atopic predisposition suffer from an exaggerated response to mold exposure, but studies addressing why such responses have evolved and if they could be advantageous are scarce. Human history is plenty of plagues and diseases connected with mold exposure, which could explain vulnerability to mold allergy. Likewise, multiorgan symptoms in DMHS are analyzed for its possible adaptive role not only in the defense of an active infection, but also as evolved mechanisms for avoidance of potentially harmful environments in an evolutionary past or present setting. PMID:28119688

A Penalized Likelihood Framework For High-Dimensional Phylogenetic Comparative Methods And An Application To New-World Monkeys Brain Evolution.

PubMed

Julien, Clavel; Leandro, Aristide; Hélène, Morlon

2018-06-19

Working with high-dimensional phylogenetic comparative datasets is challenging because likelihood-based multivariate methods suffer from low statistical performances as the number of traits p approaches the number of species n and because some computational complications occur when p exceeds n. Alternative phylogenetic comparative methods have recently been proposed to deal with the large p small n scenario but their use and performances are limited. Here we develop a penalized likelihood framework to deal with high-dimensional comparative datasets. We propose various penalizations and methods for selecting the intensity of the penalties. We apply this general framework to the estimation of parameters (the evolutionary trait covariance matrix and parameters of the evolutionary model) and model comparison for the high-dimensional multivariate Brownian (BM), Early-burst (EB), Ornstein-Uhlenbeck (OU) and Pagel's lambda models. We show using simulations that our penalized likelihood approach dramatically improves the estimation of evolutionary trait covariance matrices and model parameters when p approaches n, and allows for their accurate estimation when p equals or exceeds n. In addition, we show that penalized likelihood models can be efficiently compared using Generalized Information Criterion (GIC). We implement these methods, as well as the related estimation of ancestral states and the computation of phylogenetic PCA in the R package RPANDA and mvMORPH. Finally, we illustrate the utility of the new proposed framework by evaluating evolutionary models fit, analyzing integration patterns, and reconstructing evolutionary trajectories for a high-dimensional 3-D dataset of brain shape in the New World monkeys. We find a clear support for an Early-burst model suggesting an early diversification of brain morphology during the ecological radiation of the clade. Penalized likelihood offers an efficient way to deal with high-dimensional multivariate comparative data.

An Evolutionary-Based Framework for Analyzing Mold and Dampness-Associated Symptoms in DMHS.

PubMed

Daschner, Alvaro

2016-01-01

Among potential environmental harmful factors, fungi deserve special consideration. Their intrinsic ability to actively germinate or infect host tissues might determine a prominent trigger in host defense mechanisms. With the appearance of fungi in evolutionary history, other organisms had to evolve strategies to recognize and cope with them. Existing controversies around dampness and mold hypersensitivity syndrome (DMHS) can be due to the great variability of clinical symptoms but also of possible eliciting factors associated with mold and dampness. An hypothesis is presented, where an evolutionary analysis of the different response patterns seen in DMHS is able to explain the existing variability of disease patterns. Classical interpretation of immune responses and symptoms are addressed within the field of pathophysiology. The presented evolutionary analysis seeks for the ultimate causes of the vast array of symptoms in DMHS. Symptoms can be interpreted as induced by direct (toxic) actions of spores, mycotoxins, or other fungal metabolites, or on the other side by the host-initiated response, which aims to counterbalance and fight off potentially deleterious effects or fungal infection. Further, individual susceptibility of immune reactions can confer an exaggerated response, and magnified symptoms are then explained in terms of immunopathology. IgE-mediated allergy fits well in this scenario, where individuals with an atopic predisposition suffer from an exaggerated response to mold exposure, but studies addressing why such responses have evolved and if they could be advantageous are scarce. Human history is plenty of plagues and diseases connected with mold exposure, which could explain vulnerability to mold allergy. Likewise, multiorgan symptoms in DMHS are analyzed for its possible adaptive role not only in the defense of an active infection, but also as evolved mechanisms for avoidance of potentially harmful environments in an evolutionary past or present setting.

The evolution of a key character, or how to evolve a slipper lobster.

PubMed

Haug, Joachim T; Audo, Denis; Charbonnier, Sylvain; Palero, Ferran; Petit, Gilles; Abi Saad, Pierre; Haug, Carolin

2016-03-01

A new fossil lobster from the Cretaceous of Lebanon, Charbelicaris maronites gen. et sp. nov., is presented here, while the former species 'Cancrinos' libanensis is re-described as Paracancrinos libanensis comb. nov. P. libanensis is shown to be closer related to the contemporary slipper lobsters than to Cancrinos claviger (lithographic limestones, Jurassic, southern Germany). A finely-graded evolutionary scenario for the slipper-lobster morphotype is reconstructed based on these fossil species and extant forms. The evolutionary changes that gave rise to the current plate-like antennae of Scyllaridae, a key apomorphy of this group, are traced back through time. The antenna of what is considered the oldest slipper lobster became petaloid and consisted of about 20 fully articulated elements. For this group the name Scyllarida sensu lato tax. nov. is introduced. In a next evolutionary step, the proximal articles became conjoined and a lateral extension appeared on peduncle element 3. The entire distal petaloid region is conjoined already at the node of Verscyllarida tax. nov. In modern slipper lobsters, Neoscyllarida tax nov., the distal region is no longer petaloid in shape but asymmetrical. The study also emphasizes that exceptionally preserved fossils need to be documented with optimal documentation techniques to obtain all available information. Copyright © 2015 Elsevier Ltd. All rights reserved.

Nuclear and plastid markers reveal the persistence of genetic identity: a new perspective on the evolutionary history of Petunia exserta.

PubMed

Segatto, Ana Lúcia Anversa; Cazé, Ana Luíza Ramos; Turchetto, Caroline; Klahre, Ulrich; Kuhlemeier, Cris; Bonatto, Sandro Luis; Freitas, Loreta Brandão

2014-01-01

Recently divergent species that can hybridize are ideal models for investigating the genetic exchanges that can occur while preserving the species boundaries. Petunia exserta is an endemic species from a very limited and specific area that grows exclusively in rocky shelters. These shaded spots are an inhospitable habitat for all other Petunia species, including the closely related and widely distributed species P. axillaris. Individuals with intermediate morphologic characteristics have been found near the rocky shelters and were believed to be putative hybrids between P. exserta and P. axillaris, suggesting a situation where Petunia exserta is losing its genetic identity. In the current study, we analyzed the plastid intergenic spacers trnS/trnG and trnH/psbA and six nuclear CAPS markers in a large sampling design of both species to understand the evolutionary process occurring in this biological system. Bayesian clustering methods, cpDNA haplotype networks, genetic diversity statistics, and coalescence-based analyses support a scenario where hybridization occurs while two genetic clusters corresponding to two species are maintained. Our results reinforce the importance of coupling differentially inherited markers with an extensive geographic sample to assess the evolutionary dynamics of recently diverged species that can hybridize. Copyright © 2013 Elsevier Inc. All rights reserved.

Observational evidence of dust evolution in galactic extinction curves

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

Cecchi-Pestellini, Cesare; Casu, Silvia; Mulas, Giacomo

Although structural and optical properties of hydrogenated amorphous carbons are known to respond to varying physical conditions, most conventional extinction models are basically curve fits with modest predictive power. We compare an evolutionary model of the physical properties of carbonaceous grain mantles with their determination by homogeneously fitting observationally derived Galactic extinction curves with the same physically well-defined dust model. We find that a large sample of observed Galactic extinction curves are compatible with the evolutionary scenario underlying such a model, requiring physical conditions fully consistent with standard density, temperature, radiation field intensity, and average age of diffuse interstellar clouds.more » Hence, through the study of interstellar extinction we may, in principle, understand the evolutionary history of the diffuse interstellar clouds.« less

Divergence in Defence against Herbivores between Males and Females of Dioecious Plant Species

PubMed Central

Avila-Sakar, Germán; Romanow, Cora Anne

2012-01-01

Defensive traits may evolve differently between sexes in dioecious plant species. Our current understanding of this process hinges on a partial view of the evolution of resistance traits that may result in male-biased herbivory in dioecious populations. Here, we present a critical summary of the current state of the knowledge of herbivory in dioecious species and propose alternative evolutionary scenarios that have been neglected. These scenarios consider the potential evolutionary and functional determinants of sexual dimorphism in patterns of resource allocation to reproduction, growth, and defence. We review the evidence upon which two previous reviews of sex-biased herbivory have concluded that male-biased herbivory is a rule for dioecious species, and we caution readers about a series of shortcomings of many of these studies. Lastly, we propose a minimal standard protocol that should be followed in any studies that intend to elucidate the (co)evolution of interactions between dioecious plants and their herbivores. PMID:23320247

The evolution of respiratory O2/NO reductases: an out-of-the-phylogenetic-box perspective.

PubMed

Ducluzeau, Anne-Lise; Schoepp-Cothenet, Barbara; van Lis, Robert; Baymann, Frauke; Russell, Michael J; Nitschke, Wolfgang

2014-09-06

Complex life on our planet crucially depends on strong redox disequilibria afforded by the almost ubiquitous presence of highly oxidizing molecular oxygen. However, the history of O2-levels in the atmosphere is complex and prior to the Great Oxidation Event some 2.3 billion years ago, the amount of O2 in the biosphere is considered to have been extremely low as compared with present-day values. Therefore the evolutionary histories of life and of O2-levels are likely intricately intertwined. The obvious biological proxy for inferring the impact of changing O2-levels on life is the evolutionary history of the enzyme allowing organisms to tap into the redox power of molecular oxygen, i.e. the bioenergetic O2 reductases, alias the cytochrome and quinol oxidases. Consequently, molecular phylogenies reconstructed for this enzyme superfamily have been exploited over the last two decades in attempts to elucidate the interlocking between O2 levels in the environment and the evolution of respiratory bioenergetic processes. Although based on strictly identical datasets, these phylogenetic approaches have led to diametrically opposite scenarios with respect to the history of both the enzyme superfamily and molecular oxygen on the Earth. In an effort to overcome the deadlock of molecular phylogeny, we here review presently available structural, functional, palaeogeochemical and thermodynamic information pertinent to the evolution of the superfamily (which notably also encompasses the subfamily of nitric oxide reductases). The scenario which, in our eyes, most closely fits the ensemble of these non-phylogenetic data, sees the low O2-affinity SoxM- (or A-) type enzymes as the most recent evolutionary innovation and the high-affinity O2 reductases (SoxB or B and cbb3 or C) as arising independently from NO-reducing precursor enzymes. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

The eco-evolutionary responses of a generalist consumer to resource competition.

PubMed

Abrams, Peter A

2012-10-01

This article explores the combined evolutionary and ecological responses of resource uptake abilities in a generalist consumer to exploitative competition for one resource using a simple 2-resource model. It compares the sizes of ecologically and evolutionarily caused changes in population densities in cases where the original consumer has a strong or a weak trade-off in its abilities to consume the two resources. The analysis also compares the responses of the original species to competition when the competitor's population size is or is not limited by the shared resource. Although divergence in resource use traits in the resident generalist consumer is expected under all scenarios when resources are substitutable, the changes in population densities of the resources and resident consumer frequently differ between scenarios. The population of the original consumer often decreases as a result of its own adaptive divergence, and this decrease is often much greater than the initial ecological decrease. If the evolving consumer has a strong trade-off, the overlapped resource increases in equilibrium population density in response to being consumed by a generalist competitor. Some of these predictions differ qualitatively in alternative scenarios involving sustained variation in population densities or nutritionally essential resources. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

The Common Ancestor of Archaea and Eukarya Was Not an Archaeon

PubMed Central

Forterre, Patrick

2013-01-01

It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other. PMID:24348094

The common ancestor of archaea and eukarya was not an archaeon.

PubMed

Forterre, Patrick

2013-01-01

It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the "prokaryotic" phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.

Lucinidae/sulfur-oxidizing bacteria: ancestral heritage or opportunistic association? Further insights from the Bohol Sea (the Philippines).

PubMed

Brissac, Terry; Merçot, Hervé; Gros, Olivier

2011-01-01

The first studies of the 16S rRNA gene diversity of the bacterial symbionts found in lucinid clams did not clarify how symbiotic associations had evolved in this group. Indeed, although species-specific associations deriving from a putative ancestral symbiotic association have been described (coevolution scenario), associations between the same bacterial species and various host species (opportunistic scenario) have also been described. Here, we carried out a comparative molecular analysis of hosts, based on 18S and 28S rRNA gene sequences, and of symbionts, based on 16S rRNA gene sequences, to determine as to which evolutionary scenario led to modern lucinid/symbiont associations. For all sequences analyzed, we found only three bacterial symbiont species, two of which are harbored by lucinids colonizing mangrove swamps. The last symbiont is the most common and was found to be independent of biotope or depth. Another interesting feature is the similarity of ctenidial organization of lucinids from the Philippines to those described previously, with the exception that two bacterial morphotypes were observed in two different species (Gloverina rectangularis and Myrtea flabelliformis). Thus, there is apparently no specific association between Lucinidae and their symbionts, the association taking place according to which bacterial species is present in the environment. FEMS Microbiology Ecology © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original French government works.

Transformation and diversification in early mammal evolution.

PubMed

Luo, Zhe-Xi

2007-12-13

Evolution of the earliest mammals shows successive episodes of diversification. Lineage-splitting in Mesozoic mammals is coupled with many independent evolutionary experiments and ecological specializations. Classic scenarios of mammalian morphological evolution tend to posit an orderly acquisition of key evolutionary innovations leading to adaptive diversification, but newly discovered fossils show that evolution of such key characters as the middle ear and the tribosphenic teeth is far more labile among Mesozoic mammals. Successive diversifications of Mesozoic mammal groups multiplied the opportunities for many dead-end lineages to iteratively evolve developmental homoplasies and convergent ecological specializations, parallel to those in modern mammal groups.

The Origins of Tropical Rainforest Hyperdiversity.

PubMed

Pennington, R Toby; Hughes, Mark; Moonlight, Peter W

2015-11-01

Traditional models for tropical species richness contrast rainforests as "museums" of old species or "cradles" of recent speciation. High plant species diversity in rainforests may be more likely to reflect high episodic evolutionary turnover of species--a scenario implicating high rates of both speciation and extinction through geological time.

Life sciences biomedical research planning for Space Station

NASA Technical Reports Server (NTRS)

Primeaux, Gary R.; Michaud, Roger; Miller, Ladonna; Searcy, Jim; Dickey, Bernistine

1987-01-01

The Biomedical Research Project (BmRP), a major component of the NASA Life Sciences Space Station Program, incorporates a laboratory for the study of the effects of microgravity on the human body, and the development of techniques capable of modifying or counteracting these effects. Attention is presently given to a representative scenario of BmRP investigations and associated engineering analyses, together with an account of the evolutionary process by which the scenarios and the Space Station design requirements they entail are identified. Attention is given to a tether-implemented 'variable gravity centrifuge'.

Evolutionary mysteries in meiosis.

PubMed

Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E; Wijnker, Erik; Haag, Christoph R

2016-10-19

Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often 'weird' features. We discuss the origin of meiosis (origin of ploidy reduction and recombination, two-step meiosis), its secondary modifications (in polyploids or asexuals, inverted meiosis), its importance in punctuating life cycles (meiotic arrests, epigenetic resetting, meiotic asymmetry, meiotic fairness) and features associated with recombination (disjunction constraints, heterochiasmy, crossover interference and hotspots). We present the various evolutionary scenarios and selective pressures that have been proposed to account for these features, and we highlight that their evolutionary significance often remains largely mysterious. Resolving these mysteries will likely provide decisive steps towards understanding why sex and recombination are found in the majority of eukaryotes.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'. © 2016 The Author(s).

Evolutionary mysteries in meiosis

PubMed Central

2016-01-01

Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often ‘weird’ features. We discuss the origin of meiosis (origin of ploidy reduction and recombination, two-step meiosis), its secondary modifications (in polyploids or asexuals, inverted meiosis), its importance in punctuating life cycles (meiotic arrests, epigenetic resetting, meiotic asymmetry, meiotic fairness) and features associated with recombination (disjunction constraints, heterochiasmy, crossover interference and hotspots). We present the various evolutionary scenarios and selective pressures that have been proposed to account for these features, and we highlight that their evolutionary significance often remains largely mysterious. Resolving these mysteries will likely provide decisive steps towards understanding why sex and recombination are found in the majority of eukaryotes. This article is part of the themed issue ‘Weird sex: the underappreciated diversity of sexual reproduction’. PMID:27619705

The genome of Theobroma cacao.

PubMed

Argout, Xavier; Salse, Jerome; Aury, Jean-Marc; Guiltinan, Mark J; Droc, Gaetan; Gouzy, Jerome; Allegre, Mathilde; Chaparro, Cristian; Legavre, Thierry; Maximova, Siela N; Abrouk, Michael; Murat, Florent; Fouet, Olivier; Poulain, Julie; Ruiz, Manuel; Roguet, Yolande; Rodier-Goud, Maguy; Barbosa-Neto, Jose Fernandes; Sabot, Francois; Kudrna, Dave; Ammiraju, Jetty Siva S; Schuster, Stephan C; Carlson, John E; Sallet, Erika; Schiex, Thomas; Dievart, Anne; Kramer, Melissa; Gelley, Laura; Shi, Zi; Bérard, Aurélie; Viot, Christopher; Boccara, Michel; Risterucci, Ange Marie; Guignon, Valentin; Sabau, Xavier; Axtell, Michael J; Ma, Zhaorong; Zhang, Yufan; Brown, Spencer; Bourge, Mickael; Golser, Wolfgang; Song, Xiang; Clement, Didier; Rivallan, Ronan; Tahi, Mathias; Akaza, Joseph Moroh; Pitollat, Bertrand; Gramacho, Karina; D'Hont, Angélique; Brunel, Dominique; Infante, Diogenes; Kebe, Ismael; Costet, Pierre; Wing, Rod; McCombie, W Richard; Guiderdoni, Emmanuel; Quetier, Francis; Panaud, Olivier; Wincker, Patrick; Bocs, Stephanie; Lanaud, Claire

2011-02-01

We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.

Petrology of lunar rocks and implication to lunar evolution

NASA Technical Reports Server (NTRS)

Ridley, W. I.

1976-01-01

Recent advances in lunar petrology, based on studies of lunar rock samples available through the Apollo program, are reviewed. Samples of bedrock from both maria and terra have been collected where micrometeorite impact penetrated the regolith and brought bedrock to the surface, but no in situ cores have been taken. Lunar petrogenesis and lunar thermal history supported by studies of the rock sample are discussed and a tentative evolutionary scenario is constructed. Mare basalts, terra assemblages of breccias, soils, rocks, and regolith are subjected to elemental analysis, mineralogical analysis, trace content analysis, with studies of texture, ages and isotopic composition. Probable sources of mare basalts are indicated.

Early Human Evolution in the Western Palaearctic: Ecological Scenarios

NASA Astrophysics Data System (ADS)

Carrión, José S.; Rose, James; Stringer, Chris

2011-06-01

This review presents the themes of a special issue dealing with environmental scenarios of human evolution during the Early Pleistocene (2.6-0.78 Ma; MIS 103-MIS 19) and early Middle Pleistocene (0.78-0.47 Ma; MIS 19-base of MIS 12) within the western Palaearctic. This period is one of dramatic changes in the climates and the distribution of Palaearctic biota. These changes have played their role in generating adaptive and phyletic patterns within the human ancestry, involving several species such as Homo habilis, "Homo georgicus", Homo erectus, Homo antecessor and Homo heidelbergensis. In the archaeological record, these species include the Oldowan (Mode 1) and Acheulian (Mode 2) lithic technologies. Taphonomic considerations of palaeoecological research in hominin-bearing sites are provided and evaluated. Syntheses are provided for north Africa, western Asia, the Mediterranean Basin, Britain, and continental Europe. Palaeoenvironmental reconstructions based on multidisciplinary data are given for Ain Boucherit, Ain Hanech and El-Kherba in Algeria, Dmanisi in Georgia, Atapuerca, Cueva Negra, and the Orce Basin in Spain, Monte Poggiolo and Pirro Nord in Italy, Pont-de-Lavaud in France, and Mauer in Germany. The state of the art with the Out of Africa 1 dispersal model is reviewed. A source-sink dynamics model for Palaeolithic Europe is described to explain the morphological disparity of H. heidelbergensis (we will sometimes use the informal name "Heidelbergs") and early Neanderthals. Other aspects debated here are the selective value of habitat mosaics including reconstructions based on mammal and avian databases, and the role of geological instability combined with topographic complexity. This review is completed by addressing the question of whether the appearance of evolutionary trends within hominins is concentrated in regions of highest worldwide biological diversity (biodiversity hotspots). It is concluded that the keys for the activation of evolutionary change in hominins may have been geological instabilities, and a shifting physiographical heterogeneity combined with high biodiversity and ecological interaction.

Demographic history and gene flow during silkworm domestication

PubMed Central

2014-01-01

Background Gene flow plays an important role in domestication history of domesticated species. However, little is known about the demographic history of domesticated silkworm involving gene flow with its wild relative. Results In this study, four model-based evolutionary scenarios to describe the demographic history of B. mori were hypothesized. Using Approximate Bayesian Computation method and DNA sequence data from 29 nuclear loci, we found that the gene flow at bottleneck model is the most likely scenario for silkworm domestication. The starting time of silkworm domestication was estimated to be approximate 7,500 years ago; the time of domestication termination was 3,984 years ago. Using coalescent simulation analysis, we also found that bi-directional gene flow occurred during silkworm domestication. Conclusions Estimates of silkworm domestication time are nearly consistent with the archeological evidence and our previous results. Importantly, we found that the bi-directional gene flow might occur during silkworm domestication. Our findings add a dimension to highlight the important role of gene flow in domestication of crops and animals. PMID:25123546

The major synthetic evolutionary transitions.

PubMed

Solé, Ricard

2016-08-19

Evolution is marked by well-defined events involving profound innovations that are known as 'major evolutionary transitions'. They involve the integration of autonomous elements into a new, higher-level organization whereby the former isolated units interact in novel ways, losing their original autonomy. All major transitions, which include the origin of life, cells, multicellular systems, societies or language (among other examples), took place millions of years ago. Are these transitions unique, rare events? Have they instead universal traits that make them almost inevitable when the right pieces are in place? Are there general laws of evolutionary innovation? In order to approach this problem under a novel perspective, we argue that a parallel class of evolutionary transitions can be explored involving the use of artificial evolutionary experiments where alternative paths to innovation can be explored. These 'synthetic' transitions include, for example, the artificial evolution of multicellular systems or the emergence of language in evolved communicating robots. These alternative scenarios could help us to understand the underlying laws that predate the rise of major innovations and the possibility for general laws of evolved complexity. Several key examples and theoretical approaches are summarized and future challenges are outlined.This article is part of the themed issue 'The major synthetic evolutionary transitions'. © 2016 The Author(s).

The major synthetic evolutionary transitions

PubMed Central

Solé, Ricard

2016-01-01

Evolution is marked by well-defined events involving profound innovations that are known as ‘major evolutionary transitions'. They involve the integration of autonomous elements into a new, higher-level organization whereby the former isolated units interact in novel ways, losing their original autonomy. All major transitions, which include the origin of life, cells, multicellular systems, societies or language (among other examples), took place millions of years ago. Are these transitions unique, rare events? Have they instead universal traits that make them almost inevitable when the right pieces are in place? Are there general laws of evolutionary innovation? In order to approach this problem under a novel perspective, we argue that a parallel class of evolutionary transitions can be explored involving the use of artificial evolutionary experiments where alternative paths to innovation can be explored. These ‘synthetic’ transitions include, for example, the artificial evolution of multicellular systems or the emergence of language in evolved communicating robots. These alternative scenarios could help us to understand the underlying laws that predate the rise of major innovations and the possibility for general laws of evolved complexity. Several key examples and theoretical approaches are summarized and future challenges are outlined. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431528

Exploring an Alternative Model of Human Reproductive Capability: A Creative Learning Activity

ERIC Educational Resources Information Center

Cherif, Abour H.; Jedlicka, Dianne M.

2012-01-01

Biological and social evolutionary processes, along with social and cultural developments, have allowed humans to separate procreation from pleasurable/recreational sexual activity. As a class learning project, an alternative, hypothetical reproductive scenario is presented: "What if humans were biologically ready to conceive only during one…

Reasoning about Natural Selection: Diagnosing Contextual Competency Using the ACORNS Instrument

ERIC Educational Resources Information Center

Nehm, Ross H.; Beggrow, Elizabeth P.; Opfer, John E.; Ha, Minsu

2012-01-01

Studies of students' thinking about natural selection have revealed that the scenarios in which students reason evoke different types, magnitudes, and arrangements of knowledge elements and misconceptions. Diagnostic tests are needed that probe students' thinking across a representative array of evolutionary contexts. The ACORNS is a diagnostic…

The Structure of Phonological Theory

ERIC Educational Resources Information Center

Samuels, Bridget D.

2009-01-01

This dissertation takes a Minimalist approach to phonology, treating the phonological module as a system of abstract symbolic computation, divorced from phonetic content. I investigate the position of the phonological module within the architecture of grammar and the evolutionary scenario developed by Hauser et al. (2002a) and Fitch et al. (2005).…

Molecular evolution of the crustacean hyperglycemic hormone family in ecdysozoans

PubMed Central

2010-01-01

Background Crustacean Hyperglycemic Hormone (CHH) family peptides are neurohormones known to regulate several important functions in decapod crustaceans such as ionic and energetic metabolism, molting and reproduction. The structural conservation of these peptides, together with the variety of functions they display, led us to investigate their evolutionary history. CHH family peptides exist in insects (Ion Transport Peptides) and may be present in all ecdysozoans as well. In order to extend the evolutionary study to the entire family, CHH family peptides were thus searched in taxa outside decapods, where they have been, to date, poorly investigated. Results CHH family peptides were characterized by molecular cloning in a branchiopod crustacean, Daphnia magna, and in a collembolan, Folsomia candida. Genes encoding such peptides were also rebuilt in silico from genomic sequences of another branchiopod, a chelicerate and two nematodes. These sequences were included in updated datasets to build phylogenies of the CHH family in pancrustaceans. These phylogenies suggest that peptides found in Branchiopoda and Collembola are more closely related to insect ITPs than to crustacean CHHs. Datasets were also used to support a phylogenetic hypothesis about pancrustacean relationships, which, in addition to gene structures, allowed us to propose two evolutionary scenarios of this multigenic family in ecdysozoans. Conclusions Evolutionary scenarios suggest that CHH family genes of ecdysozoans originate from an ancestral two-exon gene, and genes of arthropods from a three-exon one. In malacostracans, the evolution of the CHH family has involved several duplication, insertion or deletion events, leading to neuropeptides with a wide variety of functions, as observed in decapods. This family could thus constitute a promising model to investigate the links between gene duplications and functional divergence. PMID:20184761

Hybridisation among groupers (genus Cephalopholis) at the eastern Indian Ocean suture zone: taxonomic and evolutionary implications

NASA Astrophysics Data System (ADS)

Payet, Samuel D.; Hobbs, Jean-Paul A.; DiBattista, Joseph D.; Newman, Stephen J.; Sinclair-Taylor, Tane; Berumen, Michael L.; McIlwain, Jennifer L.

2016-12-01

Hybridisation is a significant evolutionary process that until recently was considered rare in the marine environment. A suture zone in the eastern Indian Ocean is home to numerous hybridising sister species, providing an ideal opportunity to determine how hybridisation affects speciation and biodiversity in coral reef fishes. At this location, hybridisation between two grouper (Epinephelidae) species: Cephalopholis urodeta (Pacific Ocean) and C. nigripinnis (Indian Ocean) was investigated to determine the genetic basis of hybridisation and to compare the ecology and life history of hybrids and their parent species. This approach aimed to provide insights into the taxonomic and evolutionary consequences of hybridisation. Despite clear phenotypic differences, multiple molecular markers revealed hybrids, and their parent species were genetically homogenous within and (thousands of kilometres) outside of the hybrid zone. Hybrids were at least as fit as their parent species (in terms of growth, reproduction, and abundance) and were observed in a broad range of intermediate phenotypes. The two species appear to be interbreeding at Christmas Island due to inherent biological and ecological compatibilities, and the lack of genetic structure may be explained by three potential scenarios: (1) hybridisation and introgression; (2) discordance between morphology and genetics; and (3) incomplete lineage sorting. Further molecular analyses are necessary to discriminate these scenarios. Regardless of which applies, C. urodeta and C. nigripinnis are unlikely to evolve in reproductive isolation as they cohabit where they are common (Christmas Island) and will source congeneric mates where they are rare (Cocos Keeling Islands). Our results add to the growing body of evidence that hybridisation among coral reef fishes is a dynamic evolutionary factor.

Evolution of double-stranded DNA viruses of eukaryotes: from bacteriophages to transposons to giant viruses

PubMed Central

Koonin, Eugene V; Krupovic, Mart; Yutin, Natalya

2015-01-01

Diverse eukaryotes including animals and protists are hosts to a broad variety of viruses with double-stranded (ds) DNA genomes, from the largest known viruses, such as pandoraviruses and mimiviruses, to tiny polyomaviruses. Recent comparative genomic analyses have revealed many evolutionary connections between dsDNA viruses of eukaryotes, bacteriophages, transposable elements, and linear DNA plasmids. These findings provide an evolutionary scenario that derives several major groups of eukaryotic dsDNA viruses, including the proposed order “Megavirales,” adenoviruses, and virophages from a group of large virus-like transposons known as Polintons (Mavericks). The Polintons have been recently shown to encode two capsid proteins, suggesting that these elements lead a dual lifestyle with both a transposon and a viral phase and should perhaps more appropriately be named polintoviruses. Here, we describe the recently identified evolutionary relationships between bacteriophages of the family Tectiviridae, polintoviruses, adenoviruses, virophages, large and giant DNA viruses of eukaryotes of the proposed order “Megavirales,” and linear mitochondrial and cytoplasmic plasmids. We outline an evolutionary scenario under which the polintoviruses were the first group of eukaryotic dsDNA viruses that evolved from bacteriophages and became the ancestors of most large DNA viruses of eukaryotes and a variety of other selfish elements. Distinct lines of origin are detectable only for herpesviruses (from a different bacteriophage root) and polyoma/papillomaviruses (from single-stranded DNA viruses and ultimately from plasmids). Phylogenomic analysis of giant viruses provides compelling evidence of their independent origins from smaller members of the putative order “Megavirales,” refuting the speculations on the evolution of these viruses from an extinct fourth domain of cellular life. PMID:25727355

Phylogenetic Pattern, Evolutionary Processes and Species Delimitation in the Genus Echinococcus.

PubMed

Lymbery, A J

2017-01-01

An accurate and stable alpha taxonomy requires a clear conception of what constitutes a species and agreed criteria for delimiting different species. An evolutionary or general lineage concept defines a species as a single lineage of organisms with a common evolutionary trajectory, distinguishable from other such lineages. Delimiting evolutionary species is a two-step process. In the first step, phylogenetic reconstruction identifies putative species as groups of organisms that are monophyletic (share a common ancestor) and exclusive (more closely related to each other than to organisms outside the group). The second step is to assess whether members of the group possess genetic exchangeability (where cohesion is maintained by gene flow among populations) or ecological exchangeability (where cohesion is maintained because populations occupy the same ecological niche). Recent taxonomic reviews have recognized nine species within the genus Echinococcus. Phylogenetic reconstructions of the relationships between these putative species using mtDNA and nuclear gene sequences show that for the most part these nine species are monophyletic, although there are important incongruences that need to be resolved. Applying the criteria of genetic and ecological exchangeability suggests that seven of the currently recognized species represent evolutionarily distinct lineages. The species status of Echinococcus canadensis and Echinococcus ortleppi could not be confirmed. Coalescent-based analyses represent a promising approach to species delimitation in these closely related taxa. It seems likely, from a comparison of sister species groups, that speciation in the genus has been driven by geographic isolation, but biogeographic scenarios are largely speculative and require further testing. Copyright © 2017 Elsevier Ltd. All rights reserved.

STELLAR POPULATION AND GAS KINEMATICS OF POST-STARBURST QUASARS

NASA Astrophysics Data System (ADS)

Sanmartim, David; Storchi-Bergmann, Thaisa

2018-01-01

Post-Starburst Quasars (PSQs) are an intriguing set of galaxies that simultaneously host AGNs and post-starburst stellar populations, making them one of the most suitable objects to investigate the nature of the connection between these two components. The simultaneous presence of a post-starburst population and nuclear activity may be explained by two possible scenarios. In the secular evolutionary scenario star formation may cease due to exhaustion of the gas, while in the quenching one it may cease abruptly when the nuclear activity is triggered. In order to test these scenarios we have mapped the star formation history, manifestations of nuclear activity and excitation mechanisms in the central kpc of two nearby PSQs by using GMOS-IFU observations. In these two first exploratory studies, we have found that the young and intermediate age populations are located in a ring at ≈300-500 kpc, with some contribution of the intermediate age component also in the central region. In both of them, the gas outflow does not coincide with the young stellar population ring, which suggests that the ring is not being affected by the AGN feedback, but only the innermost regions. The individual study one of the PSQs of the sample has supported the evolutionary scenario, since the post-starburst population is not located close enough to the nucleus, where the outflow is observed. As a general behaviour, we found that outflows velocity are on the order of ~600-800 km/s and the mass outflow rates of ≈0.03-0.1 M⊙/yr, one order of magnitude greater than the AGN accretion rate, which suggests a scenario where the AGN-driven wind has entrained material from the circumnuclear region. In order to increase the statistical significance of our previous results and to distinguish between the proposed scenarios, we are conducting the same analysis to a wider sample of PSQs, which we hope will indicate more conclusively which is the favored scenario. During the meeting, we will present more detailed results of our two first exploratory studies as well for for other 3 PSQs of our sample and compare them to a control sample.

Pattern formation in individual-based systems with time-varying parameters

NASA Astrophysics Data System (ADS)

Ashcroft, Peter; Galla, Tobias

2013-12-01

We study the patterns generated in finite-time sweeps across symmetry-breaking bifurcations in individual-based models. Similar to the well-known Kibble-Zurek scenario of defect formation, large-scale patterns are generated when model parameters are varied slowly, whereas fast sweeps produce a large number of small domains. The symmetry breaking is triggered by intrinsic noise, originating from the discrete dynamics at the microlevel. Based on a linear-noise approximation, we calculate the characteristic length scale of these patterns. We demonstrate the applicability of this approach in a simple model of opinion dynamics, a model in evolutionary game theory with a time-dependent fitness structure, and a model of cell differentiation. Our theoretical estimates are confirmed in simulations. In further numerical work, we observe a similar phenomenon when the symmetry-breaking bifurcation is triggered by population growth.

An Agent-based Model for Groundwater Allocation and Management at the Bakken Shale in Western North Dakota

NASA Astrophysics Data System (ADS)

Lin, T.; Lin, Z.; Lim, S.

2017-12-01

We present an integrated modeling framework to simulate groundwater level change under the dramatic increase of hydraulic fracturing water use in the Bakken Shale oil production area. The framework combines the agent-based model (ABM) with the Fox Hills-Hell Creek (FH-HC) groundwater model. In development of the ABM, institution theory is used to model the regulation policies from the North Dakota State Water Commission, while evolutionary programming and cognitive maps are used to model the social structure that emerges from the behavior of competing individual water businesses. Evolutionary programming allows individuals to select an appropriate strategy when annually applying for potential water use permits; whereas cognitive maps endow agent's ability and willingness to compete for more water sales. All agents have their own influence boundaries that inhibit their competitive behavior toward their neighbors but not to non-neighbors. The decision-making process is constructed and parameterized with both quantitative and qualitative information, i.e., empirical water use data and knowledge gained from surveys with stakeholders. By linking institution theory, evolutionary programming, and cognitive maps, our approach addresses a higher complexity of the real decision making process. Furthermore, this approach is a new exploration for modeling the dynamics of Coupled Human and Natural System. After integrating ABM with the FH-HC model, drought and limited water accessibility scenarios are simulated to predict FH-HC ground water level changes in the future. The integrated modeling framework of ABM and FH-HC model can be used to support making scientifically sound policies in water allocation and management.

Strategic approaches to planetary base development

NASA Technical Reports Server (NTRS)

Roberts, Barney B.

1992-01-01

The evolutionary development of a planetary expansionary outpost is considered in the light of both technical and economic issues. The outline of a partnering taxonomy is set forth which encompasses both institutional and temporal issues related to establishing shared interests and investments. The purely technical issues are discussed in terms of the program components which include nonaerospace technologies such as construction engineering. Five models are proposed in which partnership and autonomy for participants are approached in different ways including: (1) the standard customer/provider relationship; (2) a service-provider scenario; (3) the joint venture; (4) a technology joint-development model; and (5) a redundancy model for reduced costs. Based on the assumed characteristics of planetary surface systems the cooperative private/public models are championed with coordinated design by NASA to facilitate outside cooperation.

Epistasis and the selective advantage of sex and recombination

NASA Astrophysics Data System (ADS)

de Oliveira, Viviane M.; da Silva, Juliana K.; Campos, Paulo R. A.

2008-09-01

The understanding of the central mechanisms favoring sex and recombination in real populations is one of the fundamental issues in evolutionary biology. Based on a previous stochastic formulation for the study of sex, here we aim to investigate the conditions under which epistasis favors the fixation of the sexual mode of reproduction in a given population. In addition, we try to identify the evolutionary forces which contribute to this process. One considers a finite population model which assumes the existence of a recombination modifier allele that can activate the recombination mechanism. We have found that sex is very little favored in a scenario of antagonistic epistasis, and this advantage only occurs in a narrow range of values of the selection coefficient sd . On the other hand, synergistic epistasis favors recombination in a very broad domain. However, the major mechanism contributing to the spreading of the modifier allele depends on the range of values of sd . At large sd , background selection favors recombination since it increases the efficacy of selection, while at low sd Muller’s ratchet is the leading mechanism.

Evolutionary games in the multiverse

PubMed Central

Gokhale, Chaitanya S.; Traulsen, Arne

2010-01-01

Evolutionary game dynamics of two players with two strategies has been studied in great detail. These games have been used to model many biologically relevant scenarios, ranging from social dilemmas in mammals to microbial diversity. Some of these games may, in fact, take place between a number of individuals and not just between two. Here we address one-shot games with multiple players. As long as we have only two strategies, many results from two-player games can be generalized to multiple players. For games with multiple players and more than two strategies, we show that statements derived for pairwise interactions no longer hold. For two-player games with any number of strategies there can be at most one isolated internal equilibrium. For any number of players with any number of strategies , there can be at most isolated internal equilibria. Multiplayer games show a great dynamical complexity that cannot be captured based on pairwise interactions. Our results hold for any game and can easily be applied to specific cases, such as public goods games or multiplayer stag hunts. PMID:20212124

Ferns diversified in the shadow of angiosperms.

PubMed

Schneider, Harald; Schuettpelz, Eric; Pryer, Kathleen M; Cranfill, Raymond; Magallón, Susana; Lupia, Richard

2004-04-01

The rise of angiosperms during the Cretaceous period is often portrayed as coincident with a dramatic drop in the diversity and abundance of many seed-free vascular plant lineages, including ferns. This has led to the widespread belief that ferns, once a principal component of terrestrial ecosystems, succumbed to the ecological predominance of angiosperms and are mostly evolutionary holdovers from the late Palaeozoic/early Mesozoic era. The first appearance of many modern fern genera in the early Tertiary fossil record implies another evolutionary scenario; that is, that the majority of living ferns resulted from a more recent diversification. But a full understanding of trends in fern diversification and evolution using only palaeobotanical evidence is hindered by the poor taxonomic resolution of the fern fossil record in the Cretaceous. Here we report divergence time estimates for ferns and angiosperms based on molecular data, with constraints from a reassessment of the fossil record. We show that polypod ferns (> 80% of living fern species) diversified in the Cretaceous, after angiosperms, suggesting perhaps an ecological opportunistic response to the diversification of angiosperms, as angiosperms came to dominate terrestrial ecosystems.

Phylogeography of Arenaria balearica L. (Caryophyllaceae): evolutionary history of a disjunct endemic from the Western Mediterranean continental islands.

PubMed

Bobo-Pinilla, Javier; Barrios de León, Sara B; Seguí Colomar, Jaume; Fenu, Giuseppe; Bacchetta, Gianluigi; Peñas de Giles, Julio; Martínez-Ortega, María Montserrat

2016-01-01

Although it has been traditionally accepted that Arenaria balearica (Caryophyllaceae) could be a relict Tertiary plant species, this has never been experimentally tested. Nor have the palaeohistorical reasons underlying the highly fragmented distribution of the species in the Western Mediterranean region been investigated. We have analysed AFLP data (213) and plastid DNA sequences (226) from a total of 250 plants from 29 populations sampled throughout the entire distribution range of the species in Majorca, Corsica, Sardinia, and the Tuscan Archipelago. The AFLP data analyses indicate very low geographic structure and population differentiation. Based on plastid DNA data, six alternative phylogeographic hypotheses were tested using Approximate Bayesian Computation (ABC). These analyses revealed ancient area fragmentation as the most probable scenario, which is in accordance with the star-like topology of the parsimony network that suggests a pattern of long term survival and subsequent in situ differentiation. Overall low levels of genetic diversity and plastid DNA variation were found, reflecting evolutionary stasis of a species preserved in locally long-term stable habitats.

Evolutionary Relations of Hexanchiformes Deep-Sea Sharks Elucidated by Whole Mitochondrial Genome Sequences

PubMed Central

Tanaka, Keiko; Tomita, Taketeru; Suzuki, Shingo; Hosomichi, Kazuyoshi; Sano, Kazumi; Doi, Hiroyuki; Kono, Azumi; Inoko, Hidetoshi; Kulski, Jerzy K.; Tanaka, Sho

2013-01-01

Hexanchiformes is regarded as a monophyletic taxon, but the morphological and genetic relationships between the five extant species within the order are still uncertain. In this study, we determined the whole mitochondrial DNA (mtDNA) sequences of seven sharks including representatives of the five Hexanchiformes, one squaliform, and one carcharhiniform and inferred the phylogenetic relationships among those species and 12 other Chondrichthyes (cartilaginous fishes) species for which the complete mitogenome is available. The monophyly of Hexanchiformes and its close relation with all other Squaliformes sharks were strongly supported by likelihood and Bayesian phylogenetic analysis of 13,749 aligned nucleotides of 13 protein coding genes and two rRNA genes that were derived from the whole mDNA sequences of the 19 species. The phylogeny suggested that Hexanchiformes is in the superorder Squalomorphi, Chlamydoselachus anguineus (frilled shark) is the sister species to all other Hexanchiformes, and the relations within Hexanchiformes are well resolved as Chlamydoselachus, (Notorynchus, (Heptranchias, (Hexanchus griseus, H. nakamurai))). Based on our phylogeny, we discussed evolutionary scenarios of the jaw suspension mechanism and gill slit numbers that are significant features in the sharks. PMID:24089661

Closed-loop optimization of chromatography column sizing strategies in biopharmaceutical manufacture.

PubMed

Allmendinger, Richard; Simaria, Ana S; Turner, Richard; Farid, Suzanne S

2014-10-01

This paper considers a real-world optimization problem involving the identification of cost-effective equipment sizing strategies for the sequence of chromatography steps employed to purify biopharmaceuticals. Tackling this problem requires solving a combinatorial optimization problem subject to multiple constraints, uncertain parameters, and time-consuming fitness evaluations. An industrially-relevant case study is used to illustrate that evolutionary algorithms can identify chromatography sizing strategies with significant improvements in performance criteria related to process cost, time and product waste over the base case. The results demonstrate also that evolutionary algorithms perform best when infeasible solutions are repaired intelligently, the population size is set appropriately, and elitism is combined with a low number of Monte Carlo trials (needed to account for uncertainty). Adopting this setup turns out to be more important for scenarios where less time is available for the purification process. Finally, a data-visualization tool is employed to illustrate how user preferences can be accounted for when it comes to selecting a sizing strategy to be implemented in a real industrial setting. This work demonstrates that closed-loop evolutionary optimization, when tuned properly and combined with a detailed manufacturing cost model, acts as a powerful decisional tool for the identification of cost-effective purification strategies. © 2013 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Closed-loop optimization of chromatography column sizing strategies in biopharmaceutical manufacture

PubMed Central

Allmendinger, Richard; Simaria, Ana S; Turner, Richard; Farid, Suzanne S

2014-01-01

BACKGROUND This paper considers a real-world optimization problem involving the identification of cost-effective equipment sizing strategies for the sequence of chromatography steps employed to purify biopharmaceuticals. Tackling this problem requires solving a combinatorial optimization problem subject to multiple constraints, uncertain parameters, and time-consuming fitness evaluations. RESULTS An industrially-relevant case study is used to illustrate that evolutionary algorithms can identify chromatography sizing strategies with significant improvements in performance criteria related to process cost, time and product waste over the base case. The results demonstrate also that evolutionary algorithms perform best when infeasible solutions are repaired intelligently, the population size is set appropriately, and elitism is combined with a low number of Monte Carlo trials (needed to account for uncertainty). Adopting this setup turns out to be more important for scenarios where less time is available for the purification process. Finally, a data-visualization tool is employed to illustrate how user preferences can be accounted for when it comes to selecting a sizing strategy to be implemented in a real industrial setting. CONCLUSION This work demonstrates that closed-loop evolutionary optimization, when tuned properly and combined with a detailed manufacturing cost model, acts as a powerful decisional tool for the identification of cost-effective purification strategies. © 2013 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. PMID:25506115

The evolution of the competition-dispersal trade-off affects α- and β-diversity in a heterogeneous metacommunity.

PubMed

Laroche, Fabien; Jarne, Philippe; Perrot, Thomas; Massol, Francois

2016-04-27

Difference in dispersal ability is a key driver of species coexistence in metacommunities. However, the available frameworks for interpreting species diversity patterns in natura often overlook trade-offs and evolutionary constraints associated with dispersal. Here, we build a metacommunity model accounting for dispersal evolution and a competition-dispersal trade-off. Depending on the distribution of carrying capacities among communities, species dispersal values are distributed either around a single strategy (evolutionarily stable strategy, ESS), or around distinct strategies (evolutionary branching, EB). We show that limited dispersal generates spatial aggregation of dispersal traits in ESS and EB scenarios, and that the competition-dispersal trade-off strengthens the pattern in the EB scenario. Importantly, individuals in larger (respectively (resp.) smaller) communities tend to harbour lower (resp. higher) dispersal, especially under the EB scenario. We explore how dispersal evolution affects species diversity patterns by comparing those from our model to the predictions of a neutral metacommunity model. The most marked difference is detected under EB, with distinctive values of both α- and β-diversity (e.g. the dissimilarity in species composition between small and large communities was significantly larger than neutral predictions). We conclude that, from an empirical perspective, jointly assessing community carrying capacity with species dispersal strategies should improve our understanding of diversity patterns in metacommunities. © 2016 The Author(s).

Evolutionary use of nuclear electric propulsion

NASA Technical Reports Server (NTRS)

Hack, K. J.; George, J. A.; Riehl, J. P.; Gilland, J. H.

1990-01-01

Evolving new propulsion technologies through a rational and conscious effort to minimize development costs and program risks while maximizing the performance benefits is intuitively practical. A phased approach to the evolution of nuclear electric propulsion from use on planetary probes, to lunar cargo vehicles, and finally to manned Mars missions with a concomitant growth in technology is considered. Technology levels and system component makeup are discussed for nuclear power systems and both ion and magnetoplasmadynamic thrusters. Mission scenarios are described, which include analysis of a probe to Pluto, a lunar cargo mission, Martian split, all-up, and quick-trip mission options. Evolutionary progression of the use of NEP in such missions is discussed.

A SYMMETRY OF FIXATION TIMES IN EVOULTIONARY DYNAMICS

PubMed Central

TAYLOR, CHRISTINE; IWASA, YOH; NOWAK, MARTIN A.

2010-01-01

In this paper, we show that for evolutionary dynamics between two types that can be described by a Moran process, the conditional fixation time of either type is the same irrespective of the selective scenario. With frequency dependent selection between two strategies A and B of an evolutionary game, regardless of whether A dominates B, A and B are best replies to themselves, or A and B are best replies to each other, the conditional fixation times of a single A and a single B mutant are identical. This does not hold for Wright-Fisher models, nor when the mutants start from multiple copies. PMID:16890959

Sensing marine biomolecules: smell, taste, and the evolutionary transition from aquatic to terrestrial life

PubMed Central

Mollo, Ernesto; Fontana, Angelo; Roussis, Vassilios; Polese, Gianluca; Amodeo, Pietro; Ghiselin, Michael T.

2014-01-01

The usual definition of smell and taste as distance and contact forms of chemoreception, respectively, has resulted in the belief that, during the shift from aquatic to terrestrial life, odorant receptors (ORs) were selected mainly to recognize airborne hydrophobic ligands, instead of the hydrophilic molecules involved in marine remote-sensing. This post-adaptive evolutionary scenario, however, neglects the fact that marine organisms 1) produce and detect a wide range of small hydrophobic and volatile molecules, especially terpenoids, and 2) contain genes coding for ORs that are able to bind those compounds. These apparent anomalies can be resolved by adopting an alternative, pre-adaptive scenario. Before becoming airborne on land, small molecules, almost insoluble in water, already played a key role in aquatic communication, but acting in “contact” forms of olfaction that did not require major molecular innovations to become effective at a distance in air. Rather, when air was “invaded” by volatile marine terpenoids, an expansion of the spatial range of olfaction was an incidental consequence rather than an adaptation. PMID:25360437

A short history of nearly every sense - The evolutionary history of vertebrate sensory cell types.

PubMed

Schlosser, Gerhard

2018-05-08

Evolving from filter feeding chordate ancestors, vertebrates adopted a more active life style. These ecological and behavioral changes went along with an elaboration of the vertebrate head including novel complex paired sense organs such as the eyes, inner ears and olfactory epithelia. However, the photoreceptors, mechanoreceptors and chemoreceptors used in these sense organs have a long evolutionary history and homologous cell types can be recognized in many other bilaterians or even cnidarians. After briefly introducing some of the major sensory cell types found in vertebrates, this review summarizes the phylogenetic distribution of sensory cell types in metazoans and presents a scenario for the evolutionary history of various sensory cell types involving several cell type diversification and fusion events. It is proposed that the evolution of novel cranial sense organs in vertebrates involved the redeployment of evolutionarily ancient sensory cell types for building larger and more complex sense organs.

Assessing Space and Satellite Environment and System Security

NASA Astrophysics Data System (ADS)

Haith, G.; Upton, S.

Satellites and other spacecraft are key assets and critical vulnerabilities in our communications, surveillance and defense infrastructure. Despite their strategic importance, there are significant gaps in our real-time knowledge of satellite security. One reason is the lack of infrastructure and applications to filter and process the overwhelming amounts of relevant data. Some efforts are addressing this challenge by fusing the data gathered from ground, air and space based sensors to detect and categorize anomalous situations. The aim is to provide decision support for Space Situational Awareness (SSA) and Defensive Counterspace (DCS). Most results have not yielded estimates of impact and cost of a given situation or suggested courses of action (level 3 data fusion). This paper describes an effort to provide high level data fusion for SSA/DCS though two complementary thrusts: threat scenario simulation with Automatic Red Teaming (ART), and historical data warehousing and mining. ART uses stochastic search algorithms (e.g., evolutionary algorithms) to evolve strategies in agent based simulations. ART provides techniques to formally specify anomalous condition scenarios envisioned by subject matter experts and to explore alternative scenarios. The simulation data can then support impact estimates and course of action evaluations. The data mining thrust has focused on finding correlations between subsystems anomalies on MightySat II and publicly available space weather data. This paper describes the ART approach, some potential correlations discovered between satellite subsystem anomalies and space weather events, and future work planned on the project.

Feature theory and the two-step hypothesis of Müllerian mimicry evolution.

PubMed

Balogh, Alexandra Catherine Victoria; Gamberale-Stille, Gabriella; Tullberg, Birgitta Sillén; Leimar, Olof

2010-03-01

The two-step hypothesis of Müllerian mimicry evolution states that mimicry starts with a major mutational leap between adaptive peaks, followed by gradual fine-tuning. The hypothesis was suggested to solve the problem of apostatic selection producing a valley between adaptive peaks, and appears reasonable for a one-dimensional phenotype. Extending the hypothesis to the realistic scenario of multidimensional phenotypes controlled by multiple genetic loci can be problematic, because it is unlikely that major mutational leaps occur simultaneously in several traits. Here we consider the implications of predator psychology on the evolutionary process. According to feature theory, single prey traits may be used by predators as features to classify prey into discrete categories. A mutational leap in such a trait could initiate mimicry evolution. We conducted individual-based evolutionary simulations in which virtual predators both categorize prey according to features and generalize over total appearances. We found that an initial mutational leap toward feature similarity in one dimension facilitates mimicry evolution of multidimensional traits. We suggest that feature-based predator categorization together with predator generalization over total appearances solves the problem of applying the two-step hypothesis to complex phenotypes, and provides a basis for a theory of the evolution of mimicry rings.

Origin of a cryptic lineage in a threatened reptile through isolation and historical hybridization.

PubMed

Sovic, M G; Fries, A C; Gibbs, H L

2016-11-01

Identifying phylogenetically distinct lineages and understanding the evolutionary processes by which they have arisen are important goals of phylogeography. This information can also help define conservation units in endangered species. Such analyses are being transformed by the availability of genomic-scale data sets and novel analytical approaches for statistically comparing different historical scenarios as causes of phylogeographic patterns. Here, we use genomic-scale restriction-site-associated DNA sequencing (RADseq) data to test for distinct lineages in the endangered Eastern Massasauga Rattlesnake (Sistrurus catenatus). We then use coalescent-based modeling techniques to identify the evolutionary mechanisms responsible for the origin of the lineages in this species. We find equivocal evidence for distinct phylogenetic lineages within S. catenatus east of the Mississippi River, but strong support for a previously unrecognized lineage on the western edge of the range of this snake, represented by populations from Iowa, USA. Snakes from these populations show patterns of genetic admixture with a nearby non-threatened sister species (Sistrurus tergeminus). Tests of historical demographic models support the hypothesis that the genetic distinctiveness of Iowa snakes is due to a combination of isolation and historical introgression between S. catenatus and S. tergeminus. Our work provides an example of how model-based analysis of genomic-scale data can help identify conservation units in rare species.

Whole planet coupling between climate, mantle, and core: Implications for rocky planet evolution

NASA Astrophysics Data System (ADS)

Foley, Bradford J.; Driscoll, Peter E.

2016-05-01

Earth's climate, mantle, and core interact over geologic time scales. Climate influences whether plate tectonics can take place on a planet, with cool climates being favorable for plate tectonics because they enhance stresses in the lithosphere, suppress plate boundary annealing, and promote hydration and weakening of the lithosphere. Plate tectonics plays a vital role in the long-term carbon cycle, which helps to maintain a temperate climate. Plate tectonics provides long-term cooling of the core, which is vital for generating a magnetic field, and the magnetic field is capable of shielding atmospheric volatiles from the solar wind. Coupling between climate, mantle, and core can potentially explain the divergent evolution of Earth and Venus. As Venus lies too close to the sun for liquid water to exist, there is no long-term carbon cycle and thus an extremely hot climate. Therefore, plate tectonics cannot operate and a long-lived core dynamo cannot be sustained due to insufficient core cooling. On planets within the habitable zone where liquid water is possible, a wide range of evolutionary scenarios can take place depending on initial atmospheric composition, bulk volatile content, or the timing of when plate tectonics initiates, among other factors. Many of these evolutionary trajectories would render the planet uninhabitable. However, there is still significant uncertainty over the nature of the coupling between climate, mantle, and core. Future work is needed to constrain potential evolutionary scenarios and the likelihood of an Earth-like evolution.

Infrared outbursts as potential tracers of common-envelope events in high-mass X-ray binary formation

NASA Astrophysics Data System (ADS)

Oskinova, Lidia M.; Bulik, Tomasz; Gómez-Morán, Ada Nebot

2018-06-01

Context. Classic massive binary evolutionary scenarios predict that a transitional common-envelope (CE) phase could be preceded as well as succeeded by the evolutionary stage when a binary consists of a compact object and a massive star, that is, a high-mass X-ray binary (HMXB). The observational manifestations of common envelope are poorly constrained. We speculate that its ejection might be observed in some cases as a transient event at mid-infrared (IR) wavelengths. Aims: We estimate the expected numbers of CE ejection events and HMXBs per star formation unit rate, and compare these theoretical estimates with observations. Methods: We compiled a list of 85 mid-IR transients of uncertain nature detected by the Spitzer Infrared Intensive Transients Survey and searched for their associations with X-ray, optical, and UV sources. Results: Confirming our theoretical estimates, we find that only one potential HMXB may be plausibly associated with an IR-transient and tentatively propose that X-ray source NGC 4490-X40 could be a precursor to the SPIRITS 16az event. Among other interesting sources, we suggest that the supernova remnant candidate [BWL2012] 063 might be associated with SPIRITS 16ajc. We also find that two SPIRITS events are likely associated with novae, and seven have potential optical counterparts. Conclusions: The massive binary evolutionary scenarios that involve CE events do not contradict currently available observations of IR transients and HMXBs in star-forming galaxies.

Living on the edge: adaptive and plastic responses of the tree Nothofagus pumilio to a long-term transplant experiment predict rear-edge upward expansion.

PubMed

Mathiasen, Paula; Premoli, Andrea C

2016-06-01

Current climate change affects the competitive ability and reproductive success of many species, leading to local extinctions, adjustment to novel local conditions by phenotypic plasticity or rapid adaptation, or tracking their optima through range shifts. However, many species have limited ability to expand to suitable areas. Altitudinal gradients, with abrupt changes in abiotic conditions over short distances, represent "natural experiments" for the evaluation of ecological and evolutionary responses under scenarios of climate change. Nothofagus pumilio is the tree species which dominates as pure stands the montane forests of Patagonia. We evaluated the adaptive value of variation in quantitative traits of N. pumilio under contrasting conditions of the altitudinal gradient with a long-term reciprocal transplant experimental design. While high-elevation plants show little response in plant, leaf, and phenological traits to the experimental trials, low-elevation ones show greater plasticity in their responses to changing environments, particularly at high elevation. Our results suggest a relatively reduced potential for evolutionary adaptation of high-elevation genotypes, and a greater evolutionary potential of low-elevation ones. Under global warming scenarios of forest upslope migration, high-elevation variants may be outperformed by low-elevation ones during this process, leading to the local extinction and/or replacement of these genotypes. These results challenge previous models and predictions expected under global warming for altitudinal gradients, on which the leading edge is considered to be the upper treeline forests.

Reservoir and vector evolutionary pressures shaped the adaptation of Borrelia.

PubMed

Estrada-Peña, Agustín; Álvarez-Jarreta, Jorge; Cabezas-Cruz, Alejandro

2018-04-12

The life cycle of spirochetes of the genus Borrelia includes complex networks of vertebrates and ticks. The tripartite association of Borrelia-vertebrate-tick has proved ecologically successful for these bacteria, which have become some of the most prominent tick-borne pathogens in the northern hemisphere. To keep evolutionary pace with its double-host life history, Borrelia must adapt to the evolutionary pressures exerted by both sets of hosts. In this review, we attempt to reconcile functional, phylogenetic, and ecological perspectives to propose a coherent scenario of Borrelia evolution. Available empirical information supports that the association of Borrelia with ticks is very old. The major split between the tick families Argasidae-Ixodidae (dated some 230-290 Mya) resulted in most relapsing fever (Rf) species being restricted to Argasidae and few associated with Ixodidae. A further key event produced the diversification of the Lyme borreliosis (Lb) species: the radiation of ticks of the genus Ixodes from the primitive stock of Ixodidae (around 217 Mya). The ecological interactions of Borrelia demonstrate that Argasidae-transmitted Rf species remain restricted to small niches of one tick species and few vertebrates. The evolutionary pressures on this group are consequently low, and speciation processes seem to be driven by geographical isolation. In contrast to Rf, Lb species circulate in nested networks of dozens of tick species and hundreds of vertebrate species. This greater variety confers a remarkably variable pool of evolutionary pressures, resulting in large speciation of the Lb group, where different species adapt to circulate through different groups of vertebrates. Available data, based on ospA and multilocus sequence typing (including eight concatenated in-house genes) phylogenetic trees, suggest that ticks could constitute a secondary bottleneck that contributes to Lb specialization. Both sets of adaptive pressures contribute to the resilience of highly adaptable meta-populations of bacteria. Copyright © 2018 Elsevier B.V. All rights reserved.

Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective.

PubMed

Inoue, Jun G; Miya, Masaki; Lam, Kevin; Tay, Boon-Hui; Danks, Janine A; Bell, Justin; Walker, Terrence I; Venkatesh, Byrappa

2010-11-01

With our increasing ability for generating whole-genome sequences, comparative analysis of whole genomes has become a powerful tool for understanding the structure, function, and evolutionary history of human and other vertebrate genomes. By virtue of their position basal to bony vertebrates, cartilaginous fishes (class Chondrichthyes) are a valuable outgroup in comparative studies of vertebrates. Recently, a holocephalan cartilaginous fish, the elephant shark, Callorhinchus milii (Subclass Holocephali: Order Chimaeriformes), has been proposed as a model genome, and low-coverage sequence of its genome has been generated. Despite such an increasing interest, the evolutionary history of the modern holocephalans-a previously successful and diverse group but represented by only 39 extant species-and their relationship with elasmobranchs and other jawed vertebrates has been poorly documented largely owing to a lack of well-preserved fossil materials after the end-Permian about 250 Ma. In this study, we assembled the whole mitogenome sequences for eight representatives from all the three families of the modern holocephalans and investigated their phylogenetic relationships and evolutionary history. Unambiguously aligned sequences from these holocephalans together with 17 other vertebrates (9,409 nt positions excluding entire third codon positions) were subjected to partitioned maximum likelihood analysis. The resulting tree strongly supported a single origin of the modern holocephalans and their sister-group relationship with elasmobranchs. The mitogenomic tree recovered the most basal callorhinchids within the chimaeriforms, which is sister to a clade comprising the remaining two families (rhinochimaerids and chimaerids). The timetree derived from a relaxed molecular clock Bayesian method suggests that the holocephalans originated in the Silurian about 420 Ma, having survived from the end-Permian (250 Ma) mass extinction and undergoing familial diversifications during the late Jurassic to early Cretaceous (170-120 Ma). This postulated evolutionary scenario agrees well with that based on the paleontological observations.

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

PubMed Central

Anselmetti, Yoann; Patterson, Murray; Ponty, Yann; B�rard, S�verine; Chauve, Cedric; Scornavacca, Celine; Daubin, Vincent; Tannier, Eric

2017-01-01

DeCoSTAR is a software that aims at reconstructing the organization of ancestral genes or genomes in the form of sets of neighborhood relations (adjacencies) between pairs of ancestral genes or gene domains. It can also improve the assembly of fragmented genomes by proposing evolutionary-induced adjacencies between scaffolding fragments. Ancestral genes or domains are deduced from reconciled phylogenetic trees under an evolutionary model that considers gains, losses, speciations, duplications, and transfers as possible events for gene evolution. Reconciliations are either given as input or computed with the ecceTERA package, into which DeCoSTAR is integrated. DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann–Gibbs distribution centered around parsimonious solutions, and statistical supports on ancestral and extant adjacencies are provided. DeCoSTAR supports the features of previously contributed tools that reconstruct ancestral adjacencies, namely DeCo, DeCoLT, ART-DeCo, and DeClone. In a few minutes, DeCoSTAR can reconstruct the evolutionary history of domains inside genes, of gene fusion and fission events, or of gene order along chromosomes, for large data sets including dozens of whole genomes from all kingdoms of life. We illustrate the potential of DeCoSTAR with several applications: ancestral reconstruction of gene orders for Anopheles mosquito genomes, multidomain proteins in Drosophila, and gene fusion and fission detection in Actinobacteria. Availability: http://pbil.univ-lyon1.fr/software/DeCoSTAR (Last accessed April 24, 2017). PMID:28402423

Integrative View of α2,3-Sialyltransferases (ST3Gal) Molecular and Functional Evolution in Deuterostomes: Significance of Lineage-Specific Losses

PubMed Central

Petit, Daniel; Teppa, Elin; Mir, Anne-Marie; Vicogne, Dorothée; Thisse, Christine; Thisse, Bernard; Filloux, Cyril; Harduin-Lepers, Anne

2015-01-01

Sialyltransferases are responsible for the synthesis of a diverse range of sialoglycoconjugates predicted to be pivotal to deuterostomes’ evolution. In this work, we reconstructed the evolutionary history of the metazoan α2,3-sialyltransferases family (ST3Gal), a subset of sialyltransferases encompassing six subfamilies (ST3Gal I–ST3Gal VI) functionally characterized in mammals. Exploration of genomic and expressed sequence tag databases and search of conserved sialylmotifs led to the identification of a large data set of st3gal-related gene sequences. Molecular phylogeny and large scale sequence similarity network analysis identified four new vertebrate subfamilies called ST3Gal III-r, ST3Gal VII, ST3Gal VIII, and ST3Gal IX. To address the issue of the origin and evolutionary relationships of the st3gal-related genes, we performed comparative syntenic mapping of st3gal gene loci combined to ancestral genome reconstruction. The ten vertebrate ST3Gal subfamilies originated from genome duplication events at the base of vertebrates and are organized in three distinct and ancient groups of genes predating the early deuterostomes. Inferring st3gal gene family history identified also several lineage-specific gene losses, the significance of which was explored in a functional context. Toward this aim, spatiotemporal distribution of st3gal genes was analyzed in zebrafish and bovine tissues. In addition, molecular evolutionary analyses using specificity determining position and coevolved amino acid predictions led to the identification of amino acid residues with potential implication in functional divergence of vertebrate ST3Gal. We propose a detailed scenario of the evolutionary relationships of st3gal genes coupled to a conceptual framework of the evolution of ST3Gal functions. PMID:25534026

Frameworks of reference: How (some) college students think about biological evolution

NASA Astrophysics Data System (ADS)

Filisky, Michael

1999-12-01

Evolution, a key concept for understanding all of biology, is often misunderstood by students from elementary school to graduate school. In order to teach evolution effectively, as well as to teach the biological concepts necessary for understanding evolution, teachers need to understand the initial ideas that students bring with them to the learning experience. Research has shown that many students are likely to hold alternative conceptions that may block their ability to learn evolution. The goal of this study is to contribute to the effectiveness of teaching evolution at the high school and college levels both by investigating concepts that students bring with them to their first college study of evolution, and by examining the conceptual frameworks that support these students as they construct new understanding. This study was executed in two stages. An initial survey of evolutionary understanding was administered to 203 undergraduate students in two courses at two universities in the area of Boston, MA. The surveys elicited short, written responses to five real and fictitious scenarios about biological inheritance and evolutionary change. Responses were coded into categories of concepts. The data were analyzed for patterns of understanding. Students exhibiting concepts from each of the major categories were randomly selected to participate in the subsequent interview stage of the study. Interviews with six of the students were conducted based on an interview guide employing scenarios similar to those from the survey. Analyses of the interview transcripts included the construction of detailed concept maps for each response followed by narratives of each interviewee's conceptual frameworks. The results of both stages of the study revealed a range of alternative conceptions about evolution, including scientifically acceptable Darwinian ideas and other ideas---including Lamarckian inheritance of acquired characteristics---are not accepted by modern science. The interviews revealed a range of reasoning styles and frameworks that explained how students could find these ideas plausible. The study concludes with recommendations for further research on the understanding of evolutionary topics; for adaptations of the research methods; and for teaching strategies to address the findings.

Population-level genetic variation and climate change in a biodiversity hotspot

PubMed Central

2017-01-01

Introduction Estimated future climate scenarios can be used to predict where hotspots of endemism may occur over the next century, but life history, ecological and genetic traits will be important in informing the varying responses within myriad taxa. Essential to predicting the consequences of climate change to individual species will be an understanding of the factors that drive genetic structure within and among populations. Here, I review the factors that influence the genetic structure of plant species in California, but are applicable elsewhere; existing levels of genetic variation, life history and ecological characteristics will affect the ability of an individual taxon to persist in the presence of anthropogenic change. Factors influencing the distribution of genetic variation Persistence in the face of climate change is likely determined by life history characteristics: dispersal ability, generation time, reproductive ability, degree of habitat specialization, plant–insect interactions, existing genetic diversity and availability of habitat or migration corridors. Existing levels of genetic diversity in plant populations vary based on a number of evolutionary scenarios that include endemism, expansion since the last glacial maximum, breeding system and current range sizes. Regional priorities and examples A number of well-documented examples are provided from the California Floristic Province. Some predictions can be made for the responses of plant taxa to rapid environmental changes based on geographic position, evolutionary history, existing genetic variation, and ecological amplitude. Conclusions, Solutions and Recommendations The prediction of how species will respond to climate change will require a synthesis drawing from population genetics, geography, palaeontology and ecology. The important integration of the historical factors that have shaped the distribution and existing genetic structure of California’s plant taxa will enable us to predict and prioritize the conservation of species and areas most likely to be impacted by rapid climate change, human disturbance and invasive species. PMID:28069633

Population-level genetic variation and climate change in a biodiversity hotspot.

PubMed

Schierenbeck, Kristina A

2017-01-01

Estimated future climate scenarios can be used to predict where hotspots of endemism may occur over the next century, but life history, ecological and genetic traits will be important in informing the varying responses within myriad taxa. Essential to predicting the consequences of climate change to individual species will be an understanding of the factors that drive genetic structure within and among populations. Here, I review the factors that influence the genetic structure of plant species in California, but are applicable elsewhere; existing levels of genetic variation, life history and ecological characteristics will affect the ability of an individual taxon to persist in the presence of anthropogenic change. Persistence in the face of climate change is likely determined by life history characteristics: dispersal ability, generation time, reproductive ability, degree of habitat specialization, plant-insect interactions, existing genetic diversity and availability of habitat or migration corridors. Existing levels of genetic diversity in plant populations vary based on a number of evolutionary scenarios that include endemism, expansion since the last glacial maximum, breeding system and current range sizes. A number of well-documented examples are provided from the California Floristic Province. Some predictions can be made for the responses of plant taxa to rapid environmental changes based on geographic position, evolutionary history, existing genetic variation, and ecological amplitude. The prediction of how species will respond to climate change will require a synthesis drawing from population genetics, geography, palaeontology and ecology. The important integration of the historical factors that have shaped the distribution and existing genetic structure of California's plant taxa will enable us to predict and prioritize the conservation of species and areas most likely to be impacted by rapid climate change, human disturbance and invasive species. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Algorithmic Trading with Developmental and Linear Genetic Programming

NASA Astrophysics Data System (ADS)

Wilson, Garnett; Banzhaf, Wolfgang

A developmental co-evolutionary genetic programming approach (PAM DGP) and a standard linear genetic programming (LGP) stock trading systemare applied to a number of stocks across market sectors. Both GP techniques were found to be robust to market fluctuations and reactive to opportunities associated with stock price rise and fall, with PAMDGP generating notably greater profit in some stock trend scenarios. Both algorithms were very accurate at buying to achieve profit and selling to protect assets, while exhibiting bothmoderate trading activity and the ability to maximize or minimize investment as appropriate. The content of the trading rules produced by both algorithms are also examined in relation to stock price trend scenarios.

Coevolution and life cycle specialization of plant cell wall degrading enzymes in a hemibiotrophic pathogen.

PubMed

Brunner, Patrick C; Torriani, Stefano F F; Croll, Daniel; Stukenbrock, Eva H; McDonald, Bruce A

2013-06-01

Zymoseptoria tritici is an important fungal pathogen on wheat that originated in the Fertile Crescent. Its closely related sister species Z. pseudotritici and Z. ardabiliae infect wild grasses in the same region. This recently emerged host-pathogen system provides a rare opportunity to investigate the evolutionary processes shaping the genome of an emerging pathogen. Here, we investigate genetic signatures in plant cell wall degrading enzymes (PCWDEs) that are likely affected by or driving coevolution in plant-pathogen systems. We hypothesize four main evolutionary scenarios and combine comparative genomics, transcriptomics, and selection analyses to assign the majority of PCWDEs in Z. tritici to one of these scenarios. We found widespread differential transcription among different members of the same gene family, challenging the idea of functional redundancy and suggesting instead that specialized enzymatic activity occurs during different stages of the pathogen life cycle. We also find that natural selection has significantly affected at least 19 of the 48 identified PCWDEs. The majority of genes showed signatures of purifying selection, typical for the scenario of conserved substrate optimization. However, six genes showed diversifying selection that could be attributed to either host adaptation or host evasion. This study provides a powerful framework to better understand the roles played by different members of multigene families and to determine which genes are the most appropriate targets for wet laboratory experimentation, for example, to elucidate enzymatic function during relevant phases of a pathogen's life cycle.

Global change and the evolution of phenotypic plasticity in plants.

PubMed

Matesanz, Silvia; Gianoli, Ernesto; Valladares, Fernando

2010-09-01

Global change drivers create new environmental scenarios and selective pressures, affecting plant species in various interacting ways. Plants respond with changes in phenology, physiology, and reproduction, with consequences for biotic interactions and community composition. We review information on phenotypic plasticity, a primary means by which plants cope with global change scenarios, recommending promising approaches for investigating the evolution of plasticity and describing constraints to its evolution. We discuss the important but largely ignored role of phenotypic plasticity in range shifts and review the extensive literature on invasive species as models of evolutionary change in novel environments. Plasticity can play a role both in the short-term response of plant populations to global change as well as in their long-term fate through the maintenance of genetic variation. In new environmental conditions, plasticity of certain functional traits may be beneficial (i.e., the plastic response is accompanied by a fitness advantage) and thus selected for. Plasticity can also be relevant in the establishment and persistence of plants in novel environments that are crucial for populations at the colonizing edge in range shifts induced by climate change. Experimental studies show taxonomically widespread plastic responses to global change drivers in many functional traits, though there is a lack of empirical support for many theoretical models on the evolution of phenotypic plasticity. Future studies should assess the adaptive value and evolutionary potential of plasticity under complex, realistic global change scenarios. Promising tools include resurrection protocols and artificial selection experiments. © 2010 New York Academy of Sciences.

Feeding of the megamouth shark (Pisces: Lamniformes: Megachasmidae) predicted by its hyoid arch: a biomechanical approach.

PubMed

Tomita, Taketeru; Sato, Keiichi; Suda, Kenta; Kawauchi, Junro; Nakaya, Kazuhiro

2011-05-01

Studies of the megamouth shark, one of three planktivorous sharks, can provide information about their evolutionary history. Megamouth shark feeding has never been observed in life animals, but two alternative hypotheses on biomechanics suggest either feeding, i.e., ram feeding or suction feeding. In this study, the second moment of area of the ceratohyal cartilages, which is an indicator of the flexural stiffness of the cartilages, is calculated for 21 species of ram- and suction-feeding sharks using computed tomography. The results indicate that suction-feeding sharks have ceratohyal cartilages with a larger second moment of area than ram-feeding sharks. The result also indicates that the ram-suction index, which is an indicator of relative contribution of ram and suction behavior, is also correlated with the second moment of area of the ceratohyal. Considering that large bending stresses are expected to be applied to the ceratohyal cartilage during suction, the larger second moment of area of the ceratohyal of suction-feeding sharks can be interpreted as an adaptation for suction feeding. Based on the small second moment of area of the ceratohyal cartilage of the megamouth shark, the feeding mode of the megamouth shark is considered to be ram feeding, similar to the planktivorous basking shark. From these results, an evolutionary scenario of feeding mechanics of three species of planktivorous sharks can be suggested. In this scenario, the planktivorous whale shark evolved ram feeding from a benthic suction-feeding ancestor. Ram feeding in the planktivorous megamouth shark and the basking shark evolved from ram feeding swimming-type ancestors and that both developed their unique filtering system to capture small-sized prey. Copyright © 2011 Wiley-Liss, Inc.

Evidence of the evolved nature of the B[e] star MWC 137

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

Muratore, M. F.; Arias, M. L.; Cidale, L.

2015-01-01

The evolutionary phase of B[e] stars is difficult to establish due to the uncertainties in their fundamental parameters. For instance, possible classifications for the Galactic B[e] star MWC 137 include pre-main-sequence and post-main-sequence phases, with a large range in luminosity. Our goal is to clarify the evolutionary stage of this peculiar object, and to study the CO molecular component of its circumstellar medium. To this purpose, we modeled the CO molecular bands using high-resolution K-band spectra. We find that MWC 137 is surrounded by a detached cool (T=1900±100 K) and dense (N=(3±1)×10{sup 21} cm{sup −2}) ring of CO gas orbitingmore » the star with a rotational velocity, projected to the line of sight, of 84 ± 2 km s{sup −1}. We also find that the molecular gas is enriched in the isotope {sup 13}C, excluding the classification of the star as a Herbig Be. The observed isotopic abundance ratio ({sup 12}C/{sup 13}C = 25 ± 2) derived from our modeling is compatible with a proto-planetary nebula, main-sequence, or supergiant evolutionary phase. However, based on some observable characteristics of MWC 137, we propose that the supergiant scenario seems to be the most plausible. Hence, we suggest that MWC 137 could be in an extremely short-lived phase, evolving from a B[e] supergiant to a blue supergiant with a bipolar ring nebula.« less

Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments.

PubMed

Gorter, Florien A; Aarts, Mark G M; Zwaan, Bas J; de Visser, J Arjan G M

2018-01-01

The fitness landscape is a concept that is widely used for understanding and predicting evolutionary adaptation. The topography of the fitness landscape depends critically on the environment, with potentially far-reaching consequences for evolution under changing conditions. However, few studies have assessed directly how empirical fitness landscapes change across conditions, or validated the predicted consequences of such change. We previously evolved replicate yeast populations in the presence of either gradually increasing, or constant high, concentrations of the heavy metals cadmium (Cd), nickel (Ni), and zinc (Zn), and analyzed their phenotypic and genomic changes. Here, we reconstructed the local fitness landscapes underlying adaptation to each metal by deleting all repeatedly mutated genes both by themselves and in combination. Fitness assays revealed that the height, and/or shape, of each local fitness landscape changed considerably across metal concentrations, with distinct qualitative differences between unconditionally (Cd) and conditionally toxic metals (Ni and Zn). This change in topography had particularly crucial consequences in the case of Ni, where a substantial part of the individual mutational fitness effects changed in sign across concentrations. Based on the Ni landscape analyses, we made several predictions about which mutations had been selected when during the evolution experiment. Deep sequencing of population samples from different time points generally confirmed these predictions, demonstrating the power of landscape reconstruction analyses for understanding and ultimately predicting evolutionary dynamics, even under complex scenarios of environmental change. Copyright © 2018 by the Genetics Society of America.

The universal ancestor

NASA Technical Reports Server (NTRS)

Woese, C.

1998-01-01

A genetic annealing model for the universal ancestor of all extant life is presented; the name of the model derives from its resemblance to physical annealing. The scenario pictured starts when "genetic temperatures" were very high, cellular entities (progenotes) were very simple, and information processing systems were inaccurate. Initially, both mutation rate and lateral gene transfer levels were elevated. The latter was pandemic and pervasive to the extent that it, not vertical inheritance, defined the evolutionary dynamic. As increasingly complex and precise biological structures and processes evolved, both the mutation rate and the scope and level of lateral gene transfer, i.e., evolutionary temperature, dropped, and the evolutionary dynamic gradually became that characteristic of modern cells. The various subsystems of the cell "crystallized," i.e., became refractory to lateral gene transfer, at different stages of "cooling," with the translation apparatus probably crystallizing first. Organismal lineages, and so organisms as we know them, did not exist at these early stages. The universal phylogenetic tree, therefore, is not an organismal tree at its base but gradually becomes one as its peripheral branchings emerge. The universal ancestor is not a discrete entity. It is, rather, a diverse community of cells that survives and evolves as a biological unit. This communal ancestor has a physical history but not a genealogical one. Over time, this ancestor refined into a smaller number of increasingly complex cell types with the ancestors of the three primary groupings of organisms arising as a result.

Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm

PubMed Central

Jin, Xiaoli; Ren, Jing; Nevo, Eviatar; Yin, Xuegui; Sun, Dongfa; Peng, Junhua

2017-01-01

NAC (NAM/ATAF/CUC) proteins constitute one of the biggest plant-specific transcription factor (TF) families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origins and distinct features were observed. It is reasonable to hypothesize that there should be divergent evolutionary patterns of NAC TFs both between dicots and monocots, and among NAC subfamilies. In this study, we compared the gene duplication and loss, evolutionary rate, and selective pattern among non-lineage specific NAC subfamilies, as well as those between dicots and monocots, through genome-wide analyses of sequence and functional data in six dicot and five grass lineages. The number of genes gained in the dicot lineages was much larger than that in the grass lineages, while fewer gene losses were observed in the grass than that in the dicots. We revealed (1) uneven constitution of Clusters of Orthologous Groups (COGs) and contrasting birth/death rates among subfamilies, and (2) two distinct evolutionary scenarios of NAC TFs between dicots and grasses. Our results demonstrated that relaxed selection, resulting from concerted gene duplications, may have permitted substitutions responsible for functional divergence of NAC genes into new lineages. The underlying mechanism of distinct evolutionary fates of NAC TFs shed lights on how evolutionary divergence contributes to differences in establishing NAC gene subfamilies and thus impacts the distinct features between dicots and grasses. PMID:28713414

Sexual division of labor: energetic and evolutionary scenarios.

PubMed

Panter-Brick, Catherine

2002-01-01

This article examines comparative energetic data on hunter-gatherers in the context of evolutionary scenarios of the sexual division of labor, with respect to both specific task allocation and overall levels of daily physical activity. The division of labor between men and women, well marked in contemporary foraging societies, was once posited as the "true watershed" for the evolution of the genus Homo. Some research on brain-wiring even links sex differences in cognitive and spatial abilities to sex-specific foraging activities. Most recent evolutionary arguments posit that men focus on hunting and women on gathering activities to realize potentially conflicting mating and parenting goals. A range of cooperative strategies (male/female and female/female) for child provisioning is also under investigation. Attention to energetic and reproductive trade-offs has usefully challenged the proposition that women are excluded from big-game hunting due to constraints of foraging ecology and reproduction. Simplistic assumptions about gender roles are thus increasingly questioned in anthropology, as well as in archaeology. Current models in behavioral ecology explore ways in which foraging practices vary with ecological circumstances, aiming to derive testable hypotheses from fine-grained data on the behavior of contemporary hunter-gatherers. Data on overall physical activity levels (PAL) can also serve to evaluate relative male/female workloads in modern groups, reconstruct hominid energy requirements and activity profiles, and examine changes with subsistence intensification. Male/female PAL ratios show that a task-specific division of labor does not readily extrapolate to 24-hour energy expenditure and that male/female differences in workloads were not necessarily reduced with the transition to agriculture. With respect to gender roles and PAL, a shift away from facile stereotypes of human behavior is evident. The challenge is to incorporate a range of behavioral responses to ecological circumstances in reconstructions of our evolutionary past. Copyright 2002 Wiley-Liss, Inc.

Where do adaptive shifts occur during invasion A multidisciplinary approach to unravel cold adaptation in a tropical ant species invading the Mediterranean zone

USDA-ARS?s Scientific Manuscript database

Although evolution is now recognized as improving the invasive success of populations, where and when key adaptation event(s) occur often remains unclear. Here we used a multidisciplinary approach to disentangle the eco-evolutionary scenario of invasion of a Mediterranean zone (i.e. Israel) by the t...

Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution.

PubMed

Rogozin, Igor B; Wolf, Yuri I; Sorokin, Alexander V; Mirkin, Boris G; Koonin, Eugene V

2003-09-02

Sequencing of eukaryotic genomes allows one to address major evolutionary problems, such as the evolution of gene structure. We compared the intron positions in 684 orthologous gene sets from 8 complete genomes of animals, plants, fungi, and protists and constructed parsimonious scenarios of evolution of the exon-intron structure for the respective genes. Approximately one-third of the introns in the malaria parasite Plasmodium falciparum are shared with at least one crown group eukaryote; this number indicates that these introns have been conserved through >1.5 billion years of evolution that separate Plasmodium from the crown group. Paradoxically, humans share many more introns with the plant Arabidopsis thaliana than with the fly or nematode. The inferred evolutionary scenario holds that the common ancestor of Plasmodium and the crown group and, especially, the common ancestor of animals, plants, and fungi had numerous introns. Most of these ancestral introns, which are retained in the genomes of vertebrates and plants, have been lost in fungi, nematodes, arthropods, and probably Plasmodium. In addition, numerous introns have been inserted into vertebrate and plant genes, whereas, in other lineages, intron gain was much less prominent.

Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor.

PubMed

Refrégier, Guislaine; Abadia, Edgar; Matsumoto, Tomoshige; Ano, Hiromi; Takashima, Tetsuya; Tsuyuguchi, Izuo; Aktas, Elif; Cömert, Füsun; Gomgnimbou, Michel Kireopori; Panaiotov, Stefan; Phelan, Jody; Coll, Francesc; McNerney, Ruth; Pain, Arnab; Clark, Taane G; Sola, Christophe

2016-11-01

Two geographically distant M. tuberculosis sublineages, Tur from Turkey and T3-Osaka from Japan, exhibit partially identical genotypic signatures (identical 12-loci MIRU-VNTR profiles, distinct spoligotyping patterns). We investigated T3-Osaka and Tur sublineages characteristics and potential genetic relatedness, first using MIRU-VNTR locus analysis on 21 and 25 samples of each sublineage respectively, and second comparing Whole Genome Sequences of 8 new samples to public data from 45 samples uncovering human tuberculosis diversity. We then tried to date their Most Recent Common Ancestor (MRCA) using three calibrations of SNP accumulation rate (long-term=0.03SNP/genome/year, derived from a tuberculosis ancestor of around 70,000years old; intermediate=0.2SNP/genome/year derived from a Peruvian mummy; short-term=0.5SNP/genome/year). To disentangle between these scenarios, we confronted the corresponding divergence times with major human history events and knowledge on human genetic divergence. We identified relatively high intrasublineage diversity for both T3-Osaka and Tur. We definitively proved their monophyly; the corresponding super-sublineage (referred to as "T3-Osa-Tur") shares a common ancestor with T3-Ethiopia and Ural sublineages but is only remotely related to other Euro-American sublineages such as X, LAM, Haarlem and S. The evolutionary scenario based on long-term evolution rate being valid until T3-Osa-Tur MRCA was not supported by Japanese fossil data. The evolutionary scenario relying on short-term evolution rate since T3-Osa-Tur MRCA was contradicted by human history and potential traces of past epidemics. T3-Osaka and Tur sublineages were found likely to have diverged between 800y and 2000years ago, potentially at the time of Mongol Empire. Altogether, this study definitively proves a strong genetic link between Turkish and Japanese tuberculosis. It provides a first hypothesis for calibrating TB Euro-American lineage molecular clock; additional studies are needed to reliably date events corresponding to intermediate depths in tuberculosis phylogeny. Copyright © 2016 Elsevier B.V. All rights reserved.

Change of niche in guanaco (Lama guanicoe): the effects of climate change on habitat suitability and lineage conservatism in Chile.

PubMed

Castillo, Andrea G; Alò, Dominique; González, Benito A; Samaniego, Horacio

2018-01-01

The main goal of this contribution was to define the ecological niche of the guanaco ( Lama guanicoe ), to describe potential distributional changes, and to assess the relative importance of niche conservatism and divergence processes between the two lineages described for the species ( L.g. cacsilensis and L.g. guanicoe ). We used maximum entropy to model lineage's climate niche from 3,321 locations throughout continental Chile, and developed future niche models under climate change for two extreme greenhouse gas emission scenarios (RCP2.6 and RCP8.5). We evaluated changes of the environmental niche and future distribution of the largest mammal in the Southern Cone of South America. Evaluation of niche conservatism and divergence were based on identity and background similarity tests. We show that: (a) the current geographic distribution of lineages is associated with different climatic requirements that are related to the geographic areas where these lineages are located; (b) future distribution models predict a decrease in the distribution surface under both scenarios; (c) a 3% decrease of areal protection is expected if the current distribution of protected areas is maintained, and this is expected to occur at the expense of a large reduction of high quality habitats under the best scenario; (d) current and future distribution ranges of guanaco mostly adhere to phylogenetic niche divergence hypotheses between lineages. Associating environmental variables with species ecological niche seems to be an important aspect of unveiling the particularities of, both evolutionary patterns and ecological features that species face in a changing environment. We report specific descriptions of how these patterns may play out under the most extreme climate change predictions and provide a grim outlook of the future potential distribution of guanaco in Chile. From an ecological perspective, while a slightly smaller distribution area is expected, this may come with an important reduction of available quality habitats. From the evolutionary perspective, we describe the limitations of this taxon as it experiences forces imposed by climate change dynamics.

Change of niche in guanaco (Lama guanicoe): the effects of climate change on habitat suitability and lineage conservatism in Chile

PubMed Central

Castillo, Andrea G.; González, Benito A.

2018-01-01

Background The main goal of this contribution was to define the ecological niche of the guanaco (Lama guanicoe), to describe potential distributional changes, and to assess the relative importance of niche conservatism and divergence processes between the two lineages described for the species (L.g. cacsilensis and L.g. guanicoe). Methods We used maximum entropy to model lineage’s climate niche from 3,321 locations throughout continental Chile, and developed future niche models under climate change for two extreme greenhouse gas emission scenarios (RCP2.6 and RCP8.5). We evaluated changes of the environmental niche and future distribution of the largest mammal in the Southern Cone of South America. Evaluation of niche conservatism and divergence were based on identity and background similarity tests. Results We show that: (a) the current geographic distribution of lineages is associated with different climatic requirements that are related to the geographic areas where these lineages are located; (b) future distribution models predict a decrease in the distribution surface under both scenarios; (c) a 3% decrease of areal protection is expected if the current distribution of protected areas is maintained, and this is expected to occur at the expense of a large reduction of high quality habitats under the best scenario; (d) current and future distribution ranges of guanaco mostly adhere to phylogenetic niche divergence hypotheses between lineages. Discussion Associating environmental variables with species ecological niche seems to be an important aspect of unveiling the particularities of, both evolutionary patterns and ecological features that species face in a changing environment. We report specific descriptions of how these patterns may play out under the most extreme climate change predictions and provide a grim outlook of the future potential distribution of guanaco in Chile. From an ecological perspective, while a slightly smaller distribution area is expected, this may come with an important reduction of available quality habitats. From the evolutionary perspective, we describe the limitations of this taxon as it experiences forces imposed by climate change dynamics. PMID:29868293

Evidence for past and present hybridization in three Antarctic icefish species provides new perspectives on an evolutionary radiation.

PubMed

Marino, I A M; Benazzo, A; Agostini, C; Mezzavilla, M; Hoban, S M; Patarnello, T; Zane, L; Bertorelle, G

2013-10-01

Determining the timing, extent and underlying causes of interspecific gene exchange during or following speciation is central to understanding species' evolution. Antarctic notothenioid fish, thanks to the acquisition of antifreeze glycoproteins during Oligocene transition to polar conditions, experienced a spectacular radiation to >100 species during Late Miocene cooling events. The impact of recent glacial cycles on this group is poorly known, but alternating warming and cooling periods may have affected species' distributions, promoted ecological divergence into recurrently opening niches and/or possibly brought allopatric species into contact. Using microsatellite markers and statistical methods including Approximate Bayesian Computation, we investigated genetic differentiation, hybridization and the possible influence of the last glaciation/deglaciation events in three icefish species of the genus Chionodraco. Our results provide strong evidence of contemporary and past introgression by showing that: (i) a substantial fraction of contemporary individuals in each species has mixed ancestry, (ii) evolutionary scenarios excluding hybridization or including it only in ancient times have small or zero posterior probabilities, (iii) the data support a scenario of interspecific gene flow associated with the two most recent interglacial periods. Glacial cycles might therefore have had a profound impact on the genetic composition of Antarctic fauna, as newly available shelf areas during the warmer intervals might have favoured secondary contacts and hybridization between diversified groups. If our findings are confirmed in other notothenioids, they offer new perspectives for understanding evolutionary dynamics of Antarctic fish and suggest a need for new predictions on the effects of global warming in this group. © 2013 John Wiley & Sons Ltd.

Evolution of Nucleotide Punctuation Marks: From Structural to Linear Signals.

PubMed

El Houmami, Nawal; Seligmann, Hervé

2017-01-01

We present an evolutionary hypothesis assuming that signals marking nucleotide synthesis (DNA replication and RNA transcription) evolved from multi- to unidimensional structures, and were carried over from transcription to translation. This evolutionary scenario presumes that signals combining secondary and primary nucleotide structures are evolutionary transitions. Mitochondrial replication initiation fits this scenario. Some observations reported in the literature corroborate that several signals for nucleotide synthesis function in translation, and vice versa. (a) Polymerase-induced frameshift mutations occur preferentially at translational termination signals (nucleotide deletion is interpreted as termination of nucleotide polymerization, paralleling the role of stop codons in translation). (b) Stem-loop hairpin presence/absence modulates codon-amino acid assignments, showing that translational signals sometimes combine primary and secondary nucleotide structures (here codon and stem-loop). (c) Homopolymer nucleotide triplets (AAA, CCC, GGG, TTT) cause transcriptional and ribosomal frameshifts. Here we find in recently described human mitochondrial RNAs that systematically lack mono-, dinucleotides after each trinucleotide (delRNAs) that delRNA triplets include 2x more homopolymers than mitogenome regions not covered by delRNA. Further analyses of delRNAs show that the natural circular code X (a little-known group of 20 translational signals enabling ribosomal frame retrieval consisting of 20 codons {AAC, AAT, ACC, ATC, ATT, CAG, CTC, CTG, GAA, GAC, GAG, GAT, GCC, GGC, GGT, GTA, GTC, GTT, TAC, TTC} universally overrepresented in coding versus other frames of gene sequences), regulates frameshift in transcription and translation. This dual transcription and translation role confirms for X the hypothesis that translational signals were carried over from transcriptional signals.

Chaos and unpredictability in evolution.

PubMed

Doebeli, Michael; Ispolatov, Iaroslav

2014-05-01

The possibility of complicated dynamic behavior driven by nonlinear feedbacks in dynamical systems has revolutionized science in the latter part of the last century. Yet despite examples of complicated frequency dynamics, the possibility of long-term evolutionary chaos is rarely considered. The concept of "survival of the fittest" is central to much evolutionary thinking and embodies a perspective of evolution as a directional optimization process exhibiting simple, predictable dynamics. This perspective is adequate for simple scenarios, when frequency-independent selection acts on scalar phenotypes. However, in most organisms many phenotypic properties combine in complicated ways to determine ecological interactions, and hence frequency-dependent selection. Therefore, it is natural to consider models for evolutionary dynamics generated by frequency-dependent selection acting simultaneously on many different phenotypes. Here we show that complicated, chaotic dynamics of long-term evolutionary trajectories in phenotype space is very common in a large class of such models when the dimension of phenotype space is large, and when there are selective interactions between the phenotypic components. Our results suggest that the perspective of evolution as a process with simple, predictable dynamics covers only a small fragment of long-term evolution. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Evolutionary dynamics of imatinib-treated leukemic cells by stochastic approach

NASA Astrophysics Data System (ADS)

Pizzolato, Nicola; Valenti, Davide; Adorno, Dominique Persano; Spagnolo, Bernardo

2009-09-01

The evolutionary dynamics of a system of cancerous cells in a model of chronic myeloid leukemia (CML) is investigated by a statistical approach. Cancer progression is explored by applying a Monte Carlo method to simulate the stochastic behavior of cell reproduction and death in a population of blood cells which can experience genetic mutations. In CML front line therapy is represented by the tyrosine kinase inhibitor imatinib which strongly affects the reproduction of leukemic cells only. In this work, we analyze the effects of a targeted therapy on the evolutionary dynamics of normal, first-mutant and cancerous cell populations. Several scenarios of the evolutionary dynamics of imatinib-treated leukemic cells are described as a consequence of the efficacy of the different modelled therapies. We show how the patient response to the therapy changes when a high value of the mutation rate from healthy to cancerous cells is present. Our results are in agreement with clinical observations. Unfortunately, development of resistance to imatinib is observed in a fraction of patients, whose blood cells are characterized by an increasing number of genetic alterations. We find that the occurrence of resistance to the therapy can be related to a progressive increase of deleterious mutations.

Synthetic transitions: towards a new synthesis

PubMed Central

Solé, Ricard

2016-01-01

The evolution of life in our biosphere has been marked by several major innovations. Such major complexity shifts include the origin of cells, genetic codes or multicellularity to the emergence of non-genetic information, language or even consciousness. Understanding the nature and conditions for their rise and success is a major challenge for evolutionary biology. Along with data analysis, phylogenetic studies and dedicated experimental work, theoretical and computational studies are an essential part of this exploration. With the rise of synthetic biology, evolutionary robotics, artificial life and advanced simulations, novel perspectives to these problems have led to a rather interesting scenario, where not only the major transitions can be studied or even reproduced, but even new ones might be potentially identified. In both cases, transitions can be understood in terms of phase transitions, as defined in physics. Such mapping (if correct) would help in defining a general framework to establish a theory of major transitions, both natural and artificial. Here, we review some advances made at the crossroads between statistical physics, artificial life, synthetic biology and evolutionary robotics. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431516

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.

Reserve design for uncertain responses of coral reefs to climate change.

PubMed

Mumby, Peter J; Elliott, Ian A; Eakin, C Mark; Skirving, William; Paris, Claire B; Edwards, Helen J; Enríquez, Susana; Iglesias-Prieto, Roberto; Cherubin, Laurent M; Stevens, Jamie R

2011-02-01

Rising sea temperatures cause mass coral bleaching and threaten reefs worldwide. We show how maps of variations in thermal stress can be used to help manage reefs for climate change. We map proxies of chronic and acute thermal stress and develop evidence-based hypotheses for the future response of corals to each stress regime. We then incorporate spatially realistic predictions of larval connectivity among reefs of the Bahamas and apply novel reserve design algorithms to create reserve networks for a changing climate. We show that scales of larval dispersal are large enough to connect reefs from desirable thermal stress regimes into a reserve network. Critically, we find that reserve designs differ according to the anticipated scope for phenotypic and genetic adaptation in corals, which remains uncertain. Attempts to provide a complete reserve design that hedged against different evolutionary outcomes achieved limited success, which emphasises the importance of considering the scope for adaptation explicitly. Nonetheless, 15% of reserve locations were selected under all evolutionary scenarios, making them a high priority for early designation. Our approach allows new insights into coral holobiont adaptation to be integrated directly into an adaptive approach to management. © 2010 Blackwell Publishing Ltd/CNRS.

Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation.

PubMed

Lopes, J S; Arenas, M; Posada, D; Beaumont, M A

2014-03-01

The estimation of parameters in molecular evolution may be biased when some processes are not considered. For example, the estimation of selection at the molecular level using codon-substitution models can have an upward bias when recombination is ignored. Here we address the joint estimation of recombination, molecular adaptation and substitution rates from coding sequences using approximate Bayesian computation (ABC). We describe the implementation of a regression-based strategy for choosing subsets of summary statistics for coding data, and show that this approach can accurately infer recombination allowing for intracodon recombination breakpoints, molecular adaptation and codon substitution rates. We demonstrate that our ABC approach can outperform other analytical methods under a variety of evolutionary scenarios. We also show that although the choice of the codon-substitution model is important, our inferences are robust to a moderate degree of model misspecification. In addition, we demonstrate that our approach can accurately choose the evolutionary model that best fits the data, providing an alternative for when the use of full-likelihood methods is impracticable. Finally, we applied our ABC method to co-estimate recombination, substitution and molecular adaptation rates from 24 published human immunodeficiency virus 1 coding data sets.

The ethical dimensions of wildlife disease management in an evolutionary context.

PubMed

Crozier, Gkd; Schulte-Hostedde, Albrecht I

2014-08-01

Best practices in wildlife disease management require robust evolutionary ecological research (EER). This means not only basing management decisions on evolutionarily sound reasoning, but also conducting management in a way that actively contributes to the on-going development of that research. Because good management requires good science, and good science is 'good' science (i.e., effective science is often science conducted ethically), good management therefore also requires practices that accord with sound ethical reasoning. To that end, we propose a two-part framework to assist decision makers to identify ethical pitfalls of wildlife disease management. The first part consists of six values - freedom, fairness, well-being, replacement, reduction, and refinement; these values, developed for the ethical evaluation of EER practices, are also well suited for evaluating the ethics of wildlife disease management. The second part consists of a decision tree to help identify the ethically salient dimensions of wildlife disease management and to guide managers toward ethically responsible practices in complex situations. While ethical reasoning cannot be used to deduce from first principles what practices should be undertaken in every given set of circumstances, it can establish parameters that bound what sorts of practices will be acceptable or unacceptable in certain types of scenarios.

From proto-mimesis to language: evidence from primatology and social neuroscience.

PubMed

Zlatev, Jordan

2008-01-01

How can we reconcile the conception of language as a conventional-normative semiotic system with a perception/action-based account of its structure and meaning? And why should linguistic meaning--as opposed to linguistic expression--be so closely related to motor activity and its neural underpinnings, as suggested by recent findings? A conceptual framework and evolutionary scenario building on the concept of bodily mimesis [Zlatev, J., 2005. What's in a schema? Bodily mimesis and the grounding of language. In: Hampe, B. (Ed.), From Perception to Meaning: Image Schemas in Cognitive Linguistics. Mouton de Gruyter, Berlin, pp. 313-343] imply answers to these questions. The article presents evidence for a particular evolutionary stage model by reviewing recent evidence on the capacity of non-human primates for intersubjectivity, imitation and gestural communication, and from neuroscientific studies of these capacities in monkeys and human subjects. It is argued that "mirror neuron" systems can subserve basic motoric and social capacities, but they need to be considerably extended in order to provide an efficient basis for bodily mimesis, and even more so for language. It is argued that while language may be ultimately "grounded" in perception and action, it is essential not to try to reduce it to them.

Is specialization an evolutionary dead end? Testing for differences in speciation, extinction and trait transition rates across diverse phylogenies of specialists and generalists.

PubMed

Day, E H; Hua, X; Bromham, L

2016-06-01

Specialization has often been claimed to be an evolutionary dead end, with specialist lineages having a reduced capacity to persist or diversify. In a phylogenetic comparative framework, an evolutionary dead end may be detectable from the phylogenetic distribution of specialists, if specialists rarely give rise to large, diverse clades. Previous phylogenetic studies of the influence of specialization on macroevolutionary processes have demonstrated a range of patterns, including examples where specialists have both higher and lower diversification rates than generalists, as well as examples where the rates of evolutionary transitions from generalists to specialists are higher, lower or equal to transitions from specialists to generalists. Here, we wish to ask whether these varied answers are due to the differences in macroevolutionary processes in different clades, or partly due to differences in methodology. We analysed ten phylogenies containing multiple independent origins of specialization and quantified the phylogenetic distribution of specialists by applying a common set of metrics to all datasets. We compared the tip branch lengths of specialists to generalists, the size of specialist clades arising from each evolutionary origin of a specialized trait and whether specialists tend to be clustered or scattered on phylogenies. For each of these measures, we compared the observed values to expectations under null models of trait evolution and expected outcomes under alternative macroevolutionary scenarios. We found that specialization is sometimes an evolutionary dead end: in two of the ten case studies (pollinator-specific plants and host-specific flies), specialization is associated with a reduced rate of diversification or trait persistence. However, in the majority of studies, we could not distinguish the observed phylogenetic distribution of specialists from null models in which specialization has no effect on diversification or trait persistence. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Evolution of endemism on a young tropical mountain.

PubMed

Merckx, Vincent S F T; Hendriks, Kasper P; Beentjes, Kevin K; Mennes, Constantijn B; Becking, Leontine E; Peijnenburg, Katja T C A; Afendy, Aqilah; Arumugam, Nivaarani; de Boer, Hugo; Biun, Alim; Buang, Matsain M; Chen, Ping-Ping; Chung, Arthur Y C; Dow, Rory; Feijen, Frida A A; Feijen, Hans; Feijen-van Soest, Cobi; Geml, József; Geurts, René; Gravendeel, Barbara; Hovenkamp, Peter; Imbun, Paul; Ipor, Isa; Janssens, Steven B; Jocqué, Merlijn; Kappes, Heike; Khoo, Eyen; Koomen, Peter; Lens, Frederic; Majapun, Richard J; Morgado, Luis N; Neupane, Suman; Nieser, Nico; Pereira, Joan T; Rahman, Homathevi; Sabran, Suzana; Sawang, Anati; Schwallier, Rachel M; Shim, Phyau-Soon; Smit, Harry; Sol, Nicolien; Spait, Maipul; Stech, Michael; Stokvis, Frank; Sugau, John B; Suleiman, Monica; Sumail, Sukaibin; Thomas, Daniel C; van Tol, Jan; Tuh, Fred Y Y; Yahya, Bakhtiar E; Nais, Jamili; Repin, Rimi; Lakim, Maklarin; Schilthuizen, Menno

2015-08-20

Tropical mountains are hot spots of biodiversity and endemism, but the evolutionary origins of their unique biotas are poorly understood. In varying degrees, local and regional extinction, long-distance colonization, and local recruitment may all contribute to the exceptional character of these communities. Also, it is debated whether mountain endemics mostly originate from local lowland taxa, or from lineages that reach the mountain by long-range dispersal from cool localities elsewhere. Here we investigate the evolutionary routes to endemism by sampling an entire tropical mountain biota on the 4,095-metre-high Mount Kinabalu in Sabah, East Malaysia. We discover that most of its unique biodiversity is younger than the mountain itself (6 million years), and comprises a mix of immigrant pre-adapted lineages and descendants from local lowland ancestors, although substantial shifts from lower to higher vegetation zones in this latter group were rare. These insights could improve forecasts of the likelihood of extinction and 'evolutionary rescue' in montane biodiversity hot spots under climate change scenarios.

Coevolutionary dynamics in large, but finite populations

NASA Astrophysics Data System (ADS)

Traulsen, Arne; Claussen, Jens Christian; Hauert, Christoph

2006-07-01

Coevolving and competing species or game-theoretic strategies exhibit rich and complex dynamics for which a general theoretical framework based on finite populations is still lacking. Recently, an explicit mean-field description in the form of a Fokker-Planck equation was derived for frequency-dependent selection with two strategies in finite populations based on microscopic processes [A. Traulsen, J. C. Claussen, and C. Hauert, Phys. Rev. Lett. 95, 238701 (2005)]. Here we generalize this approach in a twofold way: First, we extend the framework to an arbitrary number of strategies and second, we allow for mutations in the evolutionary process. The deterministic limit of infinite population size of the frequency-dependent Moran process yields the adjusted replicator-mutator equation, which describes the combined effect of selection and mutation. For finite populations, we provide an extension taking random drift into account. In the limit of neutral selection, i.e., whenever the process is determined by random drift and mutations, the stationary strategy distribution is derived. This distribution forms the background for the coevolutionary process. In particular, a critical mutation rate uc is obtained separating two scenarios: above uc the population predominantly consists of a mixture of strategies whereas below uc the population tends to be in homogeneous states. For one of the fundamental problems in evolutionary biology, the evolution of cooperation under Darwinian selection, we demonstrate that the analytical framework provides excellent approximations to individual based simulations even for rather small population sizes. This approach complements simulation results and provides a deeper, systematic understanding of coevolutionary dynamics.

Semiempirical limits on the thermal conductivity of intracluster gas

NASA Technical Reports Server (NTRS)

David, Laurence P.; Hughes, John P.; Tucker, Wallace H.

1992-01-01

A semiempirical method for establishing lower limits on the thermal conductivity of hot gas in clusters of galaxies is described. The method is based on the observation that the X-ray imaging data (e.g., Einstein IPC) for clusters are well described by the hydrostatic-isothermal beta model, even for cooling flow clusters beyond about one core radius. In addition, there are strong indications that noncooling flow clusters (like the Coma Cluster) have a large central region (up to several core radii) of nearly constant gas temperature. This suggests that thermal conduction is an effective means of transporting and redistributing the thermal energy of the gas. This in turn has implications for the extent to which magnetic fields in the cluster are effective in reducing the thermal conductivity of the gas. Time-dependent hydrodynamic simulations for the gas in the Coma Cluster under two separate evolutionary scenarios are presented. One scenario assumes that the cluster potential is static and that the gas has an initial adiabatic distribution. The second scenario uses an evolving cluster potential. These models along with analytic results show that the thermal conductivity of the gas in the Coma Cluster cannot be less than 0.1 of full Spitzer conductivity. These models also show that high gas conductivity assists rather than hinders the development of radiative cooling in the central regions of clusters.

Bridgehead Effect in the Worldwide Invasion of the Biocontrol Harlequin Ladybird

PubMed Central

Lombaert, Eric; Guillemaud, Thomas; Cornuet, Jean-Marie; Malausa, Thibaut; Facon, Benoît; Estoup, Arnaud

2010-01-01

Recent studies of the routes of worldwide introductions of alien organisms suggest that many widespread invasions could have stemmed not from the native range, but from a particularly successful invasive population, which serves as the source of colonists for remote new territories. We call here this phenomenon the invasive bridgehead effect. Evaluating the likelihood of such a scenario is heuristically challenging. We solved this problem by using approximate Bayesian computation methods to quantitatively compare complex invasion scenarios based on the analysis of population genetics (microsatellite variation) and historical (first observation dates) data. We applied this approach to the Harlequin ladybird Harmonia axyridis (HA), a coccinellid native to Asia that was repeatedly introduced as a biocontrol agent without becoming established for decades. We show that the recent burst of worldwide invasions of HA followed a bridgehead scenario, in which an invasive population in eastern North America acted as the source of the colonists that invaded the European, South American and African continents, with some admixture with a biocontrol strain in Europe. This demonstration of a mechanism of invasion via a bridgehead has important implications both for invasion theory (i.e., a single evolutionary shift in the bridgehead population versus multiple changes in case of introduced populations becoming invasive independently) and for ongoing efforts to manage invasions by alien organisms (i.e., heightened vigilance against invasive bridgeheads). PMID:20305822

Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow.

PubMed

Sachdeva, Himani; Barton, Nicholas H

2017-06-01

Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Spatial Models of Prebiotic Evolution: Soup Before Pizza?

NASA Astrophysics Data System (ADS)

Scheuring, István; Czárán, Tamás; Szabó, Péter; Károlyi, György; Toroczkai, Zoltán

2003-10-01

The problem of information integration and resistance to the invasion of parasitic mutants in prebiotic replicator systems is a notorious issue of research on the origin of life. Almost all theoretical studies published so far have demonstrated that some kind of spatial structure is indispensable for the persistence and/or the parasite resistance of any feasible replicator system. Based on a detailed critical survey of spatial models on prebiotic information integration, we suggest a possible scenario for replicator system evolution leading to the emergence of the first protocells capable of independent life. We show that even the spatial versions of the hypercycle model are vulnerable to selfish parasites in heterogeneous habitats. Contrary, the metabolic system remains persistent and coexistent with its parasites both on heterogeneous surfaces and in chaotically mixing flowing media. Persistent metabolic parasites can be converted to metabolic cooperators, or they can gradually obtain replicase activity. Our simulations show that, once replicase activity emerged, a gradual and simultaneous evolutionary improvement of replicase functionality (speed and fidelity) and template efficiency is possible only on a surface that constrains the mobility of macromolecule replicators. Based on the results of the models reviewed, we suggest that open chaotic flows (`soup') and surface dynamics (`pizza') both played key roles in the sequence of evolutionary events ultimately concluding in the appearance of the first living cell on Earth.

Origin of a cryptic lineage in a threatened reptile through isolation and historical hybridization

PubMed Central

Sovic, M G; Fries, A C; Gibbs, H L

2016-01-01

Identifying phylogenetically distinct lineages and understanding the evolutionary processes by which they have arisen are important goals of phylogeography. This information can also help define conservation units in endangered species. Such analyses are being transformed by the availability of genomic-scale data sets and novel analytical approaches for statistically comparing different historical scenarios as causes of phylogeographic patterns. Here, we use genomic-scale restriction-site-associated DNA sequencing (RADseq) data to test for distinct lineages in the endangered Eastern Massasauga Rattlesnake (Sistrurus catenatus). We then use coalescent-based modeling techniques to identify the evolutionary mechanisms responsible for the origin of the lineages in this species. We find equivocal evidence for distinct phylogenetic lineages within S. catenatus east of the Mississippi River, but strong support for a previously unrecognized lineage on the western edge of the range of this snake, represented by populations from Iowa, USA. Snakes from these populations show patterns of genetic admixture with a nearby non-threatened sister species (Sistrurus tergeminus). Tests of historical demographic models support the hypothesis that the genetic distinctiveness of Iowa snakes is due to a combination of isolation and historical introgression between S. catenatus and S. tergeminus. Our work provides an example of how model-based analysis of genomic-scale data can help identify conservation units in rare species. PMID:27460499

Sampling and counting genome rearrangement scenarios

PubMed Central

2015-01-01

Background Even for moderate size inputs, there are a tremendous number of optimal rearrangement scenarios, regardless what the model is and which specific question is to be answered. Therefore giving one optimal solution might be misleading and cannot be used for statistical inferring. Statistically well funded methods are necessary to sample uniformly from the solution space and then a small number of samples are sufficient for statistical inferring. Contribution In this paper, we give a mini-review about the state-of-the-art of sampling and counting rearrangement scenarios, focusing on the reversal, DCJ and SCJ models. Above that, we also give a Gibbs sampler for sampling most parsimonious labeling of evolutionary trees under the SCJ model. The method has been implemented and tested on real life data. The software package together with example data can be downloaded from http://www.renyi.hu/~miklosi/SCJ-Gibbs/ PMID:26452124

An evolutionary analysis of the GH57 amylopullulanases based on the DOMON_glucodextranase_like domains.

PubMed

Jiao, Yu-Liang; Wang, Shu-Jun; Lv, Ming-Sheng; Fang, Yao-Wei; Liu, Shu

2013-03-01

Thermostable amylopullulanase (TAPU) is valuable in starch saccharification industry for its capability to catalyze both α-1,4 and α-1,6 glucosidic bonds under the industrial starch liquefication condition. The majority of TAPUs belong to glycoside hydrolase family 57 (GH57). In this study, we performed a phylogenetic analysis of GH57 amylopullulanase (APU) based on the highly conserved DOMON_glucodextranase_like (DDL) domain and classified APUs according to their multidomain architectures, phylogenetic analysis and enzymatic characters. This study revealed that amylopullulanase, pullulanase, andα-amylase had passed through a long joint evolution process, in which DDL played an important role. The phylogenetic analysis of DDL domain showed that the GH57 APU is directly sharing a common ancestor with pullulanase, and the DDL domains in some species undergo evolution scenarios such as domain duplication and recombination. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Evolution of the Stem Cell Theory for Heart Failure.

PubMed

Silvestre, Jean-Sébastien; Menasché, Philippe

2015-12-01

Various stem cell-based approaches for cardiac repair have achieved encouraging results in animal experiments, often leading to their rapid proceeding to clinical testing. However, freewheeling evolutionary developments of the stem cell theory might lead to dystopian scenarios where heterogeneous sources of therapeutic cells could promote mixed clinical outcomes in un-stratified patient populations. This review focuses on the lessons that should be learnt from the first generation of stem cell-based strategies and emphasizes the absolute requirement to better understand the basic mechanisms of stem cell biology and cardiogenesis. We will also discuss about the unexpected "big bang" in the stem cell theory, "blasting" the therapeutic cells to their unchallenged ability to release paracrine factors such as extracellular membrane vesicles. Paradoxically, the natural evolution of the stem cell theory for cardiac regeneration may end with the development of cell-free strategies with multiple cellular targets including cardiomyocytes but also other infiltrating or resident cardiac cells.

The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data.

PubMed

Peters, Ralph S; Meusemann, Karen; Petersen, Malte; Mayer, Christoph; Wilbrandt, Jeanne; Ziesmann, Tanja; Donath, Alexander; Kjer, Karl M; Aspöck, Ulrike; Aspöck, Horst; Aberer, Andre; Stamatakis, Alexandros; Friedrich, Frank; Hünefeld, Frank; Niehuis, Oliver; Beutel, Rolf G; Misof, Bernhard

2014-03-20

Despite considerable progress in systematics, a comprehensive scenario of the evolution of phenotypic characters in the mega-diverse Holometabola based on a solid phylogenetic hypothesis was still missing. We addressed this issue by de novo sequencing transcriptome libraries of representatives of all orders of holometabolan insects (13 species in total) and by using a previously published extensive morphological dataset. We tested competing phylogenetic hypotheses by analyzing various specifically designed sets of amino acid sequence data, using maximum likelihood (ML) based tree inference and Four-cluster Likelihood Mapping (FcLM). By maximum parsimony-based mapping of the morphological data on the phylogenetic relationships we traced evolutionary transformations at the phenotypic level and reconstructed the groundplan of Holometabola and of selected subgroups. In our analysis of the amino acid sequence data of 1,343 single-copy orthologous genes, Hymenoptera are placed as sister group to all remaining holometabolan orders, i.e., to a clade Aparaglossata, comprising two monophyletic subunits Mecopterida (Amphiesmenoptera + Antliophora) and Neuropteroidea (Neuropterida + Coleopterida). The monophyly of Coleopterida (Coleoptera and Strepsiptera) remains ambiguous in the analyses of the transcriptome data, but appears likely based on the morphological data. Highly supported relationships within Neuropterida and Antliophora are Raphidioptera + (Neuroptera + monophyletic Megaloptera), and Diptera + (Siphonaptera + Mecoptera). ML tree inference and FcLM yielded largely congruent results. However, FcLM, which was applied here for the first time to large phylogenomic supermatrices, displayed additional signal in the datasets that was not identified in the ML trees. Our phylogenetic results imply that an orthognathous larva belongs to the groundplan of Holometabola, with compound eyes and well-developed thoracic legs, externally feeding on plants or fungi. Ancestral larvae of Aparaglossata were prognathous, equipped with single larval eyes (stemmata), and possibly agile and predacious. Ancestral holometabolan adults likely resembled in their morphology the groundplan of adult neopteran insects. Within Aparaglossata, the adult's flight apparatus and ovipositor underwent strong modifications. We show that the combination of well-resolved phylogenies obtained by phylogenomic analyses and well-documented extensive morphological datasets is an appropriate basis for reconstructing complex morphological transformations and for the inference of evolutionary histories.

New generation of elastic network models.

PubMed

López-Blanco, José Ramón; Chacón, Pablo

2016-04-01

The intrinsic flexibility of proteins and nucleic acids can be grasped from remarkably simple mechanical models of particles connected by springs. In recent decades, Elastic Network Models (ENMs) combined with Normal Model Analysis widely confirmed their ability to predict biologically relevant motions of biomolecules and soon became a popular methodology to reveal large-scale dynamics in multiple structural biology scenarios. The simplicity, robustness, low computational cost, and relatively high accuracy are the reasons behind the success of ENMs. This review focuses on recent advances in the development and application of ENMs, paying particular attention to combinations with experimental data. Successful application scenarios include large macromolecular machines, structural refinement, docking, and evolutionary conservation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Agent Based Modeling of Air Carrier Behavior for Evaluation of Technology Equipage and Adoption

NASA Technical Reports Server (NTRS)

Horio, Brant M.; DeCicco, Anthony H.; Stouffer, Virginia L.; Hasan, Shahab; Rosenbaum, Rebecca L.; Smith, Jeremy C.

2014-01-01

As part of ongoing research, the National Aeronautics and Space Administration (NASA) and LMI developed a research framework to assist policymakers in identifying impacts on the U.S. air transportation system (ATS) of potential policies and technology related to the implementation of the Next Generation Air Transportation System (NextGen). This framework, called the Air Transportation System Evolutionary Simulation (ATS-EVOS), integrates multiple models into a single process flow to best simulate responses by U.S. commercial airlines and other ATS stakeholders to NextGen-related policies, and in turn, how those responses impact the ATS. Development of this framework required NASA and LMI to create an agent-based model of airline and passenger behavior. This Airline Evolutionary Simulation (AIRLINE-EVOS) models airline decisions about tactical airfare and schedule adjustments, and strategic decisions related to fleet assignments, market prices, and equipage. AIRLINE-EVOS models its own heterogeneous population of passenger agents that interact with airlines; this interaction allows the model to simulate the cycle of action-reaction as airlines compete with each other and engage passengers. We validated a baseline configuration of AIRLINE-EVOS against Airline Origin and Destination Survey (DB1B) data and subject matter expert opinion, and we verified the ATS-EVOS framework and agent behavior logic through scenario-based experiments. These experiments demonstrated AIRLINE-EVOS's capabilities in responding to an input price shock in fuel prices, and to equipage challenges in a series of analyses based on potential incentive policies for best equipped best served, optimal-wind routing, and traffic management initiative exemption concepts..

Removal targets' classification: How time considerations modify the definition of the index

NASA Astrophysics Data System (ADS)

Zemoura, Mélissa; Hanada, Toshiya; Kawamoto, Satomi

2017-09-01

The growth of the near-Earth debris population since the beginning of human space activities is now a fact commonly admitted by space agencies worldwide. Numerous entities have warned about the danger that debris may have over time. Presently mitigation methods such as imposing post-mission disposal time after launch will no longer be sufficient; remediation processes seem necessary to limit the increase. In particular, this phenomenon is attributed to the generation of fragments due to more and more on-orbit collisions. Therefore, investigations on indexes to select potential removal targets were recently conducted, considering solely objects implicated in a collision course. This study also looks at the multiple fragmentation factors, including time through the altitude at time of impact (due to the behaviour of debris re-entering with time). The focal point is here to compare different criteria to select removal targets that enable scenarios in best adequacy with the future in question (long term, mid term or short term). Aware of the uncertainty of evolutionary models, this study also incorporates the simulation method as an impactful factor and tries to overcome the potential randomness of the results. Therefore, this paper presents a way to establish a selection criterion the most adequate for the time period focused on. In order to solve this issue, a ;double-check; method is proposed. First, an analytical evolutionary model simulates the environment over 100 years, through 100 Monte-Carlo runs. Then, among the initial population of year 2009, the objects supposed to be at the origin of the debris detected at a given time are tracked back in time into the simulations, using a collision-detecting program. The ;given period; above mentioned for the presence of debris is based on a future as such that 2029 be considered a short-term scenario, 2059 a midterm scenario and 2109 a long-term scenario. This step produces three lists of targets for removal (one for each future), and simulations are run once again, through different scenarios involving the removal of particular listed targets in order to verify the appropriateness of the proposed scenarios. The analysis of the results is based both on the mean of the simulations and on the recurrence considering each run. Three studies were conducted one for each term, and a fourth one completed the work by establishing comparison between short, mid and long-term periods. As a result, three main criteria could be established: the altitude of the objects, the number of targets necessary to remove, and the phenomenon of chain collisions. According to the future that was investigated, the most adequate criterion appeared to be different, consisting in the number of objects in the long-term analysis or the ranking position at short term (linked to the close-time consideration). As a main conclusion and further perspectives, it should be more efficient to consider the collision-probability and mass product together with the time-depending generation of fragments. This would help increasing the precision in the prediction of collision impacts. Rather than pinpointing specified targets to be removed, the aim of this study is simply to understand the mechanisms at the origin of the population increase around the Earth. Also to demonstrate that a careful definition of selection criteria would enable to adopt a suitable removal process in the period of action or for the goal to be reached.

The Mediterranean: the cradle of Anthoxanthum (Poaceae) diploid diversity.

PubMed

Chumová, Zuzana; Záveská, Eliška; Mandáková, Terezie; Krak, Karol; Trávnícek, Pavel

2017-08-01

Knowledge of diploid phylogeny and ecogeography provide a foundation for understanding plant evolutionary history, diversification patterns and taxonomy. The genus Anthoxanthum (vernal grasses, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and poorly resolved evolutionary relationships. The aims of the study were to reveal: (1) evolutionary lineages of the diploid taxa and their genetic differentiation; (2) the past distribution of the rediscovered 'Mediterranean diploid'; and (3) possible migration routes of diploids in the Mediterranean. A combined approach involving sequencing of two plastid regions ( trnL-trnF and rpl32-trnL ), nrDNA ITS, rDNA FISH analyses, climatic niche characterization and spatio-temporal modelling was used. Among the examined diploid species, only two well-differentiated evolutionary lineages were recognized: Anthoxanthum gracile and A. alpinum . The other taxa - A. aristatum, A. ovatum, A. maderense and the 'Mediterranean diploid' - form a rather intermixed group based on the examined molecular data. In situ rDNA localization enabled identification of the ancestral Anthoxanthum karyotype, shared by A. gracile and two taxa from the crown group. For the studied taxa, ancestral location probabilities for six discrete geographical regions in the Mediterranean were proposed and likely scenarios of gradual expansion from them were suggested. Modelling past and present distributions shows that the 'Mediterranean diploid' has already been occurring in the same localities for 120 000 years. Highly congruent results were obtained and dated the origin and first diversification of Anthoxanthum to the Miocene. The later divergence probably took place in the Pleistocene and started polyploid evolution within the genus. The most recent diversification event is still occurring, and incomplete lineage sorting prevents full diversification of taxa at the molecular level, despite clear separation based on climatic niches. The 'Mediterranean diploid' is hypothesized to be a possible relic of the most recent common ancestor of Anthoxanthum due to their sharing of ancestral features. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

On Helium-Dominated Stellar Evolution: The Mysterious Role of the O(He)-Type Stars

NASA Technical Reports Server (NTRS)

Reindl, N.; Rauch, T.; Werner, K.; Kruk, J. W.; Todt, H.

2014-01-01

Context. About a quarter of all post-asymptotic giant branch (AGB) stars are hydrogen-deficient. Stellar evolutionary models explain the carbon-dominated H-deficient stars by a (very) late thermal pulse scenario where the hydrogen-rich envelope is mixed with the helium-rich intershell layer. Depending on the particular time at which the final flash occurs, the entire hydrogen envelope may be burned. In contrast, helium-dominated post-AGB stars and their evolution are not yet understood. Aims. A small group of very hot, helium-dominated stars is formed by O(He)-type stars. A precise analysis of their photospheric abundances will establish constraints to their evolution. Methods. We performed a detailed spectral analysis of ultraviolet and optical spectra of four O(He) stars by means of state-of-the-art non-LTE model-atmosphere techniques. Results. We determined effective temperatures, surface gravities, and the abundances of H, He, C, N, O, F, Ne, Si, P, S, Ar, and Fe. By deriving upper limits for the mass-loss rates of the O(He) stars, we found that they do not exhibit enhanced mass-loss. The comparison with evolutionary models shows that the status of the O(He) stars remains uncertain. Their abundances match predictions of a double helium white dwarf (WD) merger scenario, suggesting that they might be the progeny of the compact and of the luminous helium-rich sdO-type stars. The existence of planetary nebulae that do not show helium enrichment around every other O(He) star precludes a merger origin for these stars. These stars must have formed in a different way, for instance via enhanced mass-loss during their post-AGB evolution or a merger within a common-envelope (CE) of a CO-WD and a red giant or AGB star. Conclusions. A helium-dominated stellar evolutionary sequence exists that may be fed by different types of mergers or CE scenarios. It appears likely that all these pass through the O(He) phase just before they become WDs.

Divergent evolutionary processes associated with colonization of offshore islands.

PubMed

Martínková, Natália; Barnett, Ross; Cucchi, Thomas; Struchen, Rahel; Pascal, Marine; Pascal, Michel; Fischer, Martin C; Higham, Thomas; Brace, Selina; Ho, Simon Y W; Quéré, Jean-Pierre; O'Higgins, Paul; Excoffier, Laurent; Heckel, Gerald; Hoelzel, A Rus; Dobney, Keith M; Searle, Jeremy B

2013-10-01

Oceanic islands have been a test ground for evolutionary theory, but here, we focus on the possibilities for evolutionary study created by offshore islands. These can be colonized through various means and by a wide range of species, including those with low dispersal capabilities. We use morphology, modern and ancient sequences of cytochrome b (cytb) and microsatellite genotypes to examine colonization history and evolutionary change associated with occupation of the Orkney archipelago by the common vole (Microtus arvalis), a species found in continental Europe but not in Britain. Among possible colonization scenarios, our results are most consistent with human introduction at least 5100 bp (confirmed by radiocarbon dating). We used approximate Bayesian computation of population history to infer the coast of Belgium as the possible source and estimated the evolutionary timescale using a Bayesian coalescent approach. We showed substantial morphological divergence of the island populations, including a size increase presumably driven by selection and reduced microsatellite variation likely reflecting founder events and genetic drift. More surprisingly, our results suggest that a recent and widespread cytb replacement event in the continental source area purged cytb variation there, whereas the ancestral diversity is largely retained in the colonized islands as a genetic 'ark'. The replacement event in the continental M. arvalis was probably triggered by anthropogenic causes (land-use change). Our studies illustrate that small offshore islands can act as field laboratories for studying various evolutionary processes over relatively short timescales, informing about the mainland source area as well as the island. © 2013 John Wiley & Sons Ltd.

ISECG Mission Scenarios and Their Role in Informing Next Steps for Human Exploration Beyond Low Earth Orbit

NASA Technical Reports Server (NTRS)

Culbert, Christopher J.; Mongrard, Olivier; Satoh, Naoki; Goodliff, Kandyce; Seaman, Calvin H.; Troutman, Patrick; Martin, Eric

2011-01-01

The International Space Exploration Coordination Group (ISECG) was established in response to The Global Exploration Strategy (GES): The Framework for Coordination developed by fourteen space agencies* and released in May 2007. This GES Framework Document recognizes that preparing for human space exploration is a stepwise process, starting with basic knowledge and culminating in a sustained human presence in deep space. ISECG has developed several optional global exploration mission scenarios enabling the phased transition from human operations in Low Earth Orbit (LEO) and utilization of the International Space Station (ISS) to human missions beyond LEO leading ultimately to human missions to cis-lunar space, the Moon, Near Earth Asteroids, Mars and its environs. Mission scenarios provide the opportunity for judging various exploration approaches in a manner consistent with agreed international goals and strategies. Each ISECG notional mission scenario reflects a series of coordinated human and robotic exploration missions over a 25-year horizon. Mission scenarios are intended to provide insights into next steps for agency investments, following on the success of the ISS. They also provide a framework for advancing the definition of Design Reference Missions (DRMs) and the concepts for capabilities contained within. Each of the human missions contained in the scenarios has been characterized by a DRM which is a top level definition of mission sequence and the capabilities needed to execute that mission. While DRMs are generally destination focused, they will comprise capabilities which are reused or evolved from capabilities used at other destinations. In this way, an evolutionary approach to developing a robust set of capabilities to sustainably explore our solar system is defined. Agencies also recognize that jointly planning for our next steps, building on the accomplishments of ISS, is important to ensuring the robustness and sustainability of any human exploration plan. Developing a shared long-term vision is important, but agencies recognize this is an evolutionary process and requires consideration of many strategic factors. Strategic factors such as the implications of an emerging commercial space industry in LEO, the opportunity provided by extending ISS lifetime to at least 2020, and the importance of defining a plan which is sustainable in light of inevitable domestic policy shifts are timely for agency consideration.

A mistletoe tale: postglacial invasion of Psittacanthus schiedeanus (Loranthaceae) to Mesoamerican cloud forests revealed by molecular data and species distribution modeling.

PubMed

Ornelas, Juan Francisco; Gándara, Etelvina; Vásquez-Aguilar, Antonio Acini; Ramírez-Barahona, Santiago; Ortiz-Rodriguez, Andrés Ernesto; González, Clementina; Mejía Saules, María Teresa; Ruiz-Sanchez, Eduardo

2016-04-12

Ecological adaptation to host taxa is thought to result in mistletoe speciation via race formation. However, historical and ecological factors could also contribute to explain genetic structuring particularly when mistletoe host races are distributed allopatrically. Using sequence data from nuclear (ITS) and chloroplast (trnL-F) DNA, we investigate the genetic differentiation of 31 Psittacanthus schiedeanus (Loranthaceae) populations across the Mesoamerican species range. We conducted phylogenetic, population and spatial genetic analyses on 274 individuals of P. schiedeanus to gain insight of the evolutionary history of these populations. Species distribution modeling, isolation with migration and Bayesian inference methods were used to infer the evolutionary transition of mistletoe invasion, in which evolutionary scenarios were compared through posterior probabilities. Our analyses revealed shallow levels of population structure with three genetic groups present across the sample area. Nine haplotypes were identified after sequencing the trnL-F intergenic spacer. These haplotypes showed phylogeographic structure, with three groups with restricted gene flow corresponding to the distribution of individuals/populations separated by habitat (cloud forest localities from San Luis Potosí to northwestern Oaxaca and Chiapas, localities with xeric vegetation in central Oaxaca, and localities with tropical deciduous forests in Chiapas), with post-glacial population expansions and potentially corresponding to post-glacial invasion types. Similarly, 44 ITS ribotypes suggest phylogeographic structure, despite the fact that most frequent ribotypes are widespread indicating effective nuclear gene flow via pollen. Gene flow estimates, a significant genetic signal of demographic expansion, and range shifts under past climatic conditions predicted by species distribution modeling suggest post-glacial invasion of P. schiedeanus mistletoes to cloud forests. However, Approximate Bayesian Computation (ABC) analyses strongly supported a scenario of simultaneous divergence among the three groups isolated recently. Our results provide support for the predominant role of isolation and environmental factors in driving genetic differentiation of Mesoamerican parrot-flower mistletoes. The ABC results are consistent with a scenario of post-glacial mistletoe invasion, independent of host identity, and that habitat types recently isolated P. schiedeanus populations, accumulating slight phenotypic differences among genetic groups due to recent migration across habitats. Under this scenario, climatic fluctuations throughout the Pleistocene would have altered the distribution of suitable habitat for mistletoes throughout Mesoamerica leading to variation in population continuity and isolation. Our findings add to an understanding of the role of recent isolation and colonization in shaping cloud forest communities in the region.

Evolution of pollen morphology in Loranthaceae

PubMed Central

Grímsson, Friðgeir; Grimm, Guido W.; Zetter, Reinhard

2018-01-01

Abstract Earlier studies indicate a strong correlation of pollen morphology and ultrastructure with taxonomy in Loranthaceae. Using high-resolution light microscopy and scanning electron microscopy imaging of the same pollen grains, we document pollen types of 35 genera including 15 studied for the first time. Using a molecular phylogenetic framework based on currently available sequence data with good genus-coverage, we reconstruct trends in the evolution of Loranthaceae pollen and pinpoint traits of high diagnostic value, partly confirming earlier intuitive hypotheses based on morphological observations. We find that pollen morphology in Loranthaceae is strongly linked to phylogenetic relationships. Some pollen types are diagnostic for discrete genera or evolutionary lineages, opening the avenue to recruit dispersed fossil pollen as age constraints for dated phylogenies and as independent data for testing biogeographic scenarios; so far based exclusively on modern-day data. Correspondences and discrepancies between palynological and molecular data and current taxonomic/systematic concepts are identified and suggestions made for future palynological and molecular investigations of Loranthaceae. PMID:29386990

Testing co-evolutionary hypotheses over geological timescales: interactions between Mesozoic non-avian dinosaurs and cycads.

PubMed

Butler, Richard J; Barrett, Paul M; Kenrick, Paul; Penn, Malcolm G

2009-02-01

The significance of co-evolution over ecological timescales is well established, yet it remains unclear to what extent co-evolutionary processes contribute to driving large-scale evolutionary and ecological changes over geological timescales. Some of the most intriguing and pervasive long-term co-evolutionary hypotheses relate to proposed interactions between herbivorous non-avian dinosaurs and Mesozoic plants, including cycads. Dinosaurs have been proposed as key dispersers of cycad seeds during the Mesozoic, and temporal variation in cycad diversity and abundance has been linked to dinosaur faunal changes. Here we assess the evidence for proposed hypotheses of trophic and evolutionary interactions between these two groups using diversity analyses, a new database of Cretaceous dinosaur and plant co-occurrence data, and a geographical information system (GIS) as a visualisation tool. Phylogenetic evidence suggests that the origins of several key biological properties of cycads (e.g. toxins, bright-coloured seeds) likely predated the origin of dinosaurs. Direct evidence of dinosaur-cycad interactions is lacking, but evidence from extant ecosystems suggests that dinosaurs may plausibly have acted as seed dispersers for cycads, although it is likely that other vertebrate groups (e.g. birds, early mammals) also played a role. Although the Late Triassic radiations of dinosaurs and cycads appear to have been approximately contemporaneous, few significant changes in dinosaur faunas coincide with the late Early Cretaceous cycad decline. No significant spatiotemporal associations between particular dinosaur groups and cycads can be identified - GIS visualisation reveals disparities between the spatiotemporal distributions of some dinosaur groups (e.g. sauropodomorphs) and cycads that are inconsistent with co-evolutionary hypotheses. The available data provide no unequivocal support for any of the proposed co-evolutionary interactions between cycads and herbivorous dinosaurs - diffuse co-evolutionary scenarios that are proposed to operate over geological timescales are plausible, but such hypotheses need to be firmly grounded on direct evidence of interaction and may be difficult to support given the patchiness of the fossil record.

A systemic approach for modeling biological evolution using Parallel DEVS.

PubMed

Heredia, Daniel; Sanz, Victorino; Urquia, Alfonso; Sandín, Máximo

2015-08-01

A new model for studying the evolution of living organisms is proposed in this manuscript. The proposed model is based on a non-neodarwinian systemic approach. The model is focused on considering several controversies and open discussions about modern evolutionary biology. Additionally, a simplification of the proposed model, named EvoDEVS, has been mathematically described using the Parallel DEVS formalism and implemented as a computer program using the DEVSLib Modelica library. EvoDEVS serves as an experimental platform to study different conditions and scenarios by means of computer simulations. Two preliminary case studies are presented to illustrate the behavior of the model and validate its results. EvoDEVS is freely available at http://www.euclides.dia.uned.es. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

A "spare" compensates for the risk of destruction of the elongated penis of earwigs (Insecta: Dermaptera)

NASA Astrophysics Data System (ADS)

Kamimura, Yoshitaka; Matsuo, Yoh

2001-11-01

Male animals in several groups have multiple intromittent organs that outnumber the corresponding female gonopore. In Dermaptera (earwigs), males of the family Anisolabididae have paired, elongated male intromittent organs (virgae), while females have a single sperm-storage organ (spermatheca). Several authors have assumed that one of the paired virgae is non-functional, because it points in the "wrong" direction. We investigated the mating success of handicapped males of Euborellia plebeja in which one of their paired virgae was removed experimentally. These handicapped males succeeded in inseminating a mate. Males with genital damage are found in the field, suggesting that the "spare" functions under natural conditions. Based on phylogenetic information on earwigs, we discuss possible evolutionary scenarios for this genital peculiarity.

Are Some Pre-Cataclysmic Variables also Post-Cataclysmic Variables?

NASA Astrophysics Data System (ADS)

Sarna, M. J.; Marks, P. B.; Smith, R. C.

1995-10-01

We propose an evolutionary scenario in which post-common-envelope binaries (PCEBs) with secondary component masses between 0.8 Msun and 1.2 M0 start semi-detached evolution almost immediately after the common-envelope (CE) phase. These systems detach due to unstable mass transfer when the secondary develops a thick convective envelope. The duration of the detached phase is a few times 108 yr, depending on the efficiency of magnetic braking and gravitational radiation. We suggest that some of the systems that have been classified as PCEBs may be in this stage of evolution and hence would be more realistically classified as pre-cataclysmic variables (PreCVs). We also propose an observational test based on measurements of the carbon and oxygen isotopic ratios from the infrared CO bands.

Evolutionary History of the Plant Pathogenic Bacterium Xanthomonas axonopodis

PubMed Central

Mhedbi-Hajri, Nadia; Hajri, Ahmed; Boureau, Tristan; Darrasse, Armelle; Durand, Karine; Brin, Chrystelle; Saux, Marion Fischer-Le; Manceau, Charles; Poussier, Stéphane; Pruvost, Olivier

2013-01-01

Deciphering mechanisms shaping bacterial diversity should help to build tools to predict the emergence of infectious diseases. Xanthomonads are plant pathogenic bacteria found worldwide. Xanthomonas axonopodis is a genetically heterogeneous species clustering, into six groups, strains that are collectively pathogenic on a large number of plants. However, each strain displays a narrow host range. We address the question of the nature of the evolutionary processes – geographical and ecological speciation – that shaped this diversity. We assembled a large collection of X. axonopodis strains that were isolated over a long period, over continents, and from various hosts. Based on the sequence analysis of seven housekeeping genes, we found that recombination occurred as frequently as point mutation in the evolutionary history of X. axonopodis. However, the impact of recombination was about three times greater than the impact of mutation on the diversity observed in the whole dataset. We then reconstructed the clonal genealogy of the strains using coalescent and genealogy approaches and we studied the diversification of the pathogen using a model of divergence with migration. The suggested scenario involves a first step of generalist diversification that spanned over the last 25 000 years. A second step of ecology-driven specialization occurred during the past two centuries. Eventually, secondary contacts between host-specialized strains probably occurred as a result of agricultural development and intensification, allowing genetic exchanges of virulence-associated genes. These transfers may have favored the emergence of novel pathotypes. Finally, we argue that the largest ecological entity within X. axonopodis is the pathovar. PMID:23505513

Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?

PubMed Central

Koonin, Eugene V.

2015-01-01

The origin of eukaryotes is a fundamental, forbidding evolutionary puzzle. Comparative genomic analysis clearly shows that the last eukaryotic common ancestor (LECA) possessed most of the signature complex features of modern eukaryotic cells, in particular the mitochondria, the endomembrane system including the nucleus, an advanced cytoskeleton and the ubiquitin network. Numerous duplications of ancestral genes, e.g. DNA polymerases, RNA polymerases and proteasome subunits, also can be traced back to the LECA. Thus, the LECA was not a primitive organism and its emergence must have resulted from extensive evolution towards cellular complexity. However, the scenario of eukaryogenesis, and in particular the relationship between endosymbiosis and the origin of eukaryotes, is far from being clear. Four recent developments provide new clues to the likely routes of eukaryogenesis. First, evolutionary reconstructions suggest complex ancestors for most of the major groups of archaea, with the subsequent evolution dominated by gene loss. Second, homologues of signature eukaryotic proteins, such as actin and tubulin that form the core of the cytoskeleton or the ubiquitin system, have been detected in diverse archaea. The discovery of this ‘dispersed eukaryome’ implies that the archaeal ancestor of eukaryotes was a complex cell that might have been capable of a primitive form of phagocytosis and thus conducive to endosymbiont capture. Third, phylogenomic analyses converge on the origin of most eukaryotic genes of archaeal descent from within the archaeal evolutionary tree, specifically, the TACK superphylum. Fourth, evidence has been presented that the origin of the major archaeal phyla involved massive acquisition of bacterial genes. Taken together, these findings make the symbiogenetic scenario for the origin of eukaryotes considerably more plausible and the origin of the organizational complexity of eukaryotic cells more readily explainable than they appeared until recently. PMID:26323764

Roots of angiosperm formins: The evolutionary history of plant FH2 domain-containing proteins

PubMed Central

2008-01-01

Background Shuffling of modular protein domains is an important source of evolutionary innovation. Formins are a family of actin-organizing proteins that share a conserved FH2 domain but their overall domain architecture differs dramatically between opisthokonts (metazoans and fungi) and plants. We performed a phylogenomic analysis of formins in most eukaryotic kingdoms, aiming to reconstruct an evolutionary scenario that may have produced the current diversity of domain combinations with focus on the origin of the angiosperm formin architectures. Results The Rho GTPase-binding domain (GBD/FH3) reported from opisthokont and Dictyostelium formins was found in all lineages except plants, suggesting its ancestral character. Instead, mosses and vascular plants possess the two formin classes known from angiosperms: membrane-anchored Class I formins and Class II formins carrying a PTEN-like domain. PTEN-related domains were found also in stramenopile formins, where they have been probably acquired independently rather than by horizontal transfer, following a burst of domain rearrangements in the chromalveolate lineage. A novel RhoGAP-related domain was identified in some algal, moss and lycophyte (but not angiosperm) formins that define a specific branch (Class III) of the formin family. Conclusion We propose a scenario where formins underwent multiple domain rearrangements in several eukaryotic lineages, especially plants and chromalveolates. In plants this replaced GBD/FH3 by a probably inactive RhoGAP-like domain, preserving a formin-mediated association between (membrane-anchored) Rho GTPases and the actin cytoskeleton. Subsequent amplification of formin genes, possibly coincident with the expansion of plants to dry land, was followed by acquisition of alternative membrane attachment mechanisms present in extant Class I and Class II formins, allowing later loss of the RhoGAP-like domain-containing formins in angiosperms. PMID:18430232

On the Reconstruction of Text Phylogeny Trees: Evaluation and Analysis of Textual Relationships

PubMed Central

Marmerola, Guilherme D.; Dias, Zanoni; Goldenstein, Siome; Rocha, Anderson

2016-01-01

Over the history of mankind, textual records change. Sometimes due to mistakes during transcription, sometimes on purpose, as a way to rewrite facts and reinterpret history. There are several classical cases, such as the logarithmic tables, and the transmission of antique and medieval scholarship. Today, text documents are largely edited and redistributed on the Web. Articles on news portals and collaborative platforms (such as Wikipedia), source code, posts on social networks, and even scientific publications or literary works are some examples in which textual content can be subject to changes in an evolutionary process. In this scenario, given a set of near-duplicate documents, it is worthwhile to find which one is the original and the history of changes that created the whole set. Such functionality would have immediate applications on news tracking services, detection of plagiarism, textual criticism, and copyright enforcement, for instance. However, this is not an easy task, as textual features pointing to the documents’ evolutionary direction may not be evident and are often dataset dependent. Moreover, side information, such as time stamps, are neither always available nor reliable. In this paper, we propose a framework for reliably reconstructing text phylogeny trees, and seamlessly exploring new approaches on a wide range of scenarios of text reusage. We employ and evaluate distinct combinations of dissimilarity measures and reconstruction strategies within the proposed framework, and evaluate each approach with extensive experiments, including a set of artificial near-duplicate documents with known phylogeny, and from documents collected from Wikipedia, whose modifications were made by Internet users. We also present results from qualitative experiments in two different applications: text plagiarism and reconstruction of evolutionary trees for manuscripts (stemmatology). PMID:27992446

A new scenario of the evolutionary derivation of the mammalian diaphragm from shoulder muscles

PubMed Central

Hirasawa, Tatsuya; Kuratani, Shigeru

2013-01-01

The evolutionary origin of the diaphragm remains unclear, due to the lack of a comparable structure in other extant taxa. However, recent researches into the developmental mechanism of this structure have yielded new insights into its origin. Here we summarize current understanding regarding the development of the diaphragm, and present a possible scenario for the evolutionary acquisition of this uniquely mammalian structure. Recent developmental analyses indicate that the diaphragm and forelimb muscles are derived from a shared cell population during embryonic development. Therefore, the embryonic positions of forelimb muscle progenitors, which correspond to the position of the brachial plexus, likely played an important role in the evolution of the diaphragm. We surveyed the literature to reexamine the position of the brachial plexus among living amniotes and confirmed that the cervico-thoracic transition in ribs reflects the brachial plexus position. Using this osteological correlate, we concluded that the anterior borders of the brachial plexuses in the stem synapsids were positioned at the level of the fourth spinal nerve, suggesting that the forelimb buds were laid in close proximity of the infrahyoid muscles. The topology of the phrenic and suprascapular nerves of mammals is similar to that of subscapular and supracoracoid nerves, respectively, of the other amniotes, suggesting that the diaphragm evolved from a muscle positioned medial to the pectoral girdle (cf. subscapular muscle). We hypothesize that the diaphragm was acquired in two steps: first, forelimb muscle cells were incorporated into tissues to form a primitive diaphragm in the stem synapsid grade, and second, the diaphragm in cynodonts became entrapped in the region controlled by pulmonary development. PMID:23448284

Environmental Influences on Mate Preferences as Assessed by a Scenario Manipulation Experiment

PubMed Central

Marzoli, Daniele; Moretto, Francesco; Monti, Aura; Tocci, Ornella; Roberts, S. Craig; Tommasi, Luca

2013-01-01

Many evolutionary psychology studies have addressed the topic of mate preferences, focusing particularly on gender and cultural differences. However, the extent to which situational and environmental variables might affect mate preferences has been comparatively neglected. We tested 288 participants in order to investigate the perceived relative importance of six traits of an ideal partner (wealth, dominance, intelligence, height, kindness, attractiveness) under four different hypothetical scenarios (status quo/nowadays, violence/post-nuclear, poverty/resource exhaustion, prosperity/global well-being). An equal number of participants (36 women, 36 men) was allotted to each scenario; each was asked to allocate 120 points across the six traits according to their perceived value. Overall, intelligence was the trait to which participants assigned most importance, followed by kindness and attractiveness, and then by wealth, dominance and height. Men appraised attractiveness as more valuable than women. Scenario strongly influenced the relative importance attributed to traits, the main finding being that wealth and dominance were more valued in the poverty and post-nuclear scenarios, respectively, compared to the other scenarios. Scenario manipulation generally had similar effects in both sexes, but women appeared particularly prone to trade off other traits for dominance in the violence scenario, and men particularly prone to trade off other traits for wealth in the poverty scenario. Our results are in line with other correlational studies of situational variables and mate preferences, and represent strong evidence of a causal relationship of environmental factors on specific mate preferences, corroborating the notion of an evolved plasticity to current ecological conditions. A control experiment seems to suggest that our scenarios can be considered as realistic descriptions of the intended ecological conditions. PMID:24069291

Progenitors of the protochordate ocellus as an evolutionary origin of the neural crest

PubMed Central

2013-01-01

The neural crest represents a highly multipotent population of embryonic stem cells found only in vertebrate embryos. Acquisition of the neural crest during the evolution of vertebrates was a great advantage, providing Chordata animals with the first cellular cartilage, bone, dentition, advanced nervous system and other innovations. Today not much is known about the evolutionary origin of neural crest cells. Here we propose a novel scenario in which the neural crest originates from neuroectodermal progenitors of the pigmented ocelli in Amphioxus-like animals. We suggest that because of changes in photoreception needs, these multipotent progenitors of photoreceptors gained the ability to migrate outside of the central nervous system and subsequently started to give rise to neural, glial and pigmented progeny at the periphery. PMID:23575111

The ultra-social animal

PubMed Central

Tomasello, Michael

2014-01-01

In evolutionary perspective, what is most remarkable about human sociality is its many and diverse forms of cooperation. Here, I provide an overview of some recent research, mostly from our laboratory, comparing human children with their nearest living relatives, the great apes, in various tests of collaboration, prosocial behavior, conformity, and group-mindedness (e.g., following and enforcing social norms). This is done in the context of a hypothetical evolutionary scenario comprising two ordered steps: a first step in which early humans began collaborating with others in unique ways in their everyday foraging and a second step in which modern humans began forming cultural groups. Humans' unique forms of sociality help to explain their unique forms of cognition and morality. © 2014. The Authors. European Journal of Social Psychology published by John Wiley & Sons, Ltd. PMID:25641998

Analytical model for orbital debris environmental management

NASA Technical Reports Server (NTRS)

Talent, David L.

1990-01-01

A differential equation, also referred to as the PIB (particle-in-a-box) model, expressing the time rate of change of the number of objects in orbit, is developed, and its applicability is illustrated. The model can be used as a tool for the assessment of LEO environment stability, and as a starting point for the development of numerical evolutionary models. Within the context of the model, evolutionary scenarios are examined, and found to be sensitive to the growth rate. It is determined that the present environment is slightly unstable to catastrophic growth, and that the number of particles on orbit will continue to increase until approximately 2250-2350 AD, with a maximum of 2,000,000. The model is expandable to the more realistic (complex) case of multiple species in a multiple-tier system.

The Use of Bioinformatics for Studying HIV Evolutionary and Epidemiological History in South America

PubMed Central

Bello, Gonzalo; Soares, Marcelo A.; Schrago, Carlos G.

2011-01-01

The South American human immunodeficiency virus type 1 (HIV-1) epidemic is driven by several subtypes (B, C, and F1) and circulating and unique recombinant forms derived from those subtypes. Those variants are heterogeneously distributed around the continent in a country-specific manner. Despite some inconsistencies mainly derived from sampling biases and analytical constrains, most of studies carried out in the area agreed in pointing out specificities in the evolutionary dynamics of the circulating HIV-1 lineages. In this paper, we covered the theoretical basis, and the application of bioinformatics methods to reconstruct the HIV spatial-temporal dynamics, unveiling relevant information to understand the origin, geographical dissemination and the current molecular scenario of the HIV epidemic in the continent, particularly in the countries of Southern Cone. PMID:22162803

The ultra-social animal.

PubMed

Tomasello, Michael

2014-04-01

In evolutionary perspective, what is most remarkable about human sociality is its many and diverse forms of cooperation. Here, I provide an overview of some recent research, mostly from our laboratory, comparing human children with their nearest living relatives, the great apes, in various tests of collaboration, prosocial behavior, conformity, and group-mindedness (e.g., following and enforcing social norms). This is done in the context of a hypothetical evolutionary scenario comprising two ordered steps: a first step in which early humans began collaborating with others in unique ways in their everyday foraging and a second step in which modern humans began forming cultural groups. Humans' unique forms of sociality help to explain their unique forms of cognition and morality. © 2014. The Authors. European Journal of Social Psychology published by John Wiley & Sons, Ltd.

Dynamics of prebiotic RNA reproduction illuminated by chemical game theory

PubMed Central

Yeates, Jessica A. M.; Hilbe, Christian; Zwick, Martin; Nowak, Martin A.; Lehman, Niles

2016-01-01

Many origins-of-life scenarios depict a situation in which there are common and potentially scarce resources needed by molecules that compete for survival and reproduction. The dynamics of RNA assembly in a complex mixture of sequences is a frequency-dependent process and mimics such scenarios. By synthesizing Azoarcus ribozyme genotypes that differ in their single-nucleotide interactions with other genotypes, we can create molecules that interact among each other to reproduce. Pairwise interplays between RNAs involve both cooperation and selfishness, quantifiable in a 2 × 2 payoff matrix. We show that a simple model of differential equations based on chemical kinetics accurately predicts the outcomes of these molecular competitions using simple rate inputs into these matrices. In some cases, we find that mixtures of different RNAs reproduce much better than each RNA type alone, reflecting a molecular form of reciprocal cooperation. We also demonstrate that three RNA genotypes can stably coexist in a rock–paper–scissors analog. Our experiments suggest a new type of evolutionary game dynamics, called prelife game dynamics or chemical game dynamics. These operate without template-directed replication, illustrating how small networks of RNAs could have developed and evolved in an RNA world. PMID:27091972

Dynamics of prebiotic RNA reproduction illuminated by chemical game theory.

PubMed

Yeates, Jessica A M; Hilbe, Christian; Zwick, Martin; Nowak, Martin A; Lehman, Niles

2016-05-03

Many origins-of-life scenarios depict a situation in which there are common and potentially scarce resources needed by molecules that compete for survival and reproduction. The dynamics of RNA assembly in a complex mixture of sequences is a frequency-dependent process and mimics such scenarios. By synthesizing Azoarcus ribozyme genotypes that differ in their single-nucleotide interactions with other genotypes, we can create molecules that interact among each other to reproduce. Pairwise interplays between RNAs involve both cooperation and selfishness, quantifiable in a 2 × 2 payoff matrix. We show that a simple model of differential equations based on chemical kinetics accurately predicts the outcomes of these molecular competitions using simple rate inputs into these matrices. In some cases, we find that mixtures of different RNAs reproduce much better than each RNA type alone, reflecting a molecular form of reciprocal cooperation. We also demonstrate that three RNA genotypes can stably coexist in a rock-paper-scissors analog. Our experiments suggest a new type of evolutionary game dynamics, called prelife game dynamics or chemical game dynamics. These operate without template-directed replication, illustrating how small networks of RNAs could have developed and evolved in an RNA world.

Promoter Motifs in NCLDVs: An Evolutionary Perspective

PubMed Central

Oliveira, Graziele Pereira; Andrade, Ana Cláudia dos Santos Pereira; Rodrigues, Rodrigo Araújo Lima; Arantes, Thalita Souza; Boratto, Paulo Victor Miranda; Silva, Ludmila Karen dos Santos; Dornas, Fábio Pio; Trindade, Giliane de Souza; Drumond, Betânia Paiva; La Scola, Bernard; Kroon, Erna Geessien; Abrahão, Jônatas Santos

2017-01-01

For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV), raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’) that could be evolved gradually by nucleotides’ gain and loss and point mutations. PMID:28117683

Archaeogenomic insights into the adaptation of plants to the human environment: pushing plant-hominin co-evolution back to the Pliocene.

PubMed

Allaby, Robin G; Kistler, Logan; Gutaker, Rafal M; Ware, Roselyn; Kitchen, James L; Smith, Oliver; Clarke, Andrew C

2015-02-01

The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plant-human process that occurred over a long time period, with evidence for the co-evolutionary relationship between plants and humans reaching ever deeper into the hominin past. This developing view is characterized by a change in emphasis on the drivers of evolution in the case of plants. Rather than individual species being passive recipients of artificial selection pressures and ultimately becoming domesticates, entire plant communities adapted to the human environment. This evolutionary scenario leads to systems level genetic expectations from models that can be explored through ancient DNA and Next Generation Sequencing approaches. Emerging evidence suggests that domesticated genomes fit well with these expectations, with periods of stable complex evolution characterized by large amounts of change associated with relatively small selective value, punctuated by periods in which changes in one-half of the plant-hominin relationship cause rapid, low-complexity adaptation in the other. A corollary of a single plant-hominin co-evolutionary process is that clues about the initiation of the domestication process may well lie deep within the hominin lineage. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

The scolopidial accessory organs and Nebenorgans in orthopteroid insects: Comparative neuroanatomy, mechanosensory function, and evolutionary origin.

PubMed

Strauß, Johannes

2017-11-01

Scolopidial sensilla in insects often form large sensory organs involved in proprioception or exteroception. Here the knowledge on Nebenorgans and accessory organs, two organs consisting of scolopidial sensory cells, is summarised. These organs are present in some insects which are model organisms for the physiology of mechanosensory systems (cockroaches and tettigoniids). Recent comparative studies documented the accessory organ in several taxa of Orthoptera (including tettigoniids, cave crickets, Jerusalem crickets) and the Nebenorgan in related insects (Mantophasmatodea). The accessory organ or Nebenorgan is usually a small organ of 8-15 sensilla located in the posterior leg tibia of all leg pairs. The physiological properties of the accessory organs and Nebenorgans are so far largely unknown. Taking together neuroanatomical and electrophysiological data from disparate taxa, there is considerable evidence that the accessory organ and Nebenorgan are vibrosensitive. They thus complement the larger vibrosensitive subgenual organ in the tibia. This review summarises the comparative studies of these sensory organs, in particular the arguments and criteria for the homology of the accessory organ and Nebenorgan among orthopteroid insects. Different scenarios of repeated evolutionary origins or losses of these sensory organs are discussed. Neuroanatomy allows to distinguish individual sensory organs for analysis of sensory physiology, and to infer scenarios of sensory evolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

The use of surrogates for an optimal management of coupled groundwater-agriculture hydrosystems

NASA Astrophysics Data System (ADS)

Grundmann, J.; Schütze, N.; Brettschneider, M.; Schmitz, G. H.; Lennartz, F.

2012-04-01

For ensuring an optimal sustainable water resources management in arid coastal environments, we develop a new simulation based integrated water management system. It aims at achieving best possible solutions for groundwater withdrawals for agricultural and municipal water use including saline water management together with a substantial increase of the water use efficiency in irrigated agriculture. To achieve a robust and fast operation of the management system regarding water quality and water quantity we develop appropriate surrogate models by combining physically based process modelling with methods of artificial intelligence. Thereby we use an artificial neural network for modelling the aquifer response, inclusive the seawater interface, which was trained on a scenario database generated by a numerical density depended groundwater flow model. For simulating the behaviour of high productive agricultural farms crop water production functions are generated by means of soil-vegetation-atmosphere-transport (SVAT)-models, adapted to the regional climate conditions, and a novel evolutionary optimisation algorithm for optimal irrigation scheduling and control. We apply both surrogates exemplarily within a simulation based optimisation environment using the characteristics of the south Batinah region in the Sultanate of Oman which is affected by saltwater intrusion into the coastal aquifer due to excessive groundwater withdrawal for irrigated agriculture. We demonstrate the effectiveness of our methodology for the evaluation and optimisation of different irrigation practices, cropping pattern and resulting abstraction scenarios. Due to contradicting objectives like profit-oriented agriculture vs. aquifer sustainability a multi-criterial optimisation is performed.

The evolution of body size in extant groups of North American freshwater fishes: speciation, size distributions, and Cope's rule.

PubMed

Knouft, Jason H; Page, Lawrence M

2003-03-01

Change in body size within an evolutionary lineage over time has been under investigation since the synthesis of Cope's rule, which suggested that there is a tendency for mammals to evolve larger body size. Data from the fossil record have subsequently been examined for several other taxonomic groups to determine whether they also displayed an evolutionary increase in body size. However, we are not aware of any species-level study that has investigated the evolution of body size within an extant continental group. Data acquired from the fossil record and data derived from the evolutionary relationships of extant species are not similar, with each set exhibiting both strengths and weaknesses related to inferring evolutionary patterns. Consequently, expectation that general trends exhibited in the fossil record will correspond to patterns in extant groups is not necessarily warranted. Using phylogenetic relationships of extant species, we show that five of nine families of North American freshwater fishes exhibit an evolutionary trend of decreasing body size. These trends result from the basal position of large species and the more derived position of small species within families. Such trends may be caused by the invasion of small streams and subsequent isolation and speciation. This pattern, potentially influenced by size-biased dispersal rates and the high percentage of small streams in North America, suggests a scenario that could result in the generation of the size-frequency distribution of North American freshwater fishes.

CnidBase: The Cnidarian Evolutionary Genomics Database

PubMed Central

Ryan, Joseph F.; Finnerty, John R.

2003-01-01

CnidBase, the Cnidarian Evolutionary Genomics Database, is a tool for investigating the evolutionary, developmental and ecological factors that affect gene expression and gene function in cnidarians. In turn, CnidBase will help to illuminate the role of specific genes in shaping cnidarian biodiversity in the present day and in the distant past. CnidBase highlights evolutionary changes between species within the phylum Cnidaria and structures genomic and expression data to facilitate comparisons to non-cnidarian metazoans. CnidBase aims to further the progress that has already been made in the realm of cnidarian evolutionary genomics by creating a central community resource which will help drive future research and facilitate more accurate classification and comparison of new experimental data with existing data. CnidBase is available at http://cnidbase.bu.edu/. PMID:12519972

Bats, Primates, and the Evolutionary Origins and Diversification of Mammalian Gammaherpesviruses

PubMed Central

Rojas-Anaya, Edith; Kolokotronis, Sergios-Orestis; Taboada, Blanca; Loza-Rubio, Elizabeth; Méndez-Ojeda, Maria L.; Osterrieder, Nikolaus

2016-01-01

ABSTRACT Gammaherpesviruses (γHVs) are generally considered host specific and to have codiverged with their hosts over millions of years. This tenet is challenged here by broad-scale phylogenetic analysis of two viral genes using the largest sample of mammalian γHVs to date, integrating for the first time bat γHV sequences available from public repositories and newly generated viral sequences from two vampire bat species (Desmodus rotundus and Diphylla ecaudata). Bat and primate viruses frequently represented deep branches within the supported phylogenies and clustered among viruses from distantly related mammalian taxa. Following evolutionary scenario testing, we determined the number of host-switching and cospeciation events. Cross-species transmissions have occurred much more frequently than previously estimated, and most of the transmissions were attributable to bats and primates. We conclude that the evolution of the Gammaherpesvirinae subfamily has been driven by both cross-species transmissions and subsequent cospeciation within specific viral lineages and that the bat and primate orders may have potentially acted as superspreaders to other mammalian taxa throughout evolutionary history. PMID:27834200

The adaptation of polar fishes to climatic changes: Structure, function and phylogeny of haemoglobin.

PubMed

Verde, Cinzia; Giordano, Daniela; di Prisco, Guido

2008-01-01

In the Antarctic, fishes of dominant suborder Notothenioidei have evolved in a unique thermal scenario. Phylogenetically related taxa of the suborder live in a wide range of latitudes, in Antarctic, sub-Antarctic and temperate oceans. Consequently, they offer a remarkable opportunity to study the physiological and biochemical characters gained and, conversely, lost during their evolutionary history. The evolutionary perspective has also been pursued by comparative studies of some features of the heme protein devoted to O(2) transport in fish living in the other polar region, the Arctic. The two polar regions differ by age and isolation. Fish living in each habitat have undergone regional constraints and fit into different evolutionary histories. The aim of this contribution is to survey the current knowledge of molecular structure, functional features, phylogeny and adaptations of the haemoglobins of fish thriving in the Antarctic, sub-Antarctic and Arctic regions (with some excursions in the temperate latitudes), in search of insights into the convergent processes evolved in response to cooling. Current climate change may disturb adaptation, calling for strategies aimed at neutralising threats to biodiversity.

Bell-Curve Based Evolutionary Strategies for Structural Optimization

NASA Technical Reports Server (NTRS)

Kincaid, Rex K.

2001-01-01

Evolutionary methods are exceedingly popular with practitioners of many fields; more so than perhaps any optimization tool in existence. Historically Genetic Algorithms (GAs) led the way in practitioner popularity. However, in the last ten years Evolutionary Strategies (ESs) and Evolutionary Programs (EPS) have gained a significant foothold. One partial explanation for this shift is the interest in using GAs to solve continuous optimization problems. The typical GA relies upon a cumbersome binary representation of the design variables. An ES or EP, however, works directly with the real-valued design variables. For detailed references on evolutionary methods in general and ES or EP in specific see Back and Dasgupta and Michalesicz. We call our evolutionary algorithm BCB (bell curve based) since it is based upon two normal distributions.

The Rise and Fall of an Evolutionary Innovation: Contrasting Strategies of Venom Evolution in Ancient and Young Animals

PubMed Central

Sunagar, Kartik; Moran, Yehu

2015-01-01

Animal venoms are theorized to evolve under the significant influence of positive Darwinian selection in a chemical arms race scenario, where the evolution of venom resistance in prey and the invention of potent venom in the secreting animal exert reciprocal selection pressures. Venom research to date has mainly focused on evolutionarily younger lineages, such as snakes and cone snails, while mostly neglecting ancient clades (e.g., cnidarians, coleoids, spiders and centipedes). By examining genome, venom-gland transcriptome and sequences from the public repositories, we report the molecular evolutionary regimes of several centipede and spider toxin families, which surprisingly accumulated low-levels of sequence variations, despite their long evolutionary histories. Molecular evolutionary assessment of over 3500 nucleotide sequences from 85 toxin families spanning the breadth of the animal kingdom has unraveled a contrasting evolutionary strategy employed by ancient and evolutionarily young clades. We show that the venoms of ancient lineages remarkably evolve under the heavy constraints of negative selection, while toxin families in lineages that originated relatively recently rapidly diversify under the influence of positive selection. We propose that animal venoms mostly employ a ‘two-speed’ mode of evolution, where the major influence of diversifying selection accompanies the earlier stages of ecological specialization (e.g., diet and range expansion) in the evolutionary history of the species–the period of expansion, resulting in the rapid diversification of the venom arsenal, followed by longer periods of purifying selection that preserve the potent toxin pharmacopeia–the period of purification and fixation. However, species in the period of purification may re-enter the period of expansion upon experiencing a major shift in ecology or environment. Thus, we highlight for the first time the significant roles of purifying and episodic selections in shaping animal venoms. PMID:26492532

Ecotypic differentiation under farmers' selection: Molecular insights into the domestication of Pachyrhizus Rich. ex DC. (Fabaceae) in the Peruvian Andes.

PubMed

Delêtre, Marc; Soengas, Beatriz; Vidaurre, Prem Jai; Meneses, Rosa Isela; Delgado Vásquez, Octavio; Oré Balbín, Isabel; Santayana, Monica; Heider, Bettina; Sørensen, Marten

2017-06-01

Understanding the distribution of crop genetic diversity in relation to environmental factors can give insights into the eco-evolutionary processes involved in plant domestication. Yam beans ( Pachyrhizus Rich. ex DC.) are leguminous crops native to South and Central America that are grown for their tuberous roots but are seed-propagated. Using a landscape genetic approach, we examined correlations between environmental factors and phylogeographic patterns of genetic diversity in Pachyrhizus landrace populations. Molecular analyses based on chloroplast DNA sequencing and a new set of nuclear microsatellite markers revealed two distinct lineages, with strong genetic differentiation between Andean landraces (lineage A) and Amazonian landraces (lineage B). The comparison of different evolutionary scenarios for the diversification history of yam beans in the Andes using approximate Bayesian computation suggests that Pachyrhizus ahipa and Pachyrhizus tuberosus share a progenitor-derivative relationship, with environmental factors playing an important role in driving selection for divergent ecotypes. The new molecular data call for a revision of the taxonomy of Pachyrhizus but are congruent with paleoclimatic and archeological evidence, and suggest that selection for determinate growth was part of ecophysiological adaptations associated with the diversification of the P. tuberosus - P. ahipa complex during the Mid-Holocene.

Phylogenomic Relationships between Amylolytic Enzymes from 85 Strains of Fungi

PubMed Central

Chen, Wanping; Xie, Ting; Shao, Yanchun; Chen, Fusheng

2012-01-01

Fungal amylolytic enzymes, including α-amylase, gluocoamylase and α-glucosidase, have been extensively exploited in diverse industrial applications such as high fructose syrup production, paper making, food processing and ethanol production. In this paper, amylolytic genes of 85 strains of fungi from the phyla Ascomycota, Basidiomycota, Chytridiomycota and Zygomycota were annotated on the genomic scale according to the classification of glycoside hydrolase (GH) from the Carbohydrate-Active enZymes (CAZy) Database. Comparisons of gene abundance in the fungi suggested that the repertoire of amylolytic genes adapted to their respective lifestyles. Amylolytic enzymes in family GH13 were divided into four distinct clades identified as heterologous α- amylases, eukaryotic α-amylases, bacterial and fungal α-amylases and GH13 α-glucosidases. Family GH15 had two branches, one for gluocoamylases, and the other with currently unknown function. GH31 α-glucosidases showed diverse branches consisting of neutral α-glucosidases, lysosomal acid α-glucosidases and a new clade phylogenetically related to the bacterial counterparts. Distribution of starch-binding domains in above fungal amylolytic enzymes was related to the enzyme source and phylogeny. Finally, likely scenarios for the evolution of amylolytic enzymes in fungi based on phylogenetic analyses were proposed. Our results provide new insights into evolutionary relationships among subgroups of fungal amylolytic enzymes and fungal evolutionary adaptation to ecological conditions. PMID:23166747

Do males pay for sex? Sex-specific selection coefficients suggest not.

PubMed

Prokop, Zofia M; Prus, Monika A; Gaczorek, Tomasz S; Sychta, Karolina; Palka, Joanna K; Plesnar-Bielak, Agata; Skarboń, Magdalena

2017-03-01

Selection acting on males can reduce mutation load of sexual relative to asexual populations, thus mitigating the twofold cost of sex, provided that it seeks and destroys the same mutations as selection acting on females, but with higher efficiency. This could happen due to sexual selection-a potent evolutionary force that in most systems predominantly affects males. We used replicate populations of red flour beetles (Tribolium castaneum) to study sex-specific selection against deleterious mutations introduced with ionizing radiation. We found no evidence for selection being stronger in males than in females; in fact, we observed a nonsignificant trend in the opposite direction. This suggests that selection on males does not reduce mutation load below the level expected under the (hypothetical) scenario of asexual reproduction. Additionally, we employed a novel approach, based on a simple model, to quantify the relative contributions of sexual and offspring viability selection to the overall selection observed in males. We found them to be similar in magnitude; however, only the offspring viability component was statistically significant. In summary, we found no support for the hypothesis that selection on males in general, and sexual selection in particular, contributes to the evolutionary maintenance of sex. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Composition bias and the origin of ORFan genes

PubMed Central

Yomtovian, Inbal; Teerakulkittipong, Nuttinee; Lee, Byungkook; Moult, John; Unger, Ron

2010-01-01

Motivation: Intriguingly, sequence analysis of genomes reveals that a large number of genes are unique to each organism. The origin of these genes, termed ORFans, is not known. Here, we explore the origin of ORFan genes by defining a simple measure called ‘composition bias’, based on the deviation of the amino acid composition of a given sequence from the average composition of all proteins of a given genome. Results: For a set of 47 prokaryotic genomes, we show that the amino acid composition bias of real proteins, random ‘proteins’ (created by using the nucleotide frequencies of each genome) and ‘proteins’ translated from intergenic regions are distinct. For ORFans, we observed a correlation between their composition bias and their relative evolutionary age. Recent ORFan proteins have compositions more similar to those of random ‘proteins’, while the compositions of more ancient ORFan proteins are more similar to those of the set of all proteins of the organism. This observation is consistent with an evolutionary scenario wherein ORFan genes emerged and underwent a large number of random mutations and selection, eventually adapting to the composition preference of their organism over time. Contact: ron@biocoml.ls.biu.ac.il Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20231229

The ethical dimensions of wildlife disease management in an evolutionary context

PubMed Central

Crozier, GKD; Schulte-Hostedde, Albrecht I

2014-01-01

Best practices in wildlife disease management require robust evolutionary ecological research (EER). This means not only basing management decisions on evolutionarily sound reasoning, but also conducting management in a way that actively contributes to the on-going development of that research. Because good management requires good science, and good science is ‘good’ science (i.e., effective science is often science conducted ethically), good management therefore also requires practices that accord with sound ethical reasoning. To that end, we propose a two-part framework to assist decision makers to identify ethical pitfalls of wildlife disease management. The first part consists of six values – freedom, fairness, well-being, replacement, reduction, and refinement; these values, developed for the ethical evaluation of EER practices, are also well suited for evaluating the ethics of wildlife disease management. The second part consists of a decision tree to help identify the ethically salient dimensions of wildlife disease management and to guide managers toward ethically responsible practices in complex situations. While ethical reasoning cannot be used to deduce from first principles what practices should be undertaken in every given set of circumstances, it can establish parameters that bound what sorts of practices will be acceptable or unacceptable in certain types of scenarios. PMID:25469160

Experimental strategies to assess the biological ramifications of multiple drivers of global ocean change-A review.

PubMed

Boyd, Philip W; Collins, Sinead; Dupont, Sam; Fabricius, Katharina; Gattuso, Jean-Pierre; Havenhand, Jonathan; Hutchins, David A; Riebesell, Ulf; Rintoul, Max S; Vichi, Marcello; Biswas, Haimanti; Ciotti, Aurea; Gao, Kunshan; Gehlen, Marion; Hurd, Catriona L; Kurihara, Haruko; McGraw, Christina M; Navarro, Jorge M; Nilsson, Göran E; Passow, Uta; Pörtner, Hans-Otto

2018-06-01

Marine life is controlled by multiple physical and chemical drivers and by diverse ecological processes. Many of these oceanic properties are being altered by climate change and other anthropogenic pressures. Hence, identifying the influences of multifaceted ocean change, from local to global scales, is a complex task. To guide policy-making and make projections of the future of the marine biosphere, it is essential to understand biological responses at physiological, evolutionary and ecological levels. Here, we contrast and compare different approaches to multiple driver experiments that aim to elucidate biological responses to a complex matrix of ocean global change. We present the benefits and the challenges of each approach with a focus on marine research, and guidelines to navigate through these different categories to help identify strategies that might best address research questions in fundamental physiology, experimental evolutionary biology and community ecology. Our review reveals that the field of multiple driver research is being pulled in complementary directions: the need for reductionist approaches to obtain process-oriented, mechanistic understanding and a requirement to quantify responses to projected future scenarios of ocean change. We conclude the review with recommendations on how best to align different experimental approaches to contribute fundamental information needed for science-based policy formulation. © 2018 John Wiley & Sons Ltd.

Evolutionary dynamics under interactive diversity

NASA Astrophysics Data System (ADS)

Su, Qi; Li, Aming; Wang, Long

2017-10-01

As evidenced by many cases in human societies, individuals often make different behavior decisions in different interactions, and adaptively adjust their behavior in changeable interactive scenarios. However, up to now, how such diverse interactive behavior affects cooperation dynamics has still remained unknown. Here we develop a general framework of interactive diversity, which models individuals’ separated behavior against distinct opponents and their adaptive adjustment in response to opponents’ strategies, to explore the evolution of cooperation. We find that interactive diversity enables individuals to reciprocate every single opponent, and thus sustains large-scale reciprocal interactions. Our work witnesses an impressive boost of cooperation for a notably extensive range of parameters and for all pairwise games. These results are robust against well-mixed and various networked populations, and against degree-normalized and cumulative payoff patterns. From the perspective of network dynamics, distinguished from individuals competing for nodes in most previous work, in this paper, the system evolves in the form of behavior disseminating along edges. We propose a theoretical method based on evolution of edges, which predicts well both the frequency of cooperation and the compact cooperation clusters. Our thorough investigation clarifies the positive role of interactive diversity in resolving social dilemmas and highlights the significance of understanding evolutionary dynamics from the viewpoint of edge dynamics.

Herbivory and body size: allometries of diet quality and gastrointestinal physiology, and implications for herbivore ecology and dinosaur gigantism.

PubMed

Clauss, Marcus; Steuer, Patrick; Müller, Dennis W H; Codron, Daryl; Hummel, Jürgen

2013-01-01

Digestive physiology has played a prominent role in explanations for terrestrial herbivore body size evolution and size-driven diversification and niche differentiation. This is based on the association of increasing body mass (BM) with diets of lower quality, and with putative mechanisms by which a higher BM could translate into a higher digestive efficiency. Such concepts, however, often do not match empirical data. Here, we review concepts and data on terrestrial herbivore BM, diet quality, digestive physiology and metabolism, and in doing so give examples for problems in using allometric analyses and extrapolations. A digestive advantage of larger BM is not corroborated by conceptual or empirical approaches. We suggest that explanatory models should shift from physiological to ecological scenarios based on the association of forage quality and biomass availability, and the association between BM and feeding selectivity. These associations mostly (but not exclusively) allow large herbivores to use low quality forage only, whereas they allow small herbivores the use of any forage they can physically manage. Examples of small herbivores able to subsist on lower quality diets are rare but exist. We speculate that this could be explained by evolutionary adaptations to the ecological opportunity of selective feeding in smaller animals, rather than by a physiologic or metabolic necessity linked to BM. For gigantic herbivores such as sauropod dinosaurs, other factors than digestive physiology appear more promising candidates to explain evolutionary drives towards extreme BM.

Herbivory and Body Size: Allometries of Diet Quality and Gastrointestinal Physiology, and Implications for Herbivore Ecology and Dinosaur Gigantism

PubMed Central

Clauss, Marcus; Steuer, Patrick; Müller, Dennis W. H.; Codron, Daryl; Hummel, Jürgen

2013-01-01

Digestive physiology has played a prominent role in explanations for terrestrial herbivore body size evolution and size-driven diversification and niche differentiation. This is based on the association of increasing body mass (BM) with diets of lower quality, and with putative mechanisms by which a higher BM could translate into a higher digestive efficiency. Such concepts, however, often do not match empirical data. Here, we review concepts and data on terrestrial herbivore BM, diet quality, digestive physiology and metabolism, and in doing so give examples for problems in using allometric analyses and extrapolations. A digestive advantage of larger BM is not corroborated by conceptual or empirical approaches. We suggest that explanatory models should shift from physiological to ecological scenarios based on the association of forage quality and biomass availability, and the association between BM and feeding selectivity. These associations mostly (but not exclusively) allow large herbivores to use low quality forage only, whereas they allow small herbivores the use of any forage they can physically manage. Examples of small herbivores able to subsist on lower quality diets are rare but exist. We speculate that this could be explained by evolutionary adaptations to the ecological opportunity of selective feeding in smaller animals, rather than by a physiologic or metabolic necessity linked to BM. For gigantic herbivores such as sauropod dinosaurs, other factors than digestive physiology appear more promising candidates to explain evolutionary drives towards extreme BM. PMID:24204552

The origin and evolution of Basigin(BSG) gene: A comparative genomic and phylogenetic analysis.

PubMed

Zhu, Xinyan; Wang, Shenglan; Shao, Mingjie; Yan, Jie; Liu, Fei

2017-07-01

Basigin (BSG), also known as extracellular matrix metalloproteinase inducer (EMMPRIN) or cluster of differentiation 147 (CD147), plays various fundamental roles in the intercellular recognition involved in immunologic phenomena, differentiation, and development. In this study, we aimed to compare the similarities and differences of BSG among organisms and explore possible evolutionary relationships based on the comparison result. We used the extensive BLAST tool to search the metazoan genomes, N-glycosylation sites, the transmembrane region and other functional sites. We then identified BSG homologs from genomic sequences and analyzed their phylogenetic relationships. We identified that BSG genes exist not only in the vertebrate metazoans but also in the invertebrate metazoans such as Amphioxus B. floridae, D. melanogaster, A. mellifera, S. japonicum, C. gigas, and T. patagoniensis. After sequence analysis, we confirmed that only vertebrate metazoans and Cephalochordate (amphioxus B. floridae) have the classic structure (a signal peptide, two Ig-like domains (IgC2 and IgI), a transmembrane region, and an intracellular domain). The invertebrate metazoans (excluding amphioxus B. floridae) lack the N-terminal signal peptides and IgC2 domain. We then generated a phylogenetic tree, genome organization comparison, and chromosomal disposition analysis based on the biological information obtained from the NCBI and Ensembl databases. Finally, we established the possible evolutionary scenario of the BSG gene, which showed the restricted exon rearrangement that has occurred during evolution, forming the present-day BSG gene. Copyright © 2017 Elsevier Ltd. All rights reserved.

On the origin of life in the zinc world: 1. Photosynthesizing, porous edifices built of hydrothermally precipitated zinc sulfide as cradles of life on Earth.

PubMed

Mulkidjanian, Armen Y

2009-08-24

The complexity of the problem of the origin of life has spawned a large number of possible evolutionary scenarios. Their number, however, can be dramatically reduced by the simultaneous consideration of various bioenergetic, physical, and geological constraints. This work puts forward an evolutionary scenario that satisfies the known constraints by proposing that life on Earth emerged, powered by UV-rich solar radiation, at photosynthetically active porous edifices made of precipitated zinc sulfide (ZnS) similar to those found around modern deep-sea hydrothermal vents. Under the high pressure of the primeval, carbon dioxide-dominated atmosphere ZnS could precipitate at the surface of the first continents, within reach of solar light. It is suggested that the ZnS surfaces (1) used the solar radiation to drive carbon dioxide reduction, yielding the building blocks for the first biopolymers, (2) served as templates for the synthesis of longer biopolymers from simpler building blocks, and (3) prevented the first biopolymers from photo-dissociation, by absorbing from them the excess radiation. In addition, the UV light may have favoured the selective enrichment of photostable, RNA-like polymers. Falsification tests of this hypothesis are described in the accompanying article (A.Y. Mulkidjanian, M.Y. Galperin, Biology Direct 2009, 4:27). The suggested "Zn world" scenario identifies the geological conditions under which photosynthesizing ZnS edifices of hydrothermal origin could emerge and persist on primordial Earth, includes a mechanism of the transient storage and utilization of solar light for the production of diverse organic compounds, and identifies the driving forces and selective factors that could have promoted the transition from the first simple, photostable polymers to more complex living organisms.

[Key morphofunctional transformations in the evolution of chiropterans (Bats, Chiroptera)].

PubMed

Kovaleva, I M

2014-01-01

Study on the morphology and morphogenesis of wing membranes in Bats has revealed some peculiarities in their structure and development. Understanding the embryogenesis of these animals, as well as attraction of data obtained on their molecular genetics and paleontology, allows one to single out some factors that could have initiated evolutionary modifications in development programs. A scenario of the key morphofunctional transformations in the forelimbs during the evolution of chiropterans is given.

Bell-Curve Based Evolutionary Strategies for Structural Optimization

NASA Technical Reports Server (NTRS)

Kincaid, Rex K.

2000-01-01

Evolutionary methods are exceedingly popular with practitioners of many fields; more so than perhaps any optimization tool in existence. Historically Genetic Algorithms (GAs) led the way in practitioner popularity (Reeves 1997). However, in the last ten years Evolutionary Strategies (ESs) and Evolutionary Programs (EPS) have gained a significant foothold (Glover 1998). One partial explanation for this shift is the interest in using GAs to solve continuous optimization problems. The typical GA relies upon a cumber-some binary representation of the design variables. An ES or EP, however, works directly with the real-valued design variables. For detailed references on evolutionary methods in general and ES or EP in specific see Back (1996) and Dasgupta and Michalesicz (1997). We call our evolutionary algorithm BCB (bell curve based) since it is based upon two normal distributions.

Insights from life history theory for an explicit treatment of trade-offs in conservation biology.

PubMed

Charpentier, Anne

2015-06-01

As economic and social contexts become more embedded within biodiversity conservation, it becomes obvious that resources are a limiting factor in conservation. This recognition is leading conservation scientists and practitioners to increasingly frame conservation decisions as trade-offs between conflicting societal objectives. However, this framing is all too often done in an intuitive way, rather than by addressing trade-offs explicitly. In contrast, the concept of trade-off is a keystone in evolutionary biology, where it has been investigated extensively. I argue that insights from evolutionary theory can provide methodological and theoretical support to evaluating and quantifying trade-offs in biodiversity conservation. I reviewed the diverse ways in which trade-offs have emerged within the context of conservation and how advances from evolutionary theory can help avoid the main pitfalls of an implicit approach. When studying both evolutionary trade-offs (e.g., reproduction vs. survival) and conservation trade-offs (e.g., biodiversity conservation vs. agriculture), it is crucial to correctly identify the limiting resource, hold constant the amount of this resource when comparing different scenarios, and choose appropriate metrics to quantify the extent to which the objectives have been achieved. Insights from studies in evolutionary theory also reveal how an inadequate selection of conservation solutions may result from considering suboptimal rather than optional solutions when examining whether a trade-off exits between 2 objectives. Furthermore, the shape of a trade-off curve (i.e., whether the relationship between 2 objectives follows a concave, convex, or linear form) is known to affect crucially the definition of optimal solutions in evolutionary biology and very likely affects decisions in biodiversity conservation planning too. This interface between evolutionary biology and biodiversity conservation can therefore provide methodological guidance to support decision makers in the difficult task of choosing among conservation solutions. © 2015 Society for Conservation Biology.

Options for the human settlement of the moon and Mars

NASA Technical Reports Server (NTRS)

Fairchild, Kyle O.; Roberts, Barney B.

1989-01-01

The evolutionary approach to space development is discussed in the framework of three overall strategies encompassing four case studies. The first strategy, human expeditions, places emphasis on highly visible, near-term manned missions to Mars or to one of the two moons of Mars. These expeditions are similar in scope and objectives to the Apollo program, with infrastructure development only conducted to the degree necessary to support one or two short-duration trips. Two such expeditionary scenarios, one to Phobus and the other to the Mars surface, are discussed. The second strategy involves the construction of science outposts, and emphasizes scientific exploration as well as investigation of technologies and operations needed for permanent habitation. A third strategy, evolutionary expansion, would explore and settle the inner solar system in a series of steps, with continued development of technologies, experience, and infrastructure.

Threatened species and the potential loss of phylogenetic diversity: conservation scenarios based on estimated extinction probabilities and phylogenetic risk analysis.

PubMed

Faith, Daniel P

2008-12-01

New species conservation strategies, including the EDGE of Existence (EDGE) program, have expanded threatened species assessments by integrating information about species' phylogenetic distinctiveness. Distinctiveness has been measured through simple scores that assign shared credit among species for evolutionary heritage represented by the deeper phylogenetic branches. A species with a high score combined with a high extinction probability receives high priority for conservation efforts. Simple hypothetical scenarios for phylogenetic trees and extinction probabilities demonstrate how such scoring approaches can provide inefficient priorities for conservation. An existing probabilistic framework derived from the phylogenetic diversity measure (PD) properly captures the idea of shared responsibility for the persistence of evolutionary history. It avoids static scores, takes into account the status of close relatives through their extinction probabilities, and allows for the necessary updating of priorities in light of changes in species threat status. A hypothetical phylogenetic tree illustrates how changes in extinction probabilities of one or more species translate into changes in expected PD. The probabilistic PD framework provided a range of strategies that moved beyond expected PD to better consider worst-case PD losses. In another example, risk aversion gave higher priority to a conservation program that provided a smaller, but less risky, gain in expected PD. The EDGE program could continue to promote a list of top species conservation priorities through application of probabilistic PD and simple estimates of current extinction probability. The list might be a dynamic one, with all the priority scores updated as extinction probabilities change. Results of recent studies suggest that estimation of extinction probabilities derived from the red list criteria linked to changes in species range sizes may provide estimated probabilities for many different species. Probabilistic PD provides a framework for single-species assessment that is well-integrated with a broader measurement of impacts on PD owing to climate change and other factors.

Nervous systems and scenarios for the invertebrate-to-vertebrate transition

PubMed Central

Holland, Nicholas D.

2016-01-01

Older evolutionary scenarios for the origin of vertebrates often gave nervous systems top billing in accordance with the notion that a big-brained Homo sapiens crowned a tree of life shaped mainly by progressive evolution. Now, however, tree thinking positions all extant organisms equidistant from the tree's root, and molecular phylogenies indicate that regressive evolution is more common than previously suspected. Even so, contemporary theories of vertebrate origin still focus on the nervous system because of its functional importance, its richness in characters for comparative biology, and its central position in the two currently prominent scenarios for the invertebrate-to-vertebrate transition, which grew out of the markedly neurocentric annelid and enteropneust theories of the nineteenth century. Both these scenarios compare phyla with diverse overall body plans. This diversity, exacerbated by the scarcity of relevant fossil data, makes it challenging to establish plausible homologies between component parts (e.g. nervous system regions). In addition, our current understanding of the relation between genotype and phenotype is too preliminary to permit us to convert gene network data into structural features in any simple way. These issues are discussed here with special reference to the evolution of nervous systems during proposed transitions from invertebrates to vertebrates. PMID:26598728

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

PubMed Central

2011-01-01

Background Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary history of this major freshwater fish clade, Otophysi, remains largely unexplored. To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families. Results Partitioned maximum likelihood analysis based on unambiguously aligned sequences (9923 bp) confidently recovered the monophyly of Otophysi and the two constituent subgroups (Cypriniformes and Characiphysi). The latter clade comprised three orders (Gymnotiformes, Characiformes, Siluriformes), and Gymnotiformes was sister to the latter two groups. One of the two suborders in Characiformes (Characoidei) was more closely related to Siluriformes than to its own suborder (Citharinoidei), rendering the characiforms paraphyletic. Although this novel relationship did not receive strong statistical support, it was supported by analyzing independent nuclear markers. A relaxed molecular clock Bayesian analysis of the divergence times and reconstruction of ancestral habitats on the timetree suggest a Pangaean origin and Mesozoic radiation of otophysans. Conclusions The present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans. This evolutionary scenario is consistent with recent arguments based on biogeographic inferences and molecular divergence time estimates. No fossil otophysan, however, has been recorded before the Albian, the early Cretaceous 100-112 Ma, creating an over 100 million year time span without fossil evidence. This formidable ghost range partially reflects a genuine difference between the estimated ages of stem group origin (molecular divergence time) and crown group morphological diversification (fossil divergence time); the ghost range, however, would be filled with discoveries of older fossils that can be used as more reasonable time constraints as well as with developments of more realistic models that capture the rates of molecular sequences accurately. PMID:21693066

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation.

PubMed

Nakatani, Masanori; Miya, Masaki; Mabuchi, Kohji; Saitoh, Kenji; Nishida, Mutsumi

2011-06-22

Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary history of this major freshwater fish clade, Otophysi, remains largely unexplored. To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families. Partitioned maximum likelihood analysis based on unambiguously aligned sequences (9923 bp) confidently recovered the monophyly of Otophysi and the two constituent subgroups (Cypriniformes and Characiphysi). The latter clade comprised three orders (Gymnotiformes, Characiformes, Siluriformes), and Gymnotiformes was sister to the latter two groups. One of the two suborders in Characiformes (Characoidei) was more closely related to Siluriformes than to its own suborder (Citharinoidei), rendering the characiforms paraphyletic. Although this novel relationship did not receive strong statistical support, it was supported by analyzing independent nuclear markers. A relaxed molecular clock Bayesian analysis of the divergence times and reconstruction of ancestral habitats on the timetree suggest a Pangaean origin and Mesozoic radiation of otophysans. The present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans. This evolutionary scenario is consistent with recent arguments based on biogeographic inferences and molecular divergence time estimates. No fossil otophysan, however, has been recorded before the Albian, the early Cretaceous 100-112 Ma, creating an over 100 million year time span without fossil evidence. This formidable ghost range partially reflects a genuine difference between the estimated ages of stem group origin (molecular divergence time) and crown group morphological diversification (fossil divergence time); the ghost range, however, would be filled with discoveries of older fossils that can be used as more reasonable time constraints as well as with developments of more realistic models that capture the rates of molecular sequences accurately.

Evolutionary Dynamics of Nitrogen Fixation in the Legume–Rhizobia Symbiosis

PubMed Central

Fujita, Hironori; Aoki, Seishiro; Kawaguchi, Masayoshi

2014-01-01

The stabilization of host–symbiont mutualism against the emergence of parasitic individuals is pivotal to the evolution of cooperation. One of the most famous symbioses occurs between legumes and their colonizing rhizobia, in which rhizobia extract nutrients (or benefits) from legume plants while supplying them with nitrogen resources produced by nitrogen fixation (or costs). Natural environments, however, are widely populated by ineffective rhizobia that extract benefits without paying costs and thus proliferate more efficiently than nitrogen-fixing cooperators. How and why this mutualism becomes stabilized and evolutionarily persists has been extensively discussed. To better understand the evolutionary dynamics of this symbiosis system, we construct a simple model based on the continuous snowdrift game with multiple interacting players. We investigate the model using adaptive dynamics and numerical simulations. We find that symbiotic evolution depends on the cost–benefit balance, and that cheaters widely emerge when the cost and benefit are similar in strength. In this scenario, the persistence of the symbiotic system is compatible with the presence of cheaters. This result suggests that the symbiotic relationship is robust to the emergence of cheaters, and may explain the prevalence of cheating rhizobia in nature. In addition, various stabilizing mechanisms, such as partner fidelity feedback, partner choice, and host sanction, can reinforce the symbiotic relationship by affecting the fitness of symbionts in various ways. This result suggests that the symbiotic relationship is cooperatively stabilized by various mechanisms. In addition, mixed nodule populations are thought to encourage cheater emergence, but our model predicts that, in certain situations, cheaters can disappear from such populations. These findings provide a theoretical basis of the evolutionary dynamics of legume–rhizobia symbioses, which is extendable to other single-host, multiple-colonizer systems. PMID:24691447

Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon

PubMed Central

Faria, Nuno Rodrigues; Suchard, Marc A; Abecasis, Ana; Sousa, J. D.; Ndembi, Nicaise; Camacho, R.J.; Vandamme, Anne-Mieke; Peeters, Martine; Lemey, Philippe

2015-01-01

Evolutionary analyses have revealed an origin of pandemic HIV-1 group M in the Congo River basin in the first part of the XXth century, but the patterns of historical viral spread in or around its epicentre remain largely unexplored. Here, we combine epidemiologic and molecular sequence data to investigate the spatiotemporal patterns of the CRF02_AG clade. By explicitly integrating prevalence counts and genetic population size estimates we date the epidemic emergence of CRF02_AG at 1973.1 (1972.1, 1975.3 95% CI). To infer their phylogeographic signature at a regional scale, we analyze pol and env time-stamped sequence data from 8 countries using a Bayesian phylogeographic approach based on a discrete asymmetric model. Our data confirms a spatial origin of this clade in the Democratic Republic of Congo (DRC) and suggests that viral dissemination to Cameroon occurred at an early stage of the evolutionary history of CRF02_AG. We find considerable support for epidemiological linkage between neighbour countries. Compilation of ethnographic data suggests that well-supported viral migration was related with chance exportation events rather than by sustained human migratory flows. Finally, using sequence data from 15 locations in Cameroon, we use relaxed random walk models to explore the spatiotemporal dynamics of CRF02_AG at a finer geographical detail. Phylogeographic dispersal in continuous space reveals that at least two distinct CRF02_AG lineages are circulating in overlapping regions that are evolving at different evolutionary and diffusion rates. Altogether, by combining molecular and epidemiological data, our results provide a time scale for CRF02_AG, place its spatial root within the putative root of group-M diversity and propose a scenario for the spatiotemporal patterns of a successful HIV-1 lineage both at a regional and country-scale. PMID:21565285

Fitness declines towards range limits and local adaptation to climate affect dispersal evolution during climate-induced range shifts.

PubMed

Hargreaves, A L; Bailey, S F; Laird, R A

2015-08-01

Dispersal ability will largely determine whether species track their climatic niches during climate change, a process especially important for populations at contracting (low-latitude/low-elevation) range limits that otherwise risk extinction. We investigate whether dispersal evolution at contracting range limits is facilitated by two processes that potentially enable edge populations to experience and adjust to the effects of climate deterioration before they cause extinction: (i) climate-induced fitness declines towards range limits and (ii) local adaptation to a shifting climate gradient. We simulate a species distributed continuously along a temperature gradient using a spatially explicit, individual-based model. We compare range-wide dispersal evolution during climate stability vs. directional climate change, with uniform fitness vs. fitness that declines towards range limits (RLs), and for a single climate genotype vs. multiple genotypes locally adapted to temperature. During climate stability, dispersal decreased towards RLs when fitness was uniform, but increased when fitness declined towards RLs, due to highly dispersive genotypes maintaining sink populations at RLs, increased kin selection in smaller populations, and an emergent fitness asymmetry that favoured dispersal in low-quality habitat. However, this initial dispersal advantage at low-fitness RLs did not facilitate climate tracking, as it was outweighed by an increased probability of extinction. Locally adapted genotypes benefited from staying close to their climate optima; this selected against dispersal under stable climates but for increased dispersal throughout shifting ranges, compared to cases without local adaptation. Dispersal increased at expanding RLs in most scenarios, but only increased at the range centre and contracting RLs given local adaptation to climate. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Epimerization of Alanyl-Alanine Induced by γ-Rays Irradiation in Aqueous Solutions.

PubMed

Munegumi, Toratane

2017-03-01

Living organisms have homochiral L-amino acids in proteins and homochiral D-mononucleotides in nucleic acids. The chemical evolutionary process to protein homochirality has been discussed for many years. Although many scenarios have been proposed for homochirality in the monomeric compounds, homochirality in amino acids and mononucleotides does not always guarantee homochirality in polypeptides and polynucleotides. Integrated scenarios containing the pathways from monomer to polymer should be proposed because in the pathways oligomers and polymers as well as monomers racemize (or epimerize), degrade, and condense. This research addresses epimerization and degradation of dipeptides under γ-rays irradiation by a cobalt-60 ( 60 Co) radiation source. The different rate constants of epimerization between diastereomeric dipeptides in the research suggest that the potential pathway toward homochirality could be much more complex.

Abundance differences among globular-cluster giants: Primordial versus evolutionary scenarios

NASA Astrophysics Data System (ADS)

Kraft, Robert P.

1994-06-01

Contrary to historical expectation, stars within a given globular cluster often exhibit wide variations in the abundance of C, N, and O as well as certain light metals, particularly Na and Al. Owing to flux limitations, studies have been confined to evolved stars, especially giants, but in few instances variations have been detected among main-sequence stars. Among giants, the variations are of two kinds. The abundances of C and N are often anticorrelated, and in the limited number of cases in which both have been measured, O and N abundances have also often proved to be anticorrelated (Pilachowski 1988; Sneden et al. 1991; Brown et al. 1991; Kraft et al. 1992). Following pioneering work by Cohen (1978) and Peterson (1980), strong evidence has recently emerged for the existence of a significant global anticorrelation between O and Na abundances (Drake et al. 1992, Kraft et al. 1993). The observations are discussed in terms of contrasting hypotheses: evolutionary versus primordial. In the former, the variations are attributed to the dredgeup of material that has been processed through the CNO cycle in the globular-cluster stars themselves. In the latter, the variations are attributed to primordial chemical inhomogeneities in the material out of which the cluster stars were formed, the composition of these 'clumps' having been determined by nuclear processing in a prior generation of more massive stars. Observational evidence supporting each of these scenarios is cited. Recent studies of stellar rotation among horizontal branch stars in certain clusters (Peterson et al. 1994) as well as new calculations of Na-23 and Al-27 production in the CNO processing regions of evolving low-mass giants (Langer et al. 1993) lend fresh support to the evolutionary hypothesis. However, such calculations do not explain the variation of C and N abundances found among cluster main-sequence stars (Suntzeff 1989; Briley et al. 1991) which therefore seem explicable only on the basis of a primordial scenario. Among mildly metal-poor giants, i.e., those in the range from solar metallicity to (Fe/H) approximately -1, recent observational evidence suggesting the existence of a substructure in the (el/Fe) ratios of the heavier alpha elements, e.g., Si, Mg, Ca, and Ti, is discussed. The possible influence of this effect on the interpretation of the integrated spectra of extragalactic globular clusters and E galaxies is noted.

Genetic evidence and the modern human origins debate.

PubMed

Relethford, J H

2008-06-01

A continued debate in anthropology concerns the evolutionary origin of 'anatomically modern humans' (Homo sapiens sapiens). Different models have been proposed to examine the related questions of (1) where and when anatomically modern humans first appeared and (2) the genetic and evolutionary relationship between modern humans and earlier human populations. Genetic data have been increasingly used to address these questions. Genetic data on living human populations have been used to reconstruct the evolutionary history of the human species by considering how global patterns of human variation could be produced given different evolutionary scenarios. Of particular interest are gene trees that reconstruct the time and place of the most recent common ancestor of humanity for a given haplotype and the analysis of regional differences in genetic diversity. Ancient DNA has also allowed a direct assessment of genetic variation in European Neandertals. Together with the fossil record, genetic data provide insight into the origin of modern humans. The evidence points to an African origin of modern humans dating back to 200,000 years followed by later expansions of moderns out of Africa across the Old World. What is less clear is what happened when these early modern humans met preexisting 'archaic human' populations outside of Africa. At present, it is difficult to distinguish between a model of total genetic replacement and a model that includes some degree of genetic mixture.

The Evolution of the Stem Cell Theory for Heart Failure

PubMed Central

Silvestre, Jean-Sébastien; Menasché, Philippe

2015-01-01

Various stem cell-based approaches for cardiac repair have achieved encouraging results in animal experiments, often leading to their rapid proceeding to clinical testing. However, freewheeling evolutionary developments of the stem cell theory might lead to dystopian scenarios where heterogeneous sources of therapeutic cells could promote mixed clinical outcomes in un-stratified patient populations. This review focuses on the lessons that should be learnt from the first generation of stem cell-based strategies and emphasizes the absolute requirement to better understand the basic mechanisms of stem cell biology and cardiogenesis. We will also discuss about the unexpected “big bang” in the stem cell theory, “blasting” the therapeutic cells to their unchallenged ability to release paracrine factors such as extracellular membrane vesicles. Paradoxically, the natural evolution of the stem cell theory for cardiac regeneration may end with the development of cell-free strategies with multiple cellular targets including cardiomyocytes but also other infiltrating or resident cardiac cells. PMID:26844266

A Real-Time Decision Support System for Voltage Collapse Avoidance in Power Supply Networks

NASA Astrophysics Data System (ADS)

Chang, Chen-Sung

This paper presents a real-time decision support system (RDSS) based on artificial intelligence (AI) for voltage collapse avoidance (VCA) in power supply networks. The RDSS scheme employs a fuzzy hyperrectangular composite neural network (FHRCNN) to carry out voltage risk identification (VRI). In the event that a threat to the security of the power supply network is detected, an evolutionary programming (EP)-based algorithm is triggered to determine the operational settings required to restore the power supply network to a secure condition. The effectiveness of the RDSS methodology is demonstrated through its application to the American Electric Power Provider System (AEP, 30-bus system) under various heavy load conditions and contingency scenarios. In general, the numerical results confirm the ability of the RDSS scheme to minimize the risk of voltage collapse in power supply networks. In other words, RDSS provides Power Provider Enterprises (PPEs) with a viable tool for performing on-line voltage risk assessment and power system security enhancement functions.

Simulating natural selection in landscape genetics

Treesearch

E. L. Landguth; S. A. Cushman; N. Johnson

2012-01-01

Linking landscape effects to key evolutionary processes through individual organism movement and natural selection is essential to provide a foundation for evolutionary landscape genetics. Of particular importance is determining how spatially- explicit, individual-based models differ from classic population genetics and evolutionary ecology models based on ideal...

Protein structure, electron transfer and evolution of prokaryotic photosynthetic reaction centers

NASA Technical Reports Server (NTRS)

Blankenship, R. E.

1994-01-01

Photosynthetic reaction centers from a variety of organisms have been isolated and characterized. The groups of prokaryotic photosynthetic organisms include the purple bacteria, the filamentous green bacteria, the green sulfur bacteria and the heliobacteria as anoxygenic representatives as well as the cyanobacteria and prochlorophytes as oxygenic representatives. This review focuses on structural and functional comparisons of the various groups of photosynthetic reaction centers and considers possible evolutionary scenarios to explain the diversity of existing photosynthetic organisms.

Designing from minimum to optimum functionality

NASA Astrophysics Data System (ADS)

Bannova, Olga; Bell, Larry

2011-04-01

This paper discusses a multifaceted strategy to link NASA Minimal Functionality Habitable Element (MFHE) requirements to a compatible growth plan; leading forward to evolutionary, deployable habitats including outpost development stages. The discussion begins by reviewing fundamental geometric features inherent in small scale, vertical and horizontal, pressurized module configuration options to characterize applicability to meet stringent MFHE constraints. A proposed scenario to incorporate a vertical core MFHE concept into an expanded architecture to provide continuity of structural form and a logical path from "minimum" to "optimum" design of a habitable module. The paper describes how habitation and logistics accommodations could be pre-integrated into a common Hab/Log Module that serves both habitation and logistics functions. This is offered as a means to reduce unnecessary redundant development costs and to avoid EVA-intensive on-site adaptation and retrofitting requirements for augmented crew capacity. An evolutionary version of the hard shell Hab/Log design would have an expandable middle section to afford larger living and working accommodations. In conclusion, the paper illustrates that a number of cargo missions referenced for NASA's 4.0.0 Lunar Campaign Scenario could be eliminated altogether to expedite progress and reduce budgets. The plan concludes with a vertical growth geometry that provides versatile and efficient site development opportunities using a combination of hard Hab/Log modules and a hybrid expandable "CLAM" (Crew Lunar Accommodations Module) element.

Strong gravitational lensing of gravitational waves from double compact binaries—perspectives for the Einstein Telescope

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

Biesiada, Marek; Ding, Xuheng; Zhu, Zong-Hong

Gravitational wave (GW) experiments are entering their advanced stage which should soon open a new observational window on the Universe. Looking into this future, the Einstein Telescope (ET) was designed to have a fantastic sensitivity improving significantly over the advanced GW detectors. One of the most important astrophysical GW sources supposed to be detected by the ET in large numbers are double compact objects (DCO) and some of such events should be gravitationally lensed by intervening galaxies. We explore the prospects of observing gravitationally lensed inspiral DCO events in the ET. This analysis is a significant extension of our previousmore » paper [1]. We are using the intrinsic merger rates of the whole class of DCO (NS-NS,BH-NS,BH-BH) located at different redshifts as calculated by [2] by using StarTrack population synthesis evolutionary code. We discuss in details predictions from each evolutionary scenario. Our general conclusion is that ET would register about 50–100 strongly lensed inspiral events per year. Only the scenario in which nascent BHs receive strong kick gives the predictions of a few events per year. Such lensed events would be dominated by the BH-BH merging binary systems. Our results suggest that during a few years of successful operation ET will provide a considerable catalog of strongly lensed events.« less

Female mating preferences determine system-level evolution in a gene network model.

PubMed

Fierst, Janna L

2013-06-01

Environmental patterns of directional, stabilizing and fluctuating selection can influence the evolution of system-level properties like evolvability and mutational robustness. Intersexual selection produces strong phenotypic selection and these dynamics may also affect the response to mutation and the potential for future adaptation. In order to to assess the influence of mating preferences on these evolutionary properties, I modeled a male trait and female preference determined by separate gene regulatory networks. I studied three sexual selection scenarios: sexual conflict, a Gaussian model of the Fisher process described in Lande (in Proc Natl Acad Sci 78(6):3721-3725, 1981) and a good genes model in which the male trait signalled his mutational condition. I measured the effects these mating preferences had on the potential for traits and preferences to evolve towards new states, and mutational robustness of both the phenotype and the individual's overall viability. All types of sexual selection increased male phenotypic robustness relative to a randomly mating population. The Fisher model also reduced male evolvability and mutational robustness for viability. Under good genes sexual selection, males evolved an increased mutational robustness for viability. Females choosing their mates is a scenario that is sufficient to create selective forces that impact genetic evolution and shape the evolutionary response to mutation and environmental selection. These dynamics will inevitably develop in any population where sexual selection is operating, and affect the potential for future adaptation.

An evolutionary perspective on the systems of adaptive immunity.

PubMed

Müller, Viktor; de Boer, Rob J; Bonhoeffer, Sebastian; Szathmáry, Eörs

2018-02-01

We propose an evolutionary perspective to classify and characterize the diverse systems of adaptive immunity that have been discovered across all major domains of life. We put forward a new function-based classification according to the way information is acquired by the immune systems: Darwinian immunity (currently known from, but not necessarily limited to, vertebrates) relies on the Darwinian process of clonal selection to 'learn' by cumulative trial-and-error feedback; Lamarckian immunity uses templated targeting (guided adaptation) to internalize heritable information on potential threats; finally, shotgun immunity operates through somatic mechanisms of variable targeting without feedback. We argue that the origin of Darwinian (but not Lamarckian or shotgun) immunity represents a radical innovation in the evolution of individuality and complexity, and propose to add it to the list of major evolutionary transitions. While transitions to higher-level units entail the suppression of selection at lower levels, Darwinian immunity re-opens cell-level selection within the multicellular organism, under the control of mechanisms that direct, rather than suppress, cell-level evolution for the benefit of the individual. From a conceptual point of view, the origin of Darwinian immunity can be regarded as the most radical transition in the history of life, in which evolution by natural selection has literally re-invented itself. Furthermore, the combination of clonal selection and somatic receptor diversity enabled a transition from limited to practically unlimited capacity to store information about the antigenic environment. The origin of Darwinian immunity therefore comprises both a transition in individuality and the emergence of a new information system - the two hallmarks of major evolutionary transitions. Finally, we present an evolutionary scenario for the origin of Darwinian immunity in vertebrates. We propose a revival of the concept of the 'Big Bang' of vertebrate immunity, arguing that its origin involved a 'difficult' (i.e. low-probability) evolutionary transition that might have occurred only once, in a common ancestor of all vertebrates. In contrast to the original concept, we argue that the limiting innovation was not the generation of somatic diversity, but the regulatory circuitry needed for the safe operation of amplifiable immune responses with somatically acquired targeting. Regulatory complexity increased abruptly by genomic duplications at the root of the vertebrate lineage, creating a rare opportunity to establish such circuitry. We discuss the selection forces that might have acted at the origin of the transition, and in the subsequent stepwise evolution leading to the modern immune systems of extant vertebrates. © 2017 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

The concept of ageing in evolutionary algorithms: Discussion and inspirations for human ageing.

PubMed

Dimopoulos, Christos; Papageorgis, Panagiotis; Boustras, George; Efstathiades, Christodoulos

2017-04-01

This paper discusses the concept of ageing as this applies to the operation of Evolutionary Algorithms, and examines its relationship to the concept of ageing as this is understood for human beings. Evolutionary Algorithms constitute a family of search algorithms which base their operation on an analogy from the evolution of species in nature. The paper initially provides the necessary knowledge on the operation of Evolutionary Algorithms, focusing on the use of ageing strategies during the implementation of the evolutionary process. Background knowledge on the concept of ageing, as this is defined scientifically for biological systems, is subsequently presented. Based on this information, the paper provides a comparison between the two ageing concepts, and discusses the philosophical inspirations which can be drawn for human ageing based on the operation of Evolutionary Algorithms. Copyright © 2017 Elsevier B.V. All rights reserved.

Testing Domestication Scenarios of Lima Bean (Phaseolus lunatus L.) in Mesoamerica: Insights from Genome-Wide Genetic Markers

PubMed Central

Chacón-Sánchez, María I.; Martínez-Castillo, Jaime

2017-01-01

Plant domestication can be seen as a long-term process that involves a complex interplay among demographic processes and evolutionary forces. Previous studies have suggested two domestication scenarios for Lima bean in Mesoamerica: two separate domestication events, one from gene pool MI in central-western Mexico and another one from gene pool MII in the area Guatemala-Costa Rica, or a single domestication from gene pool MI in central-western Mexico followed by post-domestication gene flow with wild populations. In this study we evaluated the genetic structure of the wild gene pool and tested these two competing domestication scenarios of Lima bean in Mesoamerica by applying an ABC approach to a set of genome-wide SNP markers. The results confirm the existence of three gene pools in wild Lima bean, two Mesoamerican gene pools (MI and MII) and the Andean gene pool (AI), and suggest the existence of another gene pool in central Colombia. The results indicate that although both domestication scenarios may be supported by genetic data, higher statistical support was given to the single domestication scenario in central-western Mexico followed by admixture with wild populations. Domestication would have involved strong founder effects reflected in loss of genetic diversity and increased LD levels in landraces. Genomic regions affected by selection were detected and these may harbor candidate genes related to domestication. PMID:28955351

The Formation and Evolution of Galactic Disks with APOGEE and the Gaia Survey

NASA Astrophysics Data System (ADS)

Li, Chengdong; Zhao, Gang; Zhai, Meng; Jia, Yunpeng

2018-06-01

We explore the structure and evolutionary history of Galactic disks with Apache Point Observatory Galactic Evolution Experiment data release 13 (DR13 hereafter) and Gaia Tycho-Gaia Astrometric Solution data. We use the [α/M] ratio to allocate stars into particular Galactic components to elucidate the chemical and dynamical properties of the thin and thick disks. The spatial motions of the sample stars are obtained in Galactic Cartesian and cylindrical coordinates. We analyze the abundance trends and metallicity and [α/M] gradients of the thick and thin disks. We confirm the existence of metal-weak thick-disk stars in Galactic disks. A kinematical method is used to select the thin- and thick-disk stars for comparison. We calculate the scale length and scale height of the kinematically and chemically selected thick and thin disks based on the axisymmetric Jeans equation. We conclude that the scale length of the thick disk is approximately equal to that of the thin disk via a kinematical approach. For the chemical selection, this disparity is about 1 kpc. Finally, we get the stellar orbital parameters and try to unveil the formation scenario of the thick disk. We conclude that the gas-rich merger and radial migration are more reasonable formation scenarios for the thick disk.

Evolution of social versus individual learning in a subdivided population revisited: comparative analysis of three coexistence mechanisms using the inclusive-fitness method.

PubMed

Kobayashi, Yutaka; Ohtsuki, Hisashi

2014-03-01

Learning abilities are categorized into social (learning from others) and individual learning (learning on one's own). Despite the typically higher cost of individual learning, there are mechanisms that allow stable coexistence of both learning modes in a single population. In this paper, we investigate by means of mathematical modeling how the effect of spatial structure on evolutionary outcomes of pure social and individual learning strategies depends on the mechanisms for coexistence. We model a spatially structured population based on the infinite-island framework and consider three scenarios that differ in coexistence mechanisms. Using the inclusive-fitness method, we derive the equilibrium frequency of social learners and the genetic load of social learning (defined as average fecundity reduction caused by the presence of social learning) in terms of some summary statistics, such as relatedness, for each of the three scenarios and compare the results. This comparative analysis not only reconciles previous models that made contradictory predictions as to the effect of spatial structure on the equilibrium frequency of social learners but also derives a simple mathematical rule that determines the sign of the genetic load (i.e. whether or not social learning contributes to the mean fecundity of the population). Copyright © 2013 Elsevier Inc. All rights reserved.

What is the Nondominated Formulation? A Demonstration of de Novo Water Supply Portfolio Planning Under Deep Uncertainty

NASA Astrophysics Data System (ADS)

Kasprzyk, J. R.; Reed, P. M.; Characklis, G. W.; Kirsch, B. R.

2010-12-01

This paper proposes and demonstrates a new interactive framework for sensitivity-informed de Novo programming, in which a learning approach to formulating decision problems can confront the deep uncertainty within water management problems. The framework couples global sensitivity analysis using Sobol’ variance decomposition with multiobjective evolutionary algorithms (MOEAs) to generate planning alternatives and test their robustness to new modeling assumptions and scenarios. We explore these issues within the context of a risk-based water supply management problem, where a city seeks the most efficient use of a water market. The case study examines a single city’s water supply in the Lower Rio Grande Valley (LRGV) in Texas, using both a 10-year planning horizon and an extreme single-year drought scenario. The city’s water supply portfolio comprises a volume of permanent rights to reservoir inflows and use of a water market through anticipatory thresholds for acquiring transfers of water through optioning and spot leases. Diagnostic information from the Sobol’ variance decomposition is used to create a sensitivity-informed problem formulation testing different decision variable configurations, with tradeoffs for the formulation solved using a MOEA. Subsequent analysis uses the drought scenario to expose tradeoffs between long-term and short-term planning and illustrate the impact of deeply uncertain assumptions on water availability in droughts. The results demonstrate water supply portfolios’ efficiency, reliability, and utilization of transfers in the water supply market and show how to adaptively improve the value and robustness of our problem formulations by evolving our definition of optimality to discover key tradeoffs.

Island Rule, quantitative genetics and brain–body size evolution in Homo floresiensis

PubMed Central

2017-01-01

Colonization of islands often activate a complex chain of adaptive events that, over a relatively short evolutionary time, may drive strong shifts in body size, a pattern known as the Island Rule. It is arguably difficult to perform a direct analysis of the natural selection forces behind such a change in body size. Here, we used quantitative evolutionary genetic models, coupled with simulations and pattern-oriented modelling, to analyse the evolution of brain and body size in Homo floresiensis, a diminutive hominin species that appeared around 700 kya and survived up to relatively recent times (60–90 kya) on Flores Island, Indonesia. The hypothesis of neutral evolution was rejected in 97% of the simulations, and estimated selection gradients are within the range found in living natural populations. We showed that insularity may have triggered slightly different evolutionary trajectories for body and brain size, which means explaining the exceedingly small cranial volume of H. floresiensis requires additional selective forces acting on brain size alone. Our analyses also support previous conclusions that H. floresiensis may be most likely derived from an early Indonesian H. erectus, which is coherent with currently accepted biogeographical scenario for Homo expansion out of Africa. PMID:28637851

Island Rule, quantitative genetics and brain-body size evolution in Homo floresiensis.

PubMed

Diniz-Filho, José Alexandre Felizola; Raia, Pasquale

2017-06-28

Colonization of islands often activate a complex chain of adaptive events that, over a relatively short evolutionary time, may drive strong shifts in body size, a pattern known as the Island Rule. It is arguably difficult to perform a direct analysis of the natural selection forces behind such a change in body size. Here, we used quantitative evolutionary genetic models, coupled with simulations and pattern-oriented modelling, to analyse the evolution of brain and body size in Homo floresiensis , a diminutive hominin species that appeared around 700 kya and survived up to relatively recent times (60-90 kya) on Flores Island, Indonesia. The hypothesis of neutral evolution was rejected in 97% of the simulations, and estimated selection gradients are within the range found in living natural populations. We showed that insularity may have triggered slightly different evolutionary trajectories for body and brain size, which means explaining the exceedingly small cranial volume of H. floresiensis requires additional selective forces acting on brain size alone. Our analyses also support previous conclusions that H. floresiensis may be most likely derived from an early Indonesian H. erectus , which is coherent with currently accepted biogeographical scenario for Homo expansion out of Africa. © 2017 The Author(s).

ON THE CHALLENGING VARIABILITY OF LS IV-14{sup 0}116: PULSATIONAL INSTABILITIES EXCITED BY THE {epsilon}-MECHANISM

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

Miller Bertolami, M. M.; Corsico, A. H.; Althaus, L. G., E-mail: mmiller@fcaglp.unlp.edu.ar

2011-11-01

We investigate the pulsation driving mechanism responsible for the long-period photometric variations observed in LS IV-14{sup 0}116, a subdwarf B star showing a He-enriched atmospheric composition. To this end, we perform detailed nonadiabatic pulsation computations over fully evolutionary post-He-core-flash stellar structure models, appropriate for hot subdwarf stars at evolutionary phases previous to the He-core burning stage. We found that the variability of LS IV-14{sup 0}116 can be attributed to non-radial g-mode pulsations excited by the {epsilon}-mechanism acting in the He-burning shells that appear before the star settles in the He-core burning stage. Even more interestingly, our results show that LSmore » IV-14{sup 0}116 could be the first known pulsating star in which the {epsilon}-mechanism of mode excitation is operating. Last but not the least, we find that the period range of destabilized modes is sensitive to the exact location of the burning shell, something that might help in distinguishing between the different evolutionary scenarios proposed for the formation of this star.« less

Public goods games in populations with fluctuating size.

PubMed

McAvoy, Alex; Fraiman, Nicolas; Hauert, Christoph; Wakeley, John; Nowak, Martin A

2018-05-01

Many mathematical frameworks of evolutionary game dynamics assume that the total population size is constant and that selection affects only the relative frequency of strategies. Here, we consider evolutionary game dynamics in an extended Wright-Fisher process with variable population size. In such a scenario, it is possible that the entire population becomes extinct. Survival of the population may depend on which strategy prevails in the game dynamics. Studying cooperative dilemmas, it is a natural feature of such a model that cooperators enable survival, while defectors drive extinction. Although defectors are favored for any mixed population, random drift could lead to their elimination and the resulting pure-cooperator population could survive. On the other hand, if the defectors remain, then the population will quickly go extinct because the frequency of cooperators steadily declines and defectors alone cannot survive. In a mutation-selection model, we find that (i) a steady supply of cooperators can enable long-term population survival, provided selection is sufficiently strong, and (ii) selection can increase the abundance of cooperators but reduce their relative frequency. Thus, evolutionary game dynamics in populations with variable size generate a multifaceted notion of what constitutes a trait's long-term success. Copyright © 2018 Elsevier Inc. All rights reserved.

Applying evolutionary psychology to a serious game about children's interpersonal conflict.

PubMed

Ingram, Gordon P D; Campos, Joana; Hondrou, Charline; Vasalou, Asimina; Martinho, Carlos; Joinson, Adam

2012-12-20

This article describes the use of evolutionary psychology to inform the design of a serious computer game aimed at improving 9-12-year-old children's conflict resolution skills. The design of the game will include dynamic narrative generation and emotional tagging, and there is a strong evolutionary rationale for the effect of both of these on conflict resolution. Gender differences will also be taken into consideration in designing the game. In interview research in schools in three countries (Greece, Portugal, and the UK) aimed at formalizing the game requirements, we found that gender differences varied in the extent to which they applied cross-culturally. Across the three countries, girls were less likely to talk about responding to conflict with physical aggression, talked more about feeling sad about conflict and about conflicts over friendship alliances, and talked less about conflicts in the context of sports or games. Predicted gender differences in anger and reconciliation were not found. Results are interpreted in terms of differing underlying models of friendship that are motivated by parental investment theory. This research will inform the design of the themes that we use in game scenarios for both girls and boys.

Genome Dynamics in Legionella: The Basis of Versatility and Adaptation to Intracellular Replication

PubMed Central

Gomez-Valero, Laura; Buchrieser, Carmen

2013-01-01

Legionella pneumophila is a bacterial pathogen present in aquatic environments that can cause a severe pneumonia called Legionnaires’ disease. Soon after its recognition, it was shown that Legionella replicates inside amoeba, suggesting that bacteria replicating in environmental protozoa are able to exploit conserved signaling pathways in human phagocytic cells. Comparative, evolutionary, and functional genomics suggests that the Legionella–amoeba interaction has shaped this pathogen more than previously thought. A complex evolutionary scenario involving mobile genetic elements, type IV secretion systems, and horizontal gene transfer among Legionella, amoeba, and other organisms seems to take place. This long-lasting coevolution led to the development of very sophisticated virulence strategies and a high level of temporal and spatial fine-tuning of bacteria host–cell interactions. We will discuss current knowledge of the evolution of virulence of Legionella from a genomics perspective and propose our vision of the emergence of this human pathogen from the environment. PMID:23732852

Ploidy, sex and crossing over in an evolutionary aging model

NASA Astrophysics Data System (ADS)

Lobo, Matheus P.; Onody, Roberto N.

2006-02-01

Nowadays, many forms of reproduction coexist in nature: Asexual, sexual, apomictic and meiotic parthenogenesis, hermaphroditism and parasex. The mechanisms of their evolution and what made them successful reproductive alternatives are very challenging and debated questions. Here, using a simple evolutionary aging model, we give a possible scenario. By studying the performance of populations where individuals may have diverse characteristics-different ploidies, sex with or without crossing over, as well as the absence of sex-we find an evolution sequence that may explain why there are actually two major or leading groups: Sexual and asexual. We also investigate the dependence of these characteristics on different conditions of fertility and deleterious mutations. Finally, if the primeval organisms on Earth were, in fact, asexual individuals we conjecture that the sexual form of reproduction could have more easily been set and found its niche during a period of low-intensity mutations.

FUSE Observations of He-rich sdB Stars

NASA Technical Reports Server (NTRS)

Swiegart, A. V.; Lanz, T.; Brown, T. M.; Hubeny, I.; Landsman, W. B.

2003-01-01

Most subdwarf B stars are extremely deficient in helium and selected light elements, but a minority are helium-rich. New evolutionary calculations suggest that these helium-rich sdB stars are the result of a delayed helium-core flash on the white dwarf cooling curve, which leads to extensive mixing between the hydrogen envelope and helium core. Such mixed stars should show greatly enhanced helium and carbon with respect to the other heavy elements. We have recently obtained FUSE spectra of two helium-rich sdB stars, PG1544+488 and JL87, revealing huge C Ill lines at 977 and 1176 A. Our analysis shows that PG1544+488 has a surface composition of 97% He, 2% C, and 1% N, in agreement with the new evolutionary scenario. While JL87 also reveals a large enrichment in carbon and nitrogen (1.4% and 0.4%, respectively), there is still a significant amount of hydrogen in its atmosphere.

Beyond Linear Sequence Comparisons: The use of genome-levelcharacters for phylogenetic reconstruction

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

Boore, Jeffrey L.

2004-11-27

Although the phylogenetic relationships of many organisms have been convincingly resolved by the comparisons of nucleotide or amino acid sequences, others have remained equivocal despite great effort. Now that large-scale genome sequencing projects are sampling many lineages, it is becoming feasible to compare large data sets of genome-level features and to develop this as a tool for phylogenetic reconstruction that has advantages over conventional sequence comparisons. Although it is unlikely that these will address a large number of evolutionary branch points across the broad tree of life due to the infeasibility of such sampling, they have great potential for convincinglymore » resolving many critical, contested relationships for which no other data seems promising. However, it is important that we recognize potential pitfalls, establish reasonable standards for acceptance, and employ rigorous methodology to guard against a return to earlier days of scenario-driven evolutionary reconstructions.« less

Ecology, sexual selection and speciation.

PubMed

Maan, Martine E; Seehausen, Ole

2011-06-01

The spectacular diversity in sexually selected traits among animal taxa has inspired the hypothesis that divergent sexual selection can drive speciation. Unfortunately, speciation biologists often consider sexual selection in isolation from natural selection, even though sexually selected traits evolve in an ecological context: both preferences and traits are often subject to natural selection. Conversely, while behavioural ecologists may address ecological effects on sexual communication, they rarely measure the consequences for population divergence. Herein, we review the empirical literature addressing the mechanisms by which natural selection and sexual selection can interact during speciation. We find that convincing evidence for any of these scenarios is thin. However, the available data strongly support various diversifying effects that emerge from interactions between sexual selection and environmental heterogeneity. We suggest that evaluating the evolutionary consequences of these effects requires a better integration of behavioural, ecological and evolutionary research. © 2011 Blackwell Publishing Ltd/CNRS.

Decentralized Grid Scheduling with Evolutionary Fuzzy Systems

NASA Astrophysics Data System (ADS)

Fölling, Alexander; Grimme, Christian; Lepping, Joachim; Papaspyrou, Alexander

In this paper, we address the problem of finding workload exchange policies for decentralized Computational Grids using an Evolutionary Fuzzy System. To this end, we establish a non-invasive collaboration model on the Grid layer which requires minimal information about the participating High Performance and High Throughput Computing (HPC/HTC) centers and which leaves the local resource managers completely untouched. In this environment of fully autonomous sites, independent users are assumed to submit their jobs to the Grid middleware layer of their local site, which in turn decides on the delegation and execution either on the local system or on remote sites in a situation-dependent, adaptive way. We find for different scenarios that the exchange policies show good performance characteristics not only with respect to traditional metrics such as average weighted response time and utilization, but also in terms of robustness and stability in changing environments.

In silico Evolutionary Developmental Neurobiology and the Origin of Natural Language

NASA Astrophysics Data System (ADS)

Szathmáry, Eörs; Szathmáry, Zoltán; Ittzés, Péter; Orbaán, Geroő; Zachár, István; Huszár, Ferenc; Fedor, Anna; Varga, Máté; Számadó, Szabolcs

It is justified to assume that part of our genetic endowment contributes to our language skills, yet it is impossible to tell at this moment exactly how genes affect the language faculty. We complement experimental biological studies by an in silico approach in that we simulate the evolution of neuronal networks under selection for language-related skills. At the heart of this project is the Evolutionary Neurogenetic Algorithm (ENGA) that is deliberately biomimetic. The design of the system was inspired by important biological phenomena such as brain ontogenesis, neuron morphologies, and indirect genetic encoding. Neuronal networks were selected and were allowed to reproduce as a function of their performance in the given task. The selected neuronal networks in all scenarios were able to solve the communication problem they had to face. The most striking feature of the model is that it works with highly indirect genetic encoding--just as brains do.

Genome dynamics in Legionella: the basis of versatility and adaptation to intracellular replication.

PubMed

Gomez-Valero, Laura; Buchrieser, Carmen

2013-06-01

Legionella pneumophila is a bacterial pathogen present in aquatic environments that can cause a severe pneumonia called Legionnaires' disease. Soon after its recognition, it was shown that Legionella replicates inside amoeba, suggesting that bacteria replicating in environmental protozoa are able to exploit conserved signaling pathways in human phagocytic cells. Comparative, evolutionary, and functional genomics suggests that the Legionella-amoeba interaction has shaped this pathogen more than previously thought. A complex evolutionary scenario involving mobile genetic elements, type IV secretion systems, and horizontal gene transfer among Legionella, amoeba, and other organisms seems to take place. This long-lasting coevolution led to the development of very sophisticated virulence strategies and a high level of temporal and spatial fine-tuning of bacteria host-cell interactions. We will discuss current knowledge of the evolution of virulence of Legionella from a genomics perspective and propose our vision of the emergence of this human pathogen from the environment.

Dental evidence on the hominin dispersals during the Pleistocene

PubMed Central

Martinón-Torres, M.; Bermúdez de Castro, J. M.; Gómez-Robles, A.; Arsuaga, J. L.; Carbonell, E.; Lordkipanidze, D.; Manzi, G.; Margvelashvili, A.

2007-01-01

A common assumption in the evolutionary scenario of the first Eurasian hominin populations is that they all had an African origin. This assumption also seems to apply for the Early and Middle Pleistocene populations, whose presence in Europe has been largely explained by a discontinuous flow of African emigrant waves. Only recently, some voices have speculated about the possibility of Asia being a center of speciation. However, no hard evidence has been presented to support this hypothesis. We present evidence from the most complete and up-to-date analysis of the hominin permanent dentition from Africa and Eurasia. The results show important morphological differences between the hominins found in both continents during the Pleistocene, suggesting that their evolutionary courses were relatively independent. We propose that the genetic impact of Asia in the colonization of Europe during the Early and Middle Pleistocene was stronger than that of Africa. PMID:17684093

Open Issues in Evolutionary Robotics.

PubMed

Silva, Fernando; Duarte, Miguel; Correia, Luís; Oliveira, Sancho Moura; Christensen, Anders Lyhne

2016-01-01

One of the long-term goals in evolutionary robotics is to be able to automatically synthesize controllers for real autonomous robots based only on a task specification. While a number of studies have shown the applicability of evolutionary robotics techniques for the synthesis of behavioral control, researchers have consistently been faced with a number of issues preventing the widespread adoption of evolutionary robotics for engineering purposes. In this article, we review and discuss the open issues in evolutionary robotics. First, we analyze the benefits and challenges of simulation-based evolution and subsequent deployment of controllers versus evolution on real robotic hardware. Second, we discuss specific evolutionary computation issues that have plagued evolutionary robotics: (1) the bootstrap problem, (2) deception, and (3) the role of genomic encoding and genotype-phenotype mapping in the evolution of controllers for complex tasks. Finally, we address the absence of standard research practices in the field. We also discuss promising avenues of research. Our underlying motivation is the reduction of the current gap between evolutionary robotics and mainstream robotics, and the establishment of evolutionary robotics as a canonical approach for the engineering of autonomous robots.

Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites.

PubMed

Yonezawa, Takahiro; Segawa, Takahiro; Mori, Hiroshi; Campos, Paula F; Hongoh, Yuichi; Endo, Hideki; Akiyoshi, Ayumi; Kohno, Naoki; Nishida, Shin; Wu, Jiaqi; Jin, Haofei; Adachi, Jun; Kishino, Hirohisa; Kurokawa, Ken; Nogi, Yoshifumi; Tanabe, Hideyuki; Mukoyama, Harutaka; Yoshida, Kunio; Rasoamiaramanana, Armand; Yamagishi, Satoshi; Hayashi, Yoshihiro; Yoshida, Akira; Koike, Hiroko; Akishinonomiya, Fumihito; Willerslev, Eske; Hasegawa, Masami

2017-01-09

The Palaeognathae comprise the flightless ratites and the volant tinamous, and together with the Neognathae constitute the extant members of class Aves. It is commonly believed that Palaeognathae originated in Gondwana since most of the living species are found in the Southern Hemisphere [1-3]. However, this hypothesis has been questioned because the fossil paleognaths are mostly from the Northern Hemisphere in their earliest time (Paleocene) and possessed many putative ancestral characters [4]. Uncertainties regarding the origin and evolution of Palaeognathae stem from the difficulty in estimating their divergence times [1, 2] and their remarkable morphological convergence. Here, we recovered nuclear genome fragments from extinct elephant birds, which enabled us to reconstruct a reliable phylogenomic time tree for the Palaeognathae. Based on the tree, we identified homoplasies in morphological traits of paleognaths and reconstructed their morphology-based phylogeny including fossil species without molecular data. In contrast to the prevailing theories, the fossil paleognaths from the Northern Hemisphere were placed as the basal lineages. Combined with our stable divergence time estimates that enabled a valid argument regarding the correlation with geological events, we propose a new evolutionary scenario that contradicts the traditional view. The ancestral Palaeognathae were volant, as estimated from their molecular evolutionary rates, and originated during the Late Cretaceous in the Northern Hemisphere. They migrated to the Southern Hemisphere and speciated explosively around the Cretaceous-Paleogene boundary. They then extended their distribution to the Gondwana-derived landmasses, such as New Zealand and Madagascar, by overseas dispersal. Gigantism subsequently occurred independently on each landmass. Copyright © 2017 Elsevier Ltd. All rights reserved.

Regulatory RNAs and chromatin modification in dosage compensation: a continuous path from flies to humans?

PubMed

Angelopoulou, Roxani; Lavranos, Giagkos; Manolakou, Panagiota

2008-03-20

Chromosomal sex determination is a widely distributed strategy in nature. In the most classic scenario, one sex is characterized by a homologue pair of sex chromosomes, while the other includes two morphologically and functionally distinct gonosomes. In mammalian diploid cells, the female is characterized by the presence of two identical X chromosomes, while the male features an XY pair, with the Y bearing the major genetic determinant of sex, i.e. the SRY gene. In other species, such as the fruitfly, sex is determined by the ratio of autosomes to X chromosomes. Regardless of the exact mechanism, however, all these animals would exhibit a sex-specific gene expression inequality, due to the different number of X chromosomes, a phenomenon inhibited by a series of genetic and epigenetic regulatory events described as "dosage compensation". Since adequate available data is currently restricted to worms, flies and mammals, while for other groups of animals, such as reptiles, fish and birds it is very limited, it is not yet clear whether this is an evolutionary conserved mechanism. However certain striking similarities have already been observed among evolutionary distant species, such as Drosophila melanogaster and Mus musculus. These mainly refer to a) the need for a counting mechanism, to determine the chromosomal content of the cell, i.e. the ratio of autosomes to gonosomes (a process well understood in flies, but still hypothesized in mammals), b) the implication of non-translated, sex-specific, regulatory RNAs (roX and Xist, respectively) as key elements in this process and the location of similar mediators in the Z chromosome of chicken c) the inclusion of a chromatin modification epigenetic final step, which ensures that gene expression remains stably regulated throughout the affected area of the gonosome. This review summarizes these points and proposes a possible role for comparative genetics, as they seem to constitute proof of maintained cell economy (by using the same basic regulatory elements in various different scenarios) throughout numerous centuries of evolutionary history.

Megamasers: Molecular Diagnostics of the Nuclear ISM

NASA Astrophysics Data System (ADS)

Baan, Willem A.; Klöckner, Hans-R.

Molecular emissions are powerful tracers of intense heating and star-formation processes in galactic nuclei. In this paper we consider the characteristics of molecular Megamaser emission among the population of (Ultra-) Luminous Infrared Galaxies that are powered by intense star-formation or accretion onto a massive compact object. In addition, we consider the systematic behavior of the line emission of high-density tracer molecules. An evolutionary scenario is presented for ULIRGs that may explain the molecular line ratios observed in the population of FIR galaxies.

Megamasers: Molecular Diagnostics of the Nuclear Ism

NASA Astrophysics Data System (ADS)

Baan, Willem A.; Klöckner, Hans-R.

2005-01-01

Molecular emissions are powerful tracers of intense heating and star-formation processes in galactic nuclei. In this paper we consider the characteristics of molecular Megamaser emission among the population of (Ultra-) Luminous Infrared Galaxies that are powered by intense star-formation or accretion onto a massive compact object. In addition, we consider the systematic behavior of the line emission of high-density tracer molecules. An evolutionary scenario is presented for ULIRGs that may explain the molecular line ratios observed in the population of FIR galaxies.

Satellite power system (SPS) concept definition study. Volume 3: Experimental verification definition

NASA Technical Reports Server (NTRS)

Hanley, G. M.

1980-01-01

An evolutionary Satellite Power Systems development plan was prepared. Planning analysis was directed toward the evolution of a scenario that met the stated objectives, was technically possible and economically attractive, and took into account constraining considerations, such as requirements for very large scale end-to-end demonstration in a compressed time frame, the relative cost/technical merits of ground testing versus space testing, and the need for large mass flow capability to low Earth orbit and geosynchronous orbit at reasonable cost per pound.

Kinematic signature of a rotating bar near a resonance

NASA Technical Reports Server (NTRS)

Weinberg, Martin D.

1994-01-01

Recent work based on H I, star count and emission data suggests that the Milky Way has rotating bar-like features. In this paper, I show that such features cause distinctive stellar kinematic signatures near Outer Lindblad Resonance (OLR) and Inner Lindblad Resonance (ILR). The effect of these resonances may be observable far from the peak density of the pattern and relatively nearby the solar position. The details of the kinematic signatures depend on the evolutionary history of the 'bar' and therefore velocity data, both systematic and velocity dispersion, may be used to probe the evolutionary history as well as the present state of Galaxy. Kinematic models for a variety of sample scenarios are presented. Models with evolving pattern speeds show significantly stronger dispersion signatures than those with static pattern speeds, suggesting that useful observational constraints are possible. The models are applied to the proposed rotating spheroid and bar models; we find (1) none of these models chosen to represent the proposed large-scale rotating spheroid are consistent with the stellar kinematics and (2) a Galactic bar with semimajor axis of 3 kpc will cause a large increase in velocity dispersion in the vicinity of OLR (approximately 5 kpc) with little change in the net radial motion and such a signature is suggested by K-giant velocity data. Potential future observations and analyses are discussed.

The importance of mechanisms for the evolution of cooperation

PubMed Central

van den Berg, Pieter; Weissing, Franz J.

2015-01-01

Studies aimed at explaining the evolution of phenotypic traits have often solely focused on fitness considerations, ignoring underlying mechanisms. In recent years, there has been an increasing call for integrating mechanistic perspectives in evolutionary considerations, but it is not clear whether and how mechanisms affect the course and outcome of evolution. To study this, we compare four mechanistic implementations of two well-studied models for the evolution of cooperation, the Iterated Prisoner's Dilemma (IPD) game and the Iterated Snowdrift (ISD) game. Behavioural strategies are either implemented by a 1 : 1 genotype–phenotype mapping or by a simple neural network. Moreover, we consider two different scenarios for the effect of mutations. The same set of strategies is feasible in all four implementations, but the probability that a given strategy arises owing to mutation is largely dependent on the behavioural and genetic architecture. Our individual-based simulations show that this has major implications for the evolutionary outcome. In the ISD, different evolutionarily stable strategies are predominant in the four implementations, while in the IPD each implementation creates a characteristic dynamical pattern. As a consequence, the evolved average level of cooperation is also strongly dependent on the underlying mechanism. We argue that our findings are of general relevance for the evolution of social behaviour, pleading for the integration of a mechanistic perspective in models of social evolution. PMID:26246554

Modeling Coevolution between Language and Memory Capacity during Language Origin

PubMed Central

Gong, Tao; Shuai, Lan

2015-01-01

Memory is essential to many cognitive tasks including language. Apart from empirical studies of memory effects on language acquisition and use, there lack sufficient evolutionary explorations on whether a high level of memory capacity is prerequisite for language and whether language origin could influence memory capacity. In line with evolutionary theories that natural selection refined language-related cognitive abilities, we advocated a coevolution scenario between language and memory capacity, which incorporated the genetic transmission of individual memory capacity, cultural transmission of idiolects, and natural and cultural selections on individual reproduction and language teaching. To illustrate the coevolution dynamics, we adopted a multi-agent computational model simulating the emergence of lexical items and simple syntax through iterated communications. Simulations showed that: along with the origin of a communal language, an initially-low memory capacity for acquired linguistic knowledge was boosted; and such coherent increase in linguistic understandability and memory capacities reflected a language-memory coevolution; and such coevolution stopped till memory capacities became sufficient for language communications. Statistical analyses revealed that the coevolution was realized mainly by natural selection based on individual communicative success in cultural transmissions. This work elaborated the biology-culture parallelism of language evolution, demonstrated the driving force of culturally-constituted factors for natural selection of individual cognitive abilities, and suggested that the degree difference in language-related cognitive abilities between humans and nonhuman animals could result from a coevolution with language. PMID:26544876

Population structure in relation to host-plant ecology and Wolbachia infestation in the comma butterfly.

PubMed

Kodandaramaiah, U; Weingartner, E; Janz, N; Dalén, L; Nylin, S

2011-10-01

Experimental work on Polygonia c-album, a temperate polyphagous butterfly species, has shown that Swedish, Belgian, Norwegian and Estonian females are generalists with respect to host-plant preference, whereas females from UK and Spain are specialized on Urticaceae. Female preference is known to have a strong genetic component. We test whether the specialist and generalist populations form respective genetic clusters using data from mitochondrial sequences and 10 microsatellite loci. Results do not support this hypothesis, suggesting that the specialist and generalist traits have evolved more than once independently. Mitochondrial DNA variation suggests a rapid expansion scenario, with a single widespread haplotype occurring in high frequency, whereas microsatellite data indicate strong differentiation of the Moroccan population. Based on a comparison of polymorphism in the mitochondrial data and sequences from a nuclear gene, we show that the diversity in the former is significantly less than that expected under neutral evolution. Furthermore, we found that almost all butterfly samples were infected with a single strain of Wolbachia, a maternally inherited bacterium. We reason that indirect selection on the mitochondrial genome mediated by a recent sweep of Wolbachia infection has depleted variability in the mitochondrial sequences. We also surmise that P. c-album could have expanded out of a single glacial refugium and colonized Morocco recently. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

Inactivation of tumor suppressor genes and cancer therapy: An evolutionary game theory approach.

PubMed

Khadem, Heydar; Kebriaei, Hamed; Veisi, Zahra

2017-06-01

Inactivation of alleles in tumor suppressor genes (TSG) is one of the important issues resulting in evolution of cancerous cells. In this paper, the evolution of healthy, one and two missed allele cells is modeled using the concept of evolutionary game theory and replicator dynamics. The proposed model also takes into account the interaction rates of the cells as designing parameters of the system. Different combinations of the equilibrium points of the parameterized nonlinear system is studied and categorized into some cases. In each case, the interaction rates' values are suggested in a way that the equilibrium points of the replicator dynamics are located on an appropriate region of the state space. Based on the suggested interaction rates, it is proved that the system doesn't have any undesirable interior equilibrium point as well. Therefore, the system will converge to the desirable region, where there is a scanty level of cancerous cells. In addition, the proposed conditions for interaction rates guarantee that, when a trajectory of the system reaches the boundaries, then it will stay there forever which is a desirable property since the equilibrium points have been already located on the boundaries, appropriately. The simulation results show the effectiveness of the suggestions in the elimination of the cancerous cells in different scenarios. Copyright © 2017 Elsevier Inc. All rights reserved.

Phylogenetic relationships and evolutionary history of the Mesoamerican endemic freshwater fish family Profundulidae (Cyprinodontiformes: Actinopterygii).

PubMed

Morcillo, Felipe; Ornelas-García, Claudia Patricia; Alcaraz, Lourdes; Matamoros, Wilfredo A; Doadrio, Ignacio

2016-01-01

Freshwater fishes of Profundulidae, which until now was composed of two subgenera, represent one of the few extant fish families endemic to Mesoamerica. In this study we investigated the phylogenetic relationships and evolutionary history of the eight recognized extant species (from 37 populations) of Profundulidae using three mitochondrial and one nuclear gene markers (∼2.9 Kbp). We applied a Bayesian species delimitation method as a first approach to resolving speciation patterns within Profundulidae considering two different scenarios, eight-species and twelve-species models, obtained in a previous phylogenetic analysis. Based on our results, each of the two subgenera was resolved as monophyletic, with a remarkable molecular divergence of 24.5% for mtDNA and 7.8% for nDNA uncorrected p distances, and thus we propose that they correspond to separate genera. Moreover, we propose a conservative taxonomic hypothesis with five species within Profundulus and three within Tlaloc, although both eight-species and twelve-species models were highly supported by the bayesian species delimitation analysis, providing additional evidence of higher taxonomic diversity than currently recognized in this family. According to our divergence time estimates, the family originated during the Upper Oligocene 26 Mya, and Profundulus and Tlaloc diverged in the Upper Oligocene or Lower Miocene about 20 Mya. Copyright © 2015 Elsevier Inc. All rights reserved.

Modeling Coevolution between Language and Memory Capacity during Language Origin.

PubMed

Gong, Tao; Shuai, Lan

2015-01-01

Memory is essential to many cognitive tasks including language. Apart from empirical studies of memory effects on language acquisition and use, there lack sufficient evolutionary explorations on whether a high level of memory capacity is prerequisite for language and whether language origin could influence memory capacity. In line with evolutionary theories that natural selection refined language-related cognitive abilities, we advocated a coevolution scenario between language and memory capacity, which incorporated the genetic transmission of individual memory capacity, cultural transmission of idiolects, and natural and cultural selections on individual reproduction and language teaching. To illustrate the coevolution dynamics, we adopted a multi-agent computational model simulating the emergence of lexical items and simple syntax through iterated communications. Simulations showed that: along with the origin of a communal language, an initially-low memory capacity for acquired linguistic knowledge was boosted; and such coherent increase in linguistic understandability and memory capacities reflected a language-memory coevolution; and such coevolution stopped till memory capacities became sufficient for language communications. Statistical analyses revealed that the coevolution was realized mainly by natural selection based on individual communicative success in cultural transmissions. This work elaborated the biology-culture parallelism of language evolution, demonstrated the driving force of culturally-constituted factors for natural selection of individual cognitive abilities, and suggested that the degree difference in language-related cognitive abilities between humans and nonhuman animals could result from a coevolution with language.

Local adaptation of Ruellia nudiflora (Acanthaceae) to biotic counterparts: complex scenarios revealed when two herbivore guilds are considered.

PubMed

Ortegón-Campos, I; Parra-Tabla, V; Abdala-Roberts, L; Herrera, C M

2009-11-01

This study evaluated whether the herb Ruellia nudiflora is locally adapted to a specialist insect seed predator (SP) and insect folivores, and if plant local adaptation (LA) to the former is more likely. A reciprocal transplant experiment was conducted using three sites in Yucatan (Mexico) (n = 864 plants). A third of the plants of each origin were placed at each site, and we recorded the following during a 9-month period: fruit number, leaf damage, and fruits attacked by SP. Results indicated lack of plant LA for all the variables measured. Instead, seed predation was c. 100% greater for native plants at one study site, suggesting insect LA or plant maladaptation; folivory was homogeneous across sites/origins. Based on these results, we discuss differences in the potential each herbivore guild has to promote plant LA, as well as divergent evolutionary outcomes of plant-herbivore interactions across sites.

Symbiont diversity may help coral reefs survive moderate climate change.

PubMed

Baskett, Marissa L; Gaines, Steven D; Nisbet, Roger M

2009-01-01

Given climate change, thermal stress-related mass coral-bleaching events present one of the greatest anthropogenic threats to coral reefs. While corals and their symbiotic algae may respond to future temperatures through genetic adaptation and shifts in community compositions, the climate may change too rapidly for coral response. To test this potential for response, here we develop a model of coral and symbiont ecological dynamics and symbiont evolutionary dynamics. Model results without variation in symbiont thermal tolerance predict coral reef collapse within decades under multiple future climate scenarios, consistent with previous threshold-based predictions. However, model results with genetic or community-level variation in symbiont thermal tolerance can predict coral reef persistence into the next century, provided low enough greenhouse gas emissions occur. Therefore, the level of greenhouse gas emissions will have a significant effect on the future of coral reefs, and accounting for biodiversity and biological dynamics is vital to estimating the size of this effect.

On Using Surrogates with Genetic Programming.

PubMed

Hildebrandt, Torsten; Branke, Jürgen

2015-01-01

One way to accelerate evolutionary algorithms with expensive fitness evaluations is to combine them with surrogate models. Surrogate models are efficiently computable approximations of the fitness function, derived by means of statistical or machine learning techniques from samples of fully evaluated solutions. But these models usually require a numerical representation, and therefore cannot be used with the tree representation of genetic programming (GP). In this paper, we present a new way to use surrogate models with GP. Rather than using the genotype directly as input to the surrogate model, we propose using a phenotypic characterization. This phenotypic characterization can be computed efficiently and allows us to define approximate measures of equivalence and similarity. Using a stochastic, dynamic job shop scenario as an example of simulation-based GP with an expensive fitness evaluation, we show how these ideas can be used to construct surrogate models and improve the convergence speed and solution quality of GP.

Economic viability of access broadband multiservice networks

NASA Astrophysics Data System (ADS)

Castelli, Francesco; Dammicco, Giacinto; Mocci, Ugo

1995-02-01

In this paper the economic viability of alternative architectures for optical access networks providing broad band services to different subscriber classes in a metropolitan environment, is investigated by a specific tool, NEVE (Network Economic Viability Evaluator), developed for broad band multiservice network planning, service evolutionary scenarios assessment, evaluation of tariff strategies and other actions taken at stimulating the demand growth. As the viability target can be achieved in different ways, different studies can be carried out by NEVE. In the paper some of them are discussed, particularly the ones addressed: to evaluate the impact on viability of alternative service scenarios; to determine the critical mass of broad band subscribers and the critical joint service adoption cost; to evaluate cross subsidiary policies among different subscriber classes and services; to perform sensitivity analysis with respect to variations of demand parameters and tariffs.

Reconsideration of Plant Morphological Traits: From a Structure-Based Perspective to a Function-Based Evolutionary Perspective

PubMed Central

Bai, Shu-Nong

2017-01-01

This opinion article proposes a novel alignment of traits in plant morphogenesis from a function-based evolutionary perspective. As a member species of the ecosystem on Earth, we human beings view our neighbor organisms from our own sensing system. We tend to distinguish forms and structures (i.e., “morphological traits”) mainly through vision. Traditionally, a plant was considered to be consisted of three parts, i.e., the shoot, the leaves, and the root. Based on such a “structure-based perspective,” evolutionary analyses or comparisons across species were made on particular parts or their derived structures. So far no conceptual framework has been established to incorporate the morphological traits of all three land plant phyta, i.e., bryophyta, pteridophyta and spermatophyta, for evolutionary developmental analysis. Using the tenets of the recently proposed concept of sexual reproduction cycle, the major morphological traits of land plants can be aligned into five categories from a function-based evolutionary perspective. From this perspective, and the resulting alignment, a new conceptual framework emerges, called “Plant Morphogenesis 123.” This framework views a plant as a colony of integrated plant developmental units that are each produced via one life cycle. This view provided an alternative perspective for evolutionary developmental investigation in plants. PMID:28360919

Evolving learning rules and emergence of cooperation in spatial prisoner's dilemma.

PubMed

Moyano, Luis G; Sánchez, Angel

2009-07-07

In the evolutionary Prisoner's dilemma (PD) game, agents play with each other and update their strategies in every generation according to some microscopic dynamical rule. In its spatial version, agents do not play with every other but, instead, interact only with their neighbours, thus mimicking the existing of a social or contact network that defines who interacts with whom. In this work, we explore evolutionary, spatial PD systems consisting of two types of agents, each with a certain update (reproduction, learning) rule. We investigate two different scenarios: in the first case, update rules remain fixed for the entire evolution of the system; in the second case, agents update both strategy and update rule in every generation. We show that in a well-mixed population the evolutionary outcome is always full defection. We subsequently focus on two-strategy competition with nearest-neighbour interactions on the contact network and synchronised update of strategies. Our results show that, for an important range of the parameters of the game, the final state of the system is largely different from that arising from the usual setup of a single, fixed dynamical rule. Furthermore, the results are also very different if update rules are fixed or evolve with the strategies. In these respect, we have studied representative update rules, finding that some of them may become extinct while others prevail. We describe the new and rich variety of final outcomes that arise from this co-evolutionary dynamics. We include examples of other neighbourhoods and asynchronous updating that confirm the robustness of our conclusions. Our results pave the way to an evolutionary rationale for modelling social interactions through game theory with a preferred set of update rules.

A case study of bats and white-nose syndrome demonstrating how to model population viability with evolutionary effects.

PubMed

Maslo, Brooke; Fefferman, Nina H

2015-08-01

Ecological factors generally affect population viability on rapid time scales. Traditional population viability analyses (PVA) therefore focus on alleviating ecological pressures, discounting potential evolutionary impacts on individual phenotypes. Recent studies of evolutionary rescue (ER) focus on cases in which severe, environmentally induced population bottlenecks trigger a rapid evolutionary response that can potentially reverse demographic threats. ER models have focused on shifting genetics and resulting population recovery, but no one has explored how to incorporate those findings into PVA. We integrated ER into PVA to identify the critical decision interval for evolutionary rescue (DIER) under which targeted conservation action should be applied to buffer populations undergoing ER against extinction from stochastic events and to determine the most appropriate vital rate to target to promote population recovery. We applied this model to little brown bats (Myotis lucifugus) affected by white-nose syndrome (WNS), a fungal disease causing massive declines in several North American bat populations. Under the ER scenario, the model predicted that the DIER period for little brown bats was within 11 years of initial WNS emergence, after which they stabilized at a positive growth rate (λ = 1.05). By comparing our model results with population trajectories of multiple infected hibernacula across the WNS range, we concluded that ER is a potential explanation of observed little brown bat population trajectories across multiple hibernacula within the affected range. Our approach provides a tool that can be used by all managers to provide testable hypotheses regarding the occurrence of ER in declining populations, suggest empirical studies to better parameterize the population genetics and conservation-relevant vital rates, and identify the DIER period during which management strategies will be most effective for species conservation. © 2015 Society for Conservation Biology.

Core collapse supernovae from blue supergiant progenitors : The evolutionary history of SN 1987A

NASA Astrophysics Data System (ADS)

Menon, Athira

2015-08-01

SN 1987A is historically one of the most remarkable supernova explosions to be seen from Earth. Due to the proximity of its location in the LMC, it remains the most well-studied object outside the solar system. It was also the only supernova whose progenitor was observed prior to its explosion.SN 1987A however, was a unique and enigmatic core collapse supernova. It was the first Type II supernova to have been observed to have exploded while its progenitor was a blue supergiant (BSG). Until then Type II supernovae were expected to originate from explosions of red supergiants (RSGs). A spectacular triple-ring nebula structure, rich in helium and nitrogen, was observed around the remnant, indicating a recent RSG phase before becoming a BSG. Even today it is not entirely understood what the evolutionary history may have been to cause a BSG to explode. The most commonly accepted hypothesis for its origin is the merger of a massive binary star system.An evolutionary scenario for such a binary system, was proposed by Podsiadlowski (1992) (P92). Through SPH simulations of the merger and the stellar evolution of the post-merger remnant, Ivanova & Podsiadlowski (2002) and (2003) (I&M) could successfully obtain the RSG to BSG transition of the progenitor.The aim of the present work is to produce the evolutionary history of the progenitor of SN 1987A and its explosion. We construct our models based on the results of P92 and I&M. Here, the secondary (less massive) star is accreted on the primary, while being simultaneously mixed in its envelope over a period of 100 years. The merged star is evolved until the onset of core collapse. For this work we use the 1-dimensional, implicit, hydrodynamical stellar evolution code, KEPLER. A large parameter space is explored, consisting of primary (16-20 Ms) and secondary masses (5-8 Ms), mixing boundaries, and accreting timescales. Those models whose end states match the observed properties of the progenitor of SN 1987A are exploded. The nuclear yields and light curve of the explosion are then compared with the observed data of SN 1987A.

Scalable computing for evolutionary genomics.

PubMed

Prins, Pjotr; Belhachemi, Dominique; Möller, Steffen; Smant, Geert

2012-01-01

Genomic data analysis in evolutionary biology is becoming so computationally intensive that analysis of multiple hypotheses and scenarios takes too long on a single desktop computer. In this chapter, we discuss techniques for scaling computations through parallelization of calculations, after giving a quick overview of advanced programming techniques. Unfortunately, parallel programming is difficult and requires special software design. The alternative, especially attractive for legacy software, is to introduce poor man's parallelization by running whole programs in parallel as separate processes, using job schedulers. Such pipelines are often deployed on bioinformatics computer clusters. Recent advances in PC virtualization have made it possible to run a full computer operating system, with all of its installed software, on top of another operating system, inside a "box," or virtual machine (VM). Such a VM can flexibly be deployed on multiple computers, in a local network, e.g., on existing desktop PCs, and even in the Cloud, to create a "virtual" computer cluster. Many bioinformatics applications in evolutionary biology can be run in parallel, running processes in one or more VMs. Here, we show how a ready-made bioinformatics VM image, named BioNode, effectively creates a computing cluster, and pipeline, in a few steps. This allows researchers to scale-up computations from their desktop, using available hardware, anytime it is required. BioNode is based on Debian Linux and can run on networked PCs and in the Cloud. Over 200 bioinformatics and statistical software packages, of interest to evolutionary biology, are included, such as PAML, Muscle, MAFFT, MrBayes, and BLAST. Most of these software packages are maintained through the Debian Med project. In addition, BioNode contains convenient configuration scripts for parallelizing bioinformatics software. Where Debian Med encourages packaging free and open source bioinformatics software through one central project, BioNode encourages creating free and open source VM images, for multiple targets, through one central project. BioNode can be deployed on Windows, OSX, Linux, and in the Cloud. Next to the downloadable BioNode images, we provide tutorials online, which empower bioinformaticians to install and run BioNode in different environments, as well as information for future initiatives, on creating and building such images.

Evolution of an accretion disc in binary black hole systems

NASA Astrophysics Data System (ADS)

Kimura, Shigeo S.; Takahashi, Sanemichi Z.; Toma, Kenji

2017-03-01

We investigate evolution of an accretion disc in binary black hole (BBH) systems and possible electromagnetic counterparts of the gravitational waves from mergers of BBHs. Perna et al. proposed a novel evolutionary scenario of an accretion disc in BBHs in which a disc eventually becomes 'dead', I.e. the magnetorotational instability (MRI) becomes inactive. In their scenario, the dead disc survives until a few seconds before the merger event. We improve the dead disc model and propose another scenario, taking account of effects of the tidal torque from the companion and the critical ionization degree for MRI activation more carefully. We find that the mass of the dead disc is much lower than that in the Perna's scenario. When the binary separation sufficiently becomes small, the mass inflow induced by the tidal torque reactivates MRI, restarting mass accretion on to the black hole. We also find that this disc 'revival' happens more than thousands of years before the merger. The mass accretion induced by the tidal torque increases as the separation decreases, and a relativistic jet could be launched before the merger. The emissions from these jets are too faint compared to gamma-ray bursts, but detectable if the merger events happen within ≲10 Mpc or if the masses of the black holes are as massive as ˜105 M⊙.

Nervous systems and scenarios for the invertebrate-to-vertebrate transition.

PubMed

Holland, Nicholas D

2016-01-05

Older evolutionary scenarios for the origin of vertebrates often gave nervous systems top billing in accordance with the notion that a big-brained Homo sapiens crowned a tree of life shaped mainly by progressive evolution. Now, however, tree thinking positions all extant organisms equidistant from the tree's root, and molecular phylogenies indicate that regressive evolution is more common than previously suspected. Even so, contemporary theories of vertebrate origin still focus on the nervous system because of its functional importance, its richness in characters for comparative biology, and its central position in the two currently prominent scenarios for the invertebrate-to-vertebrate transition, which grew out of the markedly neurocentric annelid and enteropneust theories of the nineteenth century. Both these scenarios compare phyla with diverse overall body plans. This diversity, exacerbated by the scarcity of relevant fossil data, makes it challenging to establish plausible homologies between component parts (e.g. nervous system regions). In addition, our current understanding of the relation between genotype and phenotype is too preliminary to permit us to convert gene network data into structural features in any simple way. These issues are discussed here with special reference to the evolution of nervous systems during proposed transitions from invertebrates to vertebrates. © 2015 The Author(s).

Combining fossil and molecular data to date the diversification of New World Primates.

PubMed

Schrago, C G; Mello, B; Soares, A E R

2013-11-01

Recent methodological advances in molecular dating associated with the growing availability of sequence data have prompted the study of the evolution of New World Anthropoidea in recent years. Motivated by questions regarding historical biogeography or the mode of evolution, these works aimed to obtain a clearer scenario of Platyrrhini origins and diversification. Although some consensus was found, disputed issues, especially those relating to the evolutionary affinities of fossil taxa, remain. The use of fossil taxa for divergence time analysis is traditionally restricted to the provision of calibration priors. However, new analytical approaches have been developed that incorporate fossils as terminals and, thus, directly assign ages to the fossil tips. In this study, we conducted a combined analysis of molecular and morphological data, including fossils, to derive the timescale of New World anthropoids. Differently from previous studies that conducted total-evidence analysis of molecules and morphology, our approach investigated the morphological clock alone. Our results corroborate the hypothesis that living platyrrhines diversified in the last 20 Ma and that Miocene Patagonian fossils compose an independent evolutionary radiation that diversified in the late Oligocene. When compared to the node ages inferred from the molecular timescale, the inclusion of fossils augmented the precision of the estimates for nodes constrained by the fossil tips. We show that morphological data can be analysed using the same methodological framework applied in relaxed molecular clock studies. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Evolutionary Study of Interethnic Cooperation

NASA Astrophysics Data System (ADS)

Kvasnicka, Vladimir; Pospichal, Jiri

The purpose of this communication is to present an evolutionary study of cooperation between two ethnic groups. The used model is stimulated by the seminal paper of J. D. Fearon and D. D. Laitin (Explaining Interethnic Cooperation, American Political Science Review, 90 (1996), pp. 715-735), where the iterated prisoner's dilemma was used to model intra- and interethnic interactions. We reformulated their approach in a form of evolutionary prisoner's dilemma method, where a population of strategies is evolved by applying simple reproduction process with a Darwin metaphor of natural selection (a probability of selection to the reproduction is proportional to a fitness). Our computer simulations show that an application of a principle of collective guilt does not lead to an emergence of an interethnic cooperation. When an administrator is introduced, then an emergence of interethnic cooperation may be observed. Furthermore, if the ethnic groups are of very different sizes, then the principle of collective guilt may be very devastating for smaller group so that intraethnic cooperation is destroyed. The second strategy of cooperation is called the personal responsibility, where agents that defected within interethnic interactions are punished inside of their ethnic groups. It means, unlikely to the principle of collective guilt, that there exists only one type of punishment, loosely speaking, agents are punished "personally." All the substantial computational results were checked and interpreted analytically within the theory of evolutionary stable strategies. Moreover, this theoretical approach offers mechanisms of simple scenarios explaining why some particular strategies are stable or not.

Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hot spot: a statistical phylogeographic study using a low-dispersal organism.

PubMed

Álvarez-Presas, M; Sánchez-Gracia, A; Carbayo, F; Rozas, J; Riutort, M

2014-06-01

The relative importance of the processes that generate and maintain biodiversity is a major and controversial topic in evolutionary biology with large implications for conservation management. The Atlantic Forest of Brazil, one of the world's richest biodiversity hot spots, is severely damaged by human activities. To formulate an efficient conservation policy, a good understanding of spatial and temporal biodiversity patterns and their underlying evolutionary mechanisms is required. With this aim, we performed a comprehensive phylogeographic study using a low-dispersal organism, the land planarian species Cephaloflexa bergi (Platyhelminthes, Tricladida). Analysing multi-locus DNA sequence variation under the Approximate Bayesian Computation framework, we evaluated two scenarios proposed to explain the diversity of Southern Atlantic Forest (SAF) region. We found that most sampled localities harbour high levels of genetic diversity, with lineages sharing common ancestors that predate the Pleistocene. Remarkably, we detected the molecular hallmark of the isolation-by-distance effect and little evidence of a recent colonization of SAF localities; nevertheless, some populations might result from very recent secondary contacts. We conclude that extant SAF biodiversity originated and has been shaped by complex interactions between ancient geological events and more recent evolutionary processes, whereas Pleistocene climate changes had a minor influence in generating present-day diversity. We also demonstrate that land planarians are an advantageous biological model for making phylogeographic and, particularly, fine-scale evolutionary inferences, and propose appropriate conservation policies.

Adding flexibility to the search for robust portfolios in non-linear water resource planning

NASA Astrophysics Data System (ADS)

Tomlinson, James; Harou, Julien

2017-04-01

To date robust optimisation of water supply systems has sought to find portfolios or strategies that are robust to a range of uncertainties or scenarios. The search for a single portfolio that is robust in all scenarios is necessarily suboptimal compared to portfolios optimised for a single scenario deterministic future. By contrast establishing a separate portfolio for each future scenario is unhelpful to the planner who must make a single decision today under deep uncertainty. In this work we show that a middle ground is possible by allowing a small number of different portfolios to be found that are each robust to a different subset of the global scenarios. We use evolutionary algorithms and a simple water resource system model to demonstrate this approach. The primary contribution is to demonstrate that flexibility can be added to the search for portfolios, in complex non-linear systems, at the expense of complete robustness across all future scenarios. In this context we define flexibility as the ability to design a portfolio in which some decisions are delayed, but those decisions that are not delayed are themselves shown to be robust to the future. We recognise that some decisions in our portfolio are more important than others. An adaptive portfolio is found by allowing no flexibility for these near-term "important" decisions, but maintaining flexibility in the remaining longer term decisions. In this sense we create an effective 2-stage decision process for a non-linear water resource supply system. We show how this reduces a measure of regret versus the inflexible robust solution for the same system.

Europa's Crust and Ocean: Origin, Composition, and the Prospects for Life

USGS Publications Warehouse

Kargel, J.S.; Kaye, J.Z.; Head, J. W.; Marion, G.M.; Sassen, R.; Crowley, J.K.; Ballesteros, O.P.; Grant, S.A.; Hogenboom, D.L.

2000-01-01

We have considered a wide array of scenarios for Europa's chemical evolution in an attempt to explain the presence of ice and hydrated materials on its surface and to understand the physical and chemical nature of any ocean that may lie below. We postulate that, following formation of the jovian system, the europan evolutionary sequence has as its major links: (a) initial carbonaceous chondrite rock, (b) global primordial aqueous differentiation and formation of an impure primordial hydrous crust, (c) brine evolution and intracrustal differentiation, (d) degassing of Europa's mantle and gas venting, (e) hydrothermal processes, and (f) chemical surface alteration. Our models were developed in the context of constraints provided by Galileo imaging, near infrared reflectance spectroscopy, and gravity and magnetometer data. Low-temperature aqueous differentiation from a carbonaceous CI or CM chondrite precursor, without further chemical processing, would result in a crust/ocean enriched in magnesium sulfate and sodium sulfate, consistent with Galileo spectroscopy. Within the bounds of this simple model, a wide range of possible layered structures may result; the final state depends on the details of intracrustal differentiation. Devolatilization of the rocky mantle and hydrothermal brine reactions could have produced very different ocean/crust compositions, e.g., an ocean/crust of sodium carbonate or sulfuric acid, or a crust containing abundant clathrate hydrates. Realistic chemical-physical evolution scenarios differ greatly in detailed predictions, but they generally call for a highly impure and chemically layered crust. Some of these models could lead also to lateral chemical heterogeneities by diapiric upwellings and/or cryovolcanism. We describe some plausible geological consequences of the physical-chemical structures predicted from these scenarios. These predicted consequences and observed aspects of Europa's geology may serve as a basis for further analys is and discrimination among several alternative scenarios. Most chemical pathways could support viable ecosystems based on analogy with the metabolic and physiological versatility of terrestrial microorganisms. ?? 2000 Academic Press.

Chemical abundances of the PRGs UGC 7576 and UGC 9796. I. Testing the formation scenario

NASA Astrophysics Data System (ADS)

Spavone, M.; Iodice, E.; Arnaboldi, M.; Longo, G.; Gerhard, O.

2011-07-01

Context. The study of both the chemical abundances of HII regions in polar ring galaxies and their implications for the evolutionary scenario of these systems has been a step forward both in tracing the formation history of the galaxy and giving hints toward the mechanisms at work during the building of a disk by cold accretion process. It is now important to establish whether such results are typical of the class of polar disk galaxies as a whole. Aims: The present work aims at checking the cold accretion of gas through a "cosmic filament" as a possible scenario for the formation of the polar structures in UGC 7576 and UGC 9796. If these form by cold accretion, we expect the HII regions abundances and metallicities to be lower than those of same-luminosity spiral disks, with values of Z ~ 1/10 Z⊙, as predicted by cosmological simulations. Methods: We used deep long-slit spectra, obtained with DOLORES@TNG in the optical wavelengths, of the brightest HII regions associated with the polar structures to derive their chemical abundances and star formation rate. We used the empirical methods, based on the intensities of easily observable lines, to derive the oxygen abundance 12 + log (O/H) of both galaxies. Such values are compared with those typical of different morphological galaxy types of comparable luminosity. Results: The average metallicity values for UGC 7576 and UGC 9796 are Z = 0.4 Z⊙ and Z = 0.1 Z⊙, respectively. Both values are lower than those measured for ordinary spirals of similar luminosity, and UGC 7576 presents no metallicity gradient along the polar structure. These data, together with other observed features available for the two PRGs in previous works, are compared with the predictions of simulations of tidal accretion, cold accretion, and merging to disentangle these scenarios.

Noise-induced bistability in the quasi-neutral coexistence of viral RNAs under different replication modes.

PubMed

Sardanyés, Josep; Arderiu, Andreu; Elena, Santiago F; Alarcón, Tomás

2018-05-01

Evolutionary and dynamical investigations into real viral populations indicate that RNA replication can range between the two extremes represented by so-called 'stamping machine replication' (SMR) and 'geometric replication' (GR). The impact of asymmetries in replication for single-stranded (+) sense RNA viruses has been mainly studied with deterministic models. However, viral replication should be better described by including stochasticity, as the cell infection process is typically initiated with a very small number of RNA macromolecules, and thus largely influenced by intrinsic noise. Under appropriate conditions, deterministic theoretical descriptions of viral RNA replication predict a quasi-neutral coexistence scenario, with a line of fixed points involving different strands' equilibrium ratios depending on the initial conditions. Recent research into the quasi-neutral coexistence in two competing populations reveals that stochastic fluctuations fundamentally alter the mean-field scenario, and one of the two species outcompetes the other. In this article, we study this phenomenon for viral RNA replication modes by means of stochastic simulations and a diffusion approximation. Our results reveal that noise has a strong impact on the amplification of viral RNAs, also causing the emergence of noise-induced bistability. We provide analytical criteria for the dominance of (+) sense strands depending on the initial populations on the line of equilibria, which are in agreement with direct stochastic simulation results. The biological implications of this noise-driven mechanism are discussed within the framework of the evolutionary dynamics of RNA viruses with different modes of replication. © 2018 The Author(s).

On the origin of life in the Zinc world: 1. Photosynthesizing, porous edifices built of hydrothermally precipitated zinc sulfide as cradles of life on Earth

PubMed Central

2009-01-01

Background The complexity of the problem of the origin of life has spawned a large number of possible evolutionary scenarios. Their number, however, can be dramatically reduced by the simultaneous consideration of various bioenergetic, physical, and geological constraints. Results This work puts forward an evolutionary scenario that satisfies the known constraints by proposing that life on Earth emerged, powered by UV-rich solar radiation, at photosynthetically active porous edifices made of precipitated zinc sulfide (ZnS) similar to those found around modern deep-sea hydrothermal vents. Under the high pressure of the primeval, carbon dioxide-dominated atmosphere ZnS could precipitate at the surface of the first continents, within reach of solar light. It is suggested that the ZnS surfaces (1) used the solar radiation to drive carbon dioxide reduction, yielding the building blocks for the first biopolymers, (2) served as templates for the synthesis of longer biopolymers from simpler building blocks, and (3) prevented the first biopolymers from photo-dissociation, by absorbing from them the excess radiation. In addition, the UV light may have favoured the selective enrichment of photostable, RNA-like polymers. Falsification tests of this hypothesis are described in the accompanying article (A.Y. Mulkidjanian, M.Y. Galperin, Biology Direct 2009, 4:27). Conclusion The suggested "Zn world" scenario identifies the geological conditions under which photosynthesizing ZnS edifices of hydrothermal origin could emerge and persist on primordial Earth, includes a mechanism of the transient storage and utilization of solar light for the production of diverse organic compounds, and identifies the driving forces and selective factors that could have promoted the transition from the first simple, photostable polymers to more complex living organisms. Reviewers This paper was reviewed by Arcady Mushegian, Simon Silver (nominated by Arcady Mushegian), Antoine Danchin (nominated by Eugene Koonin) and Dieter Braun (nominated by Sergey Maslov). PMID:19703272

Predicted extinction of unique genetic diversity in marine forests of Cystoseira spp.

PubMed

Buonomo, Roberto; Chefaoui, Rosa M; Lacida, Ricardo Bermejo; Engelen, Aschwin H; Serrão, Ester A; Airoldi, Laura

2018-07-01

Climate change is inducing shifts in species ranges across the globe. These can affect the genetic pools of species, including loss of genetic variability and evolutionary potential. In particular, geographically enclosed ecosystems, like the Mediterranean Sea, have a higher risk of suffering species loss and genetic erosion due to barriers to further range shifts and to dispersal. In this study, we address these questions for three habitat-forming seaweed species, Cystoseira tamariscifolia, C. amentacea and C. compressa, throughout their entire ranges in the Atlantic and Mediterranean regions. We aim to 1) describe their population genetic structure and diversity, 2) model the present and predict the future distribution and 3) assess the consequences of predicted future range shifts for their population genetic structure, according to two contrasting future climate change scenarios. A net loss of suitable areas was predicted in both climatic scenarios across the range of distribution of the three species. This loss was particularly severe for C. amentacea in the Mediterranean Sea (less 90% in the most extreme climatic scenario), suggesting that the species could become potentially at extinction risk. For all species, genetic data showed very differentiated populations, indicating low inter-population connectivity, and high and distinct genetic diversity in areas that were predicted to become lost, causing erosion of unique evolutionary lineages. Our results indicated that the Mediterranean Sea is the most threatened region, where future suitable Cystoseira habitats will become more limited. This is likely to have wider ecosystem impacts as there is a lack of species with the same ecological niche and functional role in the Mediterranean. The projected accelerated loss of already fragmented and disturbed populations and the long-term genetic effects highlight the urge for local scale management strategies that sustain the capacity of these habitat-forming species to persist despite climatic impacts while waiting for global emission reductions. Copyright © 2018 Elsevier Ltd. All rights reserved.

An Orthogonal Evolutionary Algorithm With Learning Automata for Multiobjective Optimization.

PubMed

Dai, Cai; Wang, Yuping; Ye, Miao; Xue, Xingsi; Liu, Hailin

2016-12-01

Research on multiobjective optimization problems becomes one of the hottest topics of intelligent computation. In order to improve the search efficiency of an evolutionary algorithm and maintain the diversity of solutions, in this paper, the learning automata (LA) is first used for quantization orthogonal crossover (QOX), and a new fitness function based on decomposition is proposed to achieve these two purposes. Based on these, an orthogonal evolutionary algorithm with LA for complex multiobjective optimization problems with continuous variables is proposed. The experimental results show that in continuous states, the proposed algorithm is able to achieve accurate Pareto-optimal sets and wide Pareto-optimal fronts efficiently. Moreover, the comparison with the several existing well-known algorithms: nondominated sorting genetic algorithm II, decomposition-based multiobjective evolutionary algorithm, decomposition-based multiobjective evolutionary algorithm with an ensemble of neighborhood sizes, multiobjective optimization by LA, and multiobjective immune algorithm with nondominated neighbor-based selection, on 15 multiobjective benchmark problems, shows that the proposed algorithm is able to find more accurate and evenly distributed Pareto-optimal fronts than the compared ones.

Evolution, appearance, and occupational success.

PubMed

Little, Anthony C; Roberts, Craig S

2012-01-01

Visual characteristics, including facial appearance, are thought to play an important role in a variety of judgments and decisions that have real occupational outcomes in many settings. Indeed, there is growing evidence suggesting that appearance influences hiring decisions and even election results. For example, attractive individuals are more likely to be hired, taller men earn more, and the facial appearance of candidates has been linked to real election outcomes. In this article, we review evidence linking physical appearance to occupational success and evaluate the hypothesis that appearance based biases are consistent with predictions based on evolutionary theories of coalition formation and leadership choice. We discuss why appearance based effects are so pervasive, addressing ideas about a "kernel of truth" in attributions and about coalitional psychology. We additionally highlight that appearance may be differently related to success at work according to the types of job or task involved. For example, leaders may be chosen because the characteristics they possess are seen as best suited to lead in particular situations. During a time of war, a dominant-appearing leader may inspire confidence and intimidate enemies while during peace-time, when negotiation and diplomacy are needed, interpersonal skills may outweigh the value of a dominant leader. In line with these ideas, masculine-faced leaders are favored in war-time scenarios while feminine-faced leaders are favored in peace-time scenarios. We suggest that such environment or task specific competencies may be prevalent during selection processes, whereby individuals whose appearance best matches perceived task competences are most likely selected, and propose the general term "task-congruent selection" to describe these effects. Overall, our review highlights how potentially adaptive biases could influence choices in the work place. With respect to certain biases, understanding their origin and current prevalence is important in order to potentially reduce discrimination in the work place.

Social Media: Menagerie of Metrics

DTIC Science & Technology

2010-01-27

intelligence, an evolutionary algorithm (EA) is a subset of evolutionary computation, a generic population-based metaheuristic optimization algorithm . An EA...Cloning - 22 Animals were cloned to date; genetic algorithms can help prediction (e.g. “elitism” - attempts to ensure selection by including performers...28, 2010 Evolutionary Algorithm • Evolutionary algorithm From Wikipedia, the free encyclopedia Artificial intelligence portal In artificial

On the challenges and mechanisms of embodied decisions

PubMed Central

Cisek, Paul; Pastor-Bernier, Alexandre

2014-01-01

Neurophysiological studies of decision-making have focused primarily on elucidating the mechanisms of classic economic decisions, for which the relevant variables are the values of expected outcomes and action is simply the means of reporting the selected choice. By contrast, here we focus on the particular challenges of embodied decision-making faced by animals interacting with their environment in real time. In such scenarios, the choices themselves as well as their relative costs and benefits are defined by the momentary geometry of the immediate environment and change continuously during ongoing activity. To deal with the demands of embodied activity, animals require an architecture in which the sensorimotor specification of potential actions, their valuation, selection and even execution can all take place in parallel. Here, we review behavioural and neurophysiological data supporting a proposed brain architecture for dealing with such scenarios, which we argue set the evolutionary foundation for the organization of the mammalian brain. PMID:25267821

A challenge to dSph formation models: are the most isolated Local Group dSph galaxies truly old?

NASA Astrophysics Data System (ADS)

Monelli, Matteo

2017-08-01

What is the origin of the different dwarf galaxy types? The classification into dwarf irregular (dIrr), spheroidal (dSph), and transition (dT) types is based on their present-day properties. However, star formation histories (SFHs) reconstructed from deep color-magnitude diagrams (CMDs) provide details on the early evolution of galaxies of all these types, and indicate only two basic evolutionary paths. One is characterized by a vigorous but brief initial star-forming event, and little or no star formation thereafter (fast evolution), and the other one by roughly continuous star formation until (nearly) the present time (slow evolution). These two paths do not map directly onto the dIrr, dT and dSph types. Thus, the present galaxy properties do not reflect their lifetime evolution. Since there are some indications that slow dwarfs were assembled in lower-density environments than fast dwarfs, Gallart et al (2015) proposed that the distinction between fast and slow dwarfs reflects the characteristic density of the environment where they formed. This scenario, and more generally scenarios where dSph galaxies formed through the interaction with a massive galaxy, are challenged by a small sample of extremely isolated dSph/dT in the outer fringes of the Local Group. This proposal targets two of these objects (VV124, KKR25) for which we will infer their SFH - through a novel technique that combines the information from their RR Lyrae stars and deep CMDs sampling the intermediate-age population - in order to test these scenarios. This is much less demanding on observing time than classical SFH derivation using full depth CMDs.

Antagonistic versus non-antagonistic models of balancing selection: Characterizing the relative timescales and hitchhiking effects of partial selective sweeps

PubMed Central

Connallon, Tim; Clark, Andrew G.

2012-01-01

Antagonistically selected alleles -- those with opposing fitness effects between sexes, environments, or fitness components -- represent an important component of additive genetic variance in fitness-related traits, with stably balanced polymorphisms often hypothesized to contribute to observed quantitative genetic variation. Balancing selection hypotheses imply that intermediate-frequency alleles disproportionately contribute to genetic variance of life history traits and fitness. Such alleles may also associate with population genetic footprints of recent selection, including reduced genetic diversity and inflated linkage disequilibrium at linked, neutral sites. Here, we compare the evolutionary dynamics of different balancing selection models, and characterize the evolutionary timescale and hitchhiking effects of partial selective sweeps generated under antagonistic versus non-antagonistic (e.g., overdominant and frequency-dependent selection) processes. We show that that the evolutionary timescales of partial sweeps tend to be much longer, and hitchhiking effects are drastically weaker, under scenarios of antagonistic selection. These results predict an interesting mismatch between molecular population genetic and quantitative genetic patterns of variation. Balanced, antagonistically selected alleles are expected to contribute more to additive genetic variance for fitness than alleles maintained by classic, non-antagonistic mechanisms. Nevertheless, classical mechanisms of balancing selection are much more likely to generate strong population genetic signatures of recent balancing selection. PMID:23461340

Phylogenomics of palearctic Formica species suggests a single origin of temporary parasitism and gives insights to the evolutionary pathway toward slave-making behaviour.

PubMed

Romiguier, Jonathan; Rolland, Jonathan; Morandin, Claire; Keller, Laurent

2018-03-28

The ants of the Formica genus are classical model species in evolutionary biology. In particular, Darwin used Formica as model species to better understand the evolution of slave-making, a parasitic behaviour where workers of another species are stolen to exploit their workforce. In his book "On the Origin of Species" (1859), Darwin first hypothesized that slave-making behaviour in Formica evolved in incremental steps from a free-living ancestor. The absence of a well-resolved phylogenetic tree of the genus prevent an assessment of whether relationships among Formica subgenera are compatible with this scenario. In this study, we resolve the relationships among the 4 palearctic Formica subgenera (Formica str. s., Coptoformica, Raptiformica and Serviformica) using a phylogenomic dataset of 945 genes for 16 species. We provide a reference tree resolving the relationships among the main Formica subgenera with high bootstrap supports. The branching order of our tree suggests that the free-living lifestyle is ancestral in the Formica genus and that parasitic colony founding could have evolved a single time, probably acting as a pre-adaptation to slave-making behaviour. This phylogenetic tree provides a solid backbone for future evolutionary studies in the Formica genus and slave-making behaviour.

Inferring Fitness Effects from Time-Resolved Sequence Data with a Delay-Deterministic Model

PubMed Central

Nené, Nuno R.; Dunham, Alistair S.; Illingworth, Christopher J. R.

2018-01-01

A common challenge arising from the observation of an evolutionary system over time is to infer the magnitude of selection acting upon a specific genetic variant, or variants, within the population. The inference of selection may be confounded by the effects of genetic drift in a system, leading to the development of inference procedures to account for these effects. However, recent work has suggested that deterministic models of evolution may be effective in capturing the effects of selection even under complex models of demography, suggesting the more general application of deterministic approaches to inference. Responding to this literature, we here note a case in which a deterministic model of evolution may give highly misleading inferences, resulting from the nondeterministic properties of mutation in a finite population. We propose an alternative approach that acts to correct for this error, and which we denote the delay-deterministic model. Applying our model to a simple evolutionary system, we demonstrate its performance in quantifying the extent of selection acting within that system. We further consider the application of our model to sequence data from an evolutionary experiment. We outline scenarios in which our model may produce improved results for the inference of selection, noting that such situations can be easily identified via the use of a regular deterministic model. PMID:29500183

Turning gold into ‘junk’: transposable elements utilize central proteins of cellular networks

PubMed Central

Abrusán, György; Szilágyi, András; Zhang, Yang; Papp, Balázs

2013-01-01

The numerous discovered cases of domesticated transposable element (TE) proteins led to the recognition that TEs are a significant source of evolutionary innovation. However, much less is known about the reverse process, whether and to what degree the evolution of TEs is influenced by the genome of their hosts. We addressed this issue by searching for cases of incorporation of host genes into the sequence of TEs and examined the systems-level properties of these genes using the Saccharomyces cerevisiae and Drosophila melanogaster genomes. We identified 51 cases where the evolutionary scenario was the incorporation of a host gene fragment into a TE consensus sequence, and we show that both the yeast and fly homologues of the incorporated protein sequences have central positions in the cellular networks. An analysis of selective pressure (Ka/Ks ratio) detected significant selection in 37% of the cases. Recent research on retrovirus-host interactions shows that virus proteins preferentially target hubs of the host interaction networks enabling them to take over the host cell using only a few proteins. We propose that TEs face a similar evolutionary pressure to evolve proteins with high interacting capacities and take some of the necessary protein domains directly from their hosts. PMID:23341038

Advances in the Neuroscience of Intelligence: from Brain Connectivity to Brain Perturbation.

PubMed

Santarnecchi, Emiliano; Rossi, Simone

2016-12-06

Our view is that intelligence, as expression of the complexity of the human brain and of its evolutionary path, represents an intriguing example of "system level brain plasticity": tangible proofs of this assertion lie in the strong links intelligence has with vital brain capacities as information processing (i.e., pure, rough capacity to transfer information in an efficient way), resilience (i.e., the ability to cope with loss of efficiency and/or loss of physical elements in a network) and adaptability (i.e., being able to efficiently rearrange its dynamics in response to environmental demands). Current evidence supporting this view move from theoretical models correlating intelligence and individual response to systematic "lesions" of brain connectivity, as well as from the field of Noninvasive Brain Stimulation (NiBS). Perturbation-based approaches based on techniques as transcranial magnetic stimulation (TMS) and transcranial alternating current stimulation (tACS), are opening new in vivo scenarios which could allow to disclose more causal relationship between intelligence and brain plasticity, overcoming the limitations of brain-behavior correlational evidence.

An Assessment of Phylogenetic Tools for Analyzing the Interplay Between Interspecific Interactions and Phenotypic Evolution.

PubMed

Drury, J P; Grether, G F; Garland, T; Morlon, H

2018-05-01

Much ecological and evolutionary theory predicts that interspecific interactions often drive phenotypic diversification and that species phenotypes in turn influence species interactions. Several phylogenetic comparative methods have been developed to assess the importance of such processes in nature; however, the statistical properties of these methods have gone largely untested. Focusing mainly on scenarios of competition between closely-related species, we assess the performance of available comparative approaches for analyzing the interplay between interspecific interactions and species phenotypes. We find that many currently used statistical methods often fail to detect the impact of interspecific interactions on trait evolution, that sister-taxa analyses are particularly unreliable in general, and that recently developed process-based models have more satisfactory statistical properties. Methods for detecting predictors of species interactions are generally more reliable than methods for detecting character displacement. In weighing the strengths and weaknesses of different approaches, we hope to provide a clear guide for empiricists testing hypotheses about the reciprocal effect of interspecific interactions and species phenotypes and to inspire further development of process-based models.

The role of evolutionary biology in research and control of liver flukes in Southeast Asia.

PubMed

Echaubard, Pierre; Sripa, Banchob; Mallory, Frank F; Wilcox, Bruce A

2016-09-01

Stimulated largely by the availability of new technology, biomedical research at the molecular-level and chemical-based control approaches arguably dominate the field of infectious diseases. Along with this, the proximate view of disease etiology predominates to the exclusion of the ultimate, evolutionary biology-based, causation perspective. Yet, historically and up to today, research in evolutionary biology has provided much of the foundation for understanding the mechanisms underlying disease transmission dynamics, virulence, and the design of effective integrated control strategies. Here we review the state of knowledge regarding the biology of Asian liver Fluke-host relationship, parasitology, phylodynamics, drug-based interventions and liver Fluke-related cancer etiology from an evolutionary biology perspective. We consider how evolutionary principles, mechanisms and research methods could help refine our understanding of clinical disease associated with infection by Liver Flukes as well as their transmission dynamics. We identify a series of questions for an evolutionary biology research agenda for the liver Fluke that should contribute to an increased understanding of liver Fluke-associated diseases. Finally, we describe an integrative evolutionary medicine approach to liver Fluke prevention and control highlighting the need to better contextualize interventions within a broader human health and sustainable development framework. Copyright © 2016 Elsevier B.V. All rights reserved.

The Role of Evolutionary Biology in Research and Control of Liver Flukes in Southeast Asia

PubMed Central

Echaubard, Pierre; Sripa, Banchob; Mallory, Frank F.; Wilcox, Bruce A.

2016-01-01

Stimulated largely by the availability of new technology, biomedical research at the molecular-level and chemical-based control approaches arguably dominate the field of infectious diseases. Along with this, the proximate view of disease etiology predominates to the exclusion of the ultimate, evolutionary biology-based, causation perspective. Yet, historically and up to today, research in evolutionary biology has provided much of the foundation for understanding the mechanisms underlying disease transmission dynamics, virulence, and the design of effective integrated control strategies. Here we review the state of knowledge regarding the biology of Asian liver Fluke-host relationship, parasitology, phylodynamics, drug-based interventions and liver Fluke-related cancer etiology from an evolutionary biology perspective. We consider how evolutionary principles, mechanisms and research methods could help refine our understanding of clinical disease associated with infection by Liver Flukes as well as their transmission dynamics. We identify a series of questions for an evolutionary biology research agenda for the liver Fluke that should contribute to an increased understanding of liver Fluke-associated diseases. Finally, we describe an integrative evolutionary medicine approach to liver Fluke prevention and control highlighting the need to better contextualize interventions within a broader human health and sustainable development framework. PMID:27197053

Multilocus approach to clarify species status and the divergence history of the Bemisia tabaci (Hemiptera: Aleyrodidae) species complex.

PubMed

Hsieh, Chia-Hung; Ko, Chiun-Cheng; Chung, Cheng-Han; Wang, Hurng-Yi

2014-07-01

The sweet potato whitefly, Bemisia tabaci, is a highly differentiated species complex. Despite consisting of several morphologically indistinguishable entities and frequent invasions on all continents with important associated economic losses, the phylogenetic relationships, species status, and evolutionary history of this species complex is still debated. We sequenced and analyzed one mitochondrial and three single-copy nuclear genes from 9 of the 12 genetic groups of B. tabaci and 5 closely related species. Bayesian species delimitation was applied to investigate the speciation events of B. tabaci. The species statuses of the different genetic groups were strongly supported under different prior settings and phylogenetic scenarios. Divergence histories were estimated by a multispecies coalescence approach implemented in (*)BEAST. Based on mitochondrial locus, B. tabaci was originated 6.47 million years ago (MYA). Nevertheless, the time was 1.25MYA based on nuclear loci. According to the method of approximate Bayesian computation, this difference is probably due to different degrees of migration among loci; i.e., although the mitochondrial locus had differentiated, gene flow at nuclear loci was still possible, a scenario similar to parapatric mode of speciation. This is the first study in whiteflies using multilocus data and incorporating Bayesian coalescence approaches, both of which provide a more biologically realistic framework for delimiting species status and delineating the divergence history of B. tabaci. Our study illustrates that gene flow during species divergence should not be overlooked and has a great impact on divergence time estimation. Copyright © 2014 Elsevier Inc. All rights reserved.

Genetic variation in a compound short tandem repeat/Alu haplotype system at the SB19.3 locus: properties and interpretation.

PubMed

Gaspar, Paulo; Seixas, Susana; Rocha, Jorge

2004-04-01

The genetic variation at a compound nonrecombining haplotype system, consisting of the previously reported SB19.3 Alu insertion polymorphism and a newly identified adjacent short tandem repeat (STR), was studied in population samples from Portugal and São Tomé (Gulf of Guinea, West Africa). Age estimates based on the linked microsatellite variation suggest that the Alu insertion occurred about 190,000 years ago. In accordance with the global patterns of distribution of human genetic variation, the highest haplotype diversity was found in the African sample. This excess in African diversity was due to both a substantial reduction in heterozygosity at the Alu polymorphism and a lower STR variability associated with the predominant Alu insertion allele in the Portuguese sample. The high level of interpopulation differentiation observed at the Alu locus (F(ST) = 0.43) was interpreted under alternative selective and demographic scenarios. The need for compatibility between patterns of variation at the STR and Alu loci could be used to restrict the range of selection coefficients in selection-driven genetic hitchhiking frameworks and to favor demographic scenarios dominated by larger pre-expansion African population sizes. Taken together, the data show that the SB19.3 Alu-STR system is an informative marker that can be included in more extended batteries of compound haplotypes used in human evolutionary studies.

A recent shark radiation: molecular phylogeny, biogeography and speciation of wobbegong sharks (family: Orectolobidae).

PubMed

Corrigan, Shannon; Beheregaray, Luciano B

2009-07-01

The elasmobranch fish are an ancient, evolutionarily successful, but under-researched vertebrate group, particularly in regard to their recent evolutionary history. Their lineage has survived four mass extinction events and most present day taxa are thought to be derived from Mesozoic forms. Here we present a molecular phylogenetic analysis of the family Orectolobidae that provides evidence for recent events of diversification in this shark group. Species interrelationships in Orectolobidae were reconstructed based on four mitochondrial and nuclear genes. In line with previous morphological work, our results do not support current taxonomic arrangements in Orectolobidae and indicate that a taxonomic revision of the family is warranted. We propose that the onset of diversification of orectolobid sharks is of Miocene age and occurred within the Indo-Australian region. Surprisingly, we also find evidence for a recent ( approximately last 2 million years) and rapid radiation of wobbegong sharks. Allopatric speciation followed by range expansion seems like the general most likely explanation to account for wobbegong relationships and distributions. We suggest that the evolution of this shark group was mostly influenced by two temporal scenarios of diversification. The oldest relates to major geological changes in the Indo-West Pacific associated with the Miocene collision of the Indo-Australian and Eurasian plates. The most recent scenario was influenced by changes in oceanography and the emergence of biogeographic barriers related to Pleistocene glacial cycles in Australian waters.

Impacts of subsidy policies on vaccination decisions in contact networks

NASA Astrophysics Data System (ADS)

Zhang, Hai-Feng; Wu, Zhi-Xi; Xu, Xiao-Ke; Small, Michael; Wang, Lin; Wang, Bing-Hong

2013-07-01

To motivate more people to participate in vaccination campaigns, various subsidy policies are often supplied by government and the health sectors. However, these external incentives may also alter the vaccination decisions of the broader public, and hence the choice of incentive needs to be carefully considered. Since human behavior and the networking-constrained interactions among individuals significantly impact the evolution of an epidemic, here we consider the voluntary vaccination on human contact networks. To this end, two categories of typical subsidy policies are considered: (1) under the free subsidy policy, the total amount of subsidy is distributed to a certain fraction of individual and who are vaccinated without personal cost, and (2) under the partial-offset subsidy policy, each vaccinated person is offset by a certain amount of subsidy. A vaccination decision model based on evolutionary game theory is established to study the effects of these different subsidy policies on disease control. Simulations suggest that, because the partial-offset subsidy policy encourages more people to take vaccination, its performance is significantly better than that of the free subsidy policy. However, an interesting phenomenon emerges in the partial-offset scenario: with limited amount of total subsidy, a moderate subsidy rate for each vaccinated individual can guarantee the group-optimal vaccination, leading to the maximal social benefits, while such an optimal phenomenon is not evident for the free subsidy scenario.

Definition of technology development missions for early space station satellite servicing, volume 2

NASA Technical Reports Server (NTRS)

1983-01-01

The results of all aspects of the early space station satellite servicing study tasks are presented. These results include identification of servicing tasks (and locations), identification of servicing mission system and detailed objectives, functional/operational requirements analyses of multiple servicing scenarios, assessment of critical servicing technology capabilities and development of an evolutionary capability plan, design and validation of selected servicing technology development missions (TDMs), identification of space station satellite servicing accommodation needs, and the cost and schedule implications of acquiring both required technology capability development and conducting the selected TDMs.

The velocity characteristics of dusty filaments in the JCMT GBS clouds

NASA Astrophysics Data System (ADS)

Buckle, J. V.; Salji, C.; Richer, J. S.

2013-07-01

Large scale, high resolution spectral and continuum imaging maps have revealed, to an unprecedented extent, the characteristics of filamentary structure in star-forming molecular clouds, and their close association with star-forming cores. The filaments are associated with the formation of dense molecular cores where star formation occurs, and recent models highlight the important relationship between filaments and star-forming clusters. Velocity-coherent filaments have been proposed as the parent structures of star forming cores in Taurus. In Serpens, accretion flows along filaments have been proposed as the continuous source of mass for the star forming cluster. An evolutionary scenario for filaments based on velocity dispersion and column density measurements has recently been proposed, which we test with large scale molecular line and dust continuum maps. The JCMT Gould Belt Survey with SCUBA-2 and HARP provides dust continuum observations at 850 and 450 micron, and 12CO/13CO/C18O J=3-2 spectral line mapping of several nearby molecular clouds, covering large angular scales at high resolution. Velocities and linewidths of optically thin species, such as C18O which traces the warm, dense gas associated with star formation, are critical for an estimate of the virial stability of filamentary structures. The data and analyses that we present provide robust statistics over a large range of starless and protostellar evolutionary states. We present the velocity characteristics of dusty filaments in Orion, probing the physics at the boundary of filamentary structure and star formation. Using C18O, we investigate the internal structure of filaments, based on fragmentation and velocity coherence in the molecular line data. Through velocity dispersion measurements, we determine whether the filamentary structures are bound, and compare results between clouds of different star formation characteristics.

The Evolutionary History of the Rediscovered Austrian Population of the Giant Centipede Scolopendra cingulata Latreille 1829 (Chilopoda, Scolopendromorpha)

PubMed Central

Oeyen, Jan Philip; Funke, Sebastian; Böhme, Wolfgang; Wesener, Thomas

2014-01-01

The thermophilous giant centipede Scolopendra cingulata is a voracious terrestrial predator, which uses its modified first leg pair and potent venom to capture prey. The highly variable species is the most common of the genus in Europe, occurring from Portugal in the west to Iran in the east. The northernmost occurrences are in Hungary and Romania, where it abides in small isolated fringe populations. We report the rediscovery of an isolated Austrian population of Scolopendra cingulata with the first explicit specimen records for more than 80 years and provide insights into the evolutionary history of the northernmost populations utilizing fragments of two mitochondrial genes, COI and 16S, comprising 1,155 base pairs. We test the previously proposed hypothesis of a speciation by distance scenario, which argued for a simple range expansion of the species from the southeast, via Romania, Hungary and finally to Austria, based on a comprehensive taxon sampling from seven countries, including the first European mainland samples. We argue that more complex patterns must have shaped the current distribution of S. cingulata and that the Austrian population should be viewed as an important biogeographical relict in a possible microrefugium. The unique haplotype of the Austrian population could constitute an important part of the species genetic diversity and we hope that this discovery will initiate protective measures not only for S. cingulata, but also for its habitat, since microrefugia are likely to host further rare thermophilous species. Furthermore, we take advantage of the unprecedented sampling to provide the first basic insights into the suitability of the COI fragment as a species identifying barcode within the centipede genus Scolopendra. PMID:25251436

On the evolution of harming and recognition in finite panmictic and infinite structured populations

PubMed Central

Lehmann, Laurent; Feldman, Marcus W.; Rousset, François

2010-01-01

Natural selection may favor two very different types of social behaviors that have costs in vital rates (fecundity and/or survival) to the actor: helping behaviors, which increase the vital rates of recipients, and harming behaviors, which reduce the vital rates of recipients. While social evolutionary theory has mainly dealt with helping behaviors, competition for limited resources creates ecological conditions where an actor may benefit from expressing behaviors that reduce the vital rates of neighbours. This may occur if the reduction in vital rates decreases the intensity of competition experienced by the actor or that experienced by its offspring. Here, we explore the joint evolution of neutral recognition markers and marker-based costly conditional harming whereby actors express harming, conditional on actor and recipient bearing different conspicuous markers. We do so for two complementary demographic scenarios: finite panmictic and infinite structured populations. We find that marker-based conditional harming can evolve under a large range of recombination rates and group sizes under both finite panmictic and infinite structured populations. Direct comparison with results for the evolution of marker-based conditional helping reveals that, if everything else is equal, marker-based conditional harming is often more likely to evolve than marker-based conditional. PMID:19624725

Evolutionary modes of emergence of short interspersed nuclear element (SINE) families in grasses.

PubMed

Kögler, Anja; Schmidt, Thomas; Wenke, Torsten

2017-11-01

Short interspersed nuclear elements (SINEs) are non-autonomous transposable elements which are propagated by retrotransposition and constitute an inherent part of the genome of most eukaryotic species. Knowledge of heterogeneous and highly abundant SINEs is crucial for de novo (or improvement of) annotation of whole genome sequences. We scanned Poaceae genome sequences of six important cereals (Oryza sativa, Triticum aestivum, Hordeum vulgare, Panicum virgatum, Sorghum bicolor, Zea mays) and Brachypodium distachyon to examine the diversity and evolution of SINE populations. We comparatively analyzed the structural features, distribution, evolutionary relation and abundance of 32 SINE families and subfamilies within grasses, comprising 11 052 individual copies. The investigation of activity profiles within the Poaceae provides insights into their species-specific diversification and amplification. We found that Poaceae SINEs (PoaS) fall into two length categories: simple SINEs of up to 180 bp and dimeric SINEs larger than 240 bp. Detailed analysis at the nucleotide level revealed that multimerization of related and unrelated SINE copies is an important evolutionary mechanism of SINE formation. We conclude that PoaS families diversify by massive reshuffling between SINE families, likely caused by insertion of truncated copies, and provide a model for this evolutionary scenario. Twenty-eight of 32 PoaS families and subfamilies show significant conservation, in particular either in the 5' or 3' regions, across Poaceae species and share large sequence stretches with one or more other PoaS families. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

The evolutionary origins of Lévy walk foraging

PubMed Central

Wosniack, Marina E.

2017-01-01

We study through a reaction-diffusion algorithm the influence of landscape diversity on the efficiency of search dynamics. Remarkably, the identical optimal search strategy arises in a wide variety of environments, provided the target density is sparse and the searcher’s information is restricted to its close vicinity. Our results strongly impact the current debate on the emergentist vs. evolutionary origins of animal foraging. The inherent character of the optimal solution (i.e., independent on the landscape for the broad scenarios assumed here) suggests an interpretation favoring the evolutionary view, as originally implied by the Lévy flight foraging hypothesis. The latter states that, under conditions of scarcity of information and sparse resources, some organisms must have evolved to exploit optimal strategies characterized by heavy-tailed truncated power-law distributions of move lengths. These results strongly suggest that Lévy strategies—and hence the selection pressure for the relevant adaptations—are robust with respect to large changes in habitat. In contrast, the usual emergentist explanation seems not able to explain how very similar Lévy walks can emerge from all the distinct non-Lévy foraging strategies that are needed for the observed large variety of specific environments. We also report that deviations from Lévy can take place in plentiful ecosystems, where locomotion truncation is very frequent due to high encounter rates. So, in this case normal diffusion strategies—performing as effectively as the optimal one—can naturally emerge from Lévy. Our results constitute the strongest theoretical evidence to date supporting the evolutionary origins of experimentally observed Lévy walks. PMID:28972973

Characterizing behavioural ‘characters’: an evolutionary framework

PubMed Central

Araya-Ajoy, Yimen G.; Dingemanse, Niels J.

2014-01-01

Biologists often study phenotypic evolution assuming that phenotypes consist of a set of quasi-independent units that have been shaped by selection to accomplish a particular function. In the evolutionary literature, such quasi-independent functional units are called ‘evolutionary characters’, and a framework based on evolutionary principles has been developed to characterize them. This framework mainly focuses on ‘fixed’ characters, i.e. those that vary exclusively between individuals. In this paper, we introduce multi-level variation and thereby expand the framework to labile characters, focusing on behaviour as a worked example. We first propose a concept of ‘behavioural characters’ based on the original evolutionary character concept. We then detail how integration of variation between individuals (cf. ‘personality’) and within individuals (cf. ‘individual plasticity’) into the framework gives rise to a whole suite of novel testable predictions about the evolutionary character concept. We further propose a corresponding statistical methodology to test whether observed behaviours should be considered expressions of a hypothesized evolutionary character. We illustrate the application of our framework by characterizing the behavioural character ‘aggressiveness’ in wild great tits, Parus major. PMID:24335984

Two possible driving forces supporting the evolution of animal communication. Comment on "Towards a Computational Comparative Neuroprimatology: Framing the language-ready brain" by Michael A. Arbib

NASA Astrophysics Data System (ADS)

Moulin-Frier, Clément; Verschure, Paul F. M. J.

2016-03-01

In the target paper [1], M.A. Arbib proposes a quite exhaustive review of the (often computational) models developed during the last decades that support his detailed scenario on language evolution (the Mirror System Hypothesis, MSH). The approach considers that language evolved from a mirror system for grasping already present in LCA-m (the last common ancestor of macaques and humans), to a simple imitation system for grasping present in LCA-c (the last common ancestor of chimpanzees and humans), to a complex imitation system for grasping that developed in the hominid line since that ancestor. MSH considers that this complex imitation system is a key evolutionary step for a language-ready brain, providing all the required elements for an open-ended gestural communication system. The transition from the gestural (bracchio-manual and visual) to the vocal (articulatory and auditory) domain is supposed to be a less important evolutionary step.

Reproductive Benefit of Oxidative Damage: An Oxidative Stress “Malevolence”?

PubMed Central

Poljsak, B.; Milisav, I.; Lampe, T.; Ostan, I.

2011-01-01

High levels of reactive oxygen species (ROS) compared to antioxidant defenses are considered to play a major role in diverse chronic age-related diseases and aging. Here we present an attempt to synthesize information about proximate oxidative processes in aging (relevant to free radical or oxidative damage hypotheses of aging) with an evolutionary scenario (credited here to Dawkins hypotheses) involving tradeoffs between the costs and benefits of oxidative stress to reproducing organisms. Oxidative stress may be considered a biological imperfection; therefore, the Dawkins' theory of imperfect adaptation of beings to environment was applied to the role of oxidative stress in processes like famine and infectious diseases and their consequences at the molecular level such as mutations and cell signaling. Arguments are presented that oxidative damage is not necessarily an evolutionary mistake but may be beneficial for reproduction; this may prevail over its harmfulness to health and longevity in evolution. Thus, Dawkins' principle of biological “malevolence” may be an additional biological paradigm for explaining the consequences of oxidative stress. PMID:21969876

Evolution of plasma characteristics for weak X-ray brightenings seen by SphinX during recent deep minimum of solar activity

NASA Astrophysics Data System (ADS)

Sylwester, Barbara; Sylwester, Janusz; Siarkowski, Marek; Gburek, Szymon; Phillips, Kenneth

Very high sensitivity of SphinX soft X-ray spectrophotometer aboard Coronas-Photon allows to observe spectra of small X-ray brightenings(microflares), many of them with maximum intensities well below the GOES or RHESSI sensitivity thresholds. Hundreds of such small flare-like events have been observed in the period between March and November 2009 with energy resolution better than 0.5 keV. The spectra have been measured in the energy range extending above 1 keV. In this study we investigate the time variability of basic plasma parameters: temperature T and emission measure EM for a number of these weak flare-like events and discuss respective evolutionary patterns on the EM-T diagnostic diagrams. For some of these events, unusual behavior is observed, different from this characteristic for a "normal" flares of higher maximum intensities. Physical scenarios providing possible explanation of such unusual evolutionary patterns will be discussed.

Onymity promotes cooperation in social dilemma experiments

PubMed Central

Wang, Zhen; Jusup, Marko; Wang, Rui-Wu; Shi, Lei; Iwasa, Yoh; Moreno, Yamir; Kurths, Jürgen

2017-01-01

One of the most elusive scientific challenges for over 150 years has been to explain why cooperation survives despite being a seemingly inferior strategy from an evolutionary point of view. Over the years, various theoretical scenarios aimed at solving the evolutionary puzzle of cooperation have been proposed, eventually identifying several cooperation-promoting mechanisms: kin selection, direct reciprocity, indirect reciprocity, network reciprocity, and group selection. We report the results of repeated Prisoner’s Dilemma experiments with anonymous and onymous pairwise interactions among individuals. We find that onymity significantly increases the frequency of cooperation and the median payoff per round relative to anonymity. Furthermore, we also show that the correlation between players’ ranks and the usage of strategies (cooperation, defection, or punishment) underwent a fundamental shift, whereby more prosocial actions are rewarded with a better ranking under onymity. Our findings prove that reducing anonymity is a valid promoter of cooperation, leading to higher payoffs for cooperators and thus suppressing an incentive—anonymity—that would ultimately favor defection. PMID:28435860

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.

Tip of the clade on the top of the World—the first fossil Lophopidae (Hemiptera: Fulgoromorpha) from the Palaeocene of Tibet

NASA Astrophysics Data System (ADS)

Szwedo, Jacek; Stroiński, Adam; Lin, Qibin

2015-06-01

Lophopidae is a family of planthoppers (Hemiptera: Fulgoromorpha) present today in tropical and subtropical zones of the Old World. The most recent taxonomic studies and phylogeny of these insects do not include the extinct representatives. Therefore, each new discovery of a fossil lophopid is of high interest, giving new insights to their evolutionary history and enabling to test the proposed relationships. The recent findings of extinct Lophopidae in Europe, in various Palaeogene deposits, put in doubts their proposed evolutionary and biogeographic scenario. The new fossil from the Palaeocene of Northern Tibet is related to one of the Lophopidae clades, Apia+ group, believed to be the most advanced one, and recently distributed in the recent Sundaland-New Guinea-Queensland area. A new genus and species Gesaris gnapo gen. et sp. n. provide information on early lophopids diversity and relationships and demonstrates the necessity for a revision of the existing hypotheses for the initial diversification and distributional pattern of the Lophopidae.

Limitations of inclusive fitness.

PubMed

Allen, Benjamin; Nowak, Martin A; Wilson, Edward O

2013-12-10

Until recently, inclusive fitness has been widely accepted as a general method to explain the evolution of social behavior. Affirming and expanding earlier criticism, we demonstrate that inclusive fitness is instead a limited concept, which exists only for a small subset of evolutionary processes. Inclusive fitness assumes that personal fitness is the sum of additive components caused by individual actions. This assumption does not hold for the majority of evolutionary processes or scenarios. To sidestep this limitation, inclusive fitness theorists have proposed a method using linear regression. On the basis of this method, it is claimed that inclusive fitness theory (i) predicts the direction of allele frequency changes, (ii) reveals the reasons for these changes, (iii) is as general as natural selection, and (iv) provides a universal design principle for evolution. In this paper we evaluate these claims, and show that all of them are unfounded. If the objective is to analyze whether mutations that modify social behavior are favored or opposed by natural selection, then no aspect of inclusive fitness theory is needed.

Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

PubMed Central

Árnason, Úlfur; Kumar, Vikas

2018-01-01

Reconstructing the evolution of baleen whales (Mysticeti) has been problematic because morphological and genetic analyses have produced different scenarios. This might be caused by genomic admixture that may have taken place among some rorquals. We present the genomes of six whales, including the blue whale (Balaenoptera musculus), to reconstruct a species tree of baleen whales and to identify phylogenetic conflicts. Evolutionary multilocus analyses of 34,192 genome fragments reveal a fast radiation of rorquals at 10.5 to 7.5 million years ago coinciding with oceanic circulation shifts. The evolutionarily enigmatic gray whale (Eschrichtius robustus) is placed among rorquals, and the blue whale genome shows a high degree of heterozygosity. The nearly equal frequency of conflicting gene trees suggests that speciation of rorqual evolution occurred under gene flow, which is best depicted by evolutionary networks. Especially in marine environments, sympatric speciation might be common; our results raise questions about how genetic divergence can be established. PMID:29632892

A radiological assessment of nuclear power and propulsion operations near Space Station Freedom

NASA Technical Reports Server (NTRS)

Bolch, Wesley E.; Thomas, J. Kelly; Peddicord, K. Lee; Nelson, Paul; Marshall, David T.; Busche, Donna M.

1990-01-01

Scenarios were identified which involve the use of nuclear power systems in the vicinity of Space Station Freedom (SSF) and their radiological impact on the SSF crew was quantified. Several of the developed scenarios relate to the use of SSF as an evolutionary transportation node for lunar and Mars missions. In particular, radiation doses delivered to SSF crew were calculated for both the launch and subsequent return of a Nuclear Electric Propulsion (NEP) cargo vehicle and a Nuclear Thermal Rocket (NTR) personnel vehicle to low earth orbit. The use of nuclear power on co-orbiting platforms and the storage and handling issues associated with radioisotope power systems were also explored as they relate to SSF. A central philosophy in these analyses was the utilization of a radiation dose budget, defined as the difference between recommended dose limits from all radiation sources and estimated doses received by crew members from natural space radiations. Consequently, for each scenario examined, the dose budget concept was used to identify and quantify constraints on operational parameters such as launch separation distances, returned vehicle parking distances, and reactor shutdown times prior to vehicle approach. The results indicate that realistic scenarios do not exist which would preclude the use of nuclear power sources in the vicinity of SSF. The radiation dose to the SSF crew can be maintained at safe levels solely by implementing proper and reasonable operating procedures.

Multilocus inference of species trees and DNA barcoding.

PubMed

Mallo, Diego; Posada, David

2016-09-05

The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree-gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

Evolutionary stability in continuous nonlinear public goods games.

PubMed

Molina, Chai; Earn, David J D

2017-01-01

We investigate a type of public goods games played in groups of individuals who choose how much to contribute towards the production of a common good, at a cost to themselves. In these games, the common good is produced based on the sum of contributions from all group members, then equally distributed among them. In applications, the dependence of the common good on the total contribution is often nonlinear (e.g., exhibiting synergy or diminishing returns). To date, most theoretical and experimental studies have addressed scenarios in which the set of possible contributions is discrete. However, in many real-world situations, contributions are continuous (e.g., individuals volunteering their time). The "n-player snowdrift games" that we analyze involve continuously varying contributions. We establish under what conditions populations of contributing (or "cooperating") individuals can evolve and persist. Previous work on snowdrift games, using adaptive dynamics, has found that what we term an "equally cooperative" strategy is locally convergently and evolutionarily stable. Using static evolutionary game theory, we find conditions under which this strategy is actually globally evolutionarily stable. All these results refer to stability to invasion by a single mutant. We broaden the scope of existing stability results by showing that the equally cooperative strategy is locally stable to potentially large population perturbations, i.e., allowing for the possibility that mutants make up a non-negligible proportion of the population (due, for example, to genetic drift, environmental variability or dispersal).

Playing evolution in the laboratory: From the first major evolutionary transition to global warming

NASA Astrophysics Data System (ADS)

Fragata, Inês; Simões, Pedro; Matos, Margarida; Szathmáry, Eörs; Santos, Mauro

2018-05-01

Experimental evolution allows testing hypotheses derived from theory or from observed patterns in nature. We have designed a droplet-based microfluidic “evolution machine” to test how transient compartmentalization (“trait-groups”) of independent molecular replicators (likely a critical step in the origin of life) could have prevented the spread of parasitic mutants; that is, inactive RNAs that have been reported to spoil a system of free replicators. In remarkable agreement with the theory, we show that this simple population structure was sufficient to prevent takeover by inactive RNAs. A more complex scenario arises when we use experimental evolution to test field-derived hypotheses; for instance, the idea that temperature is driving genetic spatiotemporal patterns of climate change. In the fly Drosophila subobscura, latitudinal clines in gene arrangement frequencies occur worldwide, and more equatorial gene arrangements are becoming more frequent at higher latitudes as a correlated response to climate change. However, the evolution at different constant temperatures in the laboratory was not consistent with patterns in nature, suggesting some limitations of experimental evolution. Finally, also in D. subobscura, we show that repeatability in experimental evolution is staggeringly consistent for life history traits, making evolution quite predictable and suggesting that laboratory selection can quickly erase differences between populations. Yet, the genetic paths used to attain the same adaptive phenotypes are complex and unpredictable. Contribution to the Focus Issue Evolutionary Modeling and Experimental Evolution edited by José Cuesta, Joachim Krug and Susanna Manrubia.

Towards a mechanistic foundation of evolutionary theory.

PubMed

Doebeli, Michael; Ispolatov, Yaroslav; Simon, Burt

2017-02-15

Most evolutionary thinking is based on the notion of fitness and related ideas such as fitness landscapes and evolutionary optima. Nevertheless, it is often unclear what fitness actually is, and its meaning often depends on the context. Here we argue that fitness should not be a basal ingredient in verbal or mathematical descriptions of evolution. Instead, we propose that evolutionary birth-death processes, in which individuals give birth and die at ever-changing rates, should be the basis of evolutionary theory, because such processes capture the fundamental events that generate evolutionary dynamics. In evolutionary birth-death processes, fitness is at best a derived quantity, and owing to the potential complexity of such processes, there is no guarantee that there is a simple scalar, such as fitness, that would describe long-term evolutionary outcomes. We discuss how evolutionary birth-death processes can provide useful perspectives on a number of central issues in evolution.

Human Exploration of Earth's Neighborhood and Mars

NASA Technical Reports Server (NTRS)

Condon, Gerald

2003-01-01

The presentation examines Mars landing scenarios, Earth to Moon transfers comparing direct vs. via libration points. Lunar transfer/orbit diagrams, comparison of opposition class and conjunction class missions, and artificial gravity for human exploration missions. Slides related to Mars landing scenarios include: mission scenario; direct entry landing locations; 2005 opportunity - Type 1; Earth-mars superior conjunction; Lander latitude accessibility; Low thrust - Earth return phase; SEP Earth return sequence; Missions - 200, 2007, 2009; and Mission map. Slides related to Earth to Moon transfers (direct vs. via libration points (L1, L2) include libration point missions, expeditionary vs. evolutionary, Earth-Moon L1 - gateway for lunar surface operations, and Lunar mission libration point vs. lunar orbit rendezvous (LOR). Slides related to lunar transfer/orbit diagrams include: trans-lunar trajectory from ISS parking orbit, trans-Earth trajectories, parking orbit considerations, and landing latitude restrictions. Slides related to comparison of opposition class (short-stay) and conjunction class (long-stay) missions for human exploration of Mars include: Mars mission planning, Earth-Mars orbital characteristics, delta-V variations, and Mars mission duration comparison. Slides related to artificial gravity for human exploration missions include: current configuration, NEP thruster location trades, minor axis rotation, and example load paths.

A Bell-Curved Based Algorithm for Mixed Continuous and Discrete Structural Optimization

NASA Technical Reports Server (NTRS)

Kincaid, Rex K.; Weber, Michael; Sobieszczanski-Sobieski, Jaroslaw

2001-01-01

An evolutionary based strategy utilizing two normal distributions to generate children is developed to solve mixed integer nonlinear programming problems. This Bell-Curve Based (BCB) evolutionary algorithm is similar in spirit to (mu + mu) evolutionary strategies and evolutionary programs but with fewer parameters to adjust and no mechanism for self adaptation. First, a new version of BCB to solve purely discrete optimization problems is described and its performance tested against a tabu search code for an actuator placement problem. Next, the performance of a combined version of discrete and continuous BCB is tested on 2-dimensional shape problems and on a minimum weight hub design problem. In the latter case the discrete portion is the choice of the underlying beam shape (I, triangular, circular, rectangular, or U).

Open Reading Frame Phylogenetic Analysis on the Cloud

PubMed Central

2013-01-01

Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus. PMID:23671843

Functional Evolution of PLP-dependent Enzymes based on Active-Site Structural Similarities

PubMed Central

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-01-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. PMID:24920327

Functional evolution of PLP-dependent enzymes based on active-site structural similarities.

PubMed

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-10-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5'-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional-fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. © 2014 Wiley Periodicals, Inc.

Ecological and evolutionary consequences of tri-trophic interactions: Spatial variation and effects of plant density.

PubMed

Abdala-Roberts, Luis; Parra-Tabla, Víctor; Moreira, Xoaquín; Ramos-Zapata, José

2017-02-01

The factors driving variation in species interactions are often unknown, and few studies have made a link between changes in interactions and the strength of selection. We report on spatial variation in functional responses by a seed predator (SP) and its parasitic wasps associated with the herb Ruellia nudiflora . We assessed the influence of plant density on consumer responses and determined whether density effects and spatial variation in functional responses altered natural selection by these consumers on the plant. We established common gardens at two sites in Yucatan, Mexico, and planted R. nudiflora at two densities in each garden. We recorded fruit output and SP and parasitoid attack; calculated relative fitness (seed number) under scenarios of three trophic levels (accounting for SP and parasitoid effects), two trophic levels (accounting for SP but not parasitoid effects), and one trophic level (no consumer effects); and compared selection strength on fruit number under these scenarios across sites and densities. There was spatial variation in SP recruitment, whereby the SP functional response was negatively density-dependent at one site but density-independent at the other; parasitoid responses were density-independent and invariant across sites. Site variation in SP attack led, in turn, to differences in SP selection on fruit output, and parasitoids did not alter SP selection. There were no significant effects of density at either site. Our results provide a link between consumer functional responses and consumer selection on plants, which deepens our understanding of geographic variation in the evolutionary outcomes of multitrophic interactions. © 2017 Botanical Society of America.

Visualization of the Eastern Renewable Generation Integration Study: Preprint

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

Gruchalla, Kenny; Novacheck, Joshua; Bloom, Aaron

The Eastern Renewable Generation Integration Study (ERGIS), explores the operational impacts of the wide spread adoption of wind and solar photovoltaics (PV) resources in the U.S. Eastern Interconnection and Quebec Interconnection (collectively, EI). In order to understand some of the economic and reliability challenges of managing hundreds of gigawatts of wind and PV generation, we developed state of the art tools, data, and models for simulating power system operations using hourly unit commitment and 5-minute economic dispatch over an entire year. Using NREL's high-performance computing capabilities and new methodologies to model operations, we found that the EI, as simulated withmore » evolutionary change in 2026, could balance the variability and uncertainty of wind and PV at a 5-minute level under a variety of conditions. A large-scale display and a combination of multiple coordinated views and small multiples were used to visually analyze the four large highly multivariate scenarios with high spatial and temporal resolutions. state of the art tools, data, and models for simulating power system operations using hourly unit commitment and 5-minute economic dispatch over an entire year. Using NRELs high-performance computing capabilities and new methodologies to model operations, we found that the EI, as simulated with evolutionary change in 2026, could balance the variability and uncertainty of wind and PV at a 5-minute level under a variety of conditions. A large-scale display and a combination of multiple coordinated views and small multiples were used to visually analyze the four large highly multivariate scenarios with high spatial and temporal resolutions.« less

Stimulating Scientific Reasoning with Drawing-Based Modeling

ERIC Educational Resources Information Center

Heijnes, Dewi; van Joolingen, Wouter; Leenaars, Frank

2018-01-01

We investigate the way students' reasoning about evolution can be supported by drawing-based modeling. We modified the drawing-based modeling tool SimSketch to allow for modeling evolutionary processes. In three iterations of development and testing, students in lower secondary education worked on creating an evolutionary model. After each…

Assessment of Surface Air Temperature over China Using Multi-criterion Model Ensemble Framework

NASA Astrophysics Data System (ADS)

Li, J.; Zhu, Q.; Su, L.; He, X.; Zhang, X.

2017-12-01

The General Circulation Models (GCMs) are designed to simulate the present climate and project future trends. It has been noticed that the performances of GCMs are not always in agreement with each other over different regions. Model ensemble techniques have been developed to post-process the GCMs' outputs and improve their prediction reliabilities. To evaluate the performances of GCMs, root-mean-square error, correlation coefficient, and uncertainty are commonly used statistical measures. However, the simultaneous achievements of these satisfactory statistics cannot be guaranteed when using many model ensemble techniques. Meanwhile, uncertainties and future scenarios are critical for Water-Energy management and operation. In this study, a new multi-model ensemble framework was proposed. It uses a state-of-art evolutionary multi-objective optimization algorithm, termed Multi-Objective Complex Evolution Global Optimization with Principle Component Analysis and Crowding Distance (MOSPD), to derive optimal GCM ensembles and demonstrate the trade-offs among various solutions. Such trade-off information was further analyzed with a robust Pareto front with respect to different statistical measures. A case study was conducted to optimize the surface air temperature (SAT) ensemble solutions over seven geographical regions of China for the historical period (1900-2005) and future projection (2006-2100). The results showed that the ensemble solutions derived with MOSPD algorithm are superior over the simple model average and any single model output during the historical simulation period. For the future prediction, the proposed ensemble framework identified that the largest SAT change would occur in the South Central China under RCP 2.6 scenario, North Eastern China under RCP 4.5 scenario, and North Western China under RCP 8.5 scenario, while the smallest SAT change would occur in the Inner Mongolia under RCP 2.6 scenario, South Central China under RCP 4.5 scenario, and South Central China under RCP 8.5 scenario.

Molecular phylogeny of black fungus gnats (Diptera: Sciaroidea: Sciaridae) and the evolution of larval habitats.

PubMed

Shin, Seunggwan; Jung, Sunghoon; Menzel, Frank; Heller, Kai; Lee, Heungsik; Lee, Seunghwan

2013-03-01

The phylogeny of the family Sciaridae is reconstructed, based on maximum likelihood, maximum parsimony, and Bayesian analyses of 4809bp from two mitochondrial (COI and 16S) and two nuclear (18S and 28S) genes for 100 taxa including the outgroup taxa. According to the present phylogenetic analyses, Sciaridae comprise three subfamilies and two genus groups: Sciarinae, Chaetosciara group, Cratyninae, and Pseudolycoriella group+Megalosphyinae. Our molecular results are largely congruent with one of the former hypotheses based on morphological data with respect to the monophyly of genera and subfamilies (Sciarinae, Megalosphyinae, and part of postulated "new subfamily"); however, the subfamily Cratyninae is shown to be polyphyletic, and the genera Bradysia, Corynoptera, Leptosciarella, Lycoriella, and Phytosciara are also recognized as non-monophyletic groups. While the ancestral larval habitat state of the family Sciaridae, based on Bayesian inference, is dead plant material (plant litter+rotten wood), the common ancestors of Phytosciara and Bradysia are inferred to living plants habitat. Therefore, shifts in larval habitats from dead plant material to living plants may have occurred within the Sciaridae at least once. Based on the results, we discuss phylogenetic relationships within the family, and present an evolutionary scenario of development of larval habitats. Copyright © 2012 Elsevier Inc. All rights reserved.

Autonomous self-organizing resource manager for multiple networked platforms

NASA Astrophysics Data System (ADS)

Smith, James F., III

2002-08-01

A fuzzy logic based expert system for resource management has been developed that automatically allocates electronic attack (EA) resources in real-time over many dissimilar autonomous naval platforms defending their group against attackers. The platforms can be very general, e.g., ships, planes, robots, land based facilities, etc. Potential foes the platforms deal with can also be general. This paper provides an overview of the resource manager including the four fuzzy decision trees that make up the resource manager; the fuzzy EA model; genetic algorithm based optimization; co-evolutionary data mining through gaming; and mathematical, computational and hardware based validation. Methods of automatically designing new multi-platform EA techniques are considered. The expert system runs on each defending platform rendering it an autonomous system requiring no human intervention. There is no commanding platform. Instead the platforms work cooperatively as a function of battlespace geometry; sensor data such as range, bearing, ID, uncertainty measures for sensor output; intelligence reports; etc. Computational experiments will show the defending networked platform's ability to self- organize. The platforms' ability to self-organize is illustrated through the output of the scenario generator, a software package that automates the underlying data mining problem and creates a computer movie of the platforms' interaction for evaluation.

A review and experimental study on the application of classifiers and evolutionary algorithms in EEG-based brain-machine interface systems

NASA Astrophysics Data System (ADS)

Tahernezhad-Javazm, Farajollah; Azimirad, Vahid; Shoaran, Maryam

2018-04-01

Objective. Considering the importance and the near-future development of noninvasive brain-machine interface (BMI) systems, this paper presents a comprehensive theoretical-experimental survey on the classification and evolutionary methods for BMI-based systems in which EEG signals are used. Approach. The paper is divided into two main parts. In the first part, a wide range of different types of the base and combinatorial classifiers including boosting and bagging classifiers and evolutionary algorithms are reviewed and investigated. In the second part, these classifiers and evolutionary algorithms are assessed and compared based on two types of relatively widely used BMI systems, sensory motor rhythm-BMI and event-related potentials-BMI. Moreover, in the second part, some of the improved evolutionary algorithms as well as bi-objective algorithms are experimentally assessed and compared. Main results. In this study two databases are used, and cross-validation accuracy (CVA) and stability to data volume (SDV) are considered as the evaluation criteria for the classifiers. According to the experimental results on both databases, regarding the base classifiers, linear discriminant analysis and support vector machines with respect to CVA evaluation metric, and naive Bayes with respect to SDV demonstrated the best performances. Among the combinatorial classifiers, four classifiers, Bagg-DT (bagging decision tree), LogitBoost, and GentleBoost with respect to CVA, and Bagging-LR (bagging logistic regression) and AdaBoost (adaptive boosting) with respect to SDV had the best performances. Finally, regarding the evolutionary algorithms, single-objective invasive weed optimization (IWO) and bi-objective nondominated sorting IWO algorithms demonstrated the best performances. Significance. We present a general survey on the base and the combinatorial classification methods for EEG signals (sensory motor rhythm and event-related potentials) as well as their optimization methods through the evolutionary algorithms. In addition, experimental and statistical significance tests are carried out to study the applicability and effectiveness of the reviewed methods.

USING ECO-EVOLUTIONARY INDIVIDUAL-BASED MODELS TO INVESTIGATE SPATIALLY-DEPENDENT PROCESSES IN CONSERVATION GENETICS

EPA Science Inventory

Eco-evolutionary population simulation models are powerful new forecasting tools for exploring management strategies for climate change and other dynamic disturbance regimes. Additionally, eco-evo individual-based models (IBMs) are useful for investigating theoretical feedbacks ...

Towards a Universal Biology: Is the Origin and Evolution of Life Predictable?

NASA Technical Reports Server (NTRS)

Rothschild, Lynn J.

2017-01-01

The origin and evolution of life seems an unpredictable oddity, based on the quirks of contingency. Celebrated by the late Stephen Jay Gould in several books, "evolution by contingency" has all the adventure of a thriller, but lacks the predictive power of the physical sciences. Not necessarily so, replied Simon Conway Morris, for convergence reassures us that certain evolutionary responses are replicable. The outcome of this debate is critical to Astrobiology. How can we understand where we came from on Earth without prophesy? Further, we cannot design a rational strategy for the search for life elsewhere - or to understand what the future will hold for life on Earth and beyond - without extrapolating from pre-biotic chemistry and evolution. There are several indirect approaches to understanding, and thus describing, what life must be. These include philosophical approaches to defining life (is there even a satisfactory definition of life?), using what we know of physics, chemistry and life to imagine alternate scenarios, using different approaches that life takes as pseudoreplicates (e.g., ribosomal vs non-ribosomal protein synthesis), and experimental approaches to understand the art of the possible. Given that: (1) Life is a process based on physical components rather than simply an object; (2). Life is likely based on organic carbon and needs a solvent for chemistry, most likely water, and (3) Looking for convergence in terrestrial evolution we can predict certain tendencies, if not quite "laws", that provide predictive power. Biological history must obey the laws of physics and chemistry, the principles of natural selection, the constraints of an evolutionary past, genetics, and developmental biology. This amalgam creates a surprising amount of predictive power in the broad outline. Critical is the apparent prevalence of organic chemistry, and uniformity in the universe of the laws of chemistry and physics. Instructive is the widespread occurrence of convergent or parallel evolution, which suggests that under certain conditions similar solutions are arrived at independently.

Modeling the Personal Health Ecosystem.

PubMed

Blobel, Bernd; Brochhausen, Mathias; Ruotsalainen, Pekka

2018-01-01

Complex ecosystems like the pHealth one combine different domains represented by a huge variety of different actors (human beings, organizations, devices, applications, components) belonging to different policy domains, coming from different disciplines, deploying different methodologies, terminologies, and ontologies, offering different levels of knowledge, skills, and experiences, acting in different scenarios and accommodating different business cases to meet the intended business objectives. For correctly modeling such systems, a system-oriented, architecture-centric, ontology-based, policy-driven approach is inevitable, thereby following established Good Modeling Best Practices. However, most of the existing standards, specifications and tools for describing, representing, implementing and managing health (information) systems reflect the advancement of information and communication technology (ICT) represented by different evolutionary levels of data modeling. The paper presents a methodology for integrating, adopting and advancing models, standards, specifications as well as implemented systems and components on the way towards the aforementioned ultimate approach, so meeting the challenge we face when transforming health systems towards ubiquitous, personalized, predictive, preventive, participative, and cognitive health and social care.

Dynamic effects of memory in a cobweb model with competing technologies

NASA Astrophysics Data System (ADS)

Agliari, Anna; Naimzada, Ahmad; Pecora, Nicolò

2017-02-01

We analyze a simple model based on the cobweb demand-supply framework with costly innovators and free imitators and study the endogenous dynamics of price and firms' fractions in a homogeneous good market. The evolutionary selection between technologies depends on a performance measure in which a memory parameter is introduced. The resulting dynamics is then described by a two-dimensional map. In addition to the locally stabilizing effect due to the presence of memory, we show the existence of a double stability threshold which entails for different dynamic scenarios occurring when the memory parameter takes extreme values (i.e. when consideration of the last profit realization prevails or it is too much neglected). The eventuality of different coexisting attractors as well as the structure of the basins of attraction that characterizes the path dependence property of the model with memory is shown. In particular, through global analysis we also illustrate particular bifurcations sequences that may increase the complexity of the related basins of attraction.

The Comet Cometh: Evolving Developmental Systems.

PubMed

Jaeger, Johannes; Laubichler, Manfred; Callebaut, Werner

In a recent opinion piece, Denis Duboule has claimed that the increasing shift towards systems biology is driving evolutionary and developmental biology apart, and that a true reunification of these two disciplines within the framework of evolutionary developmental biology (EvoDevo) may easily take another 100 years. He identifies methodological, epistemological, and social differences as causes for this supposed separation. Our article provides a contrasting view. We argue that Duboule's prediction is based on a one-sided understanding of systems biology as a science that is only interested in functional, not evolutionary, aspects of biological processes. Instead, we propose a research program for an evolutionary systems biology, which is based on local exploration of the configuration space in evolving developmental systems. We call this approach-which is based on reverse engineering, simulation, and mathematical analysis-the natural history of configuration space. We discuss a number of illustrative examples that demonstrate the past success of local exploration, as opposed to global mapping, in different biological contexts. We argue that this pragmatic mode of inquiry can be extended and applied to the mathematical analysis of the developmental repertoire and evolutionary potential of evolving developmental mechanisms and that evolutionary systems biology so conceived provides a pragmatic epistemological framework for the EvoDevo synthesis.

Radiative evolution of polyploid races of the Iberian carnation Dianthus broteri (Caryophyllaceae).

PubMed

Balao, Francisco; Valente, Luis M; Vargas, Pablo; Herrera, Javier; Talavera, Salvador

2010-07-01

*The micro-evolutionary mechanisms that drive large-scale radiations are not completely understood, partly because of a shortage of population-level studies aimed at identifying putative causes of rapid evolutionary change. The Dianthus broteri complex, representing the largest polyploid series known to date for any species in the genus (2x, 4x, 6x and 12x cytotypes), belongs to a lineage that was recently found to have diversified at unusually rapid rates. *We used a combination of genome sequencing (internal transcribed spacer (ITS), plus chloroplast DNA (cpDNA) regions trnH-psbA, psbA-trnK and trnK-matK) and amplified fragment length polymorphism (AFLP) fingerprinting in 25 populations to infer the evolutionary history of extant polyploid races. *The haplotype, ribotype and AFLP reconstructions showed a star-shaped arrangement suggesting a pattern of radiative evolution. The major, widespread haplotype occurred at all ploidy levels, whereas 20 minor haplotypes were restricted to single populations and cytotypes. In addition, AFLP analyses retrieved well-supported cytogeographic groups: six clades were clearly differentiated in terms of ploidy level and geography. Molecular data indicate that gene flow among different cytotypes is rare or nonexistent. *Our study supports a scenario of rapid diversification in carnations in which autopolyploidy and allopolyploidy, in interaction with geography and/or isolation, have played prominent roles.

The EvoDevoCI: A Concept Inventory for Gauging Students’ Understanding of Evolutionary Developmental Biology

PubMed Central

Perez, Kathryn E.; Hiatt, Anna; Davis, Gregory K.; Trujillo, Caleb; French, Donald P.; Terry, Mark; Price, Rebecca M.

2013-01-01

The American Association for the Advancement of Science 2011 report Vision and Change in Undergraduate Biology Education encourages the teaching of developmental biology as an important part of teaching evolution. Recently, however, we found that biology majors often lack the developmental knowledge needed to understand evolutionary developmental biology, or “evo-devo.” To assist in efforts to improve evo-devo instruction among undergraduate biology majors, we designed a concept inventory (CI) for evolutionary developmental biology, the EvoDevoCI. The CI measures student understanding of six core evo-devo concepts using four scenarios and 11 multiple-choice items, all inspired by authentic scientific examples. Distracters were designed to represent the common conceptual difficulties students have with each evo-devo concept. The tool was validated by experts and administered at four institutions to 1191 students during preliminary (n = 652) and final (n = 539) field trials. We used student responses to evaluate the readability, difficulty, discriminability, validity, and reliability of the EvoDevoCI, which included items ranging in difficulty from 0.22–0.55 and in discriminability from 0.19–0.38. Such measures suggest the EvoDevoCI is an effective tool for assessing student understanding of evo-devo concepts and the prevalence of associated common conceptual difficulties among both novice and advanced undergraduate biology majors. PMID:24297293

Inferring Fitness Effects from Time-Resolved Sequence Data with a Delay-Deterministic Model.

PubMed

Nené, Nuno R; Dunham, Alistair S; Illingworth, Christopher J R

2018-05-01

A common challenge arising from the observation of an evolutionary system over time is to infer the magnitude of selection acting upon a specific genetic variant, or variants, within the population. The inference of selection may be confounded by the effects of genetic drift in a system, leading to the development of inference procedures to account for these effects. However, recent work has suggested that deterministic models of evolution may be effective in capturing the effects of selection even under complex models of demography, suggesting the more general application of deterministic approaches to inference. Responding to this literature, we here note a case in which a deterministic model of evolution may give highly misleading inferences, resulting from the nondeterministic properties of mutation in a finite population. We propose an alternative approach that acts to correct for this error, and which we denote the delay-deterministic model. Applying our model to a simple evolutionary system, we demonstrate its performance in quantifying the extent of selection acting within that system. We further consider the application of our model to sequence data from an evolutionary experiment. We outline scenarios in which our model may produce improved results for the inference of selection, noting that such situations can be easily identified via the use of a regular deterministic model. Copyright © 2018 Nené et al.

Phenotypic Graphs and Evolution Unfold the Standard Genetic Code as the Optimal

NASA Astrophysics Data System (ADS)

Zamudio, Gabriel S.; José, Marco V.

2018-03-01

In this work, we explicitly consider the evolution of the Standard Genetic Code (SGC) by assuming two evolutionary stages, to wit, the primeval RNY code and two intermediate codes in between. We used network theory and graph theory to measure the connectivity of each phenotypic graph. The connectivity values are compared to the values of the codes under different randomization scenarios. An error-correcting optimal code is one in which the algebraic connectivity is minimized. We show that the SGC is optimal in regard to its robustness and error-tolerance when compared to all random codes under different assumptions.

The Systems Autonomy Demonstration Project - Catalyst for Space Station advanced automation

NASA Technical Reports Server (NTRS)

Healey, Kathleen J.

1988-01-01

The Systems Autonomy Demonstration Project (SADP) was initiated by NASA to address the advanced automation needs for the Space Station program. The application of advanced automation to the Space Station's operations management system (OMS) is discussed. The SADP's future goals and objectives are discussed with respect to OMS functional requirements, design, and desired evolutionary capabilities. Major technical challenges facing the designers, developers, and users of the OMS are identified in order to guide the definition of objectives, plans, and scenarios for future SADP demonstrations, and to focus the efforts on the supporting research.

The dynamics of magnetic flux rings

NASA Technical Reports Server (NTRS)

Deluca, E. E.; Fisher, G. H.; Patten, B. M.

1993-01-01

The evolution of magnetic fields in the presence of turbulent convection is examined using results of numerical simulations of closed magnetic flux tubes embedded in a steady 'ABC' flow field, which approximate some of the important characteristics of a turbulent convecting flow field. Three different evolutionary scenarios were found: expansion to a steady deformed ring; collapse to a compact fat flux ring, separated from the expansion type of behavior by a critical length scale; and, occasionally, evolution toward an advecting, oscillatory state. The work suggests that small-scale flows will not have a strong effect on large-scale, strong fields.

Population Genetic Structure of Cnesterodon decemmaculatus (Poeciliidae): A Freshwater Look at the Pampa Biome in Southern South America

PubMed Central

Ramos-Fregonezi, Aline M. C.; Malabarba, Luiz R.; Fagundes, Nelson J. R.

2017-01-01

The Pampas is a Neotropical biome formed primarily by low altitude grasslands and encompasses the southernmost portion of Brazil, Uruguay, and part of Argentina. Despite the high level of endemism, and its significant environmental heterogeneity, Pampean species are underrepresented in phylogeographic studies, especially aquatic organisms. The Pampean hydrological system resulted from a long history of tectonism, climate, and sea level changes since the Neogene. In this study, we examined the population genetic structure of Cnesterodon decemmaculatus, a freshwater fish species that occurs throughout most of the Pampa biome. We characterized mitochondrial and autosomal genetic lineages in populations sampled from Southern Brazil and Uruguay to investigate (1) the correspondence between current drainage systems and evolutionary lineages, (2) the demographic history for each genetic lineage, and (3) the temporal depth of these lineages. Overall, we found that the major evolutionary lineages in this species are strongly related to the main Pampean drainage systems, even though stream capture events may have affected the distribution of genetic lineages among drainages. There was evidence for recent population growth in the lineages occupying drainages closest to the shore, which may indicate the effect of quaternary sea-level changes. In general, divergence time estimates among evolutionary lineages were shallow, ranging from 20,000 to 800,000 years before present, indicating a geologically recent history for this group, as previously reported in other Pampean species. A Bayesian phylogeographical reconstruction suggested that an ancestral lineage probably colonized the Uruguay River Basin, and then expanded throughout the Pampas. This evolutionary scenario may represent useful starting models for other freshwater species having a similar distribution. PMID:29312439

Population Genetic Structure of Cnesterodon decemmaculatus (Poeciliidae): A Freshwater Look at the Pampa Biome in Southern South America.

PubMed

Ramos-Fregonezi, Aline M C; Malabarba, Luiz R; Fagundes, Nelson J R

2017-01-01

The Pampas is a Neotropical biome formed primarily by low altitude grasslands and encompasses the southernmost portion of Brazil, Uruguay, and part of Argentina. Despite the high level of endemism, and its significant environmental heterogeneity, Pampean species are underrepresented in phylogeographic studies, especially aquatic organisms. The Pampean hydrological system resulted from a long history of tectonism, climate, and sea level changes since the Neogene. In this study, we examined the population genetic structure of Cnesterodon decemmaculatus , a freshwater fish species that occurs throughout most of the Pampa biome. We characterized mitochondrial and autosomal genetic lineages in populations sampled from Southern Brazil and Uruguay to investigate (1) the correspondence between current drainage systems and evolutionary lineages, (2) the demographic history for each genetic lineage, and (3) the temporal depth of these lineages. Overall, we found that the major evolutionary lineages in this species are strongly related to the main Pampean drainage systems, even though stream capture events may have affected the distribution of genetic lineages among drainages. There was evidence for recent population growth in the lineages occupying drainages closest to the shore, which may indicate the effect of quaternary sea-level changes. In general, divergence time estimates among evolutionary lineages were shallow, ranging from 20,000 to 800,000 years before present, indicating a geologically recent history for this group, as previously reported in other Pampean species. A Bayesian phylogeographical reconstruction suggested that an ancestral lineage probably colonized the Uruguay River Basin, and then expanded throughout the Pampas. This evolutionary scenario may represent useful starting models for other freshwater species having a similar distribution.

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

Liu Jinzhong; Han Zhanwen; Zhang Fenghui

Close double white dwarfs (CDWDs) are believed to dominate the Galactic gravitational wave (GW) radiation in the frequency range 10{sup -4} to 0.1 Hz, which will be detected by the Laser Interferometer Space Antenna (LISA) detector. The aim of this detector is to detect GW radiation from astrophysical sources in the universe and to help improve our understanding of the origin of the sources and their physical properties (masses and orbital periods). In this paper, we study the probable candidate sources in the Galaxy for the LISA detector: CDWDs. We use the binary population synthesis approach of CDWDs together withmore » the latest findings of the synthesis models from Han, who proposed three evolutionary channels: (1) stable Roche lobe overflow plus common envelope (RLOF+CE), (2) CE+CE, and (3) exposed core plus CE. As a result, we systematically investigate the detailed physical properties (the distributions of masses, orbital periods, and chirp masses) of the CDWD sources for the LISA detector, examine the importance of the three evolutionary channels for the formation of CDWDs, and carry out Monte Carlo simulations. Our results show that RLOF+CE and CE+CE are the main evolutionary scenarios leading to the formation of CDWDs. For the LISA detectable sources, we also explore and discuss the importance of these three evolutionary channels. Using the calculated birth rate, we compare our results to the LISA sensitivity curve and the foreground noise floor of CDWDs. We find that our estimate for the number of CDWD sources that can be detected by the LISA detector is greater than 10,000. We also find that the detectable CDWDs are produced via the CE+CE channel and we analyze the fraction of the detectable CDWDs that are double helium (He+He), or carbon-oxygen plus helium (CO+He) WD binary systems.« less

Double neutron stars: merger rates revisited

NASA Astrophysics Data System (ADS)

Chruslinska, Martyna; Belczynski, Krzysztof; Klencki, Jakub; Benacquista, Matthew

2018-03-01

We revisit double neutron star (DNS) formation in the classical binary evolution scenario in light of the recent Laser Interferometer Gravitational-wave Observatory (LIGO)/Virgo DNS detection (GW170817). The observationally estimated Galactic DNS merger rate of R_MW = 21^{+28}_{-14} Myr-1, based on three Galactic DNS systems, fully supports our standard input physics model with RMW = 24 Myr-1. This estimate for the Galaxy translates in a non-trivial way (due to cosmological evolution of progenitor stars in chemically evolving Universe) into a local (z ≈ 0) DNS merger rate density of Rlocal = 48 Gpc-3 yr-1, which is not consistent with the current LIGO/Virgo DNS merger rate estimate (1540^{+3200}_{-1220} Gpc-3 yr-1). Within our study of the parameter space, we find solutions that allow for DNS merger rates as high as R_local ≈ 600^{+600}_{-300} Gpc-3 yr-1 which are thus consistent with the LIGO/Virgo estimate. However, our corresponding BH-BH merger rates for the models with high DNS merger rates exceed the current LIGO/Virgo estimate of local BH-BH merger rate (12-213 Gpc-3 yr-1). Apart from being particularly sensitive to the common envelope treatment, DNS merger rates are rather robust against variations of several of the key factors probed in our study (e.g. mass transfer, angular momentum loss, and natal kicks). This might suggest that either common envelope development/survival works differently for DNS (˜10-20 M⊙ stars) than for BH-BH (˜40-100 M⊙ stars) progenitors, or high black hole (BH) natal kicks are needed to meet observational constraints for both types of binaries. Our conclusion is based on a limited number of (21) evolutionary models and is valid within this particular DNS and BH-BH isolated binary formation scenario.

Producing regionally-relevant multiobjective tradeoffs to engage with Colorado water managers

NASA Astrophysics Data System (ADS)

Smith, R.; Kasprzyk, J. R.; Basdekas, L.; Dilling, L.

2016-12-01

Disseminating results from water resources systems analysis research can be challenging when there are political or regulatory barriers associated with real-world models, or when a research model does not incorporate management context to which practitioners can relate. As part of a larger transdisciplinary study, we developed a broadly-applicable case study in collaboration with our partners at six diverse water utilities in the Front Range of Colorado, USA. Our model, called the "Eldorado Utility Planning Model", incorporates realistic water management decisions and objectives and achieves a pragmatic balance between system complexity and simplicity. Using the sophisticated modeling platform RiverWare, we modeled a spatially distributed regional network in which, under varying climate scenarios, the Eldorado Utility can meet growing demand from its variety of sources and by interacting with other users in the network. In accordance with complicated Front Range water laws, ownership, priority of use, and restricted uses of water are tracked through RiverWare's accounting functionality. To achieve good system performance, Eldorado can make decisions such as expand/build a reservoir, purchase rights from one or more actors, and enact conservation. This presentation introduces the model, and motivates how it can be used to aid researchers in developing multi-objective evolutionary algorithm (MOEA)-based optimization for similar multi-reservoir systems in Colorado and the Western US. Within the optimization, system performance is quantified by 5 objectives: minimizing time in restrictions; new storage capacity; newly developed supply; and uncaptured water; and maximizing year-end storage. Our results demonstrate critical tradeoffs between the objectives and show how these tradeoffs are affected by several realistic climate change scenarios. These results were used within an interactive workshop that helped demonstrate the application of MOEA-based optimization for water management in the western US.

Classification of Medical Datasets Using SVMs with Hybrid Evolutionary Algorithms Based on Endocrine-Based Particle Swarm Optimization and Artificial Bee Colony Algorithms.

PubMed

Lin, Kuan-Cheng; Hsieh, Yi-Hsiu

2015-10-01

The classification and analysis of data is an important issue in today's research. Selecting a suitable set of features makes it possible to classify an enormous quantity of data quickly and efficiently. Feature selection is generally viewed as a problem of feature subset selection, such as combination optimization problems. Evolutionary algorithms using random search methods have proven highly effective in obtaining solutions to problems of optimization in a diversity of applications. In this study, we developed a hybrid evolutionary algorithm based on endocrine-based particle swarm optimization (EPSO) and artificial bee colony (ABC) algorithms in conjunction with a support vector machine (SVM) for the selection of optimal feature subsets for the classification of datasets. The results of experiments using specific UCI medical datasets demonstrate that the accuracy of the proposed hybrid evolutionary algorithm is superior to that of basic PSO, EPSO and ABC algorithms, with regard to classification accuracy using subsets with a reduced number of features.

Individual-based modeling of ecological and evolutionary processes

USGS Publications Warehouse

DeAngelis, Donald L.; Mooij, Wolf M.

2005-01-01

Individual-based models (IBMs) allow the explicit inclusion of individual variation in greater detail than do classical differential-equation and difference-equation models. Inclusion of such variation is important for continued progress in ecological and evolutionary theory. We provide a conceptual basis for IBMs by describing five major types of individual variation in IBMs: spatial, ontogenetic, phenotypic, cognitive, and genetic. IBMs are now used in almost all subfields of ecology and evolutionary biology. We map those subfields and look more closely at selected key papers on fish recruitment, forest dynamics, sympatric speciation, metapopulation dynamics, maintenance of diversity, and species conservation. Theorists are currently divided on whether IBMs represent only a practical tool for extending classical theory to more complex situations, or whether individual-based theory represents a radically new research program. We feel that the tension between these two poles of thinking can be a source of creativity in ecology and evolutionary theory.

Towards Co-evolution of Membranes and Metabolism

NASA Technical Reports Server (NTRS)

Wei, Chenyu; Wilson, Michael A.; Pohorille, Andrew

2014-01-01

Conceptually, the most robust way to explain how primitive cell-like structures acquired and increased their capabilities is on the basis of Darwinian evolution. A population of protocells containing material that produced more environmentally fit progeny would increase in time at the expense of other protocells. In this scenario, protocellular boundaries were inextricably connected to the metabolism they encapsulated: to be inheritable, early metabolism must have led to an increased rate of growth and division of vesicles and, similarly, transport through vesicle boundaries must have supported the evolution of metabolism. Everything that could not be delivered from the environment had to be produced and retained inside protocells. Despite their importance to the understanding of the origin of life, only a few cases of coupling between metabolism and membrane-related processes have been identified so far. For example, reactions inside fatty-acid vesicles have been linked to their competitive growth and division, and mechanisms by which membrane permeability might have coupled to information polymers have been proposed and explained. Most recently, it has been shown that a dipeptide inside fatty-acid vesicles catalyzes the formation of another dipeptide that binds to vesicle walls and, by doing so, promotes their growth at the expense of other vesicles, thus demonstrating evolutionary advantage of small, membrane-bound peptides. It has been shown that the appearance of phospholipids imparted selective advantage to protocells bound by phospholipid-containing membranes, eventually driving fatty-acid vesicles to extinction. Phospholipid membranes, however, are nearly impermeable to charged species. Yet, the ability to transport ions across membranes was vital for regulating cellular volume, pH homeostasis, generating energy and sensing the environment. To account for this, evolutionary scenarios for the emergence of simple ion channels, protein structures surrounding water-filled pores in the membrane that facilitate ion transport, have been developed. We will review recent progress in experimental and theoretical studies on coupling properties of membranes to metabolism, with the focus on how they impose constraints on scenarios for the origin of life, and discuss how these studies form the basis for future work on this topic.

Evolutionary Medicine: The Ongoing Evolution of Human Physiology and Metabolism.

PubMed

Rühli, Frank; van Schaik, Katherine; Henneberg, Maciej

2016-11-01

The field of evolutionary medicine uses evolutionary principles to understand changes in human anatomy and physiology that have occurred over time in response to environmental changes. Through this evolutionary-based approach, we can understand disease as a consequence of anatomical and physiological "trade-offs" that develop to facilitate survival and reproduction. We demonstrate how diachronic study of human anatomy and physiology is fundamental for an increased understanding of human health and disease. ©2016 Int. Union Physiol. Sci./Am. Physiol. Soc.

Models of emergency departments for reducing patient waiting times.

PubMed

Laskowski, Marek; McLeod, Robert D; Friesen, Marcia R; Podaima, Blake W; Alfa, Attahiru S

2009-07-02

In this paper, we apply both agent-based models and queuing models to investigate patient access and patient flow through emergency departments. The objective of this work is to gain insights into the comparative contributions and limitations of these complementary techniques, in their ability to contribute empirical input into healthcare policy and practice guidelines. The models were developed independently, with a view to compare their suitability to emergency department simulation. The current models implement relatively simple general scenarios, and rely on a combination of simulated and real data to simulate patient flow in a single emergency department or in multiple interacting emergency departments. In addition, several concepts from telecommunications engineering are translated into this modeling context. The framework of multiple-priority queue systems and the genetic programming paradigm of evolutionary machine learning are applied as a means of forecasting patient wait times and as a means of evolving healthcare policy, respectively. The models' utility lies in their ability to provide qualitative insights into the relative sensitivities and impacts of model input parameters, to illuminate scenarios worthy of more complex investigation, and to iteratively validate the models as they continue to be refined and extended. The paper discusses future efforts to refine, extend, and validate the models with more data and real data relative to physical (spatial-topographical) and social inputs (staffing, patient care models, etc.). Real data obtained through proximity location and tracking system technologies is one example discussed.

Recognition Without Words: Using Taste to Explore Survival Processing

PubMed Central

Hallock, Henry L.; Garman, Heather D.; Cook, Shaun P.; Gallagher, Shawn P.

2017-01-01

Many educational demonstrations of memory and recall employ word lists and number strings; items that lend themselves to semantic organization and “chunking.” By applying taste recall to the adaptive memory paradigm, which evaluates memory from a survival-based evolutionary perspective, we have developed a simple, inexpensive exercise that defies mnemonic strategies. Most adaptive memory studies have evaluated recall of words encountered while imagining survival and non-survival scenarios. Here, we’ve left the lexical domain and hypothesized that taste memory, as measured by recognition, would be best when acquisition occurs under imagined threat of personal harm, namely poisoning. We tested participants individually while they evaluated eight teas in one of three conditions: in one, they evaluated the toxicity of the tea (survival condition), in a second, they considered the marketability of the tea and, in the third, they evaluated the bitterness of the tea. After a filler task, a surprise recognition task required the participants to taste and identify the eight original teas from a group of 16 that included eight novel teas. The survival condition led to better recognition than the bitterness condition but, surprisingly, it did not yield better recognition than the marketing condition. A second experiment employed a streamlined design more appropriate for classroom settings and failed to support the hypothesis that planning enhanced recognition in survival scenarios. This simple technique has, at least, revealed a robust levels-of-processing effect for taste recognition and invites students to consider the adaptive advantages of all forms of memory. PMID:28690433

Models of Emergency Departments for Reducing Patient Waiting Times

PubMed Central

Laskowski, Marek; McLeod, Robert D.; Friesen, Marcia R.; Podaima, Blake W.; Alfa, Attahiru S.

2009-01-01

In this paper, we apply both agent-based models and queuing models to investigate patient access and patient flow through emergency departments. The objective of this work is to gain insights into the comparative contributions and limitations of these complementary techniques, in their ability to contribute empirical input into healthcare policy and practice guidelines. The models were developed independently, with a view to compare their suitability to emergency department simulation. The current models implement relatively simple general scenarios, and rely on a combination of simulated and real data to simulate patient flow in a single emergency department or in multiple interacting emergency departments. In addition, several concepts from telecommunications engineering are translated into this modeling context. The framework of multiple-priority queue systems and the genetic programming paradigm of evolutionary machine learning are applied as a means of forecasting patient wait times and as a means of evolving healthcare policy, respectively. The models' utility lies in their ability to provide qualitative insights into the relative sensitivities and impacts of model input parameters, to illuminate scenarios worthy of more complex investigation, and to iteratively validate the models as they continue to be refined and extended. The paper discusses future efforts to refine, extend, and validate the models with more data and real data relative to physical (spatial–topographical) and social inputs (staffing, patient care models, etc.). Real data obtained through proximity location and tracking system technologies is one example discussed. PMID:19572015

Directed Energy Technology Working Group Report (IDA/OSD R&M (Institute for Defense Analyses/Office of the Secretary of Defense Reliability and Maintainability) Study).

DTIC Science & Technology

1983-08-01

Missile (SLBM) Defense Scenario ............................................ B-1 C Space-Based Anti-Ballistic Missile ( ABM ) Defense Scenario...Ballistic Missile (SLBM) Defense Scenario, and at Strategic Space-Based Anti-Ballistic Missile ( ABM ) Defense Scenario. These case studies are provided...of flight. 3.5.3 Spaced-Based ABM Defense Scenario In this scenario, an orbiting battle station is operating as an element of GBMD System, and it is

Phylogenetic framework for coevolutionary studies: a compass for exploring jungles of tangled trees.

PubMed

Martínez-Aquino, Andrés

2016-08-01

Phylogenetics is used to detect past evolutionary events, from how species originated to how their ecological interactions with other species arose, which can mirror cophylogenetic patterns. Cophylogenetic reconstructions uncover past ecological relationships between taxa through inferred coevolutionary events on trees, for example, codivergence, duplication, host-switching, and loss. These events can be detected by cophylogenetic analyses based on nodes and the length and branching pattern of the phylogenetic trees of symbiotic associations, for example, host-parasite. In the past 2 decades, algorithms have been developed for cophylogetenic analyses and implemented in different software, for example, statistical congruence index and event-based methods. Based on the combination of these approaches, it is possible to integrate temporal information into cophylogenetical inference, such as estimates of lineage divergence times between 2 taxa, for example, hosts and parasites. Additionally, the advances in phylogenetic biogeography applying methods based on parametric process models and combined Bayesian approaches, can be useful for interpreting coevolutionary histories in a scenario of biogeographical area connectivity through time. This article briefly reviews the basics of parasitology and provides an overview of software packages in cophylogenetic methods. Thus, the objective here is to present a phylogenetic framework for coevolutionary studies, with special emphasis on groups of parasitic organisms. Researchers wishing to undertake phylogeny-based coevolutionary studies can use this review as a "compass" when "walking" through jungles of tangled phylogenetic trees.

Phylogenetic framework for coevolutionary studies: a compass for exploring jungles of tangled trees

PubMed Central

2016-01-01

Abstract Phylogenetics is used to detect past evolutionary events, from how species originated to how their ecological interactions with other species arose, which can mirror cophylogenetic patterns. Cophylogenetic reconstructions uncover past ecological relationships between taxa through inferred coevolutionary events on trees, for example, codivergence, duplication, host-switching, and loss. These events can be detected by cophylogenetic analyses based on nodes and the length and branching pattern of the phylogenetic trees of symbiotic associations, for example, host–parasite. In the past 2 decades, algorithms have been developed for cophylogetenic analyses and implemented in different software, for example, statistical congruence index and event-based methods. Based on the combination of these approaches, it is possible to integrate temporal information into cophylogenetical inference, such as estimates of lineage divergence times between 2 taxa, for example, hosts and parasites. Additionally, the advances in phylogenetic biogeography applying methods based on parametric process models and combined Bayesian approaches, can be useful for interpreting coevolutionary histories in a scenario of biogeographical area connectivity through time. This article briefly reviews the basics of parasitology and provides an overview of software packages in cophylogenetic methods. Thus, the objective here is to present a phylogenetic framework for coevolutionary studies, with special emphasis on groups of parasitic organisms. Researchers wishing to undertake phylogeny-based coevolutionary studies can use this review as a “compass” when “walking” through jungles of tangled phylogenetic trees. PMID:29491928

Evolutionary principles and their practical application

PubMed Central

Hendry, Andrew P; Kinnison, Michael T; Heino, Mikko; Day, Troy; Smith, Thomas B; Fitt, Gary; Bergstrom, Carl T; Oakeshott, John; Jørgensen, Peter S; Zalucki, Myron P; Gilchrist, George; Southerton, Simon; Sih, Andrew; Strauss, Sharon; Denison, Robert F; Carroll, Scott P

2011-01-01

Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology. PMID:25567966

Evolutionary principles and their practical application.

PubMed

Hendry, Andrew P; Kinnison, Michael T; Heino, Mikko; Day, Troy; Smith, Thomas B; Fitt, Gary; Bergstrom, Carl T; Oakeshott, John; Jørgensen, Peter S; Zalucki, Myron P; Gilchrist, George; Southerton, Simon; Sih, Andrew; Strauss, Sharon; Denison, Robert F; Carroll, Scott P

2011-03-01

Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology.

Toward a unifying framework for evolutionary processes.

PubMed

Paixão, Tiago; Badkobeh, Golnaz; Barton, Nick; Çörüş, Doğan; Dang, Duc-Cuong; Friedrich, Tobias; Lehre, Per Kristian; Sudholt, Dirk; Sutton, Andrew M; Trubenová, Barbora

2015-10-21

The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Evolutionary analyses of non-genealogical bonds produced by introgressive descent.

PubMed

Bapteste, Eric; Lopez, Philippe; Bouchard, Frédéric; Baquero, Fernando; McInerney, James O; Burian, Richard M

2012-11-06

All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.

Beyond Corroboration: Strengthening Model Validation by Looking for Unexpected Patterns

PubMed Central

Chérel, Guillaume; Cottineau, Clémentine; Reuillon, Romain

2015-01-01

Models of emergent phenomena are designed to provide an explanation to global-scale phenomena from local-scale processes. Model validation is commonly done by verifying that the model is able to reproduce the patterns to be explained. We argue that robust validation must not only be based on corroboration, but also on attempting to falsify the model, i.e. making sure that the model behaves soundly for any reasonable input and parameter values. We propose an open-ended evolutionary method based on Novelty Search to look for the diverse patterns a model can produce. The Pattern Space Exploration method was tested on a model of collective motion and compared to three common a priori sampling experiment designs. The method successfully discovered all known qualitatively different kinds of collective motion, and performed much better than the a priori sampling methods. The method was then applied to a case study of city system dynamics to explore the model’s predicted values of city hierarchisation and population growth. This case study showed that the method can provide insights on potential predictive scenarios as well as falsifiers of the model when the simulated dynamics are highly unrealistic. PMID:26368917

Small reactor power systems for manned planetary surface bases

NASA Technical Reports Server (NTRS)

Bloomfield, Harvey S.

1987-01-01

A preliminary feasibility study of the potential application of small nuclear reactor space power systems to manned planetary surface base missions was conducted. The purpose of the study was to identify and assess the technology, performance, and safety issues associated with integration of reactor power systems with an evolutionary manned planetary surface exploration scenario. The requirements and characteristics of a variety of human-rated modular reactor power system configurations selected for a range of power levels from 25 kWe to hundreds of kilowatts is described. Trade-off analyses for reactor power systems utilizing both man-made and indigenous shielding materials are provided to examine performance, installation and operational safety feasibility issues. The results of this study have confirmed the preliminary feasibility of a wide variety of small reactor power plant configurations for growth oriented manned planetary surface exploration missions. The capability for power level growth with increasing manned presence, while maintaining safe radiation levels, was favorably assessed for nominal 25 to 100 kWe modular configurations. No feasibility limitations or technical barriers were identified and the use of both distance and indigenous planetary soil material for human rated radiation shielding were shown to be viable and attractive options.

Population genomic analyses reveal a history of range expansion and trait evolution across the native and invaded range of yellow starthistle (Centaurea solstitialis)

PubMed Central

BARKER, BRITTANY S.; ANDONIAN, KRIKOR; SWOPE, SARAH M.; LUSTER, DOUGLAS G.; DLUGOSCH, KATRINA M.

2017-01-01

Identifying sources of genetic variation and reconstructing invasion routes for non-native introduced species is central to understanding the circumstances under which they may evolve increased invasiveness. In this study, we used genome-wide single nucleotide polymorphisms to study the colonization history of Centaurea solstitialis in its native range in Eurasia and invasions into the Americas. We leveraged this information to pinpoint key evolutionary shifts in plant size, a focal trait associated with invasiveness in this species. Our analyses revealed clear population genomic structure of potential source populations in Eurasia, including deep differentiation of a lineage found in the southern Apennine and Balkan Peninsulas and divergence among populations in Asia, eastern Europe, and western Europe. We found strongest support for an evolutionary scenario in which western European populations were derived from an ancient admixture event between populations from eastern Europe and Asia, and subsequently served as the main genetic ‘bridgehead’ for introductions to the Americas. Introductions to California appear to be from a single source region, and multiple, independent introductions of divergent genotypes likely occurred into the Pacific Northwest. Plant size has evolved significantly at three points during range expansion, including a large size increase in the lineage responsible for the aggressive invasion of California’s interior. These results reveal a long history of colonization, admixture, and trait evolution in C. solstitialis, and suggest routes for improving evidence-based management decisions for one of the most ecologically and economically damaging invasive species in the western United States. PMID:28029713

Infrasonic and Ultrasonic Hearing Evolved after the Emergence of Modern Whales.

PubMed

Mourlam, Mickaël J; Orliac, Maeva J

2017-06-19

Mysticeti (baleen whales) and Odontoceti (toothed whales) today greatly differ in their hearing abilities: Mysticeti are presumed to be sensitive to infrasonic noises [1-3], whereas Odontoceti are sensitive to ultrasonic sounds [4-6]. Two competing hypotheses exist regarding the attainment of hearing abilities in modern whales: ancestral low-frequency sensitivity [7-13] or ancestral high-frequency sensitivity [14, 15]. The significance of these evolutionary scenarios is limited by the undersampling of both early-diverging cetaceans (archaeocetes) and terrestrial hoofed relatives of cetaceans (non-cetacean artiodactyls). Here, we document for the first time the bony labyrinth, the hollow cavity housing the hearing organ, of two species of protocetid whales from Lutetian deposits (ca. 46-43 Ma) of Kpogamé, Togo. These archaeocete cetaceans, which are transitional between terrestrial and aquatic forms, prove to be a key for determining the hearing abilities of early whales. We propose a new evolutionary picture for the early stages of this history, based on qualitative and quantitative studies of the cochlear morphology of an unparalleled sample of extant and extinct land artiodactyls and cetaceans. Contrary to the hypothesis that archaeocetes have been more sensitive to high-frequency sounds than their terrestrial ancestors [15], we demonstrate that early cetaceans presented a cochlear functional pattern close to that of their terrestrial relatives, and that specialization for infrasonic or ultrasonic hearing in Mysticeti or Odontoceti, respectively, instead only occurred in fully aquatic whales, after the emergence of Neoceti (Mysticeti+Odontoceti). Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts

PubMed Central

Sikosek, Tobias; Bornberg-Bauer, Erich; Chan, Hue Sun

2012-01-01

Experimental studies have shown that some proteins exist in two alternative native-state conformations. It has been proposed that such bi-stable proteins can potentially function as evolutionary bridges at the interface between two neutral networks of protein sequences that fold uniquely into the two different native conformations. Under adaptive conflict scenarios, bi-stable proteins may be of particular advantage if they simultaneously provide two beneficial biological functions. However, computational models that simulate protein structure evolution do not yet recognize the importance of bi-stability. Here we use a biophysical model to analyze sequence space to identify bi-stable or multi-stable proteins with two or more equally stable native-state structures. The inclusion of such proteins enhances phenotype connectivity between neutral networks in sequence space. Consideration of the sequence space neighborhood of bridge proteins revealed that bi-stability decreases gradually with each mutation that takes the sequence further away from an exactly bi-stable protein. With relaxed selection pressures, we found that bi-stable proteins in our model are highly successful under simulated adaptive conflict. Inspired by these model predictions, we developed a method to identify real proteins in the PDB with bridge-like properties, and have verified a clear bi-stability gradient for a series of mutants studied by Alexander et al. (Proc Nat Acad Sci USA 2009, 106:21149–21154) that connect two sequences that fold uniquely into two different native structures via a bridge-like intermediate mutant sequence. Based on these findings, new testable predictions for future studies on protein bi-stability and evolution are discussed. PMID:23028272

Modeling the evolution of protein domain architectures using maximum parsimony.

PubMed

Fong, Jessica H; Geer, Lewis Y; Panchenko, Anna R; Bryant, Stephen H

2007-02-09

Domains are basic evolutionary units of proteins and most proteins have more than one domain. Advances in domain modeling and collection are making it possible to annotate a large fraction of known protein sequences by a linear ordering of their domains, yielding their architecture. Protein domain architectures link evolutionarily related proteins and underscore their shared functions. Here, we attempt to better understand this association by identifying the evolutionary pathways by which extant architectures may have evolved. We propose a model of evolution in which architectures arise through rearrangements of inferred precursor architectures and acquisition of new domains. These pathways are ranked using a parsimony principle, whereby scenarios requiring the fewest number of independent recombination events, namely fission and fusion operations, are assumed to be more likely. Using a data set of domain architectures present in 159 proteomes that represent all three major branches of the tree of life allows us to estimate the history of over 85% of all architectures in the sequence database. We find that the distribution of rearrangement classes is robust with respect to alternative parsimony rules for inferring the presence of precursor architectures in ancestral species. Analyzing the most parsimonious pathways, we find 87% of architectures to gain complexity over time through simple changes, among which fusion events account for 5.6 times as many architectures as fission. Our results may be used to compute domain architecture similarities, for example, based on the number of historical recombination events separating them. Domain architecture "neighbors" identified in this way may lead to new insights about the evolution of protein function.

Modeling the Evolution of Protein Domain Architectures Using Maximum Parsimony

PubMed Central

Fong, Jessica H.; Geer, Lewis Y.; Panchenko, Anna R.; Bryant, Stephen H.

2007-01-01

Domains are basic evolutionary units of proteins and most proteins have more than one domain. Advances in domain modeling and collection are making it possible to annotate a large fraction of known protein sequences by a linear ordering of their domains, yielding their architecture. Protein domain architectures link evolutionarily related proteins and underscore their shared functions. Here, we attempt to better understand this association by identifying the evolutionary pathways by which extant architectures may have evolved. We propose a model of evolution in which architectures arise through rearrangements of inferred precursor architectures and acquisition of new domains. These pathways are ranked using a parsimony principle, whereby scenarios requiring the fewest number of independent recombination events, namely fission and fusion operations, are assumed to be more likely. Using a data set of domain architectures present in 159 proteomes that represent all three major branches of the tree of life allows us to estimate the history of over 85% of all architectures in the sequence database. We find that the distribution of rearrangement classes is robust with respect to alternative parsimony rules for inferring the presence of precursor architectures in ancestral species. Analyzing the most parsimonious pathways, we find 87% of architectures to gain complexity over time through simple changes, among which fusion events account for 5.6 times as many architectures as fission. Our results may be used to compute domain architecture similarities, for example, based on the number of historical recombination events separating them. Domain architecture “neighbors” identified in this way may lead to new insights about the evolution of protein function. PMID:17166515

Scenario driven data modelling: a method for integrating diverse sources of data and data streams

DOEpatents

Brettin, Thomas S.; Cottingham, Robert W.; Griffith, Shelton D.; Quest, Daniel J.

2015-09-08

A system and method of integrating diverse sources of data and data streams is presented. The method can include selecting a scenario based on a topic, creating a multi-relational directed graph based on the scenario, identifying and converting resources in accordance with the scenario and updating the multi-directed graph based on the resources, identifying data feeds in accordance with the scenario and updating the multi-directed graph based on the data feeds, identifying analytical routines in accordance with the scenario and updating the multi-directed graph using the analytical routines and identifying data outputs in accordance with the scenario and defining queries to produce the data outputs from the multi-directed graph.

Patterns of co-speciation and host switching in primate malaria parasites.

PubMed

Garamszegi, László Zsolt

2009-05-22

The evolutionary history of many parasites is dependent on the evolution of their hosts, leading to an association between host and parasite phylogenies. However, frequent host switches across broad phylogenetic distances may weaken this close evolutionary link, especially when vectors are involved in parasites transmission, as is the case for malaria pathogens. Several studies suggested that the evolution of the primate-infective malaria lineages may be constrained by the phylogenetic relationships of their hosts, and that lateral switches between distantly related hosts may have been occurred. However, no systematic analysis has been quantified the degree of phylogenetic association between primates and their malaria parasites. Here phylogenetic approaches have been used to discriminate statistically between events due to co-divergence, duplication, extinction and host switches that can potentially cause historical association between Plasmodium parasites and their primate hosts. A Bayesian reconstruction of parasite phylogeny based on genetic information for six genes served as basis for the analyses, which could account for uncertainties about the evolutionary hypotheses of malaria parasites. Related lineages of primate-infective Plasmodium tend to infect hosts within the same taxonomic family. Different analyses testing for congruence between host and parasite phylogenies unanimously revealed a significant association between the corresponding evolutionary trees. The most important factor that resulted in this association was host switching, but depending on the parasite phylogeny considered, co-speciation and duplication may have also played some additional role. Sorting seemed to be a relatively infrequent event, and can occur only under extreme co-evolutionary scenarios. The concordance between host and parasite phylogenies is heterogeneous: while the evolution of some malaria pathogens is strongly dependent on the phylogenetic history of their primate hosts, the congruent evolution is less emphasized for other parasite lineages (e.g. for human malaria parasites). Estimation of ancestral states of host use along the phylogenetic tree of parasites revealed that lateral transfers across distantly related hosts were likely to occur in several cases. Parasites cannot infect all available hosts, and they should preferentially infect hosts that provide a similar environment for reproduction. Marginally significant evidence suggested that there might be a consistent variation within host ranges in terms of physiology. The evolution of primate malarias is constrained by the phylogenetic associations of their hosts. Some parasites can preserve a great flexibility to infect hosts across a large phylogenetic distance, thus host switching can be an important factor in mediating host ranges observed in nature. Due to this inherent flexibility and the potential exposure to various vectors, the emergence of new malaria disease in primates including humans cannot be predicted from the phylogeny of parasites.

Holocene population history of the Sabana de Bogotá region, Northern South America: An assessment of the craniofacial shape variation.

PubMed

Delgado, Miguel

2017-02-01

Several authors using multiple and independent lines of evidence investigating the biocultural continuity versus discontinuity in the Sabana de Bogotá region, in the eastern highlands of Colombia, have arrived at contradictory conclusions supporting either scenarios. This study analyzes the craniofacial size and shape variation of diachronic samples from the study region to test distinct population history scenarios that support continuity or, alternatively, divergence. A total of 92 adult skulls belonging to five chronological groups, ranging from c. 10,100 to 350 14 C YBP, were analyzed through Procrustean geometric morphometric techniques. Matrix correlation analysis, multivariate exploratory (PCA, FDA), and evolutionary quantitative genetic methods (R-matrix analysis and β-test) were used to study the diachronic craniofacial shape variation. A model that supports strong evolutionary diversification over the Holocene better explains the patterns of morphological variation observed. At least two periods of significant craniofacial size and shape change were detected: one during the middle to initial late Holocene transition (c. 4,000-3,200 14 C YBP) and other toward the final late Holocene (post-2,000 14 C YBP), which exhibit differences in the pattern and magnitude of cranial divergence. In addition, the differentiation viewed between early and mid-Holocene foragers could mark the initial entry of non-local populations into the region toward the beginnings of the middle Holocene. Distinct to previous investigations the present study supports a more complex regional population history where multiple population contractions/extinctions, dispersals and assimilations along with dietary adaptations took place during the last 10,000 years. These results are in agreement with the archaeological and paleoecological record which suggests marked periods of change rather than temporal stability. © 2016 Wiley Periodicals, Inc.

MMP-TIMP interactions in cancer invasion: An evolutionary game-theoretical framework.

PubMed

Salimi Sartakhti, Javad; Manshaei, Mohammad Hossein; Sadeghi, Mehdi

2017-01-07

One of the main steps in solid cancers to invade surrounding tissues is degradation of tissue barriers in the extracellular matrix. This operation that leads to initiate, angiogenesis and metastasis to other organs, is essentially consequence of collapsing dynamic balance between matrix metalloproteinases (MMP) and tissue inhibitors of metalloproteinases (TIMP). In this work, we model the MMP-TIMP interaction in both normal tissue and invasive cancer using evolutionary game theory. Our model explains how invasive cancer cells get the upper hand in MMP-TIMP imbalance scenarios. We investigate dynamics of them over time and discuss stable and nonstable states in the population. Numerical simulations presented here provide the identification of key genotypic features in the tumor invasion and a natural description for phenotypic variability. The simulation results are consistent with the experimental results in vitro observations presented in medical literature. Finally, by the provided results the necessary conditions to inhibit cancer invasion or prolong its course are explained. In this way, two therapeutic approaches with respect to how they could meet the required conditions are considered. Copyright © 2016 Elsevier Ltd. All rights reserved.

Estimating directional epistasis

PubMed Central

Le Rouzic, Arnaud

2014-01-01

Epistasis, i.e., the fact that gene effects depend on the genetic background, is a direct consequence of the complexity of genetic architectures. Despite this, most of the models used in evolutionary and quantitative genetics pay scant attention to genetic interactions. For instance, the traditional decomposition of genetic effects models epistasis as noise around the evolutionarily-relevant additive effects. Such an approach is only valid if it is assumed that there is no general pattern among interactions—a highly speculative scenario. Systematic interactions generate directional epistasis, which has major evolutionary consequences. In spite of its importance, directional epistasis is rarely measured or reported by quantitative geneticists, not only because its relevance is generally ignored, but also due to the lack of simple, operational, and accessible methods for its estimation. This paper describes conceptual and statistical tools that can be used to estimate directional epistasis from various kinds of data, including QTL mapping results, phenotype measurements in mutants, and artificial selection responses. As an illustration, I measured directional epistasis from a real-life example. I then discuss the interpretation of the estimates, showing how they can be used to draw meaningful biological inferences. PMID:25071828

Improved Constraints on the Disk around MWC 349A from the 23 m LBTI

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

Sallum, S.; Eisner, J. A.; Hinz, P. M.

2017-07-20

We present new spatially resolved observations of MWC 349A from the Large Binocular Telescope Interferometer (LBTI), a 23 m baseline interferometer made up of two, co-mounted 8 m telescopes. MWC 349A is a B[e] star with an unknown evolutionary state. Proposed scenarios range from a young stellar object, to a B[e] supergiant, to a tight binary system. Radio continuum and recombination line observations of this source revealed a sub-arcsecond bipolar outflow surrounding an ∼100 mas circumstellar disk. Follow-up infrared studies detected the disk, and suggested that it may have skew and an inner clearing. Our new infrared interferometric observations, whichmore » have more than twice the resolution of previously published data sets, support the presence of both skew and a compact infrared excess. They rule out inner clearings with radii greater than ∼14 mas. We show the improvements in disk parameter constraints provided by LBTI, and discuss the inferred disk parameters in the context of the posited evolutionary states for MWC 349A.« less

Impact of small groups with heterogeneous preference on behavioral evolution in population evacuation.

PubMed

Wang, Tao; Huang, Keke; Wang, Zhen; Zheng, Xiaoping

2015-01-01

Up to now, there have been a great number of mechanisms to explain the individual behavior and population traits, which seem of particular significance in evolutionary biology and social behavior analysis. Among them, small groups and heterogeneity are two useful frameworks to the above issue. However, vast majority of existing works separately consider both scenarios, which is inconsistent with realistic cases in our life. Here we propose the evolutionary games of heterogeneous small groups (namely, different small groups possess different preferences to dilemma) to study the collective behavior in population evacuation. Importantly, players usually face completely different dilemmas inside and outside the small groups. By means of numerous computation simulations, it is unveiled that the ratio of players in one certain small group directly decides the final behavior of the whole population. Moreover, it can also be concluded that heterogeneous degree of preference for different small groups plays a key role in the behavior traits of the system, which may validate some realistic social observations. The proposed framework is thus universally applicable and may shed new light into the solution of social dilemmas.

Biogeography of thermophilic phototrophic bacteria belonging to Roseiflexus genus.

PubMed

Gaisin, Vasil A; Grouzdev, Denis S; Namsaraev, Zorigto B; Sukhacheva, Marina V; Gorlenko, Vladimir M; Kuznetsov, Boris B

2016-03-01

Isolated environments such as hot springs are particularly interesting for studying the microbial biogeography. These environments create an 'island effect' leading to genetic divergence. We studied the phylogeographic pattern of thermophilic anoxygenic phototrophic bacteria, belonging to the Roseiflexus genus. The main characteristic of the observed pattern was geographic and geochronologic fidelity to the hot springs within Circum-Pacific and Alpine-Himalayan-Indonesian orogenic belts. Mantel test revealed a correlation between genetic divergence and geographic distance among the phylotypes. Cluster analysis revealed a regional differentiation of the global phylogenetic pattern. The phylogeographic pattern is in correlation with geochronologic events during the break up of Pangaea that led to the modern configuration of continents. To our knowledge this is the first geochronological scenario of intercontinental prokaryotic taxon divergence. The existence of the modern phylogeographic pattern contradicts with the existence of the ancient evolutionary history of the Roseiflexus group proposed on the basis of its deep-branching phylogenetic position. These facts indicate that evolutionary rates in Roseiflexus varied over a wide range. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Bifurcation into functional niches in adaptation.

PubMed

White, Justin S; Adami, Christoph

2004-01-01

One of the central questions in evolutionary biology concerns the dynamics of adaptation and diversification. This issue can be addressed experimentally if replicate populations adapting to identical environments can be investigated in detail. We have studied 501 such replicas using digital organisms adapting to at least two fundamentally different functional niches (survival strategies) present in the same environment: one in which fast replication is the way to live, and another where exploitation of the environment's complexity leads to complex organisms with longer life spans and smaller replication rates. While these two modes of survival are closely analogous to those expected to emerge in so-called r and K selection scenarios respectively, the bifurcation of evolutionary histories according to these functional niches occurs in identical environments, under identical selective pressures. We find that the branching occurs early, and leads to drastic phenotypic differences (in fitness, sequence length, and gestation time) that are permanent and irreversible. This study confirms an earlier experimental effort using microorganisms, in that diversification can be understood at least in part in terms of bifurcations on saddle points leading to peak shifts, as in the picture drawn by Sewall Wright.

Phenotypic divergence despite low genetic differentiation in house sparrow populations.

PubMed

Ben Cohen, Shachar; Dor, Roi

2018-01-10

Studying patterns of phenotypic variation among populations can shed light on the drivers of evolutionary processes. The house sparrow (Passer domesticus) is one of the world's most ubiquitous bird species, as well as a successful invader. We investigated phenotypic variation in house sparrow populations across a climatic gradient and in relation to a possible scenario of an invasion. We measured variation in morphological, coloration, and behavioral traits (exploratory behavior and neophobia) and compared it to the neutral genetic variation. We found that sparrows were larger and darker in northern latitudes, in accordance with Bergmann's and Gloger's biogeographic rules. Morphology and behavior mostly differed between the southernmost populations and the other regions, supporting the possibility of an invasion. Genetic differentiation was low and diversity levels were similar across populations, indicating high gene flow. Nevertheless, the southernmost and northern populations differed genetically to some extent. Furthermore, genetic differentiation (F ST ) was lower in comparison to phenotypic variation (P ST ), indicating that the phenotypic variation is shaped by directional selection or by phenotypic plasticity. This study expands our knowledge on evolutionary mechanisms and biological invasions.

Origin and early evolution of photosynthesis

NASA Technical Reports Server (NTRS)

Blankenship, R. E.

1992-01-01

Photosynthesis was well-established on the earth at least 3.5 thousand million years ago, and it is widely believed that these ancient organisms had similar metabolic capabilities to modern cyanobacteria. This requires that development of two photosystems and the oxygen evolution capability occurred very early in the earth's history, and that a presumed phase of evolution involving non-oxygen evolving photosynthetic organisms took place even earlier. The evolutionary relationships of the reaction center complexes found in all the classes of currently existing organisms have been analyzed using sequence analysis and biophysical measurements. The results indicate that all reaction centers fall into two basic groups, those with pheophytin and a pair of quinones as early acceptors, and those with iron sulfur clusters as early acceptors. No simple linear branching evolutionary scheme can account for the distribution patterns of reaction centers in existing photosynthetic organisms, and lateral transfer of genetic information is considered as a likely possibility. Possible scenarios for the development of primitive reaction centers into the heterodimeric protein structures found in existing reaction centers and for the development of organisms with two linked photosystems are presented.

STELLAR EVIDENCE THAT THE SOLAR DYNAMO MAY BE IN TRANSITION

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

Metcalfe, Travis S.; Egeland, Ricky; Van Saders, Jennifer

2016-07-20

Precise photometry from the Kepler space telescope allows not only the measurement of rotation in solar-type field stars, but also the determination of reliable masses and ages from asteroseismology. These critical data have recently provided the first opportunity to calibrate rotation–age relations for stars older than the Sun. The evolutionary picture that emerges is surprising: beyond middle-age the efficiency of magnetic braking is dramatically reduced, implying a fundamental change in angular momentum loss beyond a critical Rossby number (Ro ∼ 2). We compile published chromospheric activity measurements for the sample of Kepler asteroseismic targets that were used to establish themore » new rotation–age relations. We use these data along with a sample of well-characterized solar analogs from the Mount Wilson HK survey to develop a qualitative scenario connecting the evolution of chromospheric activity to a fundamental shift in the character of differential rotation. We conclude that the Sun may be in a transitional evolutionary phase, and that its magnetic cycle might represent a special case of stellar dynamo theory.« less

Hybrid Co-Evolutionary Motion Planning via Visibility-Based Repair

NASA Technical Reports Server (NTRS)

Dozier, Gerry; McCullough, Shaun; Brown, Edward, Jr.; Homaifar, Abdollah; Bikdash, Mar-wan

1997-01-01

This paper introduces a hybrid co-evolutionary system for global motion planning within unstructured environments. This system combines the concept of co-evolutionary search along with a concept that we refer to as the visibility-based repair to form a hybrid which quickly transforms infeasible motions into feasible ones. Also, this system makes use of a novel representation scheme for the obstacles within an environment. Our hybrid evolutionary system differs from other evolutionary motion planners in that (1) more emphasis is placed on repairing infeasible motions to develop feasible motions rather than using simulated evolution exclusively as a means of discovering feasible motions, (2) a continuous map of the environment is used rather than a discretized map, and (3) it develops global motion plans for multiple mobile destinations by co-evolving populations of sub-global motion plans. In this paper, we demonstrate the effectiveness of this system by using it to solve two challenging motion planning problems where multiple targets try to move away from a point robot.

Life is determined by its environment

NASA Astrophysics Data System (ADS)

Torday, John S.; Miller, William B.

2016-10-01

A well-developed theory of evolutionary biology requires understanding of the origins of life on Earth. However, the initial conditions (ontology) and causal (epistemology) bases on which physiology proceeded have more recently been called into question, given the teleologic nature of Darwinian evolutionary thinking. When evolutionary development is focused on cellular communication, a distinctly different perspective unfolds. The cellular communicative-molecular approach affords a logical progression for the evolutionary narrative based on the basic physiologic properties of the cell. Critical to this appraisal is recognition of the cell as a fundamental reiterative unit of reciprocating communication that receives information from and reacts to epiphenomena to solve problems. Following the course of vertebrate physiology from its unicellular origins instead of its overt phenotypic appearances and functional associations provides a robust, predictive picture for the means by which complex physiology evolved from unicellular organisms. With this foreknowledge of physiologic principles, we can determine the fundamentals of Physiology based on cellular first principles using a logical, predictable method. Thus, evolutionary creativity on our planet can be viewed as a paradoxical product of boundary conditions that permit homeostatic moments of varying length and amplitude that can productively absorb a variety of epigenetic impacts to meet environmental challenges.

Development of antibiotic regimens using graph based evolutionary algorithms.

PubMed

Corns, Steven M; Ashlock, Daniel A; Bryden, Kenneth M

2013-12-01

This paper examines the use of evolutionary algorithms in the development of antibiotic regimens given to production animals. A model is constructed that combines the lifespan of the animal and the bacteria living in the animal's gastro-intestinal tract from the early finishing stage until the animal reaches market weight. This model is used as the fitness evaluation for a set of graph based evolutionary algorithms to assess the impact of diversity control on the evolving antibiotic regimens. The graph based evolutionary algorithms have two objectives: to find an antibiotic treatment regimen that maintains the weight gain and health benefits of antibiotic use and to reduce the risk of spreading antibiotic resistant bacteria. This study examines different regimens of tylosin phosphate use on bacteria populations divided into Gram positive and Gram negative types, with a focus on Campylobacter spp. Treatment regimens were found that provided decreased antibiotic resistance relative to conventional methods while providing nearly the same benefits as conventional antibiotic regimes. By using a graph to control the information flow in the evolutionary algorithm, a variety of solutions along the Pareto front can be found automatically for this and other multi-objective problems. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Life is determined by its environment

PubMed Central

Torday, John S.; Miller, William B.

2016-01-01

A well-developed theory of evolutionary biology requires understanding of the origins of life on Earth. However, the initial conditions (ontology) and causal (epistemology) bases on which physiology proceeded have more recently been called into question, given the teleologic nature of Darwinian evolutionary thinking. When evolutionary development is focused on cellular communication, a distinctly different perspective unfolds. The cellular communicative-molecular approach affords a logical progression for the evolutionary narrative based on the basic physiologic properties of the cell. Critical to this appraisal is recognition of the cell as a fundamental reiterative unit of reciprocating communication that receives information from and reacts to epiphenomena to solve problems. Following the course of vertebrate physiology from its unicellular origins instead of its overt phenotypic appearances and functional associations provides a robust, predictive picture for the means by which complex physiology evolved from unicellular organisms. With this foreknowledge of physiologic principles, we can determine the fundamentals of Physiology based on cellular first principles using a logical, predictable method. Thus, evolutionary creativity on our planet can be viewed as a paradoxical product of boundary conditions that permit homeostatic moments of varying length and amplitude that can productively absorb a variety of epigenetic impacts to meet environmental challenges. PMID:27708547

Evolutionary Technologies: Fundamentals and Applications to Information/Communication Systems and Manufacturing/Logistics Systems

NASA Astrophysics Data System (ADS)

Gen, Mitsuo; Kawakami, Hiroshi; Tsujimura, Yasuhiro; Handa, Hisashi; Lin, Lin; Okamoto, Azuma

As efficient utilization of computational resources is increasing, evolutionary technology based on the Genetic Algorithm (GA), Genetic Programming (GP), Evolution Strategy (ES) and other Evolutionary Computations (ECs) is making rapid progress, and its social recognition and the need as applied technology are increasing. This is explained by the facts that EC offers higher robustness for knowledge information processing systems, intelligent production and logistics systems, most advanced production scheduling and other various real-world problems compared to the approaches based on conventional theories, and EC ensures flexible applicability and usefulness for any unknown system environment even in a case where accurate mathematical modeling fails in the formulation. In this paper, we provide a comprehensive survey of the current state-of-the-art in the fundamentals and applications of evolutionary technologies.

An Evolutionary Framework for Understanding the Origin of Eukaryotes.

PubMed

Blackstone, Neil W

2016-04-27

Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real-the endosymbiosis that led to the mitochondrion is often described as "non-Darwinian" because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious-all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

Ancestral assumptions and the clinical uncertainty of evolutionary medicine.

PubMed

Cournoyea, Michael

2013-01-01

Evolutionary medicine is an emerging field of medical studies that uses evolutionary theory to explain the ultimate causes of health and disease. Educational tools, online courses, and medical school modules are being developed to help clinicians and students reconceptualize health and illness in light of our evolutionary past. Yet clinical guidelines based on our ancient life histories are epistemically weak, relying on the controversial assumptions of adaptationism and advocating a strictly biophysical account of health. To fulfill the interventionist goals of clinical practice, it seems that proximate explanations are all we need to develop successful diagnostic and therapeutic guidelines. Considering these epistemic concerns, this article argues that the clinical relevance of evolutionary medicine remains uncertain at best.

A theoretical comparison of evolutionary algorithms and simulated annealing

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

Hart, W.E.

1995-08-28

This paper theoretically compares the performance of simulated annealing and evolutionary algorithms. Our main result is that under mild conditions a wide variety of evolutionary algorithms can be shown to have greater performance than simulated annealing after a sufficiently large number of function evaluations. This class of EAs includes variants of evolutionary strategie and evolutionary programming, the canonical genetic algorithm, as well as a variety of genetic algorithms that have been applied to combinatorial optimization problems. The proof of this result is based on a performance analysis of a very general class of stochastic optimization algorithms, which has implications formore » the performance of a variety of other optimization algorithm.« less

Genetic basis and fitness correlates of dynamic carotenoid-based ornamental coloration in male and female common kestrels Falco tinnunculus.

PubMed

Vergara, P; Fargallo, J A; Martínez-Padilla, J

2015-01-01

Knowledge of the genetic basis of sexual ornaments is essential to understand their evolution through sexual selection. Although carotenoid-based ornaments have been instrumental in the study of sexual selection, given the inability of animals to synthesize carotenoids de novo, they are generally assumed to be influenced solely by environmental variation. However, very few studies have directly estimated the role of genes and the environment in shaping variation in carotenoid-based traits. Using long-term individual-based data, we here explore the evolutionary potential of a dynamic, carotenoid-based ornament (namely skin coloration), in male and female common kestrels. We first estimate the amount of genetic variation underlying variation in hue, chroma and brightness. After correcting for sex differences, the chroma of the orange-yellow eye ring coloration was significantly heritable (h2±SE=0.40±0.17), whereas neither hue (h2=0) nor brightness (h2=0.02) was heritable. Second, we estimate the strength and shape of selection acting upon chromatic (hue and chroma) and achromatic (brightness) variation and show positive and negative directional selection on female but not male chroma and hue, respectively, whereas brightness was unrelated to fitness in both sexes. This suggests that different components of carotenoid-based signals traits may show different evolutionary dynamics. Overall, we show that carotenoid-based coloration is a complex and multifaceted trait. If we are to gain a better understanding of the processes responsible for the generation and maintenance of variation in carotenoid-based coloration, these complexities need to be taken into account. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Evolutionary game theory using agent-based methods.

PubMed

Adami, Christoph; Schossau, Jory; Hintze, Arend

2016-12-01

Evolutionary game theory is a successful mathematical framework geared towards understanding the selective pressures that affect the evolution of the strategies of agents engaged in interactions with potential conflicts. While a mathematical treatment of the costs and benefits of decisions can predict the optimal strategy in simple settings, more realistic settings such as finite populations, non-vanishing mutations rates, stochastic decisions, communication between agents, and spatial interactions, require agent-based methods where each agent is modeled as an individual, carries its own genes that determine its decisions, and where the evolutionary outcome can only be ascertained by evolving the population of agents forward in time. While highlighting standard mathematical results, we compare those to agent-based methods that can go beyond the limitations of equations and simulate the complexity of heterogeneous populations and an ever-changing set of interactors. We conclude that agent-based methods can predict evolutionary outcomes where purely mathematical treatments cannot tread (for example in the weak selection-strong mutation limit), but that mathematics is crucial to validate the computational simulations. Copyright © 2016 Elsevier B.V. All rights reserved.

Are hotspots of evolutionary potential adequately protected in southern California?

USGS Publications Warehouse

Vandergast, A.G.; Bohonak, A.J.; Hathaway, S.A.; Boys, J.; Fisher, R.N.

2008-01-01

Reserves are often designed to protect rare habitats, or "typical" exemplars of ecoregions and geomorphic provinces. This approach focuses on current patterns of organismal and ecosystem-level biodiversity, but typically ignores the evolutionary processes that control the gain and loss of biodiversity at these and other levels (e.g., genetic, ecological). In order to include evolutionary processes in conservation planning efforts, their spatial components must first be identified and mapped. We describe a GIS-based approach for explicitly mapping patterns of genetic divergence and diversity for multiple species (a "multi-species genetic landscape"). Using this approach, we analyzed mitochondrial DNA datasets from 21 vertebrate and invertebrate species in southern California to identify areas with common phylogeographic breaks and high intrapopulation diversity. The result is an evolutionary framework for southern California within which patterns of genetic diversity can be analyzed in the context of historical processes, future evolutionary potential and current reserve design. Our multi-species genetic landscapes pinpoint six hotspots where interpopulation genetic divergence is consistently high, five evolutionary hotspots within which genetic connectivity is high, and three hotspots where intrapopulation genetic diversity is high. These 14 hotspots can be grouped into eight geographic areas, of which five largely are unprotected at this time. The multi-species genetic landscape approach may provide an avenue to readily incorporate measures of evolutionary process into GIS-based systematic conservation assessment and land-use planning.

Evolutionary history of human disease genes reveals phenotypic connections and comorbidity among genetic diseases

NASA Astrophysics Data System (ADS)

Park, Solip; Yang, Jae-Seong; Kim, Jinho; Shin, Young-Eun; Hwang, Jihye; Park, Juyong; Jang, Sung Key; Kim, Sanguk

2012-10-01

The extent to which evolutionary changes have impacted the phenotypic relationships among human diseases remains unclear. In this work, we report that phenotypically similar diseases are connected by the evolutionary constraints on human disease genes. Human disease groups can be classified into slowly or rapidly evolving classes, where the diseases in the slowly evolving class are enriched with morphological phenotypes and those in the rapidly evolving class are enriched with physiological phenotypes. Our findings establish a clear evolutionary connection between disease classes and disease phenotypes for the first time. Furthermore, the high comorbidity found between diseases connected by similar evolutionary constraints enables us to improve the predictability of the relative risk of human diseases. We find the evolutionary constraints on disease genes are a new layer of molecular connection in the network-based exploration of human diseases.

Evolutionary history of human disease genes reveals phenotypic connections and comorbidity among genetic diseases.

PubMed

Park, Solip; Yang, Jae-Seong; Kim, Jinho; Shin, Young-Eun; Hwang, Jihye; Park, Juyong; Jang, Sung Key; Kim, Sanguk

2012-01-01

The extent to which evolutionary changes have impacted the phenotypic relationships among human diseases remains unclear. In this work, we report that phenotypically similar diseases are connected by the evolutionary constraints on human disease genes. Human disease groups can be classified into slowly or rapidly evolving classes, where the diseases in the slowly evolving class are enriched with morphological phenotypes and those in the rapidly evolving class are enriched with physiological phenotypes. Our findings establish a clear evolutionary connection between disease classes and disease phenotypes for the first time. Furthermore, the high comorbidity found between diseases connected by similar evolutionary constraints enables us to improve the predictability of the relative risk of human diseases. We find the evolutionary constraints on disease genes are a new layer of molecular connection in the network-based exploration of human diseases.

Scenario-based and scenario-neutral assessment of climate change impacts on operational performance of a multipurpose reservoir

Treesearch

Allison G. Danner; Mohammad Safeeq; Gordon E. Grant; Charlotte Wickham; Desirée Tullos; Mary V. Santelmann

2017-01-01

Scenario-based and scenario-neutral impacts assessment approaches provide complementary information about how climate change-driven effects on streamflow may change the operational performance of multipurpose dams. Examining a case study of Cougar Dam in Oregon, United States, we simulated current reservoir operations under scenarios of plausible future hydrology....

Exploring the fission and reconfiguration cycle of comet 67P/Churyumov-Gerasimenko

NASA Astrophysics Data System (ADS)

Scheeres, Daniel J.; Hirabayashi, Masatoshi; Chesley, Steven R.; McMahon, Jay W.

2016-10-01

In Hirabayashi et al. (Nature, 2016) the nucleus of comet 67P/Churyumov-Gerasimenko (67P) is studied with a focus on the straight cracks observed on the Hapi region. These cracks were shown to have formed during a period of fast rotation and led to a proposed evolutionary scenario in which the nuclei may eventually split into two components and recombine to create a new bilobate configuration. Other bilobate nuclei should be subject to such a reconfiguration process, based on the relative sizes of the components, suggesting that this evolutionary scenario may be common for bilobate nuclei which comprise the majority of comet nuclei observed at high spatial resolution. Such reconfigurations could explain the observed occurrence of comet nucleus splitting and brightening events, which still lack a definitive geophysical understanding. Motivated by the proposed theory in Hirabayashi et al., the current work explores the dynamics of the 67P nucleus' rotation rate, fission limits, and subsequent dynamics. One aspect of the theory posits that the comet's distant Jupiter flybys will cause the latitude of the sub-solar point at perihelion to vary chaotically, leading to periods of net positive and negative torques and causing the nucleus to spin-up and spin-down in a random fashion. We analyze the current 67P nucleus shape and orbit to estimate the characteristic time-scale of this rotational evolution, providing an estimate of the current nucleus lifetime in its current configuration. Once the nucleus reaches a spin period shorter than ~7 hours the components will fission into a bound orbit, with the components subsequently reimpacting at speeds less than local escape speed (about 0.4 m/s). The current study extends Hirabayashi et al., explicitly modeling the mutual gravity and orbital dynamics of the head and body, assuming that the head and body rest on each other with the current shape of the 67P nucleus. The results show that when the components are released at a spin period between 6.5 hr and 7 hr, the components will separate and subsequently collide with a low impact speed. The orbital and rotational dynamics of the system components after fission are explored as a function of the initial spin rate at fission.

An evolutionary medicine approach to understanding factors that contribute to chronic obstructive pulmonary disease.

PubMed

Aoshiba, Kazutetsu; Tsuji, Takao; Itoh, Masayuki; Yamaguchi, Kazuhiro; Nakamura, Hiroyuki

2015-01-01

Although many studies have been published on the causes and mechanisms of chronic obstructive pulmonary disease (COPD), the reason for the existence of COPD and the reasons why COPD develops in humans have hardly been studied. Evolutionary medical approaches are required to explain not only the proximate factors, such as the causes and mechanisms of a disease, but the ultimate (evolutionary) factors as well, such as why the disease is present and why the disease develops in humans. According to the concepts of evolutionary medicine, disease susceptibility is acquired as a result of natural selection during the evolutionary process of traits linked to the genes involved in disease susceptibility. In this paper, we discuss the following six reasons why COPD develops in humans based on current evolutionary medical theories: (1) evolutionary constraints; (2) mismatch between environmental changes and evolution; (3) co-evolution with pathogenic microorganisms; (4) life history trade-off; (5) defenses and their costs, and (6) reproductive success at the expense of health. Our perspective pursues evolutionary answers to the fundamental question, 'Why are humans susceptible to this common disease, COPD, despite their long evolutionary history?' We believe that the perspectives offered by evolutionary medicine are essential for researchers to better understand the significance of their work.

Evolutionary Influences on Attribution and Affect

PubMed Central

Brown, Jennie; Trafimow, David

2017-01-01

Evolutionary theory was applied to Reeder and Brewer's schematic theory and Trafimow's affect theory to extend this area of research with five new predictions involving affect and ability attributions, comparing morality and ability attributions, gender differences, and reaction times for affect and attribution ratings. The design included a 2 (Trait Dimension Type: HR, PR) × 2 (Behavior Type: morality, ability) × 2 (Valence: positive, negative) × 2 (Replication: original, replication) × 2 (Sex: female or male actor) × 2 (Gender: female or male participant) × 2 (Order: attribution portion first, affect portion first) mixed design. All factors were within participants except the order and participant gender. Participants were presented with 32 different scenarios in which an actor engaged in a concrete behavior after which they made attributions and rated their affect in response to the behavior. Reaction times were measured during attribution and affect ratings. In general, the findings from the experiment supported the new predictions. Affect was related to attributions for both morality and ability related behaviors. Morality related behaviors received more extreme attribution and affect ratings than ability related behaviors. Female actors received stronger attribution and affect ratings for diagnostic morality behaviors compared to male actors. Male and female actors received similar attribution and affect ratings for diagnostic ability behaviors. Diagnostic behaviors were associated with lower reaction times than non-diagnostic behaviors. These findings demonstrate the utility of evolutionary theory in creating new hypotheses and empirical findings in the domain of attribution. PMID:29312092

Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes.

PubMed

Novák, Lukáš; Zubáčová, Zuzana; Karnkowska, Anna; Kolisko, Martin; Hroudová, Miluše; Stairs, Courtney W; Simpson, Alastair G B; Keeling, Patrick J; Roger, Andrew J; Čepička, Ivan; Hampl, Vladimír

2016-10-06

Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.

Is the Red Wolf a Listable Unit Under the US Endangered Species Act?

PubMed

Waples, Robin S; Kays, Roland; Fredrickson, Richard J; Pacifici, Krishna; Mills, L Scott

2018-06-08

Defining units that can be afforded legal protection is a crucial, albeit challenging, step in conservation planning. As we illustrate with a case study of the red wolf (Canis rufus) from the southeastern United States, this step is especially complex when the evolutionary history of the focal taxon is uncertain. The US Endangered Species Act (ESA) allows listing of species, subspecies, or Distinct Population Segments (DPSs) of vertebrates. Red wolves were listed as an endangered species in 1973, and their status remains precarious. However, some recent genetic studies suggest that red wolves are part of a small wolf species (C. lycaon) specialized for heavily forested habitats of eastern North America, whereas other authors suggest that red wolves arose, perhaps within the last ~400 years, through hybridization between gray wolves (C. lupus) and coyotes (C. latrans). Using published genetic, morphological, behavioral, and ecological data, we evaluated whether each evolutionary hypothesis would lead to a listable unit for red wolves. Although the potential hybrid origin of red wolves, combined with abundant evidence for recent hybridization with coyotes, raises questions about status as a separate species or subspecies, we conclude that under any proposed evolutionary scenario red wolves meet both criteria to be considered a DPS: they are discrete compared with other conspecific populations, and they are Significant to the taxon to which they belong. As population-level units can qualify for legal protection under endangered-species legislation in many countries throughout the world, this general approach could potentially be applied more broadly.

Evolutionary Influences on Attribution and Affect.

PubMed

Brown, Jennie; Trafimow, David

2017-01-01

Evolutionary theory was applied to Reeder and Brewer's schematic theory and Trafimow's affect theory to extend this area of research with five new predictions involving affect and ability attributions, comparing morality and ability attributions, gender differences, and reaction times for affect and attribution ratings. The design included a 2 (Trait Dimension Type: HR, PR) × 2 (Behavior Type: morality, ability) × 2 (Valence: positive, negative) × 2 (Replication: original, replication) × 2 (Sex: female or male actor) × 2 (Gender: female or male participant) × 2 (Order: attribution portion first, affect portion first) mixed design. All factors were within participants except the order and participant gender. Participants were presented with 32 different scenarios in which an actor engaged in a concrete behavior after which they made attributions and rated their affect in response to the behavior. Reaction times were measured during attribution and affect ratings. In general, the findings from the experiment supported the new predictions. Affect was related to attributions for both morality and ability related behaviors. Morality related behaviors received more extreme attribution and affect ratings than ability related behaviors. Female actors received stronger attribution and affect ratings for diagnostic morality behaviors compared to male actors. Male and female actors received similar attribution and affect ratings for diagnostic ability behaviors. Diagnostic behaviors were associated with lower reaction times than non-diagnostic behaviors. These findings demonstrate the utility of evolutionary theory in creating new hypotheses and empirical findings in the domain of attribution.

Discrete and morphometric traits reveal contrasting patterns and processes in the macroevolutionary history of a clade of scorpions.

PubMed

Mongiardino Koch, N; Ceccarelli, F S; Ojanguren-Affilastro, A A; Ramírez, M J

2017-04-01

Many palaeontological studies have investigated the evolution of entire body plans, generally relying on discrete character-taxon matrices. In contrast, macroevolutionary studies performed by neontologists have mostly focused on morphometric traits. Although these data types are very different, some studies have suggested that they capture common patterns. Nonetheless, the tests employed to support this claim have not explicitly incorporated a phylogenetic framework and may therefore be susceptible to confounding effects due to the presence of common phylogenetic structure. We address this question using the scorpion genus Brachistosternus Pocock 1893 as case study. We make use of a time-calibrated multilocus molecular phylogeny, and compile discrete and traditional morphometric data sets, both capturing the overall morphology of the organisms. We find that morphospaces derived from these matrices are significantly different, and that the degree of discordance cannot be replicated by simulations of random character evolution. Moreover, we find strong support for contrasting modes of evolution, with discrete characters being congruent with an 'early burst' scenario whereas morphometric traits suggest species-specific adaptations to have driven morphological evolution. The inferred macroevolutionary dynamics are therefore contingent on the choice of character type. Finally, we confirm that metrics of correlation fail to detect these profound differences given common phylogenetic structure in both data sets, and that methods incorporating a phylogenetic framework and accounting for expected covariance should be favoured. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Cancer heterogeneity and multilayer spatial evolutionary games.

PubMed

Świerniak, Andrzej; Krześlak, Michał

2016-10-13

Evolutionary game theory (EGT) has been widely used to simulate tumour processes. In almost all studies on EGT models analysis is limited to two or three phenotypes. Our model contains four main phenotypes. Moreover, in a standard approach only heterogeneity of populations is studied, while cancer cells remain homogeneous. A multilayer approach proposed in this paper enables to study heterogeneity of single cells. In the extended model presented in this paper we consider four strategies (phenotypes) that can arise by mutations. We propose multilayer spatial evolutionary games (MSEG) played on multiple 2D lattices corresponding to the possible phenotypes. It enables simulation and investigation of heterogeneity on the player-level in addition to the population-level. Moreover, it allows to model interactions between arbitrary many phenotypes resulting from the mixture of basic traits. Different equilibrium points and scenarios (monomorphic and polymorphic populations) have been achieved depending on model parameters and the type of played game. However, there is a possibility of stable quadromorphic population in MSEG games for the same set of parameters like for the mean-field game. The model assumes an existence of four possible phenotypes (strategies) in the population of cells that make up tumour. Various parameters and relations between cells lead to complex analysis of this model and give diverse results. One of them is a possibility of stable coexistence of different tumour cells within the population, representing almost arbitrary mixture of the basic phenotypes. This article was reviewed by Tomasz Lipniacki, Urszula Ledzewicz and Jacek Banasiak.

Functional and Evolutionary Characterization of a Gene Transfer Agent’s Multilocus “Genome”

PubMed Central

Hynes, Alexander P.; Shakya, Migun; Mercer, Ryan G.; Grüll, Marc P.; Bown, Luke; Davidson, Fraser; Steffen, Ekaterina; Matchem, Heidi; Peach, Mandy E.; Berger, Tim; Grebe, Katherine; Zhaxybayeva, Olga; Lang, Andrew S.

2016-01-01

Gene transfer agents (GTAs) are phage-like particles that can package and transfer a random piece of the producing cell’s genome, but are unable to transfer all the genes required for their own production. As such, GTAs represent an evolutionary conundrum: are they selfish genetic elements propagating through an unknown mechanism, defective viruses, or viral structures “repurposed” by cells for gene exchange, as their name implies? In Rhodobacter capsulatus, production of the R. capsulatus GTA (RcGTA) particles is associated with a cluster of genes resembling a small prophage. Utilizing transcriptomic, genetic and biochemical approaches, we report that the RcGTA “genome” consists of at least 24 genes distributed across five distinct loci. We demonstrate that, of these additional loci, two are involved in cell recognition and binding and one in the production and maturation of RcGTA particles. The five RcGTA “genome” loci are widespread within Rhodobacterales, but not all loci have the same evolutionary histories. Specifically, two of the loci have been subject to frequent, probably virus-mediated, gene transfer events. We argue that it is unlikely that RcGTA is a selfish genetic element. Instead, our findings are compatible with the scenario that RcGTA is a virus-derived element maintained by the producing organism due to a selective advantage of within-population gene exchange. The modularity of the RcGTA “genome” is presumably a result of selection on the host organism to retain GTA functionality. PMID:27343288

The evolutionary rate dynamically tracks changes in HIV-1 epidemics

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

Maljkovic-berry, Irina; Athreya, Gayathri; Daniels, Marcus

Large-sequence datasets provide an opportunity to investigate the dynamics of pathogen epidemics. Thus, a fast method to estimate the evolutionary rate from large and numerous phylogenetic trees becomes necessary. Based on minimizing tip height variances, we optimize the root in a given phylogenetic tree to estimate the most homogenous evolutionary rate between samples from at least two different time points. Simulations showed that the method had no bias in the estimation of evolutionary rates and that it was robust to tree rooting and topological errors. We show that the evolutionary rates of HIV-1 subtype B and C epidemics have changedmore » over time, with the rate of evolution inversely correlated to the rate of virus spread. For subtype B, the evolutionary rate slowed down and tracked the start of the HAART era in 1996. Subtype C in Ethiopia showed an increase in the evolutionary rate when the prevalence increase markedly slowed down in 1995. Thus, we show that the evolutionary rate of HIV-1 on the population level dynamically tracks epidemic events.« less

The ABCs of an evolutionary education science: The academic, behavioral, and cultural implications of an evolutionary approach to education theory and practice

NASA Astrophysics Data System (ADS)

Kauffman, Rick, Jr.

Calls for improving research-informed policy in education are everywhere. Yet, while there is an increasing trend towards science-based practice, there remains little agreement over which of the sciences to consult and how to organize a collective effort between them. What Education lacks is a general theoretical framework through which policies can be constructed, implemented, and assessed. This dissertation submits that evolutionary theory can provide a suitable framework for coordinating educational policies and practice, and can provide the entire field of education with a clearer sense of how to better manage the learning environment. This dissertation explores two broad paths that outline the conceptual foundations for an Evolutionary Education Science: "Teaching Evolution" and "Using Evolution to Teach." Chapter 1 introduces both of these themes. After describing why evolutionary science is best suited for organizing education research and practice, Chapter 1 proceeds to "teach" an overview of the "evolutionary toolkit"---the mechanisms and principles that underlie the modern evolutionary perspective. The chapter then employs the "toolkit" in examining education from an evolutionary perspective, outlining the evolutionary precepts that can guide theorizing and research in education, describing how educators can "use evolution to teach.". Chapters 2-4 expand on this second theme. Chapters 2 and 3 describe an education program for at-risk 9th and 10th grade students, the Regents Academy, designed entirely with evolutionary principles in mind. The program was rigorously assessed in a randomized control design and has demonstrated success at improving students' academic performance (Chapter 2) and social & behavioral development (Chapter 3). Chapter 4 examines current teaching strategies that underlie effective curriculum-instruction-assessment practices and proposes a framework for organizing successful, evidence-based strategies for neural-/cognitive-focused learning goals. Chapter 5 explores the cognitive effects that "teaching evolution" has on the learner. This chapter examines the effects that a course on evolutionary theory has on university undergraduate students in understanding and applying evolution and how learning the evolutionary toolkit affects critical thinking skills and domain transfer of knowledge. The results demonstrate that a single course on evolutionary theory increases students' acceptance and understanding of evolution and science, and, in effect, increases critical thinking performance.

Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling.

PubMed

Andreeva, Antonina

2016-06-15

The Structural Classification of Proteins (SCOP) database has facilitated the development of many tools and algorithms and it has been successfully used in protein structure prediction and large-scale genome annotations. During the development of SCOP, numerous exceptions were found to topological rules, along with complex evolutionary scenarios and peculiarities in proteins including the ability to fold into alternative structures. This article reviews cases of structural variations observed for individual proteins and among groups of homologues, knowledge of which is essential for protein structure modelling. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

The 25 kW power module evolution study. Part 3: Conceptual designs for power module evolutions. Volume 3: Cost estimates

NASA Technical Reports Server (NTRS)

1979-01-01

Cost data generated for the evolutionary power module concepts selected are reported. The initial acquisition costs (design, development, and protoflight unit test costs) were defined and modeled for the baseline 25 kW power module configurations. By building a parametric model of this initial building block, the cost of the 50 kW and the 100 kW power modules were derived by defining only their configuration and programmatic differences from the 25 kW baseline module. Variations in cost for the quantities needed to fulfill the mission scenarios were derived by applying appropriate learning curves.

The North American Forest Sector Outlook Study 2006-2030

Treesearch

Jeffrey P. Prestemon; Joseph Buongiorno

2012-01-01

Projections for the United States and Canada to 2030 have been made with a global model to account for concurrent changes in other countries. Three future scenarios were investigated: two IPCC-based scenarios assuming the rapid growth of wood-based energy, and one IPCC-based scenario without this assumption. The model, under the IPCC scenarios, accounted for trends in...

Theoretical Analysis of Local Search and Simple Evolutionary Algorithms for the Generalized Travelling Salesperson Problem.

PubMed

Pourhassan, Mojgan; Neumann, Frank

2018-06-22

The generalized travelling salesperson problem is an important NP-hard combinatorial optimization problem for which meta-heuristics, such as local search and evolutionary algorithms, have been used very successfully. Two hierarchical approaches with different neighbourhood structures, namely a Cluster-Based approach and a Node-Based approach, have been proposed by Hu and Raidl (2008) for solving this problem. In this paper, local search algorithms and simple evolutionary algorithms based on these approaches are investigated from a theoretical perspective. For local search algorithms, we point out the complementary abilities of the two approaches by presenting instances where they mutually outperform each other. Afterwards, we introduce an instance which is hard for both approaches when initialized on a particular point of the search space, but where a variable neighbourhood search combining them finds the optimal solution in polynomial time. Then we turn our attention to analysing the behaviour of simple evolutionary algorithms that use these approaches. We show that the Node-Based approach solves the hard instance of the Cluster-Based approach presented in Corus et al. (2016) in polynomial time. Furthermore, we prove an exponential lower bound on the optimization time of the Node-Based approach for a class of Euclidean instances.

The quest for blue supergiants : The evolution of the progenitor of SN 1987A

NASA Astrophysics Data System (ADS)

Menon, Athira; Heger, Alexander

2015-08-01

SN 1987A is historically one of the most remarkable supernova explosions to be seen from Earth. Due to the proximity of its location in the LMC, it remains the most well-studied object outside the solar system. It was also the only supernova whose progenitor was observed prior to its explosion.SN 1987A however, was a unique and enigmatic core collapse supernova. It was the first Type II supernova to have been observed to have exploded while its progenitor was a blue supergiant (BSG). Until then Type II supernovae were expected to originate from explosions of red supergiants (RSGs). A spectacular triple-ring nebula structure, rich in helium and nitrogen, was observed around the remnant, indicating a recent RSG phase before becoming a BSG. Even today it is not entirely understood what the evolutionary history may have been to cause a BSG to explode. The most commonly accepted hypothesis for its origin is the merger of a massive binary star system.An evolutionary scenario for such a binary system, was proposed by Podsiadlowski (1992) (P92). Through SPH simulations of the merger and the stellar evolution of the post-merger remnant, Ivanova & Podsiadlowski (2002) and (2003) (I&M) could successfully obtain the RSG to BSG transition of the progenitor.The aim of the present work is to produce the evolutionary history of the progenitor of SN 1987A and its explosion. We construct our models based on the results of P92 and I&M. Here, the secondary (less massive) star is accreted on the primary, while being simultaneously mixed in its envelope over a period of 100 years. The merged star is evolved until the onset of core collapse. For this work we use the 1-dimensional, implicit, hydrodynamical stellar evolution code, KEPLER. A large parameter space is explored, consisting of primary (16-20 Ms) and secondary masses (5-8 Ms), mixing boundaries, and accreting timescales. Those models whose end states match the observed properties of the progenitor of SN 1987A are exploded. The nuclear yields and light curve of the explosion are then compared with the observed data of SN 1987A.

A DNA and morphology based phylogenetic framework of the ant genus Lasius with hypotheses for the evolution of social parasitism and fungiculture.

PubMed

Maruyama, Munetoshi; Steiner, Florian M; Stauffer, Christian; Akino, Toshiharu; Crozier, Ross H; Schlick-Steiner, Birgit C

2008-08-19

Ants of the genus Lasius are ecologically important and an important system for evolutionary research. Progress in evolutionary research has been hindered by the lack of a well-founded phylogeny of the subgenera, with three previous attempts disagreeing. Here we employed two mitochondrial genes (cytochrome c oxidase subunit I, 16S ribosomal RNA), comprising 1,265 bp, together with 64 morphological characters, to recover the phylogeny of Lasius by Bayesian and Maximum Parsimony inference after exploration of potential causes of phylogenetic distortion. We use the resulting framework to infer evolutionary pathways for social parasitism and fungiculture. We recovered two well supported major lineages. One includes Acanthomyops, Austrolasius, Chthonolasius, and Lasius pallitarsis, which we confirm to represent a seventh subgenus, the other clade contains Dendrolasius, and Lasius sensu stricto. The subgenus Cautolasius, displaying neither social parasitism nor fungiculture, probably belongs to the second clade, but its phylogenetic position is not resolved at the cutoff values of node support we apply. Possible causes for previous problems with reconstructing the Lasius phylogeny include use of other reconstruction techniques, possibly more prone to instabilities in some instances, and the inclusion of phylogenetically distorting characters. By establishing an updated phylogenetic framework, our study provides the basis for a later formal taxonomic revision of subgenera and for studying the evolution of various ecologically and sociobiologically relevant traits of Lasius, although there is need for future studies to include nuclear genes and additional samples from the Nearctic. Both social parasitism and fungiculture evolved twice in Lasius, once in each major lineage, which opens up new opportunities for comparative analyses. The repeated evolution of social parasitism has been established for other groups of ants, though not for temporary social parasitism as found in Lasius. For fungiculture, the independent emergence twice in a monophyletic group marks a novel scenario in ants. We present alternative hypotheses for the evolution of both traits, with one of each involving loss of the trait. Though less likely for both traits than later evolution without reversal, we consider reversal as sufficiently plausible to merit independent testing.

Tracking Advanced Planetary Systems (TAPAS) with HARPS-N. II. Super Li-rich giant HD 107028

NASA Astrophysics Data System (ADS)

Adamów, M.; Niedzielski, A.; Villaver, E.; Wolszczan, A.; Kowalik, K.; Nowak, G.; Adamczyk, M.; Deka-Szymankiewicz, B.

2015-09-01

Context. Lithium-rich giant stars are rare objects. For some of them, Li enrichment exceeds the abundance of this element found in solar system meteorites, suggesting that these stars have gone through a Li enhancement process. Aims: We identified a Li-rich giant HD 107028 with A(Li) > 3.3 in a sample of evolved stars observed within the PennState Toruń Planet Search. In this work we study different enhancement scenarios and we try to identify the one responsible for Li enrichment in HD 107028. Methods: We collected high-resolution spectra with three different instruments, covering different spectral ranges. We determined stellar parameters and abundances of selected elements with both equivalent width measurements and analysis, and spectral synthesis. We also collected multi-epoch high-precision radial velocities in an attempt to detect a companion. Results: Collected data show that HD 107028 is a star at the base of the red giant branch (RGB). Except for high Li abundance, we have not identified any other anomalies in its chemical composition, and there is no indication of a low-mass or stellar companion. We exclude Li production at the luminosity function bump on the RGB as the effective temperature and luminosity suggest that the evolutionary state is much earlier than the RGB bump. We also cannot confirm the Li enhancement by contamination as we do not observe any anomalies that are associated with this scenario. Conclusions: After evaluating various scenarios of Li enhancement we conclude that the Li-overabundance of HD 107028 originates from main-sequence evolution, and may be caused by diffusion processes. Based on observations obtained with the Hobby-Eberly Telescope, which is a joint project of the University of Texas at Austin, the Pennsylvania State University, Stanford University, Ludwig-Maximilians-Universität München, and Georg-August-Universität Göttingen.Based on observations made with the Italian Telescopio Nazionale Galileo (TNG) operated on the island of La Palma by the Fundación Galileo Galilei of the INAF (Istituto Nazionale di Astrofisica) at the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofísica de Canarias.Based on observations made with the Mercator Telescope, operated on the island of La Palma by the Flemish Community, at the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofísica de Canarias.

Why flying dogs are rare: A general theory of luck in evolutionary transitions.

PubMed

Fleming, Leonore; Brandon, Robert

2015-02-01

There is a worry that the 'major transitions in evolution' represent an arbitrary group of events. This worry is warranted, and we show why. We argue that the transition to a new level of hierarchy necessarily involves a nonselectionist chance process. Thus any unified theory of evolutionary transitions must be more like a general theory of fortuitous luck, rather than a rigid formulation of expected events. We provide a systematic account of evolutionary transitions based on a second-order regularity of chance events, as stipulated by the ZFEL (Zero Force Evolutionary Law). And in doing so, we make evolutionary transitions explainable and predictable, and so not entirely contingent after all. Copyright © 2014 Elsevier Ltd. All rights reserved.

Mean-Potential Law in Evolutionary Games

NASA Astrophysics Data System (ADS)

Nałecz-Jawecki, Paweł; Miekisz, Jacek

2018-01-01

The Letter presents a novel way to connect random walks, stochastic differential equations, and evolutionary game theory. We introduce a new concept of a potential function for discrete-space stochastic systems. It is based on a correspondence between one-dimensional stochastic differential equations and random walks, which may be exact not only in the continuous limit but also in finite-state spaces. Our method is useful for computation of fixation probabilities in discrete stochastic dynamical systems with two absorbing states. We apply it to evolutionary games, formulating two simple and intuitive criteria for evolutionary stability of pure Nash equilibria in finite populations. In particular, we show that the 1 /3 law of evolutionary games, introduced by Nowak et al. [Nature, 2004], follows from a more general mean-potential law.

Determining Selection across Heterogeneous Landscapes: A Perturbation-Based Method and Its Application to Modeling Evolution in Space.

PubMed

Wickman, Jonas; Diehl, Sebastian; Blasius, Bernd; Klausmeier, Christopher A; Ryabov, Alexey B; Brännström, Åke

2017-04-01

Spatial structure can decisively influence the way evolutionary processes unfold. To date, several methods have been used to study evolution in spatial systems, including population genetics, quantitative genetics, moment-closure approximations, and individual-based models. Here we extend the study of spatial evolutionary dynamics to eco-evolutionary models based on reaction-diffusion equations and adaptive dynamics. Specifically, we derive expressions for the strength of directional and stabilizing/disruptive selection that apply both in continuous space and to metacommunities with symmetrical dispersal between patches. For directional selection on a quantitative trait, this yields a way to integrate local directional selection across space and determine whether the trait value will increase or decrease. The robustness of this prediction is validated against quantitative genetics. For stabilizing/disruptive selection, we show that spatial heterogeneity always contributes to disruptive selection and hence always promotes evolutionary branching. The expression for directional selection is numerically very efficient and hence lends itself to simulation studies of evolutionary community assembly. We illustrate the application and utility of the expressions for this purpose with two examples of the evolution of resource utilization. Finally, we outline the domain of applicability of reaction-diffusion equations as a modeling framework and discuss their limitations.

Efficient fractal-based mutation in evolutionary algorithms from iterated function systems

NASA Astrophysics Data System (ADS)

Salcedo-Sanz, S.; Aybar-Ruíz, A.; Camacho-Gómez, C.; Pereira, E.

2018-03-01

In this paper we present a new mutation procedure for Evolutionary Programming (EP) approaches, based on Iterated Function Systems (IFSs). The new mutation procedure proposed consists of considering a set of IFS which are able to generate fractal structures in a two-dimensional phase space, and use them to modify a current individual of the EP algorithm, instead of using random numbers from different probability density functions. We test this new proposal in a set of benchmark functions for continuous optimization problems. In this case, we compare the proposed mutation against classical Evolutionary Programming approaches, with mutations based on Gaussian, Cauchy and chaotic maps. We also include a discussion on the IFS-based mutation in a real application of Tuned Mass Dumper (TMD) location and optimization for vibration cancellation in buildings. In both practical cases, the proposed EP with the IFS-based mutation obtained extremely competitive results compared to alternative classical mutation operators.

Potential applications of skip SMV with thrust engine

NASA Astrophysics Data System (ADS)

Wang, Weilin; Savvaris, Al

2016-11-01

This paper investigates the potential applications of Space Maneuver Vehicles (SMV) with skip trajectory. Due to soaring space operations over the past decades, the risk of space debris has considerably increased such as collision risks with space asset, human property on ground and even aviation. Many active debris removal methods have been investigated and in this paper, a debris remediation method is first proposed based on skip SMV. The key point is to perform controlled re-entry. These vehicles are expected to achieve a trans-atmospheric maneuver with thrust engine. If debris is released at altitude below 80 km, debris could be captured by the atmosphere drag force and re-entry interface prediction accuracy is improved. Moreover if the debris is released in a cargo at a much lower altitude, this technique protects high value space asset from break up by the atmosphere and improves landing accuracy. To demonstrate the feasibility of this concept, the present paper presents the simulation results for two specific mission profiles: (1) descent to predetermined altitude; (2) descent to predetermined point (altitude, longitude and latitude). The evolutionary collocation method is adopted for skip trajectory optimization due to its global optimality and high-accuracy. This method is actually a two-step optimization approach based on the heuristic algorithm and the collocation method. The optimal-control problem is transformed into a nonlinear programming problem (NLP) which can be efficiently and accurately solved by the sequential quadratic programming (SQP) procedure. However, such a method is sensitive to initial values. To reduce the sensitivity problem, genetic algorithm (GA) is adopted to refine the grids and provide near optimum initial values. By comparing the simulation data from different scenarios, it is found that skip SMV is feasible in active debris removal and the evolutionary collocation method gives a truthful re-entry trajectory that satisfies the path and boundary constraints.

The scenario-based generalization of radiation therapy margins.

PubMed

Fredriksson, Albin; Bokrantz, Rasmus

2016-03-07

We give a scenario-based treatment plan optimization formulation that is equivalent to planning with geometric margins if the scenario doses are calculated using the static dose cloud approximation. If the scenario doses are instead calculated more accurately, then our formulation provides a novel robust planning method that overcomes many of the difficulties associated with previous scenario-based robust planning methods. In particular, our method protects only against uncertainties that can occur in practice, it gives a sharp dose fall-off outside high dose regions, and it avoids underdosage of the target in 'easy' scenarios. The method shares the benefits of the previous scenario-based robust planning methods over geometric margins for applications where the static dose cloud approximation is inaccurate, such as irradiation with few fields and irradiation with ion beams. These properties are demonstrated on a suite of phantom cases planned for treatment with scanned proton beams subject to systematic setup uncertainty.

The Evolutionary History of Protein Domains Viewed by Species Phylogeny

PubMed Central

Yang, Song; Bourne, Philip E.

2009-01-01

Background Protein structural domains are evolutionary units whose relationships can be detected over long evolutionary distances. The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins, and the formation of the entire protein domain repertoire, are of great interest. Methodology/Principal Findings A methodology is presented for providing a parsimonious domain history based on gain, loss, vertical and horizontal transfer derived from the complete genomic domain assignments of 1015 organisms across the tree of life. When mapped to species trees the evolutionary history of domains and domain combinations is revealed, and the general evolutionary trend of domain and combination is analyzed. Conclusions/Significance We show that this approach provides a powerful tool to study how new proteins and functions emerged and to study such processes as horizontal gene transfer among more distant species. PMID:20041107

[The history of development of evolutionary methods in St. Petersburg school of computer simulation in biology].

PubMed

Menshutkin, V V; Kazanskiĭ, A B; Levchenko, V F

2010-01-01

The history of rise and development of evolutionary methods in Saint Petersburg school of biological modelling is traced and analyzed. Some pioneering works in simulation of ecological and evolutionary processes, performed in St.-Petersburg school became an exemplary ones for many followers in Russia and abroad. The individual-based approach became the crucial point in the history of the school as an adequate instrument for construction of models of biological evolution. This approach is natural for simulation of the evolution of life-history parameters and adaptive processes in populations and communities. In some cases simulated evolutionary process was used for solving a reverse problem, i. e., for estimation of uncertain life-history parameters of population. Evolutionary computations is one more aspect of this approach application in great many fields. The problems and vistas of ecological and evolutionary modelling in general are discussed.

[Evolutionary medicine: the future looking at the past].

PubMed

Carvalho, Serafim; Rosado, Margarida

2008-01-01

Evolutionary medicine is an emergent basic science that offers new and varied perspectives to the comprehension of the human health and disease, considering them as a result of a gap between our modern lives and the environment where human beings evolve. This work's goals are to understand the importance of the evolutionary theories on concepts of health and disease, providing a new insight on medicine investigation. This bibliography review is based on Medline and PsycINFO articles research between 1996 and 2007 about review and experimental studies published in English, using the key words evolutionary and medicine, psychiatry, psychology, behaviour, health, disease, gene. There were selected forty-five articles based on and with special interest on the authors' practice. There were also consulted some allusive books. The present human genome and phenotypes are essentially Palaeolithic ones: they are not adapted to the modern life style, thus favouring the so called diseases of civilization. Fitting evolutionary strategies, apparently protective ones, when excessive, are the core syndromes of many emotional disruptive behaviours and diseases. Having the stone age's genes, we are obliged to live in the space age. With the evolutionary approach, postmodern medicine is detecting better the vulnerabilities, restrictions, biases, adaptations and maladaptations of human body, its actual diseases and its preventions and treatment.

Evolutionary model selection and parameter estimation for protein-protein interaction network based on differential evolution algorithm

PubMed Central

Huang, Lei; Liao, Li; Wu, Cathy H.

2016-01-01

Revealing the underlying evolutionary mechanism plays an important role in understanding protein interaction networks in the cell. While many evolutionary models have been proposed, the problem about applying these models to real network data, especially for differentiating which model can better describe evolutionary process for the observed network urgently remains as a challenge. The traditional way is to use a model with presumed parameters to generate a network, and then evaluate the fitness by summary statistics, which however cannot capture the complete network structures information and estimate parameter distribution. In this work we developed a novel method based on Approximate Bayesian Computation and modified Differential Evolution (ABC-DEP) that is capable of conducting model selection and parameter estimation simultaneously and detecting the underlying evolutionary mechanisms more accurately. We tested our method for its power in differentiating models and estimating parameters on the simulated data and found significant improvement in performance benchmark, as compared with a previous method. We further applied our method to real data of protein interaction networks in human and yeast. Our results show Duplication Attachment model as the predominant evolutionary mechanism for human PPI networks and Scale-Free model as the predominant mechanism for yeast PPI networks. PMID:26357273

An Evolutionary Framework for Understanding the Origin of Eukaryotes

PubMed Central

Blackstone, Neil W.

2016-01-01

Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes. PMID:27128953

Remembering the evolutionary Freud.

PubMed

Young, Allan

2006-03-01

Throughout his career as a writer, Sigmund Freud maintained an interest in the evolutionary origins of the human mind and its neurotic and psychotic disorders. In common with many writers then and now, he believed that the evolutionary past is conserved in the mind and the brain. Today the "evolutionary Freud" is nearly forgotten. Even among Freudians, he is regarded to be a red herring, relevant only to the extent that he diverts attention from the enduring achievements of the authentic Freud. There are three ways to explain these attitudes. First, the evolutionary Freud's key work is the "Overview of the Transference Neurosis" (1915). But it was published at an inopportune moment, forty years after the author's death, during the so-called "Freud wars." Second, Freud eventually lost interest in the "Overview" and the prospect of a comprehensive evolutionary theory of psychopathology. The publication of The Ego and the Id (1923), introducing Freud's structural theory of the psyche, marked the point of no return. Finally, Freud's evolutionary theory is simply not credible. It is based on just-so stories and a thoroughly discredited evolutionary mechanism, Lamarckian use-inheritance. Explanations one and two are probably correct but also uninteresting. Explanation number three assumes that there is a fundamental difference between Freud's evolutionary narratives (not credible) and the evolutionary accounts of psychopathology that currently circulate in psychiatry and mainstream journals (credible). The assumption is mistaken but worth investigating.

Replaying evolutionary transitions from the dental fossil record

PubMed Central

Harjunmaa, Enni; Seidel, Kerstin; Häkkinen, Teemu; Renvoisé, Elodie; Corfe, Ian J.; Kallonen, Aki; Zhang, Zhao-Qun; Evans, Alistair R.; Mikkola, Marja L.; Salazar-Ciudad, Isaac; Klein, Ophir D.; Jernvall, Jukka

2014-01-01

The evolutionary relationships of extinct species are ascertained primarily through the analysis of morphological characters. Character inter-dependencies can have a substantial effect on evolutionary interpretations, but the developmental underpinnings of character inter-dependence remain obscure because experiments frequently do not provide detailed resolution of morphological characters. Here we show experimentally and computationally how gradual modification of development differentially affects characters in the mouse dentition. We found that intermediate phenotypes could be produced by gradually adding ectodysplasin A (EDA) protein in culture to tooth explants carrying a null mutation in the tooth-patterning gene Eda. By identifying development-based character interdependencies, we show how to predict morphological patterns of teeth among mammalian species. Finally, in vivo inhibition of sonic hedgehog signalling in Eda null teeth enabled us to reproduce characters deep in the rodent ancestry. Taken together, evolutionarily informative transitions can be experimentally reproduced, thereby providing development-based expectations for character state transitions used in evolutionary studies. PMID:25079326

Hunter-gatherer genomics: Evolutionary insights and ethical considerations

PubMed Central

Bankoff, Richard J.; Perry, George H.

2016-01-01

Hunting and gathering societies currently comprise only a small proportion of all human populations. However, the geographic and environmental diversity of modern hunter-gatherer groups, their inherent dependence on ecological resources, and their connection to patterns of behavior and subsistence that represent the vast majority of human history provide opportunities for scientific research to deliver major insights into the evolutionary history of our species. We review recent evolutionary genomic studies of hunter-gatherers, focusing especially on those that identify and functionally characterize phenotypic adaptations to local environments. We also call attention to specific ethical issues that scientists conducting hunter-gatherer genomics research ought to consider, including potential social and economic tensions between traditionally mobile hunter-gatherers and the land ownership-based nation-states by which they are governed, and the implications of genomic-based evidence of long-term evolutionary associations with particular habitats. PMID:27400119

Asymmetric Evolutionary Games.

PubMed

McAvoy, Alex; Hauert, Christoph

2015-08-01

Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner's Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games.

Using Nonlinear Stochastic Evolutionary Game Strategy to Model an Evolutionary Biological Network of Organ Carcinogenesis Under a Natural Selection Scheme

PubMed Central

Chen, Bor-Sen; Tsai, Kun-Wei; Li, Cheng-Wei

2015-01-01

Molecular biologists have long recognized carcinogenesis as an evolutionary process that involves natural selection. Cancer is driven by the somatic evolution of cell lineages. In this study, the evolution of somatic cancer cell lineages during carcinogenesis was modeled as an equilibrium point (ie, phenotype of attractor) shifting, the process of a nonlinear stochastic evolutionary biological network. This process is subject to intrinsic random fluctuations because of somatic genetic and epigenetic variations, as well as extrinsic disturbances because of carcinogens and stressors. In order to maintain the normal function (ie, phenotype) of an evolutionary biological network subjected to random intrinsic fluctuations and extrinsic disturbances, a network robustness scheme that incorporates natural selection needs to be developed. This can be accomplished by selecting certain genetic and epigenetic variations to modify the network structure to attenuate intrinsic fluctuations efficiently and to resist extrinsic disturbances in order to maintain the phenotype of the evolutionary biological network at an equilibrium point (attractor). However, during carcinogenesis, the remaining (or neutral) genetic and epigenetic variations accumulate, and the extrinsic disturbances become too large to maintain the normal phenotype at the desired equilibrium point for the nonlinear evolutionary biological network. Thus, the network is shifted to a cancer phenotype at a new equilibrium point that begins a new evolutionary process. In this study, the natural selection scheme of an evolutionary biological network of carcinogenesis was derived from a robust negative feedback scheme based on the nonlinear stochastic Nash game strategy. The evolvability and phenotypic robustness criteria of the evolutionary cancer network were also estimated by solving a Hamilton–Jacobi inequality – constrained optimization problem. The simulation revealed that the phenotypic shift of the lung cancer-associated cell network takes 54.5 years from a normal state to stage I cancer, 1.5 years from stage I to stage II cancer, and 2.5 years from stage II to stage III cancer, with a reasonable match for the statistical result of the average age of lung cancer. These results suggest that a robust negative feedback scheme, based on a stochastic evolutionary game strategy, plays a critical role in an evolutionary biological network of carcinogenesis under a natural selection scheme. PMID:26244004

The Evolution of Different Forms of Sociality: Behavioral Mechanisms and Eco-Evolutionary Feedback

PubMed Central

van der Post, Daniel J.; Verbrugge, Rineke; Hemelrijk, Charlotte K.

2015-01-01

Different forms of sociality have evolved via unique evolutionary trajectories. However, it remains unknown to what extent trajectories of social evolution depend on the specific characteristics of different species. Our approach to studying such trajectories is to use evolutionary case-studies, so that we can investigate how grouping co-evolves with a multitude of individual characteristics. Here we focus on anti-predator vigilance and foraging. We use an individual-based model, where behavioral mechanisms are specified, and costs and benefits are not predefined. We show that evolutionary changes in grouping alter selection pressures on vigilance, and vice versa. This eco-evolutionary feedback generates an evolutionary progression from “leader-follower” societies to “fission-fusion” societies, where cooperative vigilance in groups is maintained via a balance between within- and between-group selection. Group-level selection is generated from an assortment that arises spontaneously when vigilant and non-vigilant foragers have different grouping tendencies. The evolutionary maintenance of small groups, and cooperative vigilance in those groups, is therefore achieved simultaneously. The evolutionary phases, and the transitions between them, depend strongly on behavioral mechanisms. Thus, integrating behavioral mechanisms and eco-evolutionary feedback is critical for understanding what kinds of intermediate stages are involved during the evolution of particular forms of sociality. PMID:25629313

The evolution of different forms of sociality: behavioral mechanisms and eco-evolutionary feedback.

PubMed

van der Post, Daniel J; Verbrugge, Rineke; Hemelrijk, Charlotte K

2015-01-01

Different forms of sociality have evolved via unique evolutionary trajectories. However, it remains unknown to what extent trajectories of social evolution depend on the specific characteristics of different species. Our approach to studying such trajectories is to use evolutionary case-studies, so that we can investigate how grouping co-evolves with a multitude of individual characteristics. Here we focus on anti-predator vigilance and foraging. We use an individual-based model, where behavioral mechanisms are specified, and costs and benefits are not predefined. We show that evolutionary changes in grouping alter selection pressures on vigilance, and vice versa. This eco-evolutionary feedback generates an evolutionary progression from "leader-follower" societies to "fission-fusion" societies, where cooperative vigilance in groups is maintained via a balance between within- and between-group selection. Group-level selection is generated from an assortment that arises spontaneously when vigilant and non-vigilant foragers have different grouping tendencies. The evolutionary maintenance of small groups, and cooperative vigilance in those groups, is therefore achieved simultaneously. The evolutionary phases, and the transitions between them, depend strongly on behavioral mechanisms. Thus, integrating behavioral mechanisms and eco-evolutionary feedback is critical for understanding what kinds of intermediate stages are involved during the evolution of particular forms of sociality.

Linking environmental risk assessment and communication: An experiment in co-evolving scientific and social knowledge

USGS Publications Warehouse

Graffy, E.A.; Booth, N.L.

2008-01-01

Dissemination of information to decision-makers and enhanced methods of public participation are often put forward as antidotes to a perceived disconnect between risk assessment and risk communication in the public domain. However, mechanisms that support both the provision of routine, timely and relevant technical knowledge to the public and meaningful opportunities for public participation in the evaluation and management of risk are few. We argue for the need to re-conceptualise the institutional context in which risk research and communication occur as one in which scientific knowledge and public understanding are co-evolutionary instead of independent or sequential. Here, we report on an experiment to promote coevolution of environmental risk assessment and risk communication through the instrumental use of a web-based platform that dynamically links expert and public discourses through common information sources, linked scenario evaluations, and opportunities for iterative dialogue. On the basis of technical feasibility, research value and public communication capacity, we conclude that there is potential for further refinement of the methodologies presented here. Copyright ?? 2008 Inderscience Enterprises Ltd.

Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops.

PubMed

Murat, Florent; Zhang, Rongzhi; Guizard, Sébastien; Gavranović, Haris; Flores, Raphael; Steinbach, Delphine; Quesneville, Hadi; Tannier, Eric; Salse, Jérôme

2015-01-29

We used nine complete genome sequences, from grape, poplar, Arabidopsis, soybean, lotus, apple, strawberry, cacao, and papaya, to investigate the paleohistory of rosid crops. We characterized an ancestral rosid karyotype, structured into 7/21 protochomosomes, with a minimal set of 6,250 ordered protogenes and a minimum physical coding gene space of 50 megabases. We also proposed ancestral karyotypes for the Caricaceae, Brassicaceae, Malvaceae, Fabaceae, Rosaceae, Salicaceae, and Vitaceae families with 9, 8, 10, 6, 12, 9, 12, and 19 protochromosomes, respectively. On the basis of these ancestral karyotypes and present-day species comparisons, we proposed a two-step evolutionary scenario based on allohexaploidization involving the newly characterized A, B, and C diploid progenitors leading to dominant (stable) and sensitive (plastic) genomic compartments in any modern rosid crops. Finally, a new user-friendly online tool, "DicotSyntenyViewer" (available from http://urgi.versailles.inra.fr/synteny-dicot), has been made available for accurate translational genomics in rosids. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Prognostic characteristics of the lowest-mode internal waves in the Sea of Okhotsk

NASA Astrophysics Data System (ADS)

Kurkin, Andrey; Kurkina, Oxana; Zaytsev, Andrey; Rybin, Artem; Talipova, Tatiana

2017-04-01

The nonlinear dynamics of short-period internal waves on ocean shelves is well described by generalized nonlinear evolutionary models of Korteweg - de Vries type. Parameters of these models such as long wave propagation speed, nonlinear and dispersive coefficients can be calculated using hydrological data (sea water density stratification), and therefore have geographical and seasonal variations. The internal wave parameters for the basin of the Sea of Okhotsk are computed on a base of recent version of hydrological data source GDEM V3.0. Geographical and seasonal variability of internal wave characteristics is investigated. It is shown that annually or seasonally averaged data can be used for linear parameters. The nonlinear parameters are more sensitive to temporal averaging of hydrological data and detailed data are preferable to use. The zones for nonlinear parameters to change their signs (so-called "turning points") are selected. Possible internal waveforms appearing in the process of internal tide transformation including the solitary waves changing polarities are simulated for the hydrological conditions in the Sea of Okhotsk shelf to demonstrate different scenarios of internal wave adjustment, transformation, refraction and cylindrical divergence.

Genetic Diversity and Societally Important Disparities

PubMed Central

Rosenberg, Noah A.; Kang, Jonathan T. L.

2015-01-01

The magnitude of genetic diversity within human populations varies in a way that reflects the sequence of migrations by which people spread throughout the world. Beyond its use in human evolutionary genetics, worldwide variation in genetic diversity sometimes can interact with social processes to produce differences among populations in their relationship to modern societal problems. We review the consequences of genetic diversity differences in the settings of familial identification in forensic genetic testing, match probabilities in bone marrow transplantation, and representation in genome-wide association studies of disease. In each of these three cases, the contribution of genetic diversity to social differences follows from population-genetic principles. For a fourth setting that is not similarly grounded, we reanalyze with expanded genetic data a report that genetic diversity differences influence global patterns of human economic development, finding no support for the claim. The four examples describe a limit to the importance of genetic diversity for explaining societal differences while illustrating a distinction that certain biologically based scenarios do require consideration of genetic diversity for solving problems to which populations have been differentially predisposed by the unique history of human migrations. PMID:26354973

Diversification of land plants: insights from a family-level phylogenetic analysis.

PubMed

Fiz-Palacios, Omar; Schneider, Harald; Heinrichs, Jochen; Savolainen, Vincent

2011-11-21

Some of the evolutionary history of land plants has been documented based on the fossil record and a few broad-scale phylogenetic analyses, especially focusing on angiosperms and ferns. Here, we reconstructed phylogenetic relationships among all 706 families of land plants using molecular data. We dated the phylogeny using multiple fossils and a molecular clock technique. Applying various tests of diversification that take into account topology, branch length, numbers of extant species as well as extinction, we evaluated diversification rates through time. We also compared these diversification profiles against the distribution of the climate modes of the Phanerozoic. We found evidence for the radiations of ferns and mosses in the shadow of angiosperms coinciding with the rather warm Cretaceous global climate. In contrast, gymnosperms and liverworts show a signature of declining diversification rates during geological time periods of cool global climate. This broad-scale phylogenetic analysis helps to reveal the successive waves of diversification that made up the diversity of land plants we see today. Both warm temperatures and wet climate may have been necessary for the rise of the diversity under a successive lineage replacement scenario.

Pedestrian detection in crowded scenes with the histogram of gradients principle

NASA Astrophysics Data System (ADS)

Sidla, O.; Rosner, M.; Lypetskyy, Y.

2006-10-01

This paper describes a close to real-time scale invariant implementation of a pedestrian detector system which is based on the Histogram of Oriented Gradients (HOG) principle. Salient HOG features are first selected from a manually created very large database of samples with an evolutionary optimization procedure that directly trains a polynomial Support Vector Machine (SVM). Real-time operation is achieved by a cascaded 2-step classifier which uses first a very fast linear SVM (with the same features as the polynomial SVM) to reject most of the irrelevant detections and then computes the decision function with a polynomial SVM on the remaining set of candidate detections. Scale invariance is achieved by running the detector of constant size on scaled versions of the original input images and by clustering the results over all resolutions. The pedestrian detection system has been implemented in two versions: i) fully body detection, and ii) upper body only detection. The latter is especially suited for very busy and crowded scenarios. On a state-of-the-art PC it is able to run at a frequency of 8 - 20 frames/sec.

Scenario-based design: A method for connecting information system design with public health operations and emergency management

PubMed Central

Reeder, Blaine; Turner, Anne M

2011-01-01

Responding to public health emergencies requires rapid and accurate assessment of workforce availability under adverse and changing circumstances. However, public health information systems to support resource management during both routine and emergency operations are currently lacking. We applied scenario-based design as an approach to engage public health practitioners in the creation and validation of an information design to support routine and emergency public health activities. Methods: Using semi-structured interviews we identified the information needs and activities of senior public health managers of a large municipal health department during routine and emergency operations. Results: Interview analysis identified twenty-five information needs for public health operations management. The identified information needs were used in conjunction with scenario-based design to create twenty-five scenarios of use and a public health manager persona. Scenarios of use and persona were validated and modified based on follow-up surveys with study participants. Scenarios were used to test and gain feedback on a pilot information system. Conclusion: The method of scenario-based design was applied to represent the resource management needs of senior-level public health managers under routine and disaster settings. Scenario-based design can be a useful tool for engaging public health practitioners in the design process and to validate an information system design. PMID:21807120

Climate change effects on the geographic distribution of specialist tree species of the Brazilian tropical dry forests.

PubMed

Rodrigues, P M S; Silva, J O; Eisenlohr, P V; Schaefer, C E G R

2015-08-01

The aim of this study was to evaluate the ecological niche models (ENMs) for three specialist trees (Anadenanthera colubrina, Aspidosperma pyrifolium and Myracrodruon urundeuva) in seasonally dry tropical forests (SDTFs) in Brazil, considering present and future pessimist scenarios (2080) of climate change. These three species exhibit typical deciduousness and are widely distributed by SDTF in South America, being important in studies of the historical and evolutionary processes experienced by this ecosystem. The modeling of the potential geographic distribution of species was done by the method of maximum entropy (Maxent).We verified a general expansion of suitable areas for occurrence of the three species in future (c.a., 18%), although there was reduction of areas with high environmental suitability in Caatinga region. Precipitation of wettest quarter and temperature seasonality were the predictor variables that most contributed to our models. Climatic changes can provide more severe and longer dry season with increasing temperature and tree mortality in tropics. On this scenario, areas currently occupied by rainforest and savannas could become more suitable for occurrence of the SDTF specialist trees, whereas regions occupied by Caatinga could not support the future level of unsustainable (e.g., aridity). Long-term multidisciplinary studies are necessary to make reliable predictions of the plant's adaptation strategies and responses to climate changes in dry forest at community level. Based on the high deforestation rate, endemism and threat, public policies to minimize the effects of climate change on the biodiversity found within SDTFs must be undertaken rapidly.

A General Model for Estimating Macroevolutionary Landscapes.

PubMed

Boucher, Florian C; Démery, Vincent; Conti, Elena; Harmon, Luke J; Uyeda, Josef

2018-03-01

The evolution of quantitative characters over long timescales is often studied using stochastic diffusion models. The current toolbox available to students of macroevolution is however limited to two main models: Brownian motion and the Ornstein-Uhlenbeck process, plus some of their extensions. Here, we present a very general model for inferring the dynamics of quantitative characters evolving under both random diffusion and deterministic forces of any possible shape and strength, which can accommodate interesting evolutionary scenarios like directional trends, disruptive selection, or macroevolutionary landscapes with multiple peaks. This model is based on a general partial differential equation widely used in statistical mechanics: the Fokker-Planck equation, also known in population genetics as the Kolmogorov forward equation. We thus call the model FPK, for Fokker-Planck-Kolmogorov. We first explain how this model can be used to describe macroevolutionary landscapes over which quantitative traits evolve and, more importantly, we detail how it can be fitted to empirical data. Using simulations, we show that the model has good behavior both in terms of discrimination from alternative models and in terms of parameter inference. We provide R code to fit the model to empirical data using either maximum-likelihood or Bayesian estimation, and illustrate the use of this code with two empirical examples of body mass evolution in mammals. FPK should greatly expand the set of macroevolutionary scenarios that can be studied since it opens the way to estimating macroevolutionary landscapes of any conceivable shape. [Adaptation; bounds; diffusion; FPK model; macroevolution; maximum-likelihood estimation; MCMC methods; phylogenetic comparative data; selection.].

Effects of heterogeneous wealth distribution on public cooperation with collective risk

NASA Astrophysics Data System (ADS)

Wang, Jing; Fu, Feng; Wang, Long

2010-07-01

The distribution of wealth among individuals in real society can be well described by the Pareto principle or “80-20 rule.” How does such heterogeneity in initial wealth distribution affect the emergence of public cooperation, when individuals, the rich and the poor, engage in a collective-risk enterprise, not to gain a profit but to avoid a potential loss? Here we address this issue by studying a simple but effective model based on threshold public goods games. We analyze the evolutionary dynamics for two distinct scenarios, respectively: one with fair sharers versus defectors and the other with altruists versus defectors. For both scenarios, particularly, we in detail study the dynamics of the population with dichotomic initial wealth—the rich versus the poor. Moreover, we demonstrate the possible steady compositions of the population and provide the conditions for stability of these steady states. We prove that in a population with heterogeneous wealth distribution, richer individuals are more likely to cooperate than poorer ones. Participants with lower initial wealth may choose to cooperate only if all players richer than them are cooperators. The emergence of pubic cooperation largely relies on rich individuals. Furthermore, whenever the wealth gap between the rich and the poor is sufficiently large, cooperation of a few rich individuals can substantially elevate the overall level of social cooperation, which is in line with the well-known Pareto principle. Our work may offer an insight into the emergence of cooperative behavior in real social situations where heterogeneous distribution of wealth among individual is omnipresent.

Using Landscape Genetics Simulations for Planting Blister Rust Resistant Whitebark Pine in the US Northern Rocky Mountains.

PubMed

Landguth, Erin L; Holden, Zachary A; Mahalovich, Mary F; Cushman, Samuel A

2017-01-01

Recent population declines to the high elevation western North America foundation species whitebark pine, have been driven by the synergistic effects of the invasive blister rust pathogen, mountain pine beetle (MPB), fire exclusion, and climate change. This has led to consideration for listing whitebark pine (WBP) as a threatened or endangered species under the Endangered Species Act, which has intensified interest in developing management strategies for maintaining and restoring the species. An important, but poorly studied, aspect of WBP restoration is the spatial variation in adaptive genetic variation and the potential of blister rust resistant strains to maintain viable populations in the future. Here, we present a simulation modeling framework to improve understanding of the long-term genetic consequences of the blister rust pathogen, the evolution of rust resistance, and scenarios of planting rust resistant genotypes of whitebark pine. We combine climate niche modeling and eco-evolutionary landscape genetics modeling to evaluate the effects of different scenarios of planting rust-resistant genotypes and impacts of wind field direction on patterns of gene flow. Planting scenarios showed different levels for local extirpation of WBP and increased population-wide blister rust resistance, suggesting that the spatial arrangement and choice of planting locations can greatly affect survival rates of whitebark pine. This study presents a preliminary, but potentially important, framework for facilitating the conservation of whitebark pine.

Two graphical user interfaces for managing and analyzing MODFLOW groundwater-model scenarios

USGS Publications Warehouse

Banta, Edward R.

2014-01-01

Scenario Manager and Scenario Analyzer are graphical user interfaces that facilitate the use of calibrated, MODFLOW-based groundwater models for investigating possible responses to proposed stresses on a groundwater system. Scenario Manager allows a user, starting with a calibrated model, to design and run model scenarios by adding or modifying stresses simulated by the model. Scenario Analyzer facilitates the process of extracting data from model output and preparing such display elements as maps, charts, and tables. Both programs are designed for users who are familiar with the science on which groundwater modeling is based but who may not have a groundwater modeler’s expertise in building and calibrating a groundwater model from start to finish. With Scenario Manager, the user can manipulate model input to simulate withdrawal or injection wells, time-variant specified hydraulic heads, recharge, and such surface-water features as rivers and canals. Input for stresses to be simulated comes from user-provided geographic information system files and time-series data files. A Scenario Manager project can contain multiple scenarios and is self-documenting. Scenario Analyzer can be used to analyze output from any MODFLOW-based model; it is not limited to use with scenarios generated by Scenario Manager. Model-simulated values of hydraulic head, drawdown, solute concentration, and cell-by-cell flow rates can be presented in display elements. Map data can be represented as lines of equal value (contours) or as a gradated color fill. Charts and tables display time-series data obtained from output generated by a transient-state model run or from user-provided text files of time-series data. A display element can be based entirely on output of a single model run, or, to facilitate comparison of results of multiple scenarios, an element can be based on output from multiple model runs. Scenario Analyzer can export display elements and supporting metadata as a Portable Document Format file.

Contextualized Writing: Promoting Audience-Centered Writing through Scenario-Based Learning

ERIC Educational Resources Information Center

Golden, Paullett

2018-01-01

Scenario-based learning is an approach for student-centered learning used in the medical and legal fields, but is little used in liberal arts. In this study, I examine students' understanding and application of audience-centered writing techniques after a semester of formal scenario-based essays and problem-based activities. Comparing the grades…

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

Mor, Rivay; Netzer, Hagai; Trakhtenbrot, Benny

We report new Herschel observations of 25 z {approx_equal} 4.8 extremely luminous optically selected active galactic nuclei (AGNs). Five of the sources have extremely large star-forming (SF) luminosities, L{sub SF}, corresponding to SF rates (SFRs) of 2800-5600 M{sub Sun} yr{sup -1} assuming a Salpeter initial mass function. The remaining sources have only upper limits on their SFRs, but stacking their Herschel images results in a mean SFR of 700 {+-} 150 M{sub Sun} yr{sup -1}. The higher SFRs in our sample are comparable to the highest observed values so far at any redshift. Our sample does not contain obscured AGNs,more » which enables us to investigate several evolutionary scenarios connecting supermassive black holes and SF activity in the early universe. The most probable scenario is that we are witnessing the peak of SF activity in some sources and the beginning of the post-starburst decline in others. We suggest that all 25 sources, which are at their peak AGN activity, are in large mergers. AGN feedback may be responsible for diminishing the SF activity in 20 of them, but is not operating efficiently in 5 others.« less

Phylogenetic approaches reveal biodiversity threats under climate change

NASA Astrophysics Data System (ADS)

González-Orozco, Carlos E.; Pollock, Laura J.; Thornhill, Andrew H.; Mishler, Brent D.; Knerr, Nunzio; Laffan, Shawn W.; Miller, Joseph T.; Rosauer, Dan F.; Faith, Daniel P.; Nipperess, David A.; Kujala, Heini; Linke, Simon; Butt, Nathalie; Külheim, Carsten; Crisp, Michael D.; Gruber, Bernd

2016-12-01

Predicting the consequences of climate change for biodiversity is critical to conservation efforts. Extensive range losses have been predicted for thousands of individual species, but less is known about how climate change might impact whole clades and landscape-scale patterns of biodiversity. Here, we show that climate change scenarios imply significant changes in phylogenetic diversity and phylogenetic endemism at a continental scale in Australia using the hyper-diverse clade of eucalypts. We predict that within the next 60 years the vast majority of species distributions (91%) across Australia will shrink in size (on average by 51%) and shift south on the basis of projected suitable climatic space. Geographic areas currently with high phylogenetic diversity and endemism are predicted to change substantially in future climate scenarios. Approximately 90% of the current areas with concentrations of palaeo-endemism (that is, places with old evolutionary diversity) are predicted to disappear or shift their location. These findings show that climate change threatens whole clades of the phylogenetic tree, and that the outlined approach can be used to forecast areas of biodiversity losses and continental-scale impacts of climate change.

Drug resistance in vectorborne parasites: multiple actors and scenarios for an evolutionary arms race.

PubMed

Vanaerschot, Manu; Huijben, Silvie; Van den Broeck, Frederik; Dujardin, Jean-Claude

2014-01-01

Drug-resistant pathogens emerge faster than new drugs come out of drug discovery pipelines. Current and future drug options should therefore be better protected, requiring a clear understanding of the factors that contribute to the natural history of drug resistance. Although many of these factors are relatively well understood for most bacteria, this proves to be more complex for vectorborne parasites. In this review, we discuss considering three key models (Plasmodium, Leishmania and Schistosoma) how drug resistance can emerge, spread and persist. We demonstrate a multiplicity of scenarios, clearly resulting from the biological diversity of the different organisms, but also from the different modes of action of the drugs used, the specific within- and between-host ecology of the parasites, and environmental factors that may have direct or indirect effects. We conclude that integrated control of drug-resistant vectorborne parasites is not dependent upon chemotherapy only, but also requires a better insight into the ecology of these parasites and how their transmission can be impaired. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Space Station Freedom extravehicular activity systems evolution study

NASA Technical Reports Server (NTRS)

Rouen, Michael

1990-01-01

Evaluation of Space Station Freedom (SSF) support of manned exploration is in progress to identify SSF extravehicular activity (EVA) system evolution requirements and capabilities. The output from these studies will provide data to support the preliminary design process to ensure that Space Station EVA system requirements for future missions (including the transportation node) are adequately considered and reflected in the baseline design. The study considers SSF support of future missions and the EVA system baseline to determine adequacy of EVA requirements and capabilities and to identify additional requirements, capabilities, and necessary technology upgrades. The EVA demands levied by formal requirements and indicated by evolutionary mission scenarios are high for the out-years of Space Station Freedom. An EVA system designed to meet the baseline requirements can easily evolve to meet evolution demands with few exceptions. Results to date indicate that upgrades or modifications to the EVA system may be necessary to meet the full range of EVA thermal environments associated with the transportation node. Work continues to quantify the EVA capability in this regard. Evolution mission scenarios with EVA and ground unshielded nuclear propulsion engines are inconsistent with anthropomorphic EVA capabilities.

Synthetic circuit designs for earth terraformation.

PubMed

Solé, Ricard V; Montañez, Raúl; Duran-Nebreda, Salva

2015-07-18

Mounting evidence indicates that our planet might experience runaway effects associated to rising temperatures and ecosystem overexploitation, leading to catastrophic shifts on short time scales. Remediation scenarios capable of counterbalancing these effects involve geoengineering, sustainable practices and carbon sequestration, among others. None of these scenarios seems powerful enough to achieve the desired restoration of safe boundaries. We hypothesize that synthetic organisms with the appropriate engineering design could be used to safely prevent declines in some stressed ecosystems and help improving carbon sequestration. Such schemes would include engineering mutualistic dependencies preventing undesired evolutionary processes. We hypothesize that some particular design principles introduce unescapable constraints to the engineered organisms that act as effective firewalls. Testing this designed organisms can be achieved by using controlled bioreactor models, with single and heterogeneous populations, and accurate computational models including different scales (from genetic constructs and metabolic pathways to population dynamics). Our hypothesis heads towards a future anthropogenic action that should effectively act as Terraforming processes. It also implies a major challenge in the existing biosafety policies, since we suggest release of modified organisms as potentially necessary strategy for success.

Mean-Potential Law in Evolutionary Games.

PubMed

Nałęcz-Jawecki, Paweł; Miękisz, Jacek

2018-01-12

The Letter presents a novel way to connect random walks, stochastic differential equations, and evolutionary game theory. We introduce a new concept of a potential function for discrete-space stochastic systems. It is based on a correspondence between one-dimensional stochastic differential equations and random walks, which may be exact not only in the continuous limit but also in finite-state spaces. Our method is useful for computation of fixation probabilities in discrete stochastic dynamical systems with two absorbing states. We apply it to evolutionary games, formulating two simple and intuitive criteria for evolutionary stability of pure Nash equilibria in finite populations. In particular, we show that the 1/3 law of evolutionary games, introduced by Nowak et al. [Nature, 2004], follows from a more general mean-potential law.

Evolutionary Based Techniques for Fault Tolerant Field Programmable Gate Arrays

NASA Technical Reports Server (NTRS)

Larchev, Gregory V.; Lohn, Jason D.

2006-01-01

The use of SRAM-based Field Programmable Gate Arrays (FPGAs) is becoming more and more prevalent in space applications. Commercial-grade FPGAs are potentially susceptible to permanently debilitating Single-Event Latchups (SELs). Repair methods based on Evolutionary Algorithms may be applied to FPGA circuits to enable successful fault recovery. This paper presents the experimental results of applying such methods to repair four commonly used circuits (quadrature decoder, 3-by-3-bit multiplier, 3-by-3-bit adder, 440-7 decoder) into which a number of simulated faults have been introduced. The results suggest that evolutionary repair techniques can improve the process of fault recovery when used instead of or as a supplement to Triple Modular Redundancy (TMR), which is currently the predominant method for mitigating FPGA faults.

Projected timing of perceivable changes in climate extremes for terrestrial and marine ecosystems.

PubMed

Tan, Xuezhi; Gan, Thian Yew; Horton, Daniel E

2018-05-26

Human and natural systems have adapted to and evolved within historical climatic conditions. Anthropogenic climate change has the potential to alter these conditions such that onset of unprecedented climatic extremes will outpace evolutionary and adaptive capabilities. To assess whether and when future climate extremes exceed their historical windows of variability within impact-relevant socioeconomic, geopolitical, and ecological domains, we investigate the timing of perceivable changes (time of emergence; TOE) for 18 magnitude-, frequency-, and severity-based extreme temperature (10) and precipitation (8) indices using both multimodel and single-model multirealization ensembles. Under a high-emission scenario, we find that the signal of frequency- and severity-based temperature extremes is projected to rise above historical noise earliest in midlatitudes, whereas magnitude-based temperature extremes emerge first in low and high latitudes. Precipitation extremes demonstrate different emergence patterns, with severity-based indices first emerging over midlatitudes, and magnitude- and frequency-based indices emerging earliest in low and high latitudes. Applied to impact-relevant domains, simulated TOE patterns suggest (a) unprecedented consecutive dry day occurrence in >50% of 14 terrestrial biomes and 12 marine realms prior to 2100, (b) earlier perceivable changes in climate extremes in countries with lower per capita GDP, and (c) emergence of severe and frequent heat extremes well-before 2030 for the 590 most populous urban centers. Elucidating extreme-metric and domain-type TOE heterogeneities highlights the challenges adaptation planners face in confronting the consequences of elevated twenty-first century radiative forcing. © 2018 John Wiley & Sons Ltd.

High-resolution 25 μm Imaging of the Disks around Herbig Ae/Be Stars

NASA Astrophysics Data System (ADS)

Honda, M.; Maaskant, K.; Okamoto, Y. K.; Kataza, H.; Yamashita, T.; Miyata, T.; Sako, S.; Fujiyoshi, T.; Sakon, I.; Fujiwara, H.; Kamizuka, T.; Mulders, G. D.; Lopez-Rodriguez, E.; Packham, C.; Onaka, T.

2015-05-01

We imaged circumstellar disks around 22 Herbig Ae/Be stars at 25 μm using Subaru/COMICS and Gemini/T-ReCS. Our sample consists of an equal number of objects from each of the two categories defined by Meeus et al.; 11 group I (flaring disk) and II (flat disk) sources. We find that group I sources tend to show more extended emission than group II sources. Previous studies have shown that the continuous disk is difficult to resolve with 8 m class telescopes in the Q band due to the strong emission from the unresolved innermost region of the disk. This indicates that the resolved Q-band sources require a hole or gap in the disk material distribution to suppress the contribution from the innermost region of the disk. As many group I sources are resolved at 25 μm, we suggest that many, but not all, group I Herbig Ae/Be disks have a hole or gap and are (pre-)transitional disks. On the other hand, the unresolved nature of many group II sources at 25 μm supports the idea that group II disks have a continuous flat disk geometry. It has been inferred that group I disks may evolve into group II through the settling of dust grains into the mid-plane of the protoplanetary disk. However, considering the growing evidence for the presence of a hole or gap in the disk of group I sources, such an evolutionary scenario is unlikely. The difference between groups I and II may reflect different evolutionary pathways of protoplanetary disks. Based on data collected at the Subaru Telescope, via the time exchange program between Subaru and the Gemini Observatory. The Subaru Telescope is operated by the National Astronomical Observatory of Japan.

An Integrated Framework for Modeling Air Carrier Behavior, Policy, and Impacts in the U.S. Air Transportation System

NASA Technical Reports Server (NTRS)

Horio, Brant M.; Kumar, Vivek; DeCicco, Anthony H.; Hasan, Shahab; Stouffer, Virginia L.; Smith, Jeremy C.; Guerreiro, Nelson M.

2015-01-01

The implementation of the Next Generation Air Transportation System (NextGen) in the United States is an ongoing challenge for policymakers due to the complexity of the air transportation system (ATS) with its broad array of stakeholders and dynamic interdependencies between them. The successful implementation of NextGen has a hard dependency on the active participation of U.S. commercial airlines. To assist policymakers in identifying potential policy designs that facilitate the implementation of NextGen, the National Aeronautics and Space Administration (NASA) and LMI developed a research framework called the Air Transportation System Evolutionary Simulation (ATS-EVOS). This framework integrates large empirical data sets with multiple specialized models to simulate the evolution of the airline response to potential future policies and explore consequential impacts on ATS performance and market dynamics. In the ATS-EVOS configuration presented here, we leverage the Transportation Systems Analysis Model (TSAM), the Airline Evolutionary Simulation (AIRLINE-EVOS), the Airspace Concept Evaluation System (ACES), and the Aviation Environmental Design Tool (AEDT), all of which enable this research to comprehensively represent the complex facets of the ATS and its participants. We validated this baseline configuration of ATS-EVOS against Airline Origin and Destination Survey (DB1B) data and subject matter expert opinion, and we verified the ATS-EVOS framework and agent behavior logic through scenario-based experiments that explored potential implementations of a carbon tax, congestion pricing policy, and the dynamics for equipage of new technology by airlines. These experiments demonstrated ATS-EVOS's capabilities in responding to a wide range of potential NextGen-related policies and utility for decision makers to gain insights for effective policy design.

Mass elevation and lee effects markedly lift the elevational distribution of ground beetles in the Himalaya-Tibet orogen

PubMed Central

Schmidt, Joachim; Böhner, Jürgen; Brandl, Roland; Opgenoorth, Lars

2017-01-01

Mass elevation and lee effects markedly influence snow lines and tree lines in high mountain systems. However, their impact on other phenomena or groups of organisms has not yet been quantified. Here we quantitatively studied their influence in the Himalaya–Tibet orogen on the distribution of ground beetles as model organisms, specifically whether the ground beetle distribution increases from the outer to the inner parts of the orogen, against latitudinal effects. We also tested whether July temperature and solar radiation are predictors of the beetle’s elevational distribution ranges. Finally, we discussed the general importance of these effects for the distributional and evolutionary history of the biota of High Asia. We modelled spatially explicit estimates of variables characterizing temperature and solar radiation and correlated the variables with the respective lower elevational range of 118 species of ground beetles from 76 high-alpine locations. Both July temperature and solar radiation significantly positively correlated with the elevational ranges of high-alpine beetles. Against the latitudinal trend, the median elevation of the respective species distributions increased by 800 m from the Himalayan south face north to the Transhimalaya. Our results indicate that an increase in seasonal temperature due to mass elevation and lee effects substantially impact the regional distribution patterns of alpine ground beetles of the Himalaya–Tibet orogen and are likely to affect also other soil biota there and in mountain ranges worldwide. Since these effects must have changed during orogenesis, their potential impact must be considered when biogeographic scenarios based on geological models are derived. As this has not been the practice, we believe that large biases likely exist in many paleoecological and evolutionary studies dealing with the biota from the Himalaya-Tibet orogen and mountain ranges worldwide. PMID:28339461

Evolutionary adaptations: theoretical and practical implications for visual ergonomics.

PubMed

Fostervold, Knut Inge; Watten, Reidulf G; Volden, Frode

2014-01-01

The literature discussing visual ergonomics often mention that human vision is adapted to light emitted by the sun. However, theoretical and practical implications of this viewpoint is seldom discussed or taken into account. The paper discusses some of the main theoretical implications of an evolutionary approach to visual ergonomics. Based on interactional theory and ideas from ecological psychology an evolutionary stress model is proposed as a theoretical framework for future research in ergonomics and human factors. The model stresses the importance of developing work environments that fits with our evolutionary adaptations. In accordance with evolutionary psychology, the environment of evolutionary adaptedness (EEA) and evolutionarily-novel environments (EN) are used as key concepts. Using work with visual display units (VDU) as an example, the paper discusses how this knowledge can be utilized in an ergonomic analysis of risk factors in the work environment. The paper emphasises the importance of incorporating evolutionary theory in the field of ergonomics. Further, the paper encourages scientific practices that further our understanding of any phenomena beyond the borders of traditional proximal explanations.

Different evolutionary pathways underlie the morphology of wrist bones in hominoids

PubMed Central

2013-01-01

Background The hominoid wrist has been a focus of numerous morphological analyses that aim to better understand long-standing questions about the evolution of human and hominoid hand use. However, these same analyses also suggest various scenarios of complex and mosaic patterns of morphological evolution within the wrist and potentially multiple instances of homoplasy that would benefit from require formal analysis within a phylogenetic context. We identify morphological features that principally characterize primate – and, in particular, hominoid (apes, including humans) - wrist evolution and reveal the rate, process and evolutionary timing of patterns of morphological change on individual branches of the primate tree of life. Linear morphological variables of five wrist bones – the scaphoid, lunate, triquetrum, capitate and hamate – are analyzed in a diverse sample of extant hominoids (12 species, 332 specimens), Old World (8 species, 43 specimens) and New World (4 species, 26 specimens) monkeys, fossil Miocene apes (8 species, 20 specimens) and Plio-Pleistocene hominins (8 species, 18 specimens). Result Results reveal a combination of parallel and synapomorphic morphology within haplorrhines, and especially within hominoids, across individual wrist bones. Similar morphology of some wrist bones reflects locomotor behaviour shared between clades (scaphoid, triquetrum and capitate) while others (lunate and hamate) indicate clade-specific synapomorphic morphology. Overall, hominoids show increased variation in wrist bone morphology compared with other primate clades, supporting previous analyses, and demonstrate several occurrences of parallel evolution, particularly between orangutans and hylobatids, and among hominines (extant African apes, humans and fossil hominins). Conclusions Our analyses indicate that different evolutionary processes can underlie the evolution of a single anatomical unit (the wrist) to produce diversity in functional and morphological adaptations across individual wrist bones. These results exemplify a degree of evolutionary and functional independence across different wrist bones, the potential evolvability of skeletal morphology, and help to contextualize the postcranial mosaicism observed in the hominin fossil record. PMID:24148262

Evolutionary hierarchy of vertebrate-like heterotrimeric G protein families.

PubMed

Krishnan, Arunkumar; Mustafa, Arshi; Almén, Markus Sällman; Fredriksson, Robert; Williams, Michael J; Schiöth, Helgi B

2015-10-01

Heterotrimeric G proteins perform a crucial role as molecular switches controlling various cellular responses mediated by G protein-coupled receptor (GPCR) signaling pathway. Recent data have shown that the vertebrate-like G protein families are found across metazoans and their closest unicellular relatives. However, an overall evolutionary hierarchy of vertebrate-like G proteins, including gene family annotations and in particular mapping individual gene gain/loss events across diverse holozoan lineages is still incomplete. Here, with more expanded invertebrate taxon sampling, we have reconstructed phylogenetic trees for each of the G protein classes/families and provide a robust classification and hierarchy of vertebrate-like heterotrimeric G proteins. Our results further extend the evidence that the common ancestor (CA) of holozoans had at least five ancestral Gα genes corresponding to all major vertebrate Gα classes and contain a total of eight genes including two Gβ and one Gγ. Our results also indicate that the GNAI/O-like gene likely duplicated in the last CA of metazoans to give rise to GNAI- and GNAO-like genes, which are conserved across invertebrates. Moreover, homologs of GNB1-4 paralogon- and GNB5 family-like genes are found in most metazoans and that the unicellular holozoans encode two ancestral Gβ genes. Similarly, most bilaterian invertebrates encode two Gγ genes which include a representative of the GNG gene cluster and a putative homolog of GNG13. Interestingly, our results also revealed key evolutionary events such as the Drosophila melanogaster eye specific Gβ subunit that is found conserved in most arthropods and several previously unidentified species specific expansions within Gαi/o, Gαs, Gαq, Gα12/13 classes and the GNB1-4 paralogon. Also, we provide an overall proposed evolutionary scenario on the expansions of all G protein families in vertebrate tetraploidizations. Our robust classification/hierarchy is essential to further understand the differential roles of GPCR/G protein mediated intracellular signaling system across various metazoan lineages. Copyright © 2015 Elsevier Inc. All rights reserved.

Evolutionary patterns and processes in the radiation of phyllostomid bats

PubMed Central

2011-01-01

Background The phyllostomid bats present the most extensive ecological and phenotypic radiation known among mammal families. This group is an important model system for studies of cranial ecomorphology and functional optimisation because of the constraints imposed by the requirements of flight. A number of studies supporting phyllostomid adaptation have focused on qualitative descriptions or correlating functional variables and diet, but explicit tests of possible evolutionary mechanisms and scenarios for phenotypic diversification have not been performed. We used a combination of morphometric and comparative methods to test hypotheses regarding the evolutionary processes behind the diversification of phenotype (mandible shape and size) and diet during the phyllostomid radiation. Results The different phyllostomid lineages radiate in mandible shape space, with each feeding specialisation evolving towards different axes. Size and shape evolve quite independently, as the main directions of shape variation are associated with mandible elongation (nectarivores) or the relative size of tooth rows and mandibular processes (sanguivores and frugivores), which are not associated with size changes in the mandible. The early period of phyllostomid diversification is marked by a burst of shape, size, and diet disparity (before 20 Mya), larger than expected by neutral evolution models, settling later to a period of relative phenotypic and ecological stasis. The best fitting evolutionary model for both mandible shape and size divergence was an Ornstein-Uhlenbeck process with five adaptive peaks (insectivory, carnivory, sanguivory, nectarivory and frugivory). Conclusions The radiation of phyllostomid bats presented adaptive and non-adaptive components nested together through the time frame of the family's evolution. The first 10 My of the radiation were marked by strong phenotypic and ecological divergence among ancestors of modern lineages, whereas the remaining 20 My were marked by stasis around a number of probable adaptive peaks. A considerable amount of cladogenesis and speciation in this period is likely to be the result of non-adaptive allopatric divergence or adaptations to peaks within major dietary categories. PMID:21605452

Evolutionary patterns and processes in the radiation of phyllostomid bats.

PubMed

Monteiro, Leandro R; Nogueira, Marcelo R

2011-05-23

The phyllostomid bats present the most extensive ecological and phenotypic radiation known among mammal families. This group is an important model system for studies of cranial ecomorphology and functional optimisation because of the constraints imposed by the requirements of flight. A number of studies supporting phyllostomid adaptation have focused on qualitative descriptions or correlating functional variables and diet, but explicit tests of possible evolutionary mechanisms and scenarios for phenotypic diversification have not been performed. We used a combination of morphometric and comparative methods to test hypotheses regarding the evolutionary processes behind the diversification of phenotype (mandible shape and size) and diet during the phyllostomid radiation. The different phyllostomid lineages radiate in mandible shape space, with each feeding specialisation evolving towards different axes. Size and shape evolve quite independently, as the main directions of shape variation are associated with mandible elongation (nectarivores) or the relative size of tooth rows and mandibular processes (sanguivores and frugivores), which are not associated with size changes in the mandible. The early period of phyllostomid diversification is marked by a burst of shape, size, and diet disparity (before 20 Mya), larger than expected by neutral evolution models, settling later to a period of relative phenotypic and ecological stasis. The best fitting evolutionary model for both mandible shape and size divergence was an Ornstein-Uhlenbeck process with five adaptive peaks (insectivory, carnivory, sanguivory, nectarivory and frugivory). The radiation of phyllostomid bats presented adaptive and non-adaptive components nested together through the time frame of the family's evolution. The first 10 My of the radiation were marked by strong phenotypic and ecological divergence among ancestors of modern lineages, whereas the remaining 20 My were marked by stasis around a number of probable adaptive peaks. A considerable amount of cladogenesis and speciation in this period is likely to be the result of non-adaptive allopatric divergence or adaptations to peaks within major dietary categories.

[Evolutionary medicine].

PubMed

Wjst, M

2013-12-01

Evolutionary medicine allows new insights into long standing medical problems. Are we "really stoneagers on the fast lane"? This insight might have enormous consequences and will allow new answers that could never been provided by traditional anthropology. Only now this is made possible using data from molecular medicine and systems biology. Thereby evolutionary medicine takes a leap from a merely theoretical discipline to practical fields - reproductive, nutritional and preventive medicine, as well as microbiology, immunology and psychiatry. Evolutionary medicine is not another "just so story" but a serious candidate for the medical curriculum providing a universal understanding of health and disease based on our biological origin. © Georg Thieme Verlag KG Stuttgart · New York.

Development of crash imminent test scenarios for Integrated Vehicle-Based Safety Systems

DOT National Transportation Integrated Search

2007-04-01

This report identifies crash imminent test scenarios based on common pre-crash scenarios for integrated vehicle-based safety systems that alert the driver of a light vehicle or a heavy truck to an impending rear-end, lane change, or run-off-road cras...

From the scala naturae to the symbiogenetic and dynamic tree of life.

PubMed

Kutschera, Ulrich

2011-06-30

All living beings on Earth, from bacteria to humans, are connected through descent from common ancestors and represent the summation of their corresponding, ca. 3500 million year long evolutionary history. However, the evolution of phenotypic features is not predictable, and biologists no longer use terms such as "primitive" or "perfect organisms". Despite these insights, the Bible-based concept of the so-called "ladder of life" or Scala Naturae, i.e., the idea that all living beings can be viewed as representing various degrees of "perfection", with humans at the very top of this biological hierarchy, was popular among naturalists until ca. 1850 (Charles Bonnet, Jean Lamarck and others). Charles Darwin is usually credited with the establishment of a branched evolutionary "Tree of Life". This insight of 1859 was based on his now firmly corroborated proposals of common ancestry and natural selection. In this article I argue that Darwin was still influenced by "ladder thinking", a theological view that prevailed throughout the 19th century and is also part of Ernst Haeckel's famous Oak tree (of Life) of 1866, which is, like Darwin's scheme, static. In 1910, Constantin Mereschkowsky proposed an alternative, "anti-selectionist" concept of biological evolution, which became known as the symbiogenesis-theory. According to the symbiogenesis-scenario, eukaryotic cells evolved on a static Earth from archaic prokaryotes via the fusion and subsequent cooperation of certain microbes. In 1929, Alfred Wegener published his theory of continental drift, which was later corroborated, modified and extended. The resulting theory of plate tectonics is now the principal organizing concept of geology. Over millions of years, plate tectonics and hence the "dynamic Earth" has caused destructive volcanic eruptions and earthquakes. At the same time, it created mountain ranges, deep oceans, novel freshwater habitats, and deserts. As a result, these geologic processes destroyed numerous populations of organisms, and produced the environmental conditions for new species of animals, plants and microbes to adapt and evolve. In this article I propose a tree-like "symbiogenesis, natural selection, and dynamic Earth (synade)-model" of macroevolution that is based on these novel facts and data.

Solvency II solvency capital requirement for life insurance companies based on expected shortfall.

PubMed

Boonen, Tim J

2017-01-01

This paper examines the consequences for a life annuity insurance company if the solvency II solvency capital requirements (SCR) are calibrated based on expected shortfall (ES) instead of value-at-risk (VaR). We focus on the risk modules of the SCRs for the three risk classes equity risk, interest rate risk and longevity risk. The stress scenarios are determined using the calibration method proposed by EIOPA in 2014. We apply the stress-scenarios for these three risk classes to a fictitious life annuity insurance company. We find that for EIOPA's current quantile 99.5% of the VaR, the stress scenarios of the various risk classes based on ES are close to the stress scenarios based on VaR. Might EIOPA choose to calibrate the stress scenarios on a smaller quantile, the longevity SCR is relatively larger and the equity SCR is relatively smaller if ES is used instead of VaR. We derive the same conclusion if stress scenarios are determined with empirical stress scenarios.

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A

PubMed Central

Ndhlovu, Andrew; Durand, Pierre M.; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. Database URL: http://www.bioinf.wits.ac.za/software/fire/evodb PMID:26140928

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A.

PubMed

Ndhlovu, Andrew; Durand, Pierre M; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. © The Author(s) 2015. Published by Oxford University Press.

Designing, Developing and Implementing a Software Tool for Scenario Based Learning

ERIC Educational Resources Information Center

Norton, Geoff; Taylor, Mathew; Stewart, Terry; Blackburn, Greg; Jinks, Audrey; Razdar, Bahareh; Holmes, Paul; Marastoni, Enrique

2012-01-01

The pedagogical value of problem-based and inquiry-based learning activities has led to increased use of this approach in many courses. While scenarios or case studies were initially presented to learners as text-based material, the development of modern software technology provides the opportunity to deliver scenarios as e-learning modules,…

Lunar base surface mission operations. Lunar Base Systems Study (LBSS) task 4.1

NASA Technical Reports Server (NTRS)

1987-01-01

The purpose was to perform an analysis of the surface operations associated with a human-tended lunar base. Specifically, the study defined surface elements and developed mission manifests for a selected base scenario, determined the nature of surface operations associated with this scenario, generated a preliminary crew extravehicular and intravehicular activity (EVA/IVA) time resource schedule for conducting the missions, and proposed concepts for utilizing remotely operated equipment to perform repetitious or hazardous surface tasks. The operations analysis was performed on a 6 year period of human-tended lunar base operation prior to permanent occupancy. The baseline scenario was derived from a modified version of the civil needs database (CNDB) scenario. This scenario emphasizes achievement of a limited set of science and exploration objectives while emplacing the minimum habitability elements required for a permanent base.

An Interdisciplinary Model for Teaching Evolutionary Ecology.

ERIC Educational Resources Information Center

Coletta, John

1992-01-01

Describes a general systems evolutionary model and demonstrates how a previously established ecological model is a function of its past development based on the evolution of the rock, nutrient, and water cycles. Discusses the applications of the model in environmental education. (MDH)

Does the queen win it all? Queen-worker conflict over male production in the bumblebee, Bombus terrestris

NASA Astrophysics Data System (ADS)

Alaux, Cédric; Savarit, Fabrice; Jaisson, Pierre; Hefetz, Abraham

Social insects provide a useful model for studying the evolutionary balance between cooperation and conflict linked to genetic structure. We investigated the outcome of this conflict in the bumblebee, Bombus terrestris, whose annual colony life cycle is characterized by overt competition over male production. We established artificial colonies composed of a queen and unrelated workers by daily exchange of callow workers between colony pairs of distinct genetic make-up. Using microsatellite analysis, this procedure allowed an exact calculation of the proportion of worker-derived males. The development and social behavior of these artificial colonies were similar to those of normal colonies. Despite a high worker reproduction attempt (63.8% of workers had developed ovaries and 38.4% were egg-layers), we found that on average 95% of the males produced during the competition phase (CPh) were queen-derived. However, in four colonies, queen death resulted in a considerable amount of worker-derived male production. The different putative ultimate causes of this efficient control by the queen are discussed, and we suggest a possible scenario of an evolutionary arms race that may occur between these two female castes.

Mitochondrial Genome Analysis of Wild Rice (Oryza minuta) and Its Comparison with Other Related Species.

PubMed

Asaf, Sajjad; Khan, Abdul Latif; Khan, Abdur Rahim; Waqas, Muhammad; Kang, Sang-Mo; Khan, Muhammad Aaqil; Shahzad, Raheem; Seo, Chang-Woo; Shin, Jae-Ho; Lee, In-Jung

2016-01-01

Oryza minuta (Poaceae family) is a tetraploid wild relative of cultivated rice with a BBCC genome. O. minuta has the potential to resist against various pathogenic diseases such as bacterial blight (BB), white backed planthopper (WBPH) and brown plant hopper (BPH). Here, we sequenced and annotated the complete mitochondrial genome of O. minuta. The mtDNA genome is 515,022 bp, containing 60 protein coding genes, 31 tRNA genes and two rRNA genes. The mitochondrial genome organization and the gene content at the nucleotide level are highly similar (89%) to that of O. rufipogon. Comparison with other related species revealed that most of the genes with known function are conserved among the Poaceae members. Similarly, O. minuta mt genome shared 24 protein-coding genes, 15 tRNA genes and 1 ribosomal RNA gene with other rice species (indica and japonica). The evolutionary relationship and phylogenetic analysis revealed that O. minuta is more closely related to O. rufipogon than to any other related species. Such studies are essential to understand the evolutionary divergence among species and analyze common gene pools to combat risks in the current scenario of a changing environment.