Science.gov

Sample records for al bmc evolutionary

  1. BMC{trademark}: Baseline report

    SciTech Connect

    1997-07-31

    Barrier Membrane Containment (BMC){trademark} is a high-density polyethylene membrane (HOPE) groundwater barrier and pass-through system, with applications ranging from plume control and containment to groundwater manipulation coupled with in-site treatment. BMC{trademark} system can function as a permeable or impermeable reaction wall, a cut-off wall, interceptor trenches, a barrier with collection and/or monitoring system and a pass-through in a funnel and gate configuration. BMC{trademark} can be inspected with a down-hole video camera, producing a permanent VHS format tape, insuring the integrity of the wall and the interlocking joints. The joints are sealed with a ``U``-packing elastomeric gasket to prevent the flow of fluids or gases.

  2. BMC{trademark}: Baseline report; Greenbook (chapter)

    SciTech Connect

    1997-07-31

    Barrier Membrane Containment (BMC){trademark} is a high-density polyethylene membrane (HDPE) groundwater barrier and pass-through system, with applications ranging from plume control and containment to groundwater manipulation coupled with in-site treatment. BMC{trademark} system can function as a permeable or impermeable reaction wall, a cut-off wall, interceptor trenches, a barrier with collection and/or monitoring system, and a pass-through in a funnel and gate configuration. BMC{trademark} can be inspected with a down-hole video camera, producing a permanent VHS format tape, insuring the integrity of the wall and the interlocking joints.

  3. BMC-Watchdog Version 1.0

    2004-04-09

    Some machines come with a Base Motherboard Controller (BMC). This microcontroller manages a number of platform services. One of the services is a watchdog timer. The watchdog timer can be used to initiate actions after a period of time has elapsed. Typically, it is used to shut down or reset a machine when the operating system has crashed. The BMC-WATCHDOG utility sets up and manages the watchdog timer.

  4. BMC{trademark}: Baseline report; Summary

    SciTech Connect

    1997-07-31

    Barrier Membrane Containment (BMC{trademark}) is a high-density polyethylene membrane (HDPE) groundwater barrier and pass-through system, with applications ranging from plume control and containment, to groundwater manipulation, coupled with in-site treatment. BMC{trademark} system can function as a permeable or impermeable reaction wall, a cut-off wall, interceptor trenches, a barrier with collection and/or monitoring system, and a pass-through in a funnel and gate configuration. BMC{trademark} can be inspected with a down-hole video camera, producing a permanent VHS format tape, insuring the integrity of the wall and the interlocking joints. The joints are sealed with a ``U``-packing elastomeric gasket to prevent the flow of fluids or gases.

  5. A new era in sports science: the launch of BMC Sports Science, Medicine and Rehabilitation.

    PubMed

    Moylan, Elizabeth C; Horne, Genevieve

    2013-03-28

    This Editorial celebrates the launch of BMC Sports Science, Medicine and Rehabilitation within the BMC series of journals published by BioMed Central. BMC Sports Science, Medicine and Rehabilitation incorporates the recently closed Sports Medicine, Arthroscopy, Rehabilitation, Therapy & Technology (SMARTT) with an expanded scope and Editorial Board. BMC Sports Science, Medicine and Rehabilitation will fill its own niche in the BMC series alongside other companion journals including BMC Physiology, BMC Musculoskeletal Disorders and BMC Surgery.

  6. BMC Ecology image competition: the winning images

    PubMed Central

    2013-01-01

    BMC Ecology announces the winning entries in its inaugural Ecology Image Competition, open to anyone affiliated with a research institute. The competition, which received more than 200 entries from international researchers at all career levels and a wide variety of scientific disciplines, was looking for striking visual interpretations of ecological processes. In this Editorial, our academic Section Editors and guest judge Dr Yan Wong explain what they found most appealing about their chosen winning entries, and highlight a few of the outstanding images that didn’t quite make it to the top prize. PMID:23517630

  7. Prediction of femoral neck and spine bone mineral content from the BMC of the radius or ulna and the relationship between bone strength and BMC

    NASA Technical Reports Server (NTRS)

    Wilson, C. R.

    1974-01-01

    The bone mineral content (BMC) is extensively used to provide information about the status of an entire skeleton. Changes in BMC are employed to evaluate the effect of various drugs, disease states, weightlessness, exercise, renal dialysis and others on the skeleton. Clinical and functional information is discussed that may be derived from the BMC of a limited region of the skeleton. In particular there is a fairly high degree of correlation between the BMC of the radius or ulna and that of the femoral neck, r about 0.85 and a somewhat lower relationship between the BMC of the radius or ulna and the thoracic vertebrae, r about 0.65. Also the BMC is highly related to the strength of bone at that scan site.

  8. BMC Ecology Image Competition 2015: the winning images.

    PubMed

    Potenski, Catherine J; Porzecanski, Ana Luz; Baguette, Michel; Clobert, Jean; Hughes, David; Settele, Josef

    2015-07-29

    For the third time, BMC Ecology is delighted to announce the winners of our Image Competition. This year featured entries from all over the world and showcased not only the creativity and talent of the participants, but also the exquisite beauty and diversity of our planet. We are pleased to present the winning selections of the editorial board of the journal and guest judge Dr. Ana Luz Porzecanski, as well as some highly commended images that are sure to impress.

  9. BMC Ecology Image Competition 2016: the winning images.

    PubMed

    Simundza, Julia; Palmer, Matthew; Settele, Josef; Jacobus, Luke M; Hughes, David P; Mazzi, Dominique; Blanchet, Simon

    2016-01-01

    The 2016 BMC Ecology Image Competition marked another celebration of the astounding biodiversity, natural beauty, and biological interactions documented by talented ecologists worldwide. For our fourth annual competition, we welcomed guest judge Dr. Matthew Palmer of Columbia University, who chose the winning image from over 140 entries. In this editorial, we highlight the award winning images along with a selection of highly commended honorable mentions. PMID:27503341

  10. BMC Ecology image competition 2014: the winning images.

    PubMed

    Harold, Simon; Henderson, Caspar; Baguette, Michel; Bonsall, Michael B; Hughes, David; Settele, Josef

    2014-08-29

    BMC Ecology showcases the winning entries from its second Ecology Image Competition. More than 300 individual images were submitted from an international array of research scientists, depicting life on every continent on earth. The journal's Editorial Board and guest judge Caspar Henderson outline why their winning selections demonstrated high levels of technical skill and aesthetic sense in depicting the science of ecology, and we also highlight a small selection of highly commended images that we simply couldn't let you miss out on.

  11. BMC Ecology image competition 2014: the winning images

    PubMed Central

    2014-01-01

    BMC Ecology showcases the winning entries from its second Ecology Image Competition. More than 300 individual images were submitted from an international array of research scientists, depicting life on every continent on earth. The journal’s Editorial Board and guest judge Caspar Henderson outline why their winning selections demonstrated high levels of technical skill and aesthetic sense in depicting the science of ecology, and we also highlight a small selection of highly commended images that we simply couldn’t let you miss out on. PMID:25178017

  12. Phylo-evo-devo: combining phylogenetics with evolutionary developmental biology.

    PubMed

    Minelli, Alessandro

    2009-01-01

    As a result of the integration of molecular and morphological approaches for the reconstruction of phylogenies, and of the intertwining of developmental and evolutionary biology, further prospects are open for a fruitful interaction between these two fields in what we may call a phylo-evo-devo approach.Wiegmann et al.'s molecular phylogeny of the holometabolous insect orders, recently published in BMC Biology, offers a good opportunity to revisit the inverted positions of wings and halteres in the Diptera and the Strepsiptera in terms of a putative homeotic mutation in the Hox gene Ultrabithorax. The main finding of this paper is that Strepsiptera are closely related to the Coleoptera rather than Diptera, as recently claimed. Through this exemplary case, the paper demonstrates the value of the reciprocal illumination we can expect from the integration of a good phylogeny and a sound knowledge of the evolvability of developmental mechanisms. PMID:19558647

  13. Application of waste bulk moulded composite (BMC) as a filler for isotactic polypropylene composites.

    PubMed

    Barczewski, Mateusz; Matykiewicz, Danuta; Andrzejewski, Jacek; Skórczewska, Katarzyna

    2016-05-01

    The aim of this study was to produce isotactic polypropylene based composites filled with waste thermosetting bulk moulded composite (BMC). The influence of BMC waste addition (5, 10, 20 wt%) on composites structure and properties was investigated. Moreover, additional studies of chemical treatment of the filler were prepared. Modification of BMC waste by calcium stearate (CaSt) powder allows to assess the possibility of the production of composites with better dispersion of the filler and more uniform properties. The mechanical, processing, and thermal properties, as well as structural investigations were examined by means of static tensile test, Dynstat impact strength test, differential scanning calorimetry (DSC), wide angle X-ray scattering (WAXS), melt flow index (MFI) and scanning electron microscopy (SEM). Developed composites with different amounts of non-reactive filler exhibited satisfactory thermal and mechanical properties. Moreover, application of the low cost modifier (CaSt) allows to obtain composites with better dispersion of the filler and improved processability.

  14. The Practical Application of Body-Mind Centering[R] (BMC) in Dance Pedagogy

    ERIC Educational Resources Information Center

    Eddy, Martha

    2006-01-01

    Based in bodily awareness, somatic education has many points of relationship with dance education. Body-Mind Centering[R] (BMC), with some of its roots in Laban Movement Analysis/Bartenieff Fundamentals (LMA/BF), has a particularly easy link to dance. When studying Body-Mind Centering, the theoretical components are often taught through dance…

  15. Finite element analysis and simulation of rheological properties of bulk molding compound (BMC)

    NASA Astrophysics Data System (ADS)

    Ergin, M. Fatih; Aydin, Ismail

    2013-12-01

    Bulk molding compound (BMC) is one of the important composite materials with various engineering applications. BMC is a thermoset plastic resin blend of various inert fillers, fiber reinforcements, catalysts, stabilizers and pigments that form a viscous, molding compound. Depending on the end-use application, bulk molding compounds are formulated to achieve close dimensional control, flame and scratch resistance, electrical insulation, corrosion and stain resistance, superior mechanical properties, low shrink and color stability. Its excellent flow characteristics, dielectric properties, and flame resistance make this thermoset material well-suited to a wide variety of applications requiring precision in detail and dimensions as well as high performance. When a BMC is used for these purposes, the rheological behavior and properties of the BMC is the main concern. In this paper, finite element analysis of rheological properties of bulk molding composite material was studied. For this purpose, standard samples of composite material were obtained by means of uniaxial hot pressing. 3 point flexural tests were then carried out by using a universal testing machine. Finite element analyses were then performed with defined material properties within a specific constitutive material behavior. Experimental and numerical results were then compared. Good correlation between the numerical simulation and the experimental results was obtained. It was expected with this study that effects of various process parameters and boundary conditions on the rheological behavior of bulk molding compounds could be determined by means of numerical analysis without detailed experimental work.

  16. The effects of calcium-regulating-hormone on BMC in patients with CRF.

    PubMed

    Lü, Y M; Xiao, H W; Liang, K H

    1995-01-01

    By means of single photon absorptiometry, bone material content (BMC) on centerbrachium was detected in 34 patients with chronic renal failure (CRF) and 34 sex-age-matched normal controls, and their serum parathyroid hormone (PTH), calcitonin (CT) were also measured by radioimmunoassay. It was found that (1) the mean BMC was obviously lower in patients with CRF than that in the normal controls; (2) PTH and CT obviously rose in patients with CRF; (3) the decrease of BMC was strongly correlated with that of creatinine clearance (Ccr). Furthermore, the more Ccr decreases, the more PTH in blood increases; no relations have been found between BMC and the serum levels of CT. The authors suggest that the development of osteoporosis with CRF is due to the secondary increase of PTH in blood but the effect of increased serum CT levels was not so obvious. Therefore, lowering blood PTH concentrations by parathyroidectomy or renal transplantation may be beneficial to curing osteoporosis of patients with CRF. PMID:8731961

  17. Application of waste bulk moulded composite (BMC) as a filler for isotactic polypropylene composites.

    PubMed

    Barczewski, Mateusz; Matykiewicz, Danuta; Andrzejewski, Jacek; Skórczewska, Katarzyna

    2016-05-01

    The aim of this study was to produce isotactic polypropylene based composites filled with waste thermosetting bulk moulded composite (BMC). The influence of BMC waste addition (5, 10, 20 wt%) on composites structure and properties was investigated. Moreover, additional studies of chemical treatment of the filler were prepared. Modification of BMC waste by calcium stearate (CaSt) powder allows to assess the possibility of the production of composites with better dispersion of the filler and more uniform properties. The mechanical, processing, and thermal properties, as well as structural investigations were examined by means of static tensile test, Dynstat impact strength test, differential scanning calorimetry (DSC), wide angle X-ray scattering (WAXS), melt flow index (MFI) and scanning electron microscopy (SEM). Developed composites with different amounts of non-reactive filler exhibited satisfactory thermal and mechanical properties. Moreover, application of the low cost modifier (CaSt) allows to obtain composites with better dispersion of the filler and improved processability. PMID:27222742

  18. Application of waste bulk moulded composite (BMC) as a filler for isotactic polypropylene composites

    PubMed Central

    Barczewski, Mateusz; Matykiewicz, Danuta; Andrzejewski, Jacek; Skórczewska, Katarzyna

    2016-01-01

    The aim of this study was to produce isotactic polypropylene based composites filled with waste thermosetting bulk moulded composite (BMC). The influence of BMC waste addition (5, 10, 20 wt%) on composites structure and properties was investigated. Moreover, additional studies of chemical treatment of the filler were prepared. Modification of BMC waste by calcium stearate (CaSt) powder allows to assess the possibility of the production of composites with better dispersion of the filler and more uniform properties. The mechanical, processing, and thermal properties, as well as structural investigations were examined by means of static tensile test, Dynstat impact strength test, differential scanning calorimetry (DSC), wide angle X-ray scattering (WAXS), melt flow index (MFI) and scanning electron microscopy (SEM). Developed composites with different amounts of non-reactive filler exhibited satisfactory thermal and mechanical properties. Moreover, application of the low cost modifier (CaSt) allows to obtain composites with better dispersion of the filler and improved processability. PMID:27222742

  19. Evolutionary considerations on complex emotions and music-induced emotions. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

    NASA Astrophysics Data System (ADS)

    Gingras, Bruno; Marin, Manuela M.

    2015-06-01

    Recent efforts to uncover the neural underpinnings of emotional experiences have provided a foundation for novel neurophysiological theories of emotions, adding to the existing body of psychophysiological, motivational, and evolutionary theories. Besides explicitly modeling human-specific emotions and considering the interactions between emotions and language, Koelsch et al.'s original contribution to this challenging endeavor is to identify four brain areas as distinct "affect systems" which differ in terms of emotional qualia and evolutionary pathways [1]. Here, we comment on some features of this promising Quartet Theory of Emotions, focusing particularly on evolutionary and biological aspects related to the four affect systems and their relation to prevailing emotion theories, as well as on the role of music-induced emotions.

  20. Mathematical universality and direct applicability of evolutionary games. Comment on "Universal scaling for the dilemma strength in evolutionary games", by Z. Wang et al.

    NASA Astrophysics Data System (ADS)

    Arranz, Jordi; Traulsen, Arne

    2015-09-01

    The application of classical game theory to biological sciences allowed researchers to successfully approach problems in theoretical and evolutionary biology in a novel manner [1]. Among those, the evolution of cooperation is the most popular application of evolutionary game theory. The evolution of cooperation is traditionally modeled through games, in particular social dilemmas. These depict situations, in which the interest of an individual is in conflict with the interest of the group, thus games offer an ideal ground to study how cooperation can emerge in the face of natural selection, where individual advantage triumphs over group benefits.

  1. Evolutionary-based Design and Control of Geometry Aims for AMD-manufacturing of Ti-6Al-4V Parts

    NASA Astrophysics Data System (ADS)

    Möller, Mauritz; Baramsky, Nicolaj; Ewald, Ake; Emmelmann, Claus; Schlattmann, Josef

    Additive Metal Deposition (AMD) is an additive manufacturing process building parts based on a nozzle-fed powder by laser assisted solidification. The AMD technology offers unique advantages for the production of near net-shape parts. In contrast to the powder bed-based technologies it provides a high productivity grade. Today AMD lacks reproducible process strategies manufacturing large parts in narrow tolerances. The building height of a single layer and the geometrical shape of a whole part alter progressively with increasing part dimensions - consecutively leading to a higher effort in the manufacturing-process development for such parts. To reduce this effort, in this paper first an iterative identification of optimal process parameters is performed by following an evolutionary algorithm under varied BC. Based on the geometry-related parameter sets, tolerances are defined. The process strategies and tolerances are validated for a prototype application considering the defined quality aims. Finally the results are discussed and summarized in an a-priori process design guideline for AMD Ti6Al4V-parts.

  2. Vitamin D and Calcium Intakes, Physical Activity, and Calcaneus BMC among School-Going 13-Year Old Malaysian Adolescents

    PubMed Central

    Suriawati, A. A.; Abdul Majid, Hazreen; Al-Sadat, Nabilla; Mohamed, Mohd Nahar Azmi; Jalaludin, Muhammad Yazid

    2016-01-01

    Background: Dietary calcium and vitamin D are essential for bone development. Apart from diet, physical activity may potentially improve and sustain bone health. Objective: To investigate the relationship between the dietary intake of calcium and vitamin D, physical activity, and bone mineral content (BMC) in 13-year-old Malaysian adolescents. Design: Cross-sectional. Setting: Selected public secondary schools from the central and northern regions of Peninsular Malaysia. Participants: The subjects were from the Malaysian Health and Adolescents Longitudinal Research Team Cohort study (MyHeARTs). Methods: The data included seven-day diet histories, anthropometric measurements, and the BMC of calcaneal bone using a portable broadband ultrasound bone densitometer. Nutritionist Pro software was used to calculate the dietary calcium and vitamin D intakes from the diet histories, based on the Nutrient Composition of Malaysian Food Database guidance for the dietary calcium intake and the Singapore Energy and Nutrient Composition of Food Database for vitamin D intake. Results: A total of 289 adolescents (65.7% females) were recruited. The average dietary intakes of calcium and vitamin D were 377 ± 12 mg/day and 2.51 ± 0.12 µg/day, respectively, with the majority of subjects failing to meet the Recommended Nutrient Intake (RNI) of Malaysia for dietary calcium and vitamin D. All the subjects had a normal Z-score for the BMC (−2.00 or higher) with a mean of 0.55 ± 0.01. From the statistical analysis of the factors contributing to BMC, it was found that for those subjects with a higher intake of vitamin D, a higher combination of the intake of vitamin D and calcium resulted in significantly higher BMC quartiles. The regression analysis showed that the BMC might have been influenced by the vitamin D intake. Conclusions: A combination of the intake of vitamin D and calcium is positively associated with the BMC. PMID:27783041

  3. An open future for ecological and evolutionary data?

    PubMed Central

    2014-01-01

    As part of BioMed Central’s open science mission, we are pleased to announce that two of our journals have integrated with the open data repository Dryad. Authors submitting their research to either BMC Ecology or BMC Evolutionary Biology will now have the opportunity to deposit their data directly into the Dryad archive and will receive a permanent, citable link to their dataset. Although this does not affect any of our current data deposition policies at these journals, we hope to encourage a more widespread adoption of open data sharing in the fields of ecology and evolutionary biology by facilitating this process for our authors. We also take this opportunity to discuss some of the wider issues that may concern researchers when making their data openly available. Although we offer a number of positive examples from different fields of biology, we also recognise that reticence to data sharing still exists, and that change must be driven from within research communities in order to create future science that is fit for purpose in the digital age. This editorial was published jointly in both BMC Ecology and BMC Evolutionary Biology. PMID:24690275

  4. An open future for ecological and evolutionary data?

    PubMed Central

    2014-01-01

    As part of BioMed Central’s open science mission, we are pleased to announce that two of our journals have integrated with the open data repository Dryad. Authors submitting their research to either BMC Ecology or BMC Evolutionary Biology will now have the opportunity to deposit their data directly into the Dryad archive and will receive a permanent, citable link to their dataset. Although this does not affect any of our current data deposition policies at these journals, we hope to encourage a more widespread adoption of open data sharing in the fields of ecology and evolutionary biology by facilitating this process for our authors. We also take this opportunity to discuss some of the wider issues that may concern researchers when making their data openly available. Although we offer a number of positive examples from different fields of biology, we also recognise that reticence to data sharing still exists, and that change must be driven from within research communities in order to create future science that is fit for purpose in the digital age. This editorial was published jointly in both BMC Ecology and BMC Evolutionary Biology. PMID:24690219

  5. An open future for ecological and evolutionary data?

    PubMed

    Kenall, Amye; Harold, Simon; Foote, Christopher

    2014-04-02

    As part of BioMed Central's open science mission, we are pleased to announce that two of our journals have integrated with the open data repository Dryad. Authors submitting their research to either BMC Ecology or BMC Evolutionary Biology will now have the opportunity to deposit their data directly into the Dryad archive and will receive a permanent, citable link to their dataset. Although this does not affect any of our current data deposition policies at these journals, we hope to encourage a more widespread adoption of open data sharing in the fields of ecology and evolutionary biology by facilitating this process for our authors. We also take this opportunity to discuss some of the wider issues that may concern researchers when making their data openly available. Although we offer a number of positive examples from different fields of biology, we also recognise that reticence to data sharing still exists, and that change must be driven from within research communities in order to create future science that is fit for purpose in the digital age. This editorial was published jointly in both BMC Ecology and BMC Evolutionary Biology.

  6. A fresh insight into the evolutionary status and third body hypothesis of the eclipsing binaries AD Andromedae, AL Camelopardalis, and V338 Herculis

    NASA Astrophysics Data System (ADS)

    Liakos, A.; Niarchos, P.; Budding, E.

    2012-03-01

    Aims: We aim to derive the absolute parameters of the components of AD And, AL Cam, and V338 Her, interpret their orbital period changes and discuss their evolutionary status. Methods: New and complete multi-filter light curves of the eclipsing binaries AD And, AL Cam, and V338 Her were obtained and analysed with modern methods. Using all reliably observed times of minimum light, we examined orbital period irregularities using the least squares method. In addition, we acquired new spectroscopic observations during the secondary eclipses for AL Cam and V338 Her. Results: For AL Cam and V338 Her, we derive reliable spectral types for their primary stars. Statistical checks of orbital period analysis for all systems are very reassuring in the cases of V338 Her and AD And, although less so for AL Cam. The LIght-Time Effect (LITE) results are checked by inclusion of a third light option in the photometric analyses. Light curve solutions provide the means to calculate the absolute parameters of the components of the systems and reliably estimate their present evolutionary status. Conclusions: AL Cam and V338 Her are confirmed as classical Algols of relatively low mass in similar configurations. Unlike AL Cam, however, V338 Her is still transferring matter between its components, raising interest in the determinability of the evolutionary histories of Algols. AD And is found to be a detached system in which both close stars are of age ~109 yr and is probably a "non-classical" young triple, at an interesting stage of its dynamical evolution. The spectra and reduced photometric data are available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/539/A129

  7. Embedded CLIPS for SDI BM/C3 simulation and analysis

    NASA Technical Reports Server (NTRS)

    Gossage, Brett; Nanney, Van

    1990-01-01

    Nichols Research Corporation is developing the BM/C3 Requirements Analysis Tool (BRAT) for the U.S. Army Strategic Defense Command. BRAT uses embedded CLIPS/Ada to model the decision making processes used by the human commander of a defense system. Embedding CLlPS/Ada in BRAT allows the user to explore the role of the human in Command and Control (C2) and the use of expert systems for automated C2. BRAT models assert facts about the current state of the system, the simulated scenario, and threat information into CLIPS/Ada. A user-defined rule set describes the decision criteria for the commander. We have extended CLIPS/Ada with user-defined functions that allow the firing of a rule to invoke a system action such as weapons release or a change in strategy. The use of embedded CLIPS/Ada will provide a powerful modeling tool for our customer at minimal cost.

  8. 76 FR 61741 - Bmc Software, Inc. Including On-Site Leased Workers From COMSYS ITS Including Remote Workers...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-05

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF LABOR Employment and Training Administration Bmc Software, Inc. Including On-Site Leased Workers From COMSYS ITS Including Remote Workers Located Throughout the United States; Houston, TX; Amended Certification Regarding Eligibility To Apply for Worker...

  9. Draft Genome Sequence of Exiguobacterium sp. Strain BMC-KP, an Environmental Isolate from Bryn Mawr, Pennsylvania

    PubMed Central

    Hyson, Peter; Shapiro, Joshua A.

    2015-01-01

    Exiguobacterium sp. strain BMC-KP was isolated as part of a student environmental sampling project at Bryn Mawr College, PA. Sequencing of bacterial DNA assembled a 3.32-Mb draft genome. Analysis suggests the presence of genes for tolerance to cold and toxic metals, broad carbohydrate metabolism, and genes derived from phage. PMID:26450734

  10. The law of cooperation: Comment on "Universal scaling for the dilemma strength in evolutionary games" by Z. Wang et al.

    NASA Astrophysics Data System (ADS)

    Ichinose, Genki

    2015-09-01

    Cooperation is a behavior that benefits others while incurring costs to the actor. Thus, natural selection favors defection (non-cooperation), which unilaterally takes the benefits without paying any costs, rather than cooperation. Despite this logical consequence, reality is the opposite: Cooperation is ubiquitous at any level from genomes to human societies. This contradiction is known as the puzzle of the evolution of cooperation. For a long time, evolutionary game theorists have used the prisoner's dilemma game (PD) and the chicken game (CH) as the standard models to solve this puzzle. For these researchers, it is recognized that a specific mechanism is needed for the evolution of cooperation [1]. Five mechanisms are proposed: kin selection, direct reciprocity, indirect reciprocity, network reciprocity, and group selection. By using the donor and recipient game (D&R), which is one of the particular forms of PD, Nowak theoretically showed that once benefit (b), cost (c), and the other one or two parameters for each mechanism are given, we (evolutionary game theorists) can immediately know whether cooperation evolves [1]. The point here is that he included those unique parameters for each mechanism into PD and then reformulated the payoff matrix. Therefore, we can use this extended PD as the first scaling parameters.

  11. Different evolutionary pathways from B4 to B1 phase in AlN and InN: metadynamics investigations.

    PubMed

    Duan, Yifeng; Qin, Lixia; Liu, Hanyu

    2016-05-25

    Pressure-induced B4-B1 phase transitions of AlN and InN at ambient temperature are systematically investigated using density functional-based metadynamics simulations. A homogeneous deformation path, which is energetically favorable, is through a hexagonal structure for AlN, and through a tetragonal structure for InN. Furthermore, the dynamical stability, instead of the mechanical stability, is crucial to determining the phase-transition paths: the intermediate hexagonal structure can remain stable, whereas the tetragonal structure is always unstable. The B4 phase always shows the direct band gap before the occurrence of structure transition, while the band gap of stable intermediate hexagonal phase is indirect for AlN. Finally, the band gap of the ultimate cubic phase is direct for AlN and indirect for InN, due to the strong p-d repulsion at the R point. PMID:27120439

  12. Scaling behavior can be tricky: Comment on "Universal scaling for the dilemma strength in evolutionary games" by Z. Wang et al.

    NASA Astrophysics Data System (ADS)

    Hui, Pak Ming; Xu, Chen

    2015-09-01

    Evolutionary game theory is a powerful tool for studying the emergence of cooperation among competing individuals [1]. Popularly studied games include the prisoner's dilemma [2], snowdrift game [3] and stag hunt game [4]. They have been extensively studied for the extent of cooperative behavior under different dilemma strengths. Generally, the games can be defined by a 2 × 2 matrix and thus four payoff elements, T, R, P, and S, for the possible payoffs to players when they use pure strategies against each other. Detailed definitions of the four payoffs are given in the review by Wang et al. [5]. For simplicity, it is often the case that fewer parameters are invoked, e.g. a single parameter [3] and more generally two parameters [6]. Generally speaking, reducing the number of parameters has the effect of restricting the system to a certain subspace of the unreduced case. In addition, the spatial structures, such as a well-mixed population or a population forming a complex network, that govern the competing relationship and environment of the agents, and the evolutionary rules, that govern how agents update their strategies, are vital in determining how cooperation evolves, as well documented in the references of [5].

  13. Correspondence: Some general points regarding Ledberg and Wennberg, BMC Medical Research Methodology 2014 April 27;14:58.

    PubMed

    Böhning, Dankmar; van der Heijden, Peter G M

    2015-07-07

    The purpose of this note is to contribute some general points on a recent paper by Ledberg and Wennberg (BMC Med Res Meth 14:58, 2014) which need to be rectified. They advocate the capture-removal estimator. First, we will discuss drawbacks of this estimator in comparison to the Lincoln-Petersen estimator. Second, we show that their evaluation of the Chao estimator is flawed. We conclude that some statements in Ledberg and Wennberg with respect to Chao's estimator and removal estimation need to be taken with great caution.

  14. A tale of two theorems. Comment on "Universal scaling for the dilemma strength in evolutionary games" by Z. Wang et al.

    NASA Astrophysics Data System (ADS)

    Tudge, Simon J.; Brede, Markus

    2015-09-01

    Wang et al. [12] give an extensive review on evolutionary game theory, with a particular focus on the evolution of cooperation; an area that is of central importance to understanding many disparate biological topics [1,2,8,9]. One of the key focuses of the paper is that there are potentially two differing ways of defining two-by-two games so that they can be parameterised with only two variables. This is a highly worthwhile endeavour in that it allows one to systematically investigate and categorise all such games with much greater ease. Perhaps the key result of the paper is that the authors argue that one such parameterisation is far superior to the other, as it retains predictive power even with the additional assumption of a number of reciprocity mechanisms, such as network reciprocity. We wish to draw attention to the fact that these two parameterisations can be understood as the application of two invariance theorems in evolutionary game theory. Furthermore, we complement the authors' extensive simulations with a mathematical argument that might help explain their result in a more transparent way. We will show that one of these invariance theorems generalises to the case of an assorted population and the other does not. It may be argued that many, if not all, of the particular mechanisms of reciprocity crucially rely on the positive assortment of cooperative behaviours [3-7,10]; if one accepts this then our result acts as an argument towards why only one game parameterisation will be sufficient for models of reciprocity.

  15. Short-term lower-body plyometric training improves whole body BMC, bone metabolic markers, and physical fitness in early pubertal male basketball players.

    PubMed

    Zribi, Anis; Zouch, Mohamed; Chaari, Hamada; Bouajina, Elyes; Ben Nasr, Hela; Zaouali, Monia; Tabka, Zouhair

    2014-02-01

    The effects of a 9-week lower-body plyometric training program on bone mass, bone markers and physical fitness was examined in 51 early pubertal male basketball players divided randomly into a plyometric group (PG: 25 participants) and a control group (CG: 26 participants). Areal bone mineral density (aBMD), bone mineral content (BMC), and bone area (BA) in the whole body, L2-L4 vertebrae, and in total hip, serum levels of osteocalcin (Oc) and C-terminal telopeptide fragment of Type I collagen (CTx), jump, sprint and power abilities were assessed at baseline and 9 weeks. Group comparisons were done by independent student's t-test between means and analyses of (ANOVA) and covariance (ANCOVA), adjusting for baseline values. PG experienced a significant increase in Oc (p < .01) and all physical fitness except for the 5-jump test. However, there was no improvement in aBMD, BMC and BA in any measured site, except in whole body BMC of the PG. A positive correlation was observed between percentage increase (Δ%) of physical fitness and those of (Oc) for the PG. In summary, biweekly sessions of lower body plyometric training program were successful for improving whole body BMC, bone formation marker (Oc) and physical fitness in early pubertal male basketball players.

  16. Developmental dynamics and contemporary evolutionary psychology: status quo or irreconcilable views? Reply to Bjorklund (2003), Krebs (2003), Buss and Reeve (2003), Crawford (2003), and Tooby et Al. (2003).

    PubMed

    Lickliter, Robert; Honeycutt, Hunter

    2003-11-01

    The authors address commentaries by D. F. Bjorklund (2003); D. M. Buss and H. K. Reeve (2003); C. B. Crawford (2003); D. L. Krebs (2003); and J. Tooby, L. Cosmides, and H. C. Barrett (2003) on their analysis of the underlying assumptions of contemporary evolutionary psychology (R. Lickliter & H. Honeycutt, 2003). The authors argue that evolutionary psychology currently offers no coherent framework for how to integrate genetic, environmental, and experiential factors into a theory of behavioral or cognitive phenotypes. The authors propose that this absence is due to a lack of developmental analysis in the major works of evolutionary psychology, resulting in an almost exclusive focus on adaptationist accounts of evolution by natural selection rather than a more broad-based focus on the process and products of evolution by epigenetic developmental dynamics.

  17. Changes in Bone Biomarkers, BMC, and Insulin Resistance Following a 10-Week Whole Body Vibration Exercise Program in Overweight Latino Boys

    PubMed Central

    Erceg, David N.; Anderson, Lindsey J.; Nickles, Chun M.; Lane, Christianne J.; Weigensberg, Marc J.; Schroeder, E. Todd

    2015-01-01

    Purpose: With the childhood obesity epidemic, efficient methods of exercise are sought to improve health. We tested whether whole body vibration (WBV) exercise can positively affect bone metabolism and improve insulin/glucose dynamics in sedentary overweight Latino boys. Methods: Twenty Latino boys 8-10 years of age were randomly assigned to either a control (CON) or 3 days/wk WBV exercise (VIB) for 10-wk. Results: Significant increases in BMC (4.5±3.2%; p=0.01) and BMD (1.3±1.3%; p<0.01) were observed for the VIB group when compared to baseline values. For the CON group BMC significantly increased (2.0±2.2%; p=0.02), with no change in BMD (0.8±1.3%; p=0.11). There were no significant between group changes in BMC or BMD. No significant change was observed for osteocalcin and (collagen type I C-telopeptide) CTx for the VIB group. However, osteocalcin showed a decreasing trend (p=0.09) and CTx significantly increased (p<0.03) for the CON group. This increase in CTx was significantly different between groups (p<0.02) and the effect size of between-group difference in change was large (-1.09). There were no significant correlations between osteocalcin and measures of fat mass or insulin resistance for collapsed data. Conclusion: Although bone metabolism was altered by WBV training, no associations were apparent between osteocalcin and insulin resistance. These findings suggest WBV exercise may positively increase BMC and BMD by decreasing bone resorption in overweight Latino boys. PMID:26078710

  18. Evolutionary thinking

    PubMed Central

    Hunt, Tam

    2014-01-01

    Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution—both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place—has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps’ book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging “integral” or “evolutionary” cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps. PMID:26478766

  19. Evolutionary awareness.

    PubMed

    Gorelik, Gregory; Shackelford, Todd K

    2014-08-27

    In this article, we advance the concept of "evolutionary awareness," a metacognitive framework that examines human thought and emotion from a naturalistic, evolutionary perspective. We begin by discussing the evolution and current functioning of the moral foundations on which our framework rests. Next, we discuss the possible applications of such an evolutionarily-informed ethical framework to several domains of human behavior, namely: sexual maturation, mate attraction, intrasexual competition, culture, and the separation between various academic disciplines. Finally, we discuss ways in which an evolutionary awareness can inform our cross-generational activities-which we refer to as "intergenerational extended phenotypes"-by helping us to construct a better future for ourselves, for other sentient beings, and for our environment.

  20. Evolutionary medicine.

    PubMed

    Swynghedauw, B

    2004-04-01

    Nothing in biology makes sense except in the light of evolution. Evolutionary, or darwinian, medicine takes the view that contemporary diseases result from incompatibility between the conditions under which the evolutionary pressure had modified our genetic endowment and the lifestyle and dietary habits in which we are currently living, including the enhanced lifespan, the changes in dietary habits and the lack of physical activity. An evolutionary trait express a genetic polymorphism which finally improve fitness, it needs million years to become functional. A limited genetic diversity is a necessary prerequisite for evolutionary medicine. Nevertheless, search for a genetic endowment would become nearly impossible if the human races were genetically different. From a genetic point of view, homo sapiens, is homogeneous, and the so-called human races have only a socio-economic definition. Historically, Heart Failure, HF, had an infectious origin and resulted from mechanical overload which triggered mechanoconversion by using phylogenically ancient pleiotropic pathways. Adaptation was mainly caused by negative inotropism. Recently, HF was caused by a complex remodelling caused by the trophic effects of mechanics, ischemia, senescence, diabetes and, neurohormones. The generally admitted hypothesis is that cancers were largely caused by a combination of modern reproductive and dietary lifestyles mismatched with genotypic traits, plus the longer time available for a confrontation. Such a concept is illustrated for skin and breast cancers, and also for the link between cancer risk and dietary habits.

  1. A trans-ethnic genome-wide association study identifies gender-specific loci influencing pediatric aBMD and BMC at the distal radius

    PubMed Central

    Chesi, Alessandra; Mitchell, Jonathan A.; Kalkwarf, Heidi J.; Bradfield, Jonathan P.; Lappe, Joan M.; McCormack, Shana E.; Gilsanz, Vicente; Oberfield, Sharon E.; Hakonarson, Hakon; Shepherd, John A.; Kelly, Andrea; Zemel, Babette S.; Grant, Struan F.A.

    2015-01-01

    Childhood fractures are common, with the forearm being the most common site. Genome-wide association studies (GWAS) have identified more than 60 loci associated with bone mineral density (BMD) in adults but less is known about genetic influences specific to bone in childhood. To identify novel genetic factors that influence pediatric bone strength at a common site for childhood fractures, we performed a sex-stratified trans-ethnic genome-wide association study of areal BMD (aBMD) and bone mineral content (BMC) Z-scores measured by dual energy X-ray absorptiometry at the one-third distal radius, in a cohort of 1399 children without clinical abnormalities in bone health. We tested signals with P < 5 × 10−6 for replication in an independent, same-age cohort of 486 Caucasian children. Two loci yielded a genome-wide significant combined P-value: rs7797976 within CPED1 in females [P = 2.4 × 10−11, β =− 0.30 standard deviations (SD) per T allele; aBMD-Z] and rs7035284 at 9p21.3 in males (P = 1.2 × 10−8, β = 0.28 SD per G allele; BMC-Z). Signals at the CPED1-WNT16-FAM3C locus have been previously associated with BMD at other skeletal sites in adults and children. Our result at the distal radius underscores the importance of this locus at multiple skeletal sites. The 9p21.3 locus is within a gene desert, with the nearest gene flanking each side being MIR31HG and MTAP, neither of which has been implicated in BMD or BMC previously. These findings suggest that genetic determinants of childhood bone accretion at the radius, a skeletal site that is primarily cortical bone, exist and also differ by sex. PMID:26041818

  2. Oversimplifying Evolutionary Psychology Leads to Explanatory Gaps

    ERIC Educational Resources Information Center

    Tate, Chuck; Ledbetter, Jay N.

    2010-01-01

    Comments on Evolutionary psychology: Controversies, questions, prospects, and limitations by Confer et al. They argued that SST cannot explain the existence of either homosexuality or suicide within the human species. We contend that a sufficiently nuanced evolutionary position has no difficulties explaining either phenomenon. Also in this…

  3. A manual collection of Syt, Esyt, Rph3a, Rph3al, Doc2, and Dblc2 genes from 46 metazoan genomes - an open access resource for neuroscience and evolutionary biology

    PubMed Central

    2010-01-01

    Background Synaptotagmin proteins were first identified in nervous tissue, residing in synaptic vesicles. Synaptotagmins were subsequently found to form a large family, some members of which play important roles in calcium triggered exocytic events. These members have been investigated intensively, but other family members are not well understood, making it difficult to grasp the meaning of family membership in functional terms. Further difficulty arises as families are defined quite legitimately in different ways: by common descent or by common possession of distinguishing features. One definition does not necessarily imply the other. The evolutionary range of genome sequences now available, can shed more light on synaptotagmin gene phylogeny and clarify family relationships. The aim of compiling this open access collection of synaptotagmin and synaptotagmin-like sequences, is that its use may lead to greater understanding of the biological function of these proteins in an evolutionary context. Results 46 metazoan genomes were examined and their complement of Syt, Esyt, Rph3a, Rph3al, Doc2 and Dblc2 genes identified. All of the sequences were compared, named, then examined in detail. Esyt genes were formerly named Fam62. The species in this collection are Trichoplax, Nematostella, Capitella, Helobdella, Lottia, Ciona, Strongylocentrotus, Branchiostoma, Ixodes, Daphnia, Acyrthosiphon, Tribolium, Nasonia, Apis, Anopheles, Drosophila, Caenorhabditis, Takifugu, Tetraodon, Gasterosteus, Oryzias, Danio, Xenopus, Anolis, Gallus, Taeniopygia,Ornithorhynchus, Monodelphis, Mus and Homo. All of the data described in this paper is available as additional files. Conclusions Only a subset of synaptotagmin proteins appear able to function as calcium triggers. Syt1, Syt7 and Syt9 are ancient conserved synaptotagmins of this type. Some animals carry extensive repertoires of synaptotagmin genes. Other animals of no less complexity, carry only a small repertoire. Current

  4. Human evolutionary history and contemporary evolutionary theory provide insight when assessing cultural group selection.

    PubMed

    Fuentes, Agustin; Kissel, Marc

    2016-01-01

    Richerson et al. provide a much needed roadmap for assessing cultural group selection (CGS) theory and for applying it to understanding variation between contemporary human groups. However, the current proposal lacks connection to relevant evidence from the human evolutionary record and requires a better integration with contemporary evolutionary theory. The article also misapplies the F st statistic. PMID:27562510

  5. [Evolution of evolutionary physiology].

    PubMed

    Natochin, Iu V

    2008-09-01

    In 19th century and at the beginning 20th century, reports appeared in the field of comparative and ontogenetic physiology and the value of these methods for understanding of evolution of functions. The term "evolutionary physiology" was suggested by A. N. Severtsov in 1914. In the beginning of 30s, in the USSR, laboratories for researches in problems of evolutionary physiology were created, the results of these researches having been published. In 1956 in Leningrad, the Institute of Evolutionary Physiology was founded by L. A. Orbeli. He formulates the goals and methods of evolutionary physiology. In the following half a century, the evolutionary physiology was actively developed. The evolutionary physiology solves problems of evolution of function of functions evolution, often involving methods of adjacent sciences, including biochemistry, morphology, molecular biology.

  6. Trade-offs, individual differences, and misunderstandings about evolutionary psychology.

    PubMed

    Perilloux, Carin; Lewis, David M G; Goetz, Cari D; Fleischman, Diana S; Easton, Judith A; Confer, Jaime C; Buss, David M

    2010-12-01

    Replies to comments on Evolutionary psychology: Controversies, questions, prospects, and limitations (see record 2010-02208-001) by Confer et al. The purpose of which was to clarify the logic of evolutionary psychology and clear up some of the more common misunderstandings about it. In this response, we address the key points raised by the commentators.

  7. When theory trumps ideology: Lessons from evolutionary psychology.

    PubMed

    Tybur, Joshua M; Navarrete, Carlos David

    2015-01-01

    Evolutionary psychologists are personally liberal, just as social psychologists are. Yet their research has rarely been perceived as liberally biased--if anything, it has been erroneously perceived as motivated by conservative political agendas. Taking a closer look at evolutionary psychologists might offer the broader social psychology community guidance in neutralizing some of the biases Duarte et al. discuss.

  8. Trade-Offs, Individual Differences, and Misunderstandings about Evolutionary Psychology

    ERIC Educational Resources Information Center

    Perilloux, Carin; Lewis, David M. G.; Goetz, Cari D.; Fleischman, Diana S.; Easton, Judith A.; Confer, Jaime C.; Buss, David M.

    2010-01-01

    Replies to comments on Evolutionary psychology: Controversies, questions, prospects, and limitations by Confer et al. The purpose of which was to clarify the logic of evolutionary psychology and clear up some of the more common misunderstandings about it. In this response, we address the key points raised by the commentators.

  9. On evolutionary causes and evolutionary processes.

    PubMed

    Laland, Kevin N

    2015-08-01

    In this essay I consider how biologists understand 'causation' and 'evolutionary process', drawing attention to some idiosyncrasies in the use of these terms. I suggest that research within the evolutionary sciences has been channeled in certain directions and not others by scientific conventions, many of which have now become counterproductive. These include the views (i) that evolutionary processes are restricted to those phenomena that directly change gene frequencies, (ii) that understanding the causes of both ecological change and ontogeny is beyond the remit of evolutionary biology, and (iii) that biological causation can be understood by a dichotomous proximate-ultimate distinction, with developmental processes perceived as solely relevant to proximate causation. I argue that the notion of evolutionary process needs to be broadened to accommodate phenomena such as developmental bias and niche construction that bias the course of evolution, but do not directly change gene frequencies, and that causation in biological systems is fundamentally reciprocal in nature. This article is part of a Special Issue entitled: In Honor of Jerry Hogan.

  10. 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.

  11. Accuracy of DXA scanning of the thoracic spine: cadaveric studies comparing BMC, areal BMD and geometric estimates of volumetric BMD against ash weight and CT measures of bone volume.

    PubMed

    Sran, Meena M; Khan, Karim M; Keiver, Kathy; Chew, Jason B; McKay, Heather A; Oxland, Thomas R

    2005-12-01

    Biomechanical studies of the thoracic spine often scan cadaveric segments by dual energy X-ray absorptiometry (DXA) to obtain measures of bone mass. Only one study has reported the accuracy of lateral scans of thoracic vertebral bodies. The accuracy of DXA scans of thoracic spine segments and of anterior-posterior (AP) thoracic scans has not been investigated. We have examined the accuracy of AP and lateral thoracic DXA scans by comparison with ash weight, the gold-standard for measuring bone mineral content (BMC). We have also compared three methods of estimating volumetric bone mineral density (vBMD) with a novel standard-ash weight (g)/bone volume (cm3) as measured by computed tomography (CT). Twelve T5-T8 spine segments were scanned with DXA (AP and lateral) and CT. The T6 vertebrae were excised, the posterior elements removed and then the vertebral bodies were ashed in a muffle furnace. We proposed a new method of estimating vBMD and compared it with two previously published methods. BMC values from lateral DXA scans displayed the strongest correlation with ash weight (r=0.99) and were on average 12.8% higher (p<0.001). As expected, BMC (AP or lateral) was more strongly correlated with ash weight than areal bone mineral density (aBMD; AP: r=0.54, or lateral: r=0.71) or estimated vBMD. Estimates of vBMD with either of the three methods were strongly and similarly correlated with volumetric BMD calculated by dividing ash weight by CT-derived volume. These data suggest that readily available DXA scanning is an appropriate surrogate measure for thoracic spine bone mineral and that the lateral scan might be the scan method of choice. PMID:15616862

  12. Polymorphic Evolutionary Games.

    PubMed

    Fishman, Michael A

    2016-06-01

    In this paper, I present an analytical framework for polymorphic evolutionary games suitable for explicitly modeling evolutionary processes in diploid populations with sexual reproduction. The principal aspect of the proposed approach is adding diploid genetics cum sexual recombination to a traditional evolutionary game, and switching from phenotypes to haplotypes as the new game׳s pure strategies. Here, the relevant pure strategy׳s payoffs derived by summing the payoffs of all the phenotypes capable of producing gametes containing that particular haplotype weighted by the pertinent probabilities. The resulting game is structurally identical to the familiar Evolutionary Games with non-linear pure strategy payoffs (Hofbauer and Sigmund, 1998. Cambridge University Press), and can be analyzed in terms of an established analytical framework for such games. And these results can be translated into the terms of genotypic, and whence, phenotypic evolutionary stability pertinent to the original game.

  13. A single amino acid substitution within the transmembrane domain of the human immunodeficiency virus type 1 Vpu protein renders simian-human immunodeficiency virus (SHIV{sub KU-1bMC33}) susceptible to rimantadine

    SciTech Connect

    Hout, David R.; Gomez, Lisa M.; Pacyniak, Erik; Miller, Jean-Marie; Hill, M. Sarah; Stephens, Edward B. . E-mail: estephen@kumc.edu

    2006-05-10

    Previous studies from our laboratory have shown that the transmembrane domain (TM) of the Vpu protein of human immunodeficiency virus type 1 (HIV-1) contributes to the pathogenesis of SHIV{sub KU-1bMC33} in macaques and that the TM domain of Vpu could be replaced with the M2 protein viroporin from influenza A virus. Recently, we showed that the replacement of the TM domain of Vpu with that of the M2 protein of influenza A virus resulted in a virus (SHIV{sub M2}) that was sensitive to rimantadine [Hout, D.R., Gomez, M.L., Pacyniak, E., Gomez, L.M., Inbody, S.H., Mulcahy, E.R., Culley, N., Pinson, D.M., Powers, M.F., Wong, S.W., Stephens, E.B., 2006. Substitution of the transmembrane domain of Vpu in simian human immunodeficiency virus (SHIV{sub KU-1bMC33}) with that of M2 of influenza A results in a virus that is sensitive to inhibitors of the M2 ion channel and is pathogenic for pig-tailed macaques. Virology 344, 541-558]. Based on previous studies of the M2 protein which have shown that the His-X-X-X-Trp motif within the M2 is essential to the function of the M2 proton channel, we have constructed a novel SHIV in which the alanine at position 19 of the TM domain was replaced with a histidine residue resulting in the motif His-Ile-Leu-Val-Trp. The SHIV{sub VpuA19H} replicated with similar kinetics as the parental SHIV{sub KU-1bMC33} and pulse-chase analysis revealed that the processing of viral proteins was similar to SHIV{sub KU-1bMC33}. This SHIV{sub VpuA19H} virus was found to be more sensitive to the M2 ion channel blocker rimantadine than SHIV{sub M2}. Electron microscopic examination of SHIV{sub VpuA19H}-infected cells treated with rimantadine revealed an accumulation of viral particles at the cell surface and within intracellular vesicles, which was similar to that previously observed to SHIV{sub M2}-infected cells treated with rimantadine. These data indicate that the Vpu protein of HIV-1 can be converted into a rimantadine-sensitive ion channel with the

  14. Ancient hyaenas highlight the old problem of estimating evolutionary rates.

    PubMed

    Shapiro, Beth; Ho, Simon Y W

    2014-02-01

    Phylogenetic analyses of ancient DNA data can provide a timeline for evolutionary change even in the absence of fossils. The power to infer the evolutionary rate is, however, highly dependent on the number and age of samples, the information content of the sequence data and the demographic history of the sampled population. In this issue of Molecular Ecology, Sheng et al. (2014) analysed mitochondrial DNA sequences isolated from a combination of ancient and present-day hyaenas, including three Pleistocene samples from China. Using an evolutionary rate inferred from the ages of the ancient sequences, they recalibrated the timing of hyaena diversification and suggest a much more recent evolutionary history than was believed previously. Their results highlight the importance of accurately estimating the evolutionary rate when inferring timescales of geographical and evolutionary diversification. PMID:24450980

  15. Ancient hyaenas highlight the old problem of estimating evolutionary rates.

    PubMed

    Shapiro, Beth; Ho, Simon Y W

    2014-02-01

    Phylogenetic analyses of ancient DNA data can provide a timeline for evolutionary change even in the absence of fossils. The power to infer the evolutionary rate is, however, highly dependent on the number and age of samples, the information content of the sequence data and the demographic history of the sampled population. In this issue of Molecular Ecology, Sheng et al. (2014) analysed mitochondrial DNA sequences isolated from a combination of ancient and present-day hyaenas, including three Pleistocene samples from China. Using an evolutionary rate inferred from the ages of the ancient sequences, they recalibrated the timing of hyaena diversification and suggest a much more recent evolutionary history than was believed previously. Their results highlight the importance of accurately estimating the evolutionary rate when inferring timescales of geographical and evolutionary diversification.

  16. Evolutionary tree reconstruction

    NASA Technical Reports Server (NTRS)

    Cheeseman, Peter; Kanefsky, Bob

    1990-01-01

    It is described how Minimum Description Length (MDL) can be applied to the problem of DNA and protein evolutionary tree reconstruction. If there is a set of mutations that transform a common ancestor into a set of the known sequences, and this description is shorter than the information to encode the known sequences directly, then strong evidence for an evolutionary relationship has been found. A heuristic algorithm is described that searches for the simplest tree (smallest MDL) that finds close to optimal trees on the test data. Various ways of extending the MDL theory to more complex evolutionary relationships are discussed.

  17. Evolutionary biology of language.

    PubMed Central

    Nowak, M A

    2000-01-01

    Language is the most important evolutionary invention of the last few million years. It was an adaptation that helped our species to exchange information, make plans, express new ideas and totally change the appearance of the planet. How human language evolved from animal communication is one of the most challenging questions for evolutionary biology The aim of this paper is to outline the major principles that guided language evolution in terms of mathematical models of evolutionary dynamics and game theory. I will discuss how natural selection can lead to the emergence of arbitrary signs, the formation of words and syntactic communication. PMID:11127907

  18. Evolutionary Mechanisms for Loneliness

    PubMed Central

    Cacioppo, John T.; Cacioppo, Stephanie; Boomsma, Dorret I.

    2013-01-01

    Robert Weiss (1973) conceptualized loneliness as perceived social isolation, which he described as a gnawing, chronic disease without redeeming features. On the scale of everyday life, it is understandable how something as personally aversive as loneliness could be regarded as a blight on human existence. However, evolutionary time and evolutionary forces operate at such a different scale of organization than we experience in everyday life that personal experience is not sufficient to understand the role of loneliness in human existence. Research over the past decade suggests a very different view of loneliness than suggested by personal experience, one in which loneliness serves a variety of adaptive functions in specific habitats. We review evidence on the heritability of loneliness and outline an evolutionary theory of loneliness, with an emphasis on its potential adaptive value in an evolutionary timescale. PMID:24067110

  19. Evolutionary behavioral genetics

    PubMed Central

    Zietsch, Brendan P.; de Candia, Teresa R; Keller, Matthew C.

    2014-01-01

    We describe the scientific enterprise at the intersection of evolutionary psychology and behavioral genetics—a field that could be termed Evolutionary Behavioral Genetics—and how modern genetic data is revolutionizing our ability to test questions in this field. We first explain how genetically informative data and designs can be used to investigate questions about the evolution of human behavior, and describe some of the findings arising from these approaches. Second, we explain how evolutionary theory can be applied to the investigation of behavioral genetic variation. We give examples of how new data and methods provide insight into the genetic architecture of behavioral variation and what this tells us about the evolutionary processes that acted on the underlying causal genetic variants. PMID:25587556

  20. Rethinking evolutionary individuality

    PubMed Central

    Ereshefsky, Marc; Pedroso, Makmiller

    2015-01-01

    This paper considers whether multispecies biofilms are evolutionary individuals. Numerous multispecies biofilms have characteristics associated with individuality, such as internal integrity, division of labor, coordination among parts, and heritable adaptive traits. However, such multispecies biofilms often fail standard reproductive criteria for individuality: they lack reproductive bottlenecks, are comprised of multiple species, do not form unified reproductive lineages, and fail to have a significant division of reproductive labor among their parts. If such biofilms are good candidates for evolutionary individuals, then evolutionary individuality is achieved through other means than frequently cited reproductive processes. The case of multispecies biofilms suggests that standard reproductive requirements placed on individuality should be reconsidered. More generally, the case of multispecies biofilms indicates that accounts of individuality that focus on single-species eukaryotes are too restrictive and that a pluralistic and open-ended account of evolutionary individuality is needed. PMID:26039982

  1. The major evolutionary transitions.

    PubMed

    Szathmáry, E; Smith, J M

    1995-03-16

    There is no theoretical reason to expect evolutionary lineages to increase in complexity with time, and no empirical evidence that they do so. Nevertheless, eukaryotic cells are more complex than prokaryotic ones, animals and plants are more complex than protists, and so on. This increase in complexity may have been achieved as a result of a series of major evolutionary transitions. These involved changes in the way information is stored and transmitted.

  2. Proteomics in evolutionary ecology.

    PubMed

    Baer, B; Millar, A H

    2016-03-01

    Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein

  3. Applying evolutionary anthropology.

    PubMed

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

    Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution.

  4. Paleoanthropology and evolutionary theory.

    PubMed

    Tattersall, Ian

    2012-01-01

    Paleoanthropologists of the first half of the twentieth century were little concerned either with evolutionary theory or with the technicalities and broader implications of zoological nomenclature. In consequence, the paleoanthropological literature of the period consisted largely of a series of descriptions accompanied by authoritative pronouncements, together with a huge excess of hominid genera and species. Given the intellectual flimsiness of the resulting paleoanthropological framework, it is hardly surprising that in 1950 the ornithologist Ernst Mayr met little resistance when he urged the new postwar generation of paleoanthropologists to accept not only the elegant reductionism of the Evolutionary Synthesis but a vast oversimplification of hominid phylogenetic history and nomenclature. Indeed, the impact of Mayr's onslaught was so great that even when developments in evolutionary biology during the last quarter of the century brought other paleontologists to the realization that much more has been involved in evolutionary histories than the simple action of natural selection within gradually transforming lineages, paleoanthropologists proved highly reluctant to follow. Even today, paleoanthropologists are struggling to reconcile an intuitive realization that the burgeoning hominid fossil record harbors a substantial diversity of species (bringing hominid evolutionary patterns into line with that of other successful mammalian families), with the desire to cram a huge variety of morphologies into an unrealistically minimalist systematic framework. As long as this theoretical ambivalence persists, our perception of events in hominid phylogeny will continue to be distorted.

  5. Applying Evolutionary Anthropology

    PubMed Central

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

    Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. PMID:25684561

  6. Evolutionary perspectives on emotions and their link to intentions, dispositions and behavior. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

    NASA Astrophysics Data System (ADS)

    Wildgruber, Dirk; Kreifelts, Benjamin

    2015-06-01

    Koelsch and coworkers present a sophisticated neuroanatomical model of emotions comprising four affect-systems and four output-systems, each bound to a specific brain area [1]. Moreover, they suggest the emergence of distinct components of subjective feelings or "emotion percepts" due to integration of the activation across these subsystems. Incorporating numerous neurobiological, psychological and philosophical findings on human emotions, the model reflects an extensive interdisciplinary approach. Considering an evolutionary perspective, however, we would like to address some issues concerning emotions and their link to intentions, dispositions and behavior that are not fully covered by the Quartet Model. Charles Darwin pointed out that individuals that are better adapted to their environment have increased chances of survival and reproduction. Therefore, natural selection leads to a rising prevalence of properties offering a survival benefit across generations [2]. To better understand the biological functions of emotions we propose to ask the question: How do emotions provide a benefit for survival and reproduction?

  7. Is the universal scaling for the dilemma strength still available in populations with heterogeneous connectivity or activities?. Comment on "Universal scaling for the dilemma strength in evolutionary games" by Z. Wang et al.

    NASA Astrophysics Data System (ADS)

    Xia, Cheng-Yi; Wang, Lin

    2015-09-01

    The emergence and maintenance of cooperative behavior are widely observed in various realistic systems, such as cellular organisms, vertebrates, and human society [1]. Understanding the ubiquity of cooperation is a challenging problem, attracting great interest from diverse communities. The development of evolutionary game theory contributes to valuable tools for studying the origin of cooperative behavior and solving related social dilemmas [2]. Five key reciprocal mechanisms to promote the cooperation, including direct reciprocity, indirect reciprocity, network reciprocity, group selection, and kin selection, have been identified [3], inspiring much effort in exploring the effects of game dynamics and population's connectivity structure on the patterns of cooperation. Most of current works generate conclusions by focusing on specific game models or mechanisms, which imply the probable existence of some effective and universal laws.

  8. Ecological and evolutionary traps

    USGS Publications Warehouse

    Schlaepfer, Martin A.; Runge, M.C.; Sherman, P.W.

    2002-01-01

    Organisms often rely on environmental cues to make behavioral and life-history decisions. However, in environments that have been altered suddenly by humans, formerly reliable cues might no longer be associated with adaptive outcomes. In such cases, organisms can become 'trapped' by their evolutionary responses to the cues and experience reduced survival or reproduction. Ecological traps occur when organisms make poor habitat choices based on cues that correlated formerly with habitat quality. Ecological traps are part of a broader phenomenon, evolutionary traps, involving a dissociation between cues that organisms use to make any behavioral or life-history decision and outcomes normally associated with that decision. A trap can lead to extinction if a population falls below a critical size threshold before adaptation to the novel environment occurs. Conservation and management protocols must be designed in light of, rather than in spite of, the behavioral mechanisms and evolutionary history of populations and species to avoid 'trapping' them.

  9. Evolutionary Debunking Arguments

    PubMed Central

    Kahane, Guy

    2011-01-01

    Evolutionary debunking arguments (EDAs) are arguments that appeal to the evolutionary origins of evaluative beliefs to undermine their justification. This paper aims to clarify the premises and presuppositions of EDAs—a form of argument that is increasingly put to use in normative ethics. I argue that such arguments face serious obstacles. It is often overlooked, for example, that they presuppose the truth of metaethical objectivism. More importantly, even if objectivism is assumed, the use of EDAs in normative ethics is incompatible with a parallel and more sweeping global evolutionary debunking argument that has been discussed in recent metaethics. After examining several ways of responding to this global debunking argument, I end by arguing that even if we could resist it, this would still not rehabilitate the current targeted use of EDAs in normative ethics given that, if EDAs work at all, they will in any case lead to a truly radical revision of our evaluative outlook. PMID:21949447

  10. Human nutrition: evolutionary perspectives.

    PubMed

    Barnicot, N A

    2005-01-01

    In recent decades, much new evidence relating to the ape forerunners of modern humans has come to hand and diet appears to be an important factor. At some stage, there must have been a transition from a largely vegetarian ape diet to a modern human hunting economy providing significant amounts of meat. On an even longer evolutionary time scale the change was more complex. The mechanisms of evolutionary change are now better understood than they were in Darwin's time, thanks largely to great advances in genetics, both experimental and theoretical. It is virtually certain that diet, as a major component of the human environment, must have exerted evolutionary effects, but researchers still have little good evidence. PMID:17393680

  11. Investigating human evolutionary history

    PubMed Central

    WOOD, BERNARD

    2000-01-01

    We rely on fossils for the interpretation of more than 95% of our evolutionary history. Fieldwork resulting in the recovery of fresh fossil evidence is an important component of reconstructing human evolutionary history, but advances can also be made by extracting additional evidence for the existing fossil record, and by improving the methods used to interpret the fossil evidence. This review shows how information from imaging and dental microstructure has contributed to improving our understanding of the hominin fossil record. It also surveys recent advances in the use of the fossil record for phylogenetic inference. PMID:10999269

  12. The fastest evolutionary trajectory

    PubMed Central

    Traulsen, Arne; Iwasa, Yoh; Nowak, Martin A.

    2008-01-01

    Given two mutants, A and B, separated by n mutational steps, what is the evolutionary trajectory which allows a homogeneous population of A to reach B in the shortest time? We show that the optimum evolutionary trajectory (fitness landscape) has the property that the relative fitness increase between any two consecutive steps is constant. Hence, the optimum fitness landscape between A and B is given by an exponential function. Our result is precise for small mutation rates and excluding back mutations. We discuss deviations for large mutation rates and including back mutations. For very large mutation rates, the optimum fitness landscape is flat and has a single peak at type B. PMID:17900629

  13. Hybridization facilitates evolutionary rescue

    PubMed Central

    Stelkens, Rike B; Brockhurst, Michael A; Hurst, Gregory D D; Greig, Duncan

    2014-01-01

    The resilience of populations to rapid environmental degradation is a major concern for biodiversity conservation. When environments deteriorate to lethal levels, species must evolve to adapt to the new conditions to avoid extinction. Here, we test the hypothesis that evolutionary rescue may be enabled by hybridization, because hybridization increases genetic variability. Using experimental evolution, we show that interspecific hybrid populations of Saccharomyces yeast adapt to grow in more highly degraded environments than intraspecific and parental crosses, resulting in survival rates far exceeding those of their ancestors. We conclude that hybridization can increase evolutionary responsiveness and that taxa able to exchange genes with distant relatives may better survive rapid environmental change. PMID:25558281

  14. The curiously long absence of cooking in evolutionary thought.

    PubMed

    Wrangham, R

    2016-06-01

    Beran et al. (2015, p. 1) characterized the idea that "cooked food was integral in human evolution" as a "long-held hypothesis" favored by Darwin and Engels. In fact, however, although Darwin and Engels considered the use of cooked food to be an important influence on behavior and society, neither of them suggested that its effects were evolutionary in the sense of affecting biology. Explicit discussion of the possible evolutionary impacts of cooking did not begin until the twentieth century. PMID:27059233

  15. EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

    PubMed Central

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

    2015-01-01

    Evolution has long provided a foundation for population genetics, but many major advances in evolutionary biology from the 20th century are only now being applied in molecular medicine. They include the distinction between proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are further transforming evolutionary biology and creating yet more opportunities for progress at the interface of evolution with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and others to speed the development of evolutionary molecular medicine. PMID:22544168

  16. Origins of evolutionary transitions.

    PubMed

    Clarke, Ellen

    2014-04-01

    An 'evolutionary transition in individuality' or 'major transition' is a transformation in the hierarchical level at which natural selection operates on a population. In this article I give an abstract (i.e. level-neutral and substrate-neutral) articulation of the transition process in order to precisely understand how such processes can happen, especially how they can get started. PMID:24736161

  17. Evolutionary Developmental Psychology.

    ERIC Educational Resources Information Center

    Geary, David C.; Bjorklund, David F.

    2000-01-01

    Describes evolutionary developmental psychology as the study of the genetic and ecological mechanisms that govern the development of social and cognitive competencies common to all human beings and the epigenetic (gene-environment interactions) processes that adapt these competencies to local conditions. Outlines basic assumptions and domains of…

  18. Evolutionary developmental psychology.

    PubMed

    King, Ashley C; Bjorklund, David F

    2010-02-01

    The field of evolutionary developmental psychology can potentially broaden the horizons of mainstream evolutionary psychology by combining the principles of Darwinian evolution by natural selection with the study of human development, focusing on the epigenetic effects that occur between humans and their environment in a way that attempts to explain how evolved psychological mechanisms become expressed in the phenotypes of adults. An evolutionary developmental perspective includes an appreciation of comparative research and we, among others, argue that contrasting the cognition of humans with that of nonhuman primates can provide a framework with which to understand how human cognitive abilities and intelligence evolved. Furthermore, we argue that several aspects of childhood (e.g., play and immature cognition) serve both as deferred adaptations as well as imparting immediate benefits. Intense selection pressure was surely exerted on childhood over human evolutionary history and, as a result, neglecting to consider the early developmental period of children when studying their later adulthood produces an incomplete picture of the evolved adaptations expressed through human behavior and cognition.

  19. Learning: An Evolutionary Analysis

    ERIC Educational Resources Information Center

    Swann, Joanna

    2009-01-01

    This paper draws on the philosophy of Karl Popper to present a descriptive evolutionary epistemology that offers philosophical solutions to the following related problems: "What happens when learning takes place?" and "What happens in human learning?" It provides a detailed analysis of how learning takes place without any direct transfer of…

  20. Evolutionary pattern search algorithms

    SciTech Connect

    Hart, W.E.

    1995-09-19

    This paper defines a class of evolutionary algorithms called evolutionary pattern search algorithms (EPSAs) and analyzes their convergence properties. This class of algorithms is closely related to evolutionary programming, evolutionary strategie and real-coded genetic algorithms. EPSAs are self-adapting systems that modify the step size of the mutation operator in response to the success of previous optimization steps. The rule used to adapt the step size can be used to provide a stationary point convergence theory for EPSAs on any continuous function. This convergence theory is based on an extension of the convergence theory for generalized pattern search methods. An experimental analysis of the performance of EPSAs demonstrates that these algorithms can perform a level of global search that is comparable to that of canonical EAs. We also describe a stopping rule for EPSAs, which reliably terminated near stationary points in our experiments. This is the first stopping rule for any class of EAs that can terminate at a given distance from stationary points.

  1. Evolutionary Theories of Detection

    SciTech Connect

    Fitch, J P

    2005-04-29

    Current, mid-term and long range technologies for detection of pathogens and toxins are briefly described in the context of performance metrics and operational scenarios. Predictive (evolutionary) and speculative (revolutionary) assessments are given with trade-offs identified, where possible, among competing performance goals.

  2. [Schizophrenia and evolutionary psychopathology].

    PubMed

    Kelemen, Oguz; Kéri, Szabolcs

    2007-01-01

    Evolution can shape any characteristic appearing as a phenotype that is genetically rooted and possesses a long history. The stress-diathesis model suggests that psychiatric disorders have some genetic roots, and therefore the theory of evolution may be relevant for psychiatry. Schizophrenia is present in every human culture with approximately the same incidence. The great evolutionary paradox is: how can such illness persist despite fundamental reproductive disadvantages? Since the 1960s, several evolutionary explanations have been raised to explain the origins of schizophrenia. This article reviews all the major evolutionary theories about the possible origins of this disease. On the one hand, some researchers have proposed that schizophrenia is an evolutionary disadvantageous byproduct of human brain evolution (e.g. the evolution of hemispheric specialization, social brain or language skills). On the other hand, others have suggested that a compensatory advantage must exist either in the biological system of patients with schizophrenia (e.g. resistance against infectious diseases), or within the social domain (e.g. greater creativity of the relatives). According to some theories, shamanism and religion demonstrate some similarities to psychosis and provide clues regarding the origins of schizophrenia. At the end of this article we discuss this last theory in detail listing arguments for and against.

  3. Evolutionary Theory under Fire.

    ERIC Educational Resources Information Center

    Lewin, Roger

    1980-01-01

    Summarizes events of a conference on evolutionary biology in Chicago entitled: "Macroevolution." Reviews the theory of modern synthesis, a term used to explain Darwinism in terms of population biology and genetics. Issues presented at the conference are discussed in detail. (CS)

  4. A Simple General Model of Evolutionary Dynamics

    NASA Astrophysics Data System (ADS)

    Thurner, Stefan

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

  5. Reciprocity Mechanisms meet together. A previous step to bridge the gap with experiments?. Comment on "Universal scaling for the dilemma strength in evolutionary games", by Z. Wang, et al.

    NASA Astrophysics Data System (ADS)

    Gómez-Gardeñes, Jesús

    2015-09-01

    As it is well-recognized, powerful theoretical schemes for the promotion of cooperation fall into the following five categories: direct reciprocity, indirect reciprocity, kin selection, group selection, and network reciprocity, all of which got a great deal of attention and theoretical validation during the past decades [1,2]. In [3] Wang et al. briefly explain how reciprocity mechanisms work, illustrating the huge amount of theoretical work done in the area during the last decades, to finally pose some of the still unsolved puzzles that need to be solved in order to achieve a full (theoretical) understanding of the mechanisms that allow cooperative traits to survive in different scenarios.

  6. Evolutionary biology of cancer.

    PubMed

    Crespi, Bernard; Summers, Kyle

    2005-10-01

    Cancer is driven by the somatic evolution of cell lineages that have escaped controls on replication and by the population-level evolution of genes that influence cancer risk. We describe here how recent evolutionary ecological studies have elucidated the roles of predation by the immune system and competition among normal and cancerous cells in the somatic evolution of cancer. Recent analyses of the evolution of cancer at the population level show how rapid changes in human environments have augmented cancer risk, how strong selection has frequently led to increased cancer risk as a byproduct, and how anticancer selection has led to tumor-suppression systems, tissue designs that slow somatic evolution, constraints on morphological evolution and even senescence itself. We discuss how applications of the tools of ecology and evolutionary biology are poised to revolutionize our understanding and treatment of this disease.

  7. Evolutionary Determinants of Cancer

    PubMed Central

    Greaves, Mel

    2015-01-01

    ‘Nothing in biology makes sense except in the light of evolution’ Th. Dobzhansky, 1973 Our understanding of cancer is being transformed by exploring clonal diversity, drug resistance and causation within an evolutionary framework. The therapeutic resilience of advanced cancer is a consequence of its character as complex, dynamic and adaptive ecosystem engendering robustness, underpinned by genetic diversity and epigenetic plasticity. The risk of mutation-driven escape by self-renewing cells is intrinsic to multicellularity but is countered by multiple restraints facilitating increasing complexity and longevity of species. But our own has disrupted this historical narrative by rapidly escalating intrinsic risk. Evolutionary principles illuminate these challenges and provide new avenues to explore for more effective control. PMID:26193902

  8. Evolutionary game theory

    NASA Astrophysics Data System (ADS)

    Smith, John Maynard

    1986-10-01

    It is often the case that the best thing for an animal or plant to do depends on what other members of the population are doing. In more technical language, the fitnesses of different phenotypes are frequency-dependent. Evolutionary game theory has been developed to analyse such cases. In this paper I aim to do three things. First, I describe the concepts of evolutionary game theory in the context of a simple game, the Hawk-Dove game, and compare them with the concepts of classical game theory originating with Von Neumann and Morgenstern (1953) [1]. Second, I list some of the applications of the theory. Finally, I suggest how the theory can tell us something about the evolution of learning.

  9. Predicting evolutionary dynamics

    NASA Astrophysics Data System (ADS)

    Balazsi, Gabor

    We developed an ordinary differential equation-based model to predict the evolutionary dynamics of yeast cells carrying a synthetic gene circuit. The predicted aspects included the speed at which the ancestral genotype disappears from the population; as well as the types of mutant alleles that establish in each environmental condition. We validated these predictions by experimental evolution. The agreement between our predictions and experimental findings suggests that cellular and population fitness landscapes can be useful to predict short-term evolution.

  10. Evolutionary theory of cancer.

    PubMed

    Attolini, Camille Stephan-Otto; Michor, Franziska

    2009-06-01

    As Theodosius Dobzhansky famously noted in 1973, "Nothing in biology makes sense except in the light of evolution," and cancer is no exception to this rule. Our understanding of cancer initiation, progression, treatment, and resistance has advanced considerably by regarding cancer as the product of evolutionary processes. Here we review the literature of mathematical models of cancer evolution and provide a synthesis and discussion of the field.

  11. Evolutionary theory and teleology.

    PubMed

    O'Grady, R T

    1984-04-21

    The order within and among living systems can be explained rationally by postulating a process of descent with modification, effected by factors which are extrinsic or intrinsic to the organisms. Because at the time Darwin proposed his theory of evolution there was no concept of intrinsic factors which could evolve, he postulated a process of extrinsic effects--natural selection. Biological order was thus seen as an imposed, rather than an emergent, property. Evolutionary change was seen as being determined by the functional efficiency (adaptedness) of the organism in its environment, rather than by spontaneous changes in intrinsically generated organizing factors. The initial incompleteness of Darwin's explanatory model, and the axiomatization of its postulates in neo-Darwinism, has resulted in a theory of functionalism, rather than structuralism. As such, it introduces an unnecessary teleology which confounds evolutionary studies and reduces the usefulness of the theory. This problem cannot be detected from within the neo-Darwinian paradigm because the different levels of end-directed activity--teleomatic, teleonomic, and teleological--are not recognized. They are, in fact, considered to influence one another. The theory of nonequilibrium evolution avoids these problems by returning to the basic principles of biological order and developing a structuralist explanation of intrinsically generated change. Extrinsic factors may affect the resultant evolutionary pattern, but they are neither necessary nor sufficient for evolution to occur.

  12. 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'.

  13. Asymmetric Evolutionary Games

    PubMed Central

    McAvoy, Alex; Hauert, Christoph

    2015-01-01

    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. PMID:26308326

  14. Evolutionary consequences of autopolyploidy.

    PubMed

    Parisod, Christian; Holderegger, Rolf; Brochmann, Christian

    2010-04-01

    Autopolyploidy is more common in plants than traditionally assumed, but has received little attention compared with allopolyploidy. Hence, the advantages and disadvantages of genome doubling per se compared with genome doubling coupled with hybridizations in allopolyploids remain unclear. Autopolyploids are characterized by genomic redundancy and polysomic inheritance, increasing effective population size. To shed light on the evolutionary consequences of autopolyploidy, we review a broad range of studies focusing on both synthetic and natural autopolyploids encompassing levels of biological organization from genes to evolutionary lineages. The limited evidence currently available suggests that autopolyploids neither experience strong genome restructuring nor wide reorganization of gene expression during the first generations following genome doubling, but that these processes may become more important in the longer term. Biogeographic and ecological surveys point to an association between the formation of autopolyploid lineages and environmental change. We thus hypothesize that polysomic inheritance may provide a short-term evolutionary advantage for autopolyploids compared to diploid relatives when environmental change enforces range shifts. In addition, autopolyploids should possess increased genome flexibility, allowing them to adapt and persist across heterogeneous landscapes in the long run. PMID:20070540

  15. 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'. PMID:27619705

  16. Oversimplifying evolutionary psychology leads to explanatory gaps.

    PubMed

    Tate, Chuck; Ledbetter, Jay N

    2010-12-01

    Comments on Evolutionary psychology: Controversies, questions, prospects, and limitations (see record 2010-02208-001) by Confer et al. They argued that SST cannot explain the existence of either homosexuality or suicide within the human species. We contend that a sufficiently nuanced evolutionary position has no difficulties explaining either phenomenon. Also in this account, it is assumed that all psychological functioning must serve survival and reproduction. However, since evolution selects against certain qualities (it does not select for qualities, as it is commonly, but incorrectly, described), two types of qualities should remain intact for any species: (a) those that facilitate survival and reproduction and (b) those that do not impede survival and reproduction at the population level.

  17. Evolutionary Design in Biology

    NASA Astrophysics Data System (ADS)

    Wiese, Kay C.

    Much progress has been achieved in recent years in molecular biology and genetics. The sheer volume of data in the form of biological sequences has been enormous and efficient methods for dealing with these huge amounts of data are needed. In addition, the data alone does not provide information on the workings of biological systems; hence much research effort has focused on designing mathematical and computational models to address problems from molecular biology. Often, the terms bioinformatics and computational biology are used to refer to the research fields concerning themselves with designing solutions to molecular problems in biology. However, there is a slight distinction between bioinformatics and computational biology: the former is concerned with managing the enormous amounts of biological data and extracting information from it, while the latter is more concerned with the design and development of new algorithms to address problems such as protein or RNA folding. However, the boundary is blurry, and there is no consistent usage of the terms. We will use the term bioinformatics to encompass both fields. To cover all areas of research in bioinformatics is beyond the scope of this section and we refer the interested reader to [2] for a general introduction. A large part of what bioinformatics is concerned about is evolution and function of biological systems on a molecular level. Evolutionary computation and evolutionary design are concerned with developing computational systems that "mimic" certain aspects of natural evolution (mutation, crossover, selection, fitness). Much of the inner workings of natural evolutionary systems have been copied, sometimes in modified format into evolutionary computation systems. Artificial neural networks mimic the functioning of simple brain cell clusters. Fuzzy systems are concerned with the "fuzzyness" in decision making, similar to a human expert. These three computational paradigms fall into the category of

  18. On evolutionary systems.

    PubMed

    Alvarez de Lorenzana, J M; Ward, L M

    1987-01-01

    This paper develops a metatheoretical framework for understanding evolutionary systems (systems that develop in ways that increase their own variety). The framework addresses shortcomings seen in other popular systems theories. It concerns both living and nonliving systems, and proposes a metahierarchy of hierarchical systems. Thus, it potentially addresses systems at all descriptive levels. We restrict our definition of system to that of a core system whose parts have a different ontological status than the system, and characterize the core system in terms of five global properties: minimal length interval, minimal time interval, system cycle, total receptive capacity, and system potential. We propose two principles through the interaction of which evolutionary systems develop. The Principle of Combinatorial Expansion describes how a core system realizes its developmental potential through a process of progressive differentiation of the single primal state up to a limit stage. The Principle of Generative Condensation describes how the components of the last stage of combinatorial expansion condense and become the environment for and components of new, enriched systems. The early evolution of the Universe after the "big bang" is discussed in light of these ideas as an example of the application of the framework.

  19. On evolutionary systems.

    PubMed

    Alvarez de Lorenzana, J M; Ward, L M

    1987-01-01

    This paper develops a metatheoretical framework for understanding evolutionary systems (systems that develop in ways that increase their own variety). The framework addresses shortcomings seen in other popular systems theories. It concerns both living and nonliving systems, and proposes a metahierarchy of hierarchical systems. Thus, it potentially addresses systems at all descriptive levels. We restrict our definition of system to that of a core system whose parts have a different ontological status than the system, and characterize the core system in terms of five global properties: minimal length interval, minimal time interval, system cycle, total receptive capacity, and system potential. We propose two principles through the interaction of which evolutionary systems develop. The Principle of Combinatorial Expansion describes how a core system realizes its developmental potential through a process of progressive differentiation of the single primal state up to a limit stage. The Principle of Generative Condensation describes how the components of the last stage of combinatorial expansion condense and become the environment for and components of new, enriched systems. The early evolution of the Universe after the "big bang" is discussed in light of these ideas as an example of the application of the framework. PMID:3689299

  20. Evolutionary models of binaries

    NASA Astrophysics Data System (ADS)

    van Rensbergen, Walter; Mennekens, Nicki; de Greve, Jean-Pierre; Jansen, Kim; de Loore, Bert

    2011-07-01

    We have put on CDS a catalog containing 561 evolutionary models of binaries: J/A+A/487/1129 (Van Rensbergen+, 2008). The catalog covers a grid of binaries with a B-type primary at birth, different values for the initial mass ratio and a wide range of initial orbital periods. The evolution was calculated with the Brussels code in which we introduced the spinning up and the creation of a hot spot on the gainer or its accretion disk, caused by impacting mass coming from the donor. When the kinetic energy of fast rotation added to the radiative energy of the hot spot exceeds the binding energy, a fraction of the transferred matter leaves the system: the evolution is liberal during a short lasting era of rapid mass transfer. The spin-up of the gainer was modulated using both strong and weak tides. The catalog shows the results for both types. For comparison, we included the evolutionary tracks calculated with the conservative assumption. Binaries with an initial primary below 6 Msolar show hardly any mass loss from the system and thus evolve conservatively. Above this limit differences between liberal and conservative evolution grow with increasing initial mass of the primary star.

  1. Evolutionary status of Polaris

    NASA Astrophysics Data System (ADS)

    Fadeyev, Yu. A.

    2015-05-01

    Hydrodynamic models of short-period Cepheids were computed to determine the pulsation period as a function of evolutionary time during the first and third crossings of the instability strip. The equations of radiation hydrodynamics and turbulent convection for radial stellar pulsations were solved with the initial conditions obtained from the evolutionary models of Population I stars (X = 0.7, Z = 0.02) with masses from 5.2 to 6.5 M⊙ and the convective core overshooting parameter 0.1 ≤ αov ≤ 0.3. In Cepheids with period of 4 d the rate of pulsation period change during the first crossing of the instability strip is over 50 times larger than that during the third crossing. Polaris is shown to cross the instability strip for the first time and to be the fundamental mode pulsator. The best agreement between the predicted and observed rates of period change was obtained for the model with mass of 5.4 M⊙ and the overshooting parameter αov = 0.25. The bolometric luminosity and radius are L = 1.26 × 103 L⊙ and R = 37.5 R⊙, respectively. In the HR diagram, Polaris is located at the red edge of the instability strip.

  2. Man's Evolutionary Future

    ERIC Educational Resources Information Center

    Dobzhansky, Theodosius

    1972-01-01

    Man can aspire to control his evolution and direct it towards goals which he finds good, salutary, worth living for....The one most 'natural' thing for man is to modify nature by means of his knowledge." (Author/AL)

  3. Spore: Spawning Evolutionary Misconceptions?

    NASA Astrophysics Data System (ADS)

    Bean, Thomas E.; Sinatra, Gale M.; Schrader, P. G.

    2010-10-01

    The use of computer simulations as educational tools may afford the means to develop understanding of evolution as a natural, emergent, and decentralized process. However, special consideration of developmental constraints on learning may be necessary when using these technologies. Specifically, the essentialist (biological forms possess an immutable essence), teleological (assignment of purpose to living things and/or parts of living things that may not be purposeful), and intentionality (assumption that events are caused by an intelligent agent) biases may be reinforced through the use of computer simulations, rather than addressed with instruction. We examine the video game Spore for its depiction of evolutionary content and its potential to reinforce these cognitive biases. In particular, we discuss three pedagogical strategies to mitigate weaknesses of Spore and other computer simulations: directly targeting misconceptions through refutational approaches, targeting specific principles of scientific inquiry, and directly addressing issues related to models as cognitive tools.

  4. Child Development and Evolutionary Psychology.

    ERIC Educational Resources Information Center

    Bjorklund, David F.; Pellegrini, Anthony D.

    2000-01-01

    Argues that an evolutionary account provides insight into developmental function and individual differences. Outlines some assumptions of evolutionary psychology related to development. Introduces the developmental systems approach, differential influence of natural selection at different points in ontogeny, and development of evolved…

  5. 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.

  6. Observability in dynamic evolutionary models.

    PubMed

    López, I; Gámez, M; Carreño, R

    2004-02-01

    In the paper observability problems are considered in basic dynamic evolutionary models for sexual and asexual populations. Observability means that from the (partial) knowledge of certain phenotypic characteristics the whole evolutionary process can be uniquely recovered. Sufficient conditions are given to guarantee observability for both sexual and asexual populations near an evolutionarily stable state.

  7. Islamic Medicine and Evolutionary Medicine: A Comparative Analysis

    PubMed Central

    Saniotis, Arthur

    2012-01-01

    The advent of evolutionary medicine in the last two decades has provided new insights into the causes of human disease and possible preventative strategies. One of the strengths of evolutionary medicine is that it follows a multi-disciplinary approach. Such an approach is vital to future biomedicine as it enables for the infiltration of new ideas. Although evolutionary medicine uses Darwinian evolution as a heuristic for understanding human beings’ susceptibility to disease, this is not necessarily in conflict with Islamic medicine. It should be noted that current evolutionary theory was first expounded by various Muslim scientists such as al-Jāḥiẓ, al-Ṭūsī, Ibn Khaldūn and Ibn Maskawayh centuries before Darwin and Wallace. In this way, evolution should not be viewed as being totally antithetical to Islam. This article provides a comparative overview of Islamic medicine and Evolutionary medicine as well as drawing points of comparison between the two approaches which enables their possible future integration. PMID:23864992

  8. Islamic medicine and evolutionary medicine: a comparative analysis.

    PubMed

    Saniotis, Arthur

    2012-01-01

    The advent of evolutionary medicine in the last two decades has provided new insights into the causes of human disease and possible preventative strategies. One of the strengths of evolutionary medicine is that it follows a multi-disciplinary approach. Such an approach is vital to future biomedicine as it enables for the infiltration of new ideas. Although evolutionary medicine uses Darwinian evolution as a heuristic for understanding human beings' susceptibility to disease, this is not necessarily in conflict with Islamic medicine. It should be noted that current evolutionary theory was first expounded by various Muslim scientists such as al-Jāḥiẓ, al-Ṭūsī, Ibn Khaldūn and Ibn Maskawayh centuries before Darwin and Wallace. In this way, evolution should not be viewed as being totally antithetical to Islam. This article provides a comparative overview of Islamic medicine and Evolutionary medicine as well as drawing points of comparison between the two approaches which enables their possible future integration.

  9. The evolutionary advantage of limited network knowledge.

    PubMed

    Larson, Jennifer M

    2016-06-01

    Groups of individuals have social networks that structure interactions within the groups; evolutionary theory increasingly uses this fact to explain the emergence of cooperation (Eshel and Cavalli-Sforza, 1982; Boyd and Richerson, 1988, 1989; Ohtsuki et al., 2006; Nowak et al., 2010; Van Veelen et al., 2012). This approach has resulted in a number of important insights for the evolution of cooperation in the biological and social sciences, but omits a key function of social networks that has persisted throughout recent evolutionary history (Apicella et al., 2012): their role in transmitting gossip about behavior within a group. Accounting for this well-established role of social networks among rational agents in a setting of indirect reciprocity not only shows a new mechanism by which the structure of networks is fitness-relevant, but also reveals that knowledge of social networks can be fitness-relevant as well. When groups enforce cooperation by sanctioning peers whom gossip reveals to have deviated, individuals in certain peripheral network positions are tempting targets of uncooperative behavior because gossip they share about misbehavior spreads slowly through the network. The ability to identify these individuals creates incentives to behave uncooperatively. Consequently, groups comprised of individuals who knew precise information about their social networks would be at a fitness disadvantage relative to groups of individuals with a coarser knowledge of their networks. Empirical work has consistently shown that modern humans know little about the structure of their own social networks and perform poorly when tasked with learning new ones. This robust empirical regularity may be the product of natural selection in an environment of strong selective pressure at the group level. Imprecise views of networks make enforcing cooperation easier. PMID:27012517

  10. The evolutionary advantage of limited network knowledge.

    PubMed

    Larson, Jennifer M

    2016-06-01

    Groups of individuals have social networks that structure interactions within the groups; evolutionary theory increasingly uses this fact to explain the emergence of cooperation (Eshel and Cavalli-Sforza, 1982; Boyd and Richerson, 1988, 1989; Ohtsuki et al., 2006; Nowak et al., 2010; Van Veelen et al., 2012). This approach has resulted in a number of important insights for the evolution of cooperation in the biological and social sciences, but omits a key function of social networks that has persisted throughout recent evolutionary history (Apicella et al., 2012): their role in transmitting gossip about behavior within a group. Accounting for this well-established role of social networks among rational agents in a setting of indirect reciprocity not only shows a new mechanism by which the structure of networks is fitness-relevant, but also reveals that knowledge of social networks can be fitness-relevant as well. When groups enforce cooperation by sanctioning peers whom gossip reveals to have deviated, individuals in certain peripheral network positions are tempting targets of uncooperative behavior because gossip they share about misbehavior spreads slowly through the network. The ability to identify these individuals creates incentives to behave uncooperatively. Consequently, groups comprised of individuals who knew precise information about their social networks would be at a fitness disadvantage relative to groups of individuals with a coarser knowledge of their networks. Empirical work has consistently shown that modern humans know little about the structure of their own social networks and perform poorly when tasked with learning new ones. This robust empirical regularity may be the product of natural selection in an environment of strong selective pressure at the group level. Imprecise views of networks make enforcing cooperation easier.

  11. How competition affects evolutionary rescue

    PubMed Central

    Osmond, Matthew Miles; de Mazancourt, Claire

    2013-01-01

    Populations facing novel environments can persist by adapting. In nature, the ability to adapt and persist will depend on interactions between coexisting individuals. Here we use an adaptive dynamic model to assess how the potential for evolutionary rescue is affected by intra- and interspecific competition. Intraspecific competition (negative density-dependence) lowers abundance, which decreases the supply rate of beneficial mutations, hindering evolutionary rescue. On the other hand, interspecific competition can aid evolutionary rescue when it speeds adaptation by increasing the strength of selection. Our results clarify this point and give an additional requirement: competition must increase selection pressure enough to overcome the negative effect of reduced abundance. We therefore expect evolutionary rescue to be most likely in communities which facilitate rapid niche displacement. Our model, which aligns to previous quantitative and population genetic models in the absence of competition, provides a first analysis of when competitors should help or hinder evolutionary rescue. PMID:23209167

  12. ALS Association

    MedlinePlus

    ... toward a world without ALS! Walk to Defeat ALS® Walk to Defeat ALS® draws people of all ... We need your help. I Will Advocate National ALS Registry The National ALS Registry is a congressionally ...

  13. Evolutionary dynamics of microsatellite DNA.

    PubMed

    Schlötterer, C

    2000-09-01

    Within the past decade microsatellites have developed into one of the most popular genetic markers. Despite the widespread use of microsatellite analysis, an integral picture of the mutational dynamics of microsatellite DNA is just beginning to emerge. Here, I review both generally agreed and controversial results about the mutational dynamics of microsatellite DNA. Microsatellites are short DNA sequence stretches in which a motif of one to six bases is tandemly repeated. It has been known for some time that these sequences can differ in repeat number among individuals. With the advent of polymerase chain reaction (PCR) technology this property of microsatellite DNA was converted into a highly versatile genetic marker (Litt and Luty 1989; Tautz 1989; Weber and May 1989). Polymerase chain reaction products of different length can be amplified with primers flanking the variable microsatellite region. Due to the availability of high-throughput capillary sequencers or mass spectrography the sizing of alleles is no longer a bottleneck in microsatellite analysis. The almost random distribution of microsatellites and their high level of polymorphism greatly facilitated the construction of genetic maps (Dietrich et al. 1994; Dib et al. 1996) and enabled subsequent positional cloning of several genes. Almost at the same time, microsatellites were established as the marker of choice for the identification of individuals and paternity testing. The high sensitivity of PCR-based microsatellite analysis was not only of great benefit for forensics, but opened completely new research areas, such as the analysis of samples with limited DNA amounts (e.g., many social insects) or degraded DNA (e.g., feces, museum material) (Schlötterer and Pemberton 1998). More recently, microsatellite analysis has also been employed in population genetics (Goldstein and Schlötterer 1999). Compared with allozymes, microsatellites offer the advantage that, in principle, several thousand potentially

  14. RNA based evolutionary optimization.

    PubMed

    Schuster, P

    1993-12-01

    The notion of an RNA world has been introduced for a prebiotic scenario that is dominated by RNA molecules and their properties, in particular their capabilities to act as templates for reproduction and as catalysts for several cleavage and ligation reactions of polynucleotides and polypeptides. This notion is used here also for simple experimental assays which are well suited to study evolution in the test tube. In molecular evolution experiments fitness is determined in essence by the molecular structures of RNA molecules. Evidence is presented for adaptation to environment in cell-free media. RNA based molecular evolution experiments have led to interesting spin-offs in biotechnology, commonly called 'applied molecular evolution', which make use of Darwinian trial-and-error strategies in order to synthesize new pharmacological compounds and other advanced materials on a biological basis. Error-propagation in RNA replication leads to formation of mutant spectra called 'quasispecies'. An increase in the error rate broadens the mutant spectrum. There exists a sharply defined threshold beyond which heredity breaks down and evolutionary adaptation becomes impossible. Almost all RNA viruses studied so far operate at conditions close to this error threshold. Quasispecies and error thresholds are important for an understanding of RNA virus evolution, and they may help to develop novel antiviral strategies. Evolution of RNA molecules can be studied and interpreted by considering secondary structures. The notion of sequence space introduces a distance between pairs of RNA sequences which is tantamount to counting the minimal number of point mutations required to convert the sequences into each other. The mean sensitivity of RNA secondary structures to mutation depends strongly on the base pairing alphabet: structures from sequences which contain only one base pair (GC or AU are much less stable against mutation than those derived from the natural (AUGC) sequences

  15. Histocompatible chicken inbred lines: homogeneities in the major histocompatibility complex antigens of the GSP, GSN/1, PNP/DO and BM-C inbred lines assessed by hemagglutination, mixed lymphocyte reaction and skin transplantation.

    PubMed

    Valdez, Marcos B; Mizutani, Makoto; Fujiwara, Akira; Yazawa, Hajime; Yamagata, Takahiro; Shimada, Kiyoshi; Namikawa, Takao

    2007-10-01

    Chicken inbred lines of the GSP, GSN/1, PNP/DO and BM-C have been established by selection of a specific allele at the B blood group locus (MHC B-G region) and other polymorphic loci through pedigree mating. To extend the potential of these inbred lines as experimental animals in Aves, we assessed the antigenic homogeneities of the MHC antigens by three immunological methods. Antigenic variations of red blood cells (RBCs) were surveyed in the inbred lines and a random-bred line (NG) derived from the Nagoya breed by using ten kinds of intact antisera produced in the inbred line of chickens against RBCs of a red junglefowl and hybrids. In the hemagglutination test, no individual variations were found within the inbred line at all, while all the ten antisera detected highly heterogeneous reactions in individuals of the NG. The reciprocal one-way mixed lymphocyte reactions gave constantly higher stimulation responses (P<0.01) between individual pairs from the inbred lines having different B alleles compared to pairs within the inbred line, while lower stimulation was observed between pairs of the GSP and GSN/1 inbred lines both having the B(21) allele. In reciprocal skin transplantation, the transplanted skingrafts within the inbred line and between individuals from the GSP and GSN/1 inbred lines survived more than 100 days, while all the skingrafts showed signs of rejection within 7 days among the inbred lines having different B alleles. The results obtained by the three practical methods coincidentally indicated that the individuals in the respective four inbred lines were histocompatible, and further, that the GSP and GSN/1 individuals were histocompatible. PMID:18075192

  16. Evolutionary theory, psychiatry, and psychopharmacology.

    PubMed

    Stein, Dan J

    2006-07-01

    Darwin's seminal publications in the nineteenth century laid the foundation for an evolutionary approach to psychology and psychiatry. Advances in 20th century evolutionary theory facilitated the development of evolutionary psychology and psychiatry as recognized areas of scientific investigation. In this century, advances in understanding the molecular basis of evolution, of the mind, and of psychopathology, offer the possibility of an integrated approach to understanding the proximal (psychobiological) and distal (evolutionary) mechanisms of interest to psychiatry and psychopharmacology. There is, for example, growing interest in the question of whether specific genetic variants mediate psychobiological processes that have evolutionary value in specific contexts, and of the implications of this for understanding the vulnerability to psychopathology and for considering the advantages and limitations of pharmacotherapy. The evolutionary value, and gene-environmental mediation, of early life programming is potentially a particularly rich area of investigation. Although evolutionary approaches to psychology and to medicine face important conceptual and methodological challenges, current work is increasingly sophisticated, and may prove to be an important foundational discipline for clinicians and researchers in psychiatry and psychopharmacology.

  17. Evolutionary rescue beyond the models

    PubMed Central

    Gomulkiewicz, Richard; Shaw, Ruth G.

    2013-01-01

    Laboratory model systems and mathematical models have shed considerable light on the fundamental properties and processes of evolutionary rescue. But it remains to determine the extent to which these model-based findings can help biologists predict when evolution will fail or succeed in rescuing natural populations that are facing novel conditions that threaten their persistence. In this article, we present a prospectus for transferring our basic understanding of evolutionary rescue to wild and other non-laboratory populations. Current experimental and theoretical results emphasize how the interplay between inheritance processes and absolute fitness in changed environments drive population dynamics and determine prospects of extinction. We discuss the challenge of inferring these elements of the evolutionary rescue process in field and natural settings. Addressing this challenge will contribute to a more comprehensive understanding of population persistence that combines processes of evolutionary rescue with developmental and ecological mechanisms. PMID:23209173

  18. Army ants: an evolutionary bestseller?

    PubMed

    Berghoff, Stefanie M

    2003-09-01

    Army ants are characterized by a complex combination of behavioral and morphological traits. Molecular data now indicate that army ant behavior has a unique evolutionary origin and has been conserved for over more than 100 million years.

  19. Evolutionary constraints or opportunities?

    PubMed Central

    Sharov, Alexei A.

    2014-01-01

    Natural selection is traditionally viewed as a leading factor of evolution, whereas variation is assumed to be random and non-directional. Any order in variation is attributed to epigenetic or developmental constraints that can hinder the action of natural selection. In contrast I consider the positive role of epigenetic mechanisms in evolution because they provide organisms with opportunities for rapid adaptive change. Because the term “constraint” has negative connotations, I use the term “regulated variation” to emphasize the adaptive nature of phenotypic variation, which helps populations and species to survive and evolve in changing environments. The capacity to produce regulated variation is a phenotypic property, which is not described in the genome. Instead, the genome acts as a switchboard, where mostly random mutations switch “on” or “off” preexisting functional capacities of organism components. Thus, there are two channels of heredity: informational (genomic) and structure-functional (phenotypic). Functional capacities of organisms most likely emerged in a chain of modifications and combinations of more simple ancestral functions. The role of DNA has been to keep records of these changes (without describing the result) so that they can be reproduced in the following generations. Evolutionary opportunities include adjustments of individual functions, multitasking, connection between various components of an organism, and interaction between organisms. The adaptive nature of regulated variation can be explained by the differential success of lineages in macro-evolution. Lineages with more advantageous patterns of regulated variation are likely to produce more species and secure more resources (i.e., long-term lineage selection). PMID:24769155

  20. Evolutionary constraints or opportunities?

    PubMed

    Sharov, Alexei A

    2014-04-22

    Natural selection is traditionally viewed as a leading factor of evolution, whereas variation is assumed to be random and non-directional. Any order in variation is attributed to epigenetic or developmental constraints that can hinder the action of natural selection. In contrast I consider the positive role of epigenetic mechanisms in evolution because they provide organisms with opportunities for rapid adaptive change. Because the term "constraint" has negative connotations, I use the term "regulated variation" to emphasize the adaptive nature of phenotypic variation, which helps populations and species to survive and evolve in changing environments. The capacity to produce regulated variation is a phenotypic property, which is not described in the genome. Instead, the genome acts as a switchboard, where mostly random mutations switch "on" or "off" preexisting functional capacities of organism components. Thus, there are two channels of heredity: informational (genomic) and structure-functional (phenotypic). Functional capacities of organisms most likely emerged in a chain of modifications and combinations of more simple ancestral functions. The role of DNA has been to keep records of these changes (without describing the result) so that they can be reproduced in the following generations. Evolutionary opportunities include adjustments of individual functions, multitasking, connection between various components of an organism, and interaction between organisms. The adaptive nature of regulated variation can be explained by the differential success of lineages in macro-evolution. Lineages with more advantageous patterns of regulated variation are likely to produce more species and secure more resources (i.e., long-term lineage selection).

  1. Evolutionary constraints or opportunities?

    PubMed

    Sharov, Alexei A

    2014-09-01

    Natural selection is traditionally viewed as a leading factor of evolution, whereas variation is assumed to be random and non-directional. Any order in variation is attributed to epigenetic or developmental constraints that can hinder the action of natural selection. In contrast I consider the positive role of epigenetic mechanisms in evolution because they provide organisms with opportunities for rapid adaptive change. Because the term "constraint" has negative connotations, I use the term "regulated variation" to emphasize the adaptive nature of phenotypic variation, which helps populations and species to survive and evolve in changing environments. The capacity to produce regulated variation is a phenotypic property, which is not described in the genome. Instead, the genome acts as a switchboard, where mostly random mutations switch "on" or "off" preexisting functional capacities of organism components. Thus, there are two channels of heredity: informational (genomic) and structure-functional (phenotypic). Functional capacities of organisms most likely emerged in a chain of modifications and combinations of more simple ancestral functions. The role of DNA has been to keep records of these changes (without describing the result) so that they can be reproduced in the following generations. Evolutionary opportunities include adjustments of individual functions, multitasking, connection between various components of an organism, and interaction between organisms. The adaptive nature of regulated variation can be explained by the differential success of lineages in macro-evolution. Lineages with more advantageous patterns of regulated variation are likely to produce more species and secure more resources (i.e., long-term lineage selection).

  2. Molluscan Evolutionary Genomics

    SciTech Connect

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  3. Evolutionary status of Be stars

    NASA Astrophysics Data System (ADS)

    Zorec, J.; Frémat, Y.; Cidale, L.

    2004-12-01

    Fundamental parameters of nearly 50 field Be stars have been determined. Correcting these parameters from gravity darkening effects induced the fast rotation, we deduced the evolutionary phase of the studied stars. We show that the evolutionary phase at which appear the Be phenomenon is mass dependent: the smaller the stellar mass the elder the phase in the main sequence at which the Be phenomenon seem to appear.

  4. Substitution of the transmembrane domain of Vpu in simian-human immunodeficiency virus (SHIV{sub KU1bMC33}) with that of M2 of influenza A results in a virus that is sensitive to inhibitors of the M2 ion channel and is pathogenic for pig-tailed macaques

    SciTech Connect

    Hout, David R.; Gomez, Melissa L.; Pacyniak, Erik; Gomez, Lisa M.; Fegley, Barbara; Mulcahy, Ellyn R.; Hill, M. Sarah; Culley, Nathan; Pinson, David M.; Nothnick, Warren; Powers, Michael F.; Wong, Scott W.; Stephens, Edward B. . E-mail: estephen@kumc.edu

    2006-01-20

    The Vpu protein of human immunodeficiency virus type 1 has been shown to shunt the CD4 receptor molecule to the proteasome for degradation and to enhance virus release from infected cells. The exact mechanism by which the Vpu protein enhances virus release is currently unknown but some investigators have shown that this function is associated with the transmembrane domain and potential ion channel properties. In this study, we determined if the transmembrane domain of Vpu could be functionally substituted with that of the prototypical viroporin, the M2 protein of influenza A virus. We constructed chimeric vpu gene in which the transmembrane domain of Vpu was replaced with that of the M2 protein of influenza. This chimeric vpu gene was substituted for the vpu gene in the genome of a pathogenic simian human immunodeficiency virus, SHIV{sub KU-1bMC33}. The resulting virus, SHIV{sub M2}, synthesized a Vpu protein that had a slightly different M{sub r} compared to the parental SHIV{sub KU-1bMC33}, reflecting the different sizes of the two Vpu proteins. The SHIV{sub M2} was shown to replicate with slightly reduced kinetics when compared to the parental SHIV{sub KU-1bMC33} but electron microscopy revealed that the site of maturation was similar to the parental virus SHIV{sub KU1bMC33}. We show that the replication and spread of SHIV{sub M2} could be blocked with the antiviral drug rimantadine, which is known to target the M2 ion channel. Our results indicate a dose dependent inhibition of SHIV{sub M2} with 100 {mu}M rimantadine resulting in a >95% decrease in p27 released into the culture medium. Rimantadine did not affect the replication of the parental SHIV{sub KU-1bMC33}. Examination of SHIV{sub M2}-infected cells treated with 50 {mu}M rimantadine revealed numerous viral particles associated with the cell plasma membrane and within intracytoplasmic vesicles, which is similar to HIV-1 mutants lacking a functional vpu. To determine if SHIV{sub M2} was as pathogenic as

  5. Toward a theory of evolutionary computation.

    PubMed

    Eberbach, Eugene

    2005-10-01

    We outline a theory of evolutionary computation using a formal model of evolutionary computation--the Evolutionary Turing Machine--which is introduced as the extension of the Turing Machine model. Evolutionary Turing Machines provide a better and a more complete model for evolutionary computing than conventional Turing Machines, algorithms, and Markov chains. The convergence and convergence rate are defined and investigated in terms of this new model. The sufficient conditions needed for the completeness and optimality of evolutionary search are investigated. In particular, the notion of the total optimality as an instance of the multiobjective optimization of the Universal Evolutionary Turing Machine is introduced. This provides an automatic way to deal with the intractability of evolutionary search by optimizing the quality of solutions and search costs simultaneously. Based on a new model a very flexible classification of optimization problem hardness for the evolutionary techniques is proposed. The expressiveness of evolutionary computation is investigated. We show that the problem of the best evolutionary algorithm is undecidable independently of whether the fitness function is time dependent or fixed. It is demonstrated that the evolutionary computation paradigm is more expressive than Turing Machines, and thus the conventional computer science based on them. We show that an Evolutionary Turing Machine is able to solve nonalgorithmically the halting problem of the Universal Turing Machine and, asymptotically, the best evolutionary algorithm problem. In other words, the best evolutionary algorithm does not exist, but it can be potentially indefinitely approximated using evolutionary techniques.

  6. ALS - resources

    MedlinePlus

    Resources - ALS ... The following organizations are good resources for information on amyotrophic lateral sclerosis : Muscular Dystrophy Association -- mda.org/disease/amyotrophic-lateral-sclerosis National Amyotrophic Lateral Sclerosis (ALS) Registry -- ...

  7. Evolutionary inevitability of sexual antagonism.

    PubMed

    Connallon, Tim; Clark, Andrew G

    2014-02-01

    Sexual antagonism, whereby mutations are favourable in one sex and disfavourable in the other, is common in natural populations, yet the root causes of sexual antagonism are rarely considered in evolutionary theories of adaptation. Here, we explore the evolutionary consequences of sex-differential selection and genotype-by-sex interactions for adaptation in species with separate sexes. We show that sexual antagonism emerges naturally from sex differences in the direction of selection on phenotypes expressed by both sexes or from sex-by-genotype interactions affecting the expression of such phenotypes. Moreover, modest sex differences in selection or genotype-by-sex effects profoundly influence the long-term evolutionary trajectories of populations with separate sexes, as these conditions trigger the evolution of strong sexual antagonism as a by-product of adaptively driven evolutionary change. The theory demonstrates that sexual antagonism is an inescapable by-product of adaptation in species with separate sexes, whether or not selection favours evolutionary divergence between males and females.

  8. Evolutionary genetics of maternal effects

    PubMed Central

    Wolf, Jason B.; Wade, Michael J.

    2016-01-01

    Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single‐locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype‐phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype‐phenotype relationship frequency dependent, resulting in the appearance of negative frequency‐dependent selection, while additive MGEs contribute a component of parent‐of‐origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be “available” to the evolving population. PMID:26969266

  9. 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'. PMID:27431528

  10. 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'.

  11. Environmental changes bridge evolutionary valleys

    PubMed Central

    Steinberg, Barrett; Ostermeier, Marc

    2016-01-01

    In the basic fitness landscape metaphor for molecular evolution, evolutionary pathways are presumed to follow uphill steps of increasing fitness. How evolution can cross fitness valleys is an open question. One possibility is that environmental changes alter the fitness landscape such that low-fitness sequences reside on a hill in alternate environments. We experimentally test this hypothesis on the antibiotic resistance gene TEM-15 β-lactamase by comparing four evolutionary strategies shaped by environmental changes. The strategy that included initial steps of selecting for low antibiotic resistance (negative selection) produced superior alleles compared with the other three strategies. We comprehensively examined possible evolutionary pathways leading to one such high-fitness allele and found that an initially deleterious mutation is key to the allele’s evolutionary history. This mutation is an initial gateway to an otherwise relatively inaccessible area of sequence space and participates in higher-order, positive epistasis with a number of neutral to slightly beneficial mutations. The ability of negative selection and environmental changes to provide access to novel fitness peaks has important implications for natural evolutionary mechanisms and applied directed evolution. PMID:26844293

  12. Evolutionary foundations for cancer biology

    PubMed Central

    Aktipis, C Athena; Nesse, Randolph M

    2013-01-01

    New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles—cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations—provide a foundation for understanding, preventing, and treating cancer. PMID:23396885

  13. 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

  14. Structural symmetry in evolutionary games

    PubMed Central

    McAvoy, Alex; Hauert, Christoph

    2015-01-01

    In evolutionary game theory, an important measure of a mutant trait (strategy) is its ability to invade and take over an otherwise-monomorphic population. Typically, one quantifies the success of a mutant strategy via the probability that a randomly occurring mutant will fixate in the population. However, in a structured population, this fixation probability may depend on where the mutant arises. Moreover, the fixation probability is just one quantity by which one can measure the success of a mutant; fixation time, for instance, is another. We define a notion of homogeneity for evolutionary games that captures what it means for two single-mutant states, i.e. two configurations of a single mutant in an otherwise-monomorphic population, to be ‘evolutionarily equivalent’ in the sense that all measures of evolutionary success are the same for both configurations. Using asymmetric games, we argue that the term ‘homogeneous’ should apply to the evolutionary process as a whole rather than to just the population structure. For evolutionary matrix games in graph-structured populations, we give precise conditions under which the resulting process is homogeneous. Finally, we show that asymmetric matrix games can be reduced to symmetric games if the population structure possesses a sufficient degree of symmetry. PMID:26423436

  15. Evolutionary genomics of environmental pollution.

    PubMed

    Whitehead, Andrew

    2014-01-01

    Chemical toxins have been a persistent source of evolutionary challenges throughout the history of life, and deep within the genomic storehouse of evolutionary history lay ancient adaptations to diverse chemical poisons. However, the rate of change of contemporary environments mediated by human-introduced pollutants is rapidly screening this storehouse and severely testing the adaptive potential of many species. In this chapter, we briefly review the deep history of evolutionary adaptation to environmental toxins, and then proceed to describe the attributes of stressors and populations that may facilitate contemporary adaptation to pollutants introduced by humans. We highlight that phenotypes derived to enable persistence in polluted habitats may be multi-dimensional, requiring global genome-scale tools and approaches to uncover their mechanistic basis, and include examples of recent progress in the field. The modern tools of genomics offer promise for discovering how pollutants interact with genomes on physiological timescales, and also for discovering what genomic attributes of populations may enable resistance to pollutants over evolutionary timescales. Through integration of these sophisticated genomics tools and approaches with an understanding of the deep historical forces that shaped current populations, a more mature understanding of the mechanistic basis of contemporary ecological-evolutionary dynamics should emerge.

  16. Evolutionary genetics of maternal effects.

    PubMed

    Wolf, Jason B; Wade, Michael J

    2016-04-01

    Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single-locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype-phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype-phenotype relationship frequency dependent, resulting in the appearance of negative frequency-dependent selection, while additive MGEs contribute a component of parent-of-origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be "available" to the evolving population. PMID:26969266

  17. Evolutionary psychology and intelligence research.

    PubMed

    Kanazawa, Satoshi

    2010-01-01

    This article seeks to unify two subfields of psychology that have hitherto stood separately: evolutionary psychology and intelligence research/differential psychology. I suggest that general intelligence may simultaneously be an evolved adaptation and an individual-difference variable. Tooby and Cosmides's (1990a) notion of random quantitative variation on a monomorphic design allows us to incorporate heritable individual differences in evolved adaptations. The Savanna-IQ Interaction Hypothesis, which is one consequence of the integration of evolutionary psychology and intelligence research, can potentially explain why less intelligent individuals enjoy TV more, why liberals are more intelligent than conservatives, and why night owls are more intelligent than morning larks, among many other findings. The general approach proposed here will allow us to integrate evolutionary psychology with any other aspect of differential psychology.

  18. Evolutionary engineering for industrial microbiology.

    PubMed

    Vanee, Niti; Fisher, Adam B; Fong, Stephen S

    2012-01-01

    Superficially, evolutionary engineering is a paradoxical field that balances competing interests. In natural settings, evolution iteratively selects and enriches subpopulations that are best adapted to a particular ecological niche using random processes such as genetic mutation. In engineering desired approaches utilize rational prospective design to address targeted problems. When considering details of evolutionary and engineering processes, more commonality can be found. Engineering relies on detailed knowledge of the problem parameters and design properties in order to predict design outcomes that would be an optimized solution. When detailed knowledge of a system is lacking, engineers often employ algorithmic search strategies to identify empirical solutions. Evolution epitomizes this iterative optimization by continuously diversifying design options from a parental design, and then selecting the progeny designs that represent satisfactory solutions. In this chapter, the technique of applying the natural principles of evolution to engineer microbes for industrial applications is discussed to highlight the challenges and principles of evolutionary engineering.

  19. Theoretical developments in evolutionary computation

    NASA Astrophysics Data System (ADS)

    Fogel, David B.

    1999-11-01

    Recent developments in the theory of evolutionary computation offer evidence and proof that overturns several conventionally held beliefs. In particular, the no free lunch theorem and other related theorems show that there can be no best evolutionary algorithm, and that no particular variation operator or selection mechanism provides a general advantage over another choice. Furthermore, the fundamental nature of the notion of schema processing is called into question by recent theory that shows that the schema theorem does not hold when schema fitness is stochastic. Moreover, the analysis that underlies schema theory, namely the k- armed bandit analysis, does not generate a sampling plan that yields an optimal allocation of trials, as has been suggested in the literature for almost 25 years. The importance of these new findings is discussed in the context of future progress in the field of evolutionary computation.

  20. Neuronal boost to evolutionary dynamics

    PubMed Central

    de Vladar, Harold P.; Szathmáry, Eörs

    2015-01-01

    Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild. PMID:26640653

  1. Neuronal boost to evolutionary dynamics.

    PubMed

    de Vladar, Harold P; Szathmáry, Eörs

    2015-12-01

    Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild.

  2. Evolutionary models of interstellar chemistry

    NASA Technical Reports Server (NTRS)

    Prasad, Sheo S.

    1987-01-01

    The goal of evolutionary models of interstellar chemistry is to understand how interstellar clouds came to be the way they are, how they will change with time, and to place them in an evolutionary sequence with other celestial objects such as stars. An improved Mark II version of an earlier model of chemistry in dynamically evolving clouds is presented. The Mark II model suggests that the conventional elemental C/O ratio less than one can explain the observed abundances of CI and the nondetection of O2 in dense clouds. Coupled chemical-dynamical models seem to have the potential to generate many observable discriminators of the evolutionary tracks. This is exciting, because, in general, purely dynamical models do not yield enough verifiable discriminators of the predicted tracks.

  3. An inquiry into evolutionary inquiry

    NASA Astrophysics Data System (ADS)

    Donovan, Samuel S.

    2005-11-01

    While evolution education has received a great deal of attention within the science education research community it still poses difficult teaching and learning challenges. Understanding evolutionary biology has been given high priority in national science education policy because of its role in coordinating our understanding of the life sciences, its importance in our intellectual history, its role in the perception of humans' position in nature, and its impact on our current medical, agricultural, and conservation practices. The rhetoric used in evolution education policy statements emphasizes familiarity with the nature of scientific inquiry as an important learning outcome associated with understanding evolution but provide little guidance with respect to how one might achieve this goal. This dissertation project explores the nature of evolutionary inquiry and how understanding the details of disciplinary reasoning can inform evolution education. The first analysis involves recasting the existing evolution education research literature to assess educational outcomes related to students ability to reason about data using evolutionary biology methods and models. This is followed in the next chapter by a detailed historical and philosophical characterization of evolutionary biology with the goal of providing a richer context for considering what exactly it is we want students to know about evolution as a discipline. Chapter 4 describes the development and implementation of a high school evolution curriculum that engages students with many aspects of model based reasoning. The final component of this reframing of evolution education involves an empirical study characterizing students' understanding of evolutionary biology as a modeling enterprise. Each chapter addresses a different aspect of evolution education and explores the implications of foregrounding disciplinary reasoning as an educational outcome. The analyses are coordinated with one another in the sense

  4. The evolutionary psychology of violence.

    PubMed

    Goetz, Aaron T

    2010-02-01

    This paper reviews theory and research on the evolutionary psychology of violence. First, I examine evidence suggesting that humans have experienced an evolutionary history of violence. Next, I discuss violence as a context-sensitive strategy that might have provided benefits to our ancestors under certain circumstances. I then focus on the two most common forms of violence that plague humans -violence over status contests and intimate partner violence- outlining psychological mechanisms involved in each. Finally, I suggest that greater progress will be made by shifting the study from contexts to mechanisms.

  5. The evolutionary psychology of hunger.

    PubMed

    Al-Shawaf, Laith

    2016-10-01

    An evolutionary psychological perspective suggests that emotions can be understood as coordinating mechanisms whose job is to regulate various psychological and physiological programs in the service of solving an adaptive problem. This paper suggests that it may also be fruitful to approach hunger from this coordinating mechanism perspective. To this end, I put forward an evolutionary task analysis of hunger, generating novel a priori hypotheses about the coordinating effects of hunger on psychological processes such as perception, attention, categorization, and memory. This approach appears empirically fruitful in that it yields a bounty of testable new hypotheses.

  6. The evolutionary psychology of hunger.

    PubMed

    Al-Shawaf, Laith

    2016-10-01

    An evolutionary psychological perspective suggests that emotions can be understood as coordinating mechanisms whose job is to regulate various psychological and physiological programs in the service of solving an adaptive problem. This paper suggests that it may also be fruitful to approach hunger from this coordinating mechanism perspective. To this end, I put forward an evolutionary task analysis of hunger, generating novel a priori hypotheses about the coordinating effects of hunger on psychological processes such as perception, attention, categorization, and memory. This approach appears empirically fruitful in that it yields a bounty of testable new hypotheses. PMID:27328100

  7. Deep evolutionary origins of neurobiology

    PubMed Central

    Mancuso, Stefano

    2009-01-01

    It is generally assumed, both in common-sense argumentations and scientific concepts, that brains and neurons represent late evolutionary achievements which are present only in more advanced animals. Here we overview recently published data clearly revealing that our understanding of bacteria, unicellular eukaryotic organisms, plants, brains and neurons, rooted in the Aristotelian philosophy is flawed. Neural aspects of biological systems are obvious already in bacteria and unicellular biological units such as sexual gametes and diverse unicellular eukaryotic organisms. Altogether, processes and activities thought to represent evolutionary ‘recent’ specializations of the nervous system emerge rather to represent ancient and fundamental cell survival processes. PMID:19513267

  8. Evolutionary Dynamics of Biological Games

    NASA Astrophysics Data System (ADS)

    Nowak, Martin A.; Sigmund, Karl

    2004-02-01

    Darwinian dynamics based on mutation and selection form the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short- and long-term evolution in phenotype space and have found applications ranging from animal behavior and ecology to speciation, macroevolution, and human language. Evolutionary game theory is an essential component of a mathematical and computational approach to biology.

  9. The Evolving Theory of Evolutionary Radiations.

    PubMed

    Simões, M; Breitkreuz, L; Alvarado, M; Baca, S; Cooper, J C; Heins, L; Herzog, K; Lieberman, B S

    2016-01-01

    Evolutionary radiations have intrigued biologists for more than 100 years, and our understanding of the patterns and processes associated with these radiations continues to grow and evolve. Recently it has been recognized that there are many different types of evolutionary radiation beyond the well-studied adaptive radiations. We focus here on multifarious types of evolutionary radiations, paying special attention to the abiotic factors that might trigger diversification in clades. We integrate concepts such as exaptation, species selection, coevolution, and the turnover-pulse hypothesis (TPH) into the theoretical framework of evolutionary radiations. We also discuss other phenomena that are related to, but distinct from, evolutionary radiations that have relevance for evolutionary biology.

  10. Euryhalinity in an evolutionary context

    USGS Publications Warehouse

    Schultz, Eric T.; McCormick, Stephen D.; McCormick, Stephen D.; Farrell, Anthony Peter; Brauner, Colin J.

    2013-01-01

    This chapter focuses on the evolutionary importance and taxonomic distribution of euryhalinity. Euryhalinity refers to broad halotolerance and broad halohabitat distribution. Salinity exposure experiments have demonstrated that species vary tenfold in their range of tolerable salinity levels, primarily because of differences in upper limits. Halotolerance breadth varies with the species’ evolutionary history, as represented by its ordinal classification, and with the species’ halohabitat. Freshwater and seawater species tolerate brackish water; their empirically-determined fundamental haloniche is broader than their realized haloniche, as revealed by the halohabitats they occupy. With respect to halohabitat distribution, a minority of species (<10%) are euryhaline. Habitat-euryhalinity is prevalent among basal actinopterygian fishes, is largely absent from orders arising from intermediate nodes, and reappears in the most derived taxa. There is pronounced family-level variability in the tendency to be halohabitat-euryhaline, which may have arisen during a burst of diversification following the Cretaceous-Palaeogene extinction. Low prevalence notwithstanding, euryhaline species are potent sources of evolutionary diversity. Euryhalinity is regarded as a key innovation trait whose evolution enables exploitation of new adaptive zone, triggering cladogenesis. We review phylogenetically-informed studies that demonstrate freshwater species diversifying from euryhaline ancestors through processes such as landlocking. These studies indicate that some euryhaline taxa are particularly susceptible to changes in halohabitat and subsequent diversification, and some geographic regions have been hotspots for transitions to freshwater. Comparative studies on mechanisms among multiple taxa and at multiple levels of biological integration are needed to clarify evolutionary pathways to, and from, euryhalinity.

  11. Erotomanic stalking in evolutionary perspective.

    PubMed

    Brüne, Martin

    2003-01-01

    Erotomania, the delusion of being loved by another person, comprises marked sex differences concerning prevalence rates and behavior. Whereas traditional psychiatry has considered erotomania to be almost entirely restricted to women, recent studies have revealed that criminal offenses associated with the condition occur much more frequently in men. The main hypothesis of this article is that these findings may be explained in terms of evolutionary theory. Erotomania, accordingly, may be viewed as a pathological variant of a specific sexual strategy that evolved under selection pressures of the human environment of evolutionary adaptedness. The overt behavior is related to the pursuit of long-term mating, its potentially beneficial effect on inclusive fitness of the individual, and disparate strategies of the sexes to ensure sexual fidelity of the potential partner. Therefore, the evolutionary approach provides a plausible explanation as to why forensically relevant erotomania prevails in men. The pathological process of delusional misinterpretation of perceived signals from the social environment itself may result from poor reality testing due to a failure of social meta-cognition. The evolutionary perspective may provide additional insights into the nature of sex-specific behaviors and may improve our understanding of forensically relevant behaviors. PMID:12579619

  12. Evolutionary Psychology and Intelligence Research

    ERIC Educational Resources Information Center

    Kanazawa, Satoshi

    2010-01-01

    This article seeks to unify two subfields of psychology that have hitherto stood separately: evolutionary psychology and intelligence research/differential psychology. I suggest that general intelligence may simultaneously be an evolved adaptation and an individual-difference variable. Tooby and Cosmides's (1990a) notion of random quantitative…

  13. Current Issues in Evolutionary Paleontology.

    ERIC Educational Resources Information Center

    Scully, Erik Paul

    1987-01-01

    Describes some of the contributions made by the field of paleontology to theories in geology and biology. Suggests that the two best examples of modern evolutionary paleontology relate to the theory of punctuated equilibria, and the possibility that mass extinctions may be cyclic. (TW)

  14. Evolutionary Perspective in Child Growth

    PubMed Central

    Hochberg, Ze’ev

    2011-01-01

    Hereditary, environmental, and stochastic factors determine a child’s growth in his unique environment, but their relative contribution to the phenotypic outcome and the extent of stochastic programming that is required to alter human phenotypes is not known because few data are available. This is an attempt to use evolutionary life-history theory in understanding child growth in a broad evolutionary perspective, using the data and theory of evolutionary predictive adaptive growth-related strategies. Transitions from one life-history phase to the next have inherent adaptive plasticity in their timing. Humans evolved to withstand energy crises by decreasing their body size, and evolutionary short-term adaptations to energy crises utilize a plasticity that modifies the timing of transition from infancy into childhood, culminating in short stature in times of energy crisis. Transition to juvenility is part of a strategy of conversion from a period of total dependence on the family and tribe for provision and security to self-supply, and a degree of adaptive plasticity is provided and determines body composition. Transition to adolescence entails plasticity in adapting to energy resources, other environmental cues, and the social needs of the maturing adolescent to determine life-span and the period of fecundity and fertility. Fundamental questions are raised by a life-history approach to the unique growth pattern of each child in his given genetic background and current environment. PMID:23908815

  15. Evolutionary perspective in child growth.

    PubMed

    Hochberg, Ze'ev

    2011-07-01

    Hereditary, environmental, and stochastic factors determine a child's growth in his unique environment, but their relative contribution to the phenotypic outcome and the extent of stochastic programming that is required to alter human phenotypes is not known because few data are available. This is an attempt to use evolutionary life-history theory in understanding child growth in a broad evolutionary perspective, using the data and theory of evolutionary predictive adaptive growth-related strategies. Transitions from one life-history phase to the next have inherent adaptive plasticity in their timing. Humans evolved to withstand energy crises by decreasing their body size, and evolutionary short-term adaptations to energy crises utilize a plasticity that modifies the timing of transition from infancy into childhood, culminating in short stature in times of energy crisis. Transition to juvenility is part of a strategy of conversion from a period of total dependence on the family and tribe for provision and security to self-supply, and a degree of adaptive plasticity is provided and determines body composition. Transition to adolescence entails plasticity in adapting to energy resources, other environmental cues, and the social needs of the maturing adolescent to determine life-span and the period of fecundity and fertility. Fundamental questions are raised by a life-history approach to the unique growth pattern of each child in his given genetic background and current environment.

  16. Computational Physics and Evolutionary Dynamics

    NASA Astrophysics Data System (ADS)

    Fontana, Walter

    2000-03-01

    One aspect of computational physics deals with the characterization of statistical regularities in materials. Computational physics meets biology when these materials can evolve. RNA molecules are a case in point. The folding of RNA sequences into secondary structures (shapes) inspires a simple biophysically grounded genotype-phenotype map that can be explored computationally and in the laboratory. We have identified some statistical regularities of this map and begin to understand their evolutionary consequences. (1) ``typical shapes'': Only a small subset of shapes realized by the RNA folding map is typical, in the sense of containing shapes that are realized significantly more often than others. Consequence: evolutionary histories mostly involve typical shapes, and thus exhibit generic properties. (2) ``neutral networks'': Sequences folding into the same shape are mutationally connected into a network that reaches across sequence space. Consequence: Evolutionary transitions between shapes reflect the fraction of boundary shared by the corresponding neutral networks in sequence space. The notion of a (dis)continuous transition can be made rigorous. (3) ``shape space covering'': Given a random sequence, a modest number of mutations suffices to reach a sequence realizing any typical shape. Consequence: The effective search space for evolutionary optimization is greatly reduced, and adaptive success is less dependent on initial conditions. (4) ``plasticity mirrors variability'': The repertoire of low energy shapes of a sequence is an indicator of how much and in which ways its energetically optimal shape can be altered by a single point mutation. Consequence: (i) Thermodynamic shape stability and mutational robustness are intimately linked. (ii) When natural selection favors the increase of stability, extreme mutational robustness -- to the point of an evolutionary dead-end -- is produced as a side effect. (iii) The hallmark of robust shapes is modularity.

  17. Evolutionary branching under multi-dimensional evolutionary constraints.

    PubMed

    Ito, Hiroshi; Sasaki, Akira

    2016-10-21

    The fitness of an existing phenotype and of a potential mutant should generally depend on the frequencies of other existing phenotypes. Adaptive evolution driven by such frequency-dependent fitness functions can be analyzed effectively using adaptive dynamics theory, assuming rare mutation and asexual reproduction. When possible mutations are restricted to certain directions due to developmental, physiological, or physical constraints, the resulting adaptive evolution may be restricted to subspaces (constraint surfaces) with fewer dimensionalities than the original trait spaces. To analyze such dynamics along constraint surfaces efficiently, we develop a Lagrange multiplier method in the framework of adaptive dynamics theory. On constraint surfaces of arbitrary dimensionalities described with equality constraints, our method efficiently finds local evolutionarily stable strategies, convergence stable points, and evolutionary branching points. We also derive the conditions for the existence of evolutionary branching points on constraint surfaces when the shapes of the surfaces can be chosen freely. PMID:27444402

  18. Evolutionary inspirations for drug discovery.

    PubMed

    Zhang, Hong-Yu; Chen, Ling-Ling; Li, Xue-Juan; Zhang, Jian

    2010-10-01

    Conceptual innovations are needed to address the challenge of 'more investments, fewer drugs' in the pharmaceutical industry. Since the publication of The Origin of Species by Charles Darwin 150 years ago, evolution has been a central concept in biology. In this article, we show that evolutionary concepts are also helpful to streamline the drug-discovery pipeline through facilitating the discovery of targets and drug candidates. Furthermore, the antioxidant paradox can be addressed by an evolutionary methodology. Through examining the evolved biological roles of natural polyphenols (which dominate current antioxidant drug discovery), we reveal that polyphenols (particularly flavonoids) are not evolved for scavenging free radicals. This finding provides new clues to understanding why the strong in vitro antioxidant activities of polyphenols cannot be translated into in vivo effects. Polyphenols have evolved a superior ability to bind various proteins, so we also argue that they are good starting points for multi-target drugs. PMID:20724009

  19. Evolutionary model of stock markets

    NASA Astrophysics Data System (ADS)

    Kaldasch, Joachim

    2014-12-01

    The paper presents an evolutionary economic model for the price evolution of stocks. Treating a stock market as a self-organized system governed by a fast purchase process and slow variations of demand and supply the model suggests that the short term price distribution has the form a logistic (Laplace) distribution. The long term return can be described by Laplace-Gaussian mixture distributions. The long term mean price evolution is governed by a Walrus equation, which can be transformed into a replicator equation. This allows quantifying the evolutionary price competition between stocks. The theory suggests that stock prices scaled by the price over all stocks can be used to investigate long-term trends in a Fisher-Pry plot. The price competition that follows from the model is illustrated by examining the empirical long-term price trends of two stocks.

  20. Ultimate Realities: Deterministic and Evolutionary

    PubMed Central

    Moxley, Roy A

    2007-01-01

    References to ultimate reality commonly turn up in the behavioral literature as references to determinism. However, this determinism is often difficult to interpret. There are different kinds of determinisms as well as different kinds of ultimate realities for a behaviorist to consider. To clarify some of the issues involved, the views of ultimate realities are treated as falling along a continuum, with extreme views of complete indeterminism and complete determinism at either end and various mixes in between. Doing so brings into play evolutionary realities and the movement from indeterminism to determinism, as in Peirce's evolutionary cosmology. In addition, this framework helps to show how the views of determinism by B. F. Skinner and other behaviorists have shifted over time. PMID:22478489

  1. Evolutionary inspirations for drug discovery.

    PubMed

    Zhang, Hong-Yu; Chen, Ling-Ling; Li, Xue-Juan; Zhang, Jian

    2010-10-01

    Conceptual innovations are needed to address the challenge of 'more investments, fewer drugs' in the pharmaceutical industry. Since the publication of The Origin of Species by Charles Darwin 150 years ago, evolution has been a central concept in biology. In this article, we show that evolutionary concepts are also helpful to streamline the drug-discovery pipeline through facilitating the discovery of targets and drug candidates. Furthermore, the antioxidant paradox can be addressed by an evolutionary methodology. Through examining the evolved biological roles of natural polyphenols (which dominate current antioxidant drug discovery), we reveal that polyphenols (particularly flavonoids) are not evolved for scavenging free radicals. This finding provides new clues to understanding why the strong in vitro antioxidant activities of polyphenols cannot be translated into in vivo effects. Polyphenols have evolved a superior ability to bind various proteins, so we also argue that they are good starting points for multi-target drugs.

  2. Evolutionary speed of species invasions.

    PubMed

    García-Ramos, Gisela; Rodríguez, Diego

    2002-04-01

    Successful invasion may depend of the capacity of a species to adjust genetically to a spatially varying environment. This research modeled a species invasion by examining the interaction between a quantitative genetic trait and population density. It assumed: (I) a quantitative genetic trait describes the adaptation of an individual to its local ecological conditions; (2) populations far from the local optimum grow more slowly than those near the optimum; and (3) the evolution of a trait depends on local population density, because differences in local population densities cause asymmetrical gene flow. This genetics-density interaction determined the propagation speed of populations. Numerical simulations showed that populations spread by advancing as two synchronic traveling waves, one for population density and one for trait adaptation. The form of the density wave was a step front that advances homogenizing populations at their carrying capacity; the adaptation wave was a curve with finite slope that homogenizes populations at full adaptation. The largest speed of population expansion, for a dimensionless analysis, corresponded to an almost homogeneous spatial environment when this model approached an ecological description such as the Fisher-Skellam's model. A large genetic response also favored faster speeds. Evolutionary speeds, in a natural scale, showed a wide range of rates that were also slower compared to models that only consider demographics. This evolutionary speed increased with high heritability, strong stabilizing selection, and high intrinsic growth rate. It decreased for steeper environmental gradients. Also indicated was an optimal dispersal rate over which evolutionary speed declined. This is expected because dispersal moves individuals further, but homogenizes populations genetically, making them maladapted. The evolutionary speed was compared to observed data. Furthermore, a moderate increase in the speed of expansion was predicted for

  3. Exaptation, adaptation, and evolutionary psychology.

    PubMed

    Schulz, Armin

    2013-01-01

    One of the most well known methodological criticisms of evolutionary psychology is Gould's claim that the program pays too much attention to adaptations, and not enough to exaptations. Almost as well known is the standard rebuttal of that criticism: namely, that the study of exaptations in fact depends on the study of adaptations. However, as I try to show in this paper, it is premature to think that this is where this debate ends. First, the notion of exaptation that is commonly used in this debate is different from the one that Gould and Vrba originally defined. Noting this is particularly important, since, second, the standard reply to Gould's criticism only works if the criticism is framed in terms of the former notion of exaptation, and not the latter. However, third, this ultimately does not change the outcome of the debate much, as evolutionary psychologists can respond to the revamped criticism of their program by claiming that the original notion of exaptation is theoretically and empirically uninteresting. By discussing these issues further, I also seek to determine, more generally, which ways of approaching the adaptationism debate in evolutionary biology are useful, and which not.

  4. Cancer research meets evolutionary biology

    PubMed Central

    Pepper, John W; Scott Findlay, C; Kassen, Rees; Spencer, Sabrina L; Maley, Carlo C

    2009-01-01

    There is increasing evidence that Darwin's theory of evolution by natural selection provides insights into the etiology and treatment of cancer. On a microscopic scale, neoplastic cells meet the conditions for evolution by Darwinian selection: cell reproduction with heritable variability that affects cell survival and replication. This suggests that, like other areas of biological and biomedical research, Darwinian theory can provide a general framework for understanding many aspects of cancer, including problems of great clinical importance. With the availability of raw molecular data increasing rapidly, this theory may provide guidance in translating data into understanding and progress. Several conceptual and analytical tools from evolutionary biology can be applied to cancer biology. Two clinical problems may benefit most from the application of Darwinian theory: neoplastic progression and acquired therapeutic resistance. The Darwinian theory of cancer has especially profound implications for drug development, both in terms of explaining past difficulties, and pointing the way toward new approaches. Because cancer involves complex evolutionary processes, research should incorporate both tractable (simplified) experimental systems, and also longitudinal observational studies of the evolutionary dynamics of cancer in laboratory animals and in human patients. Cancer biology will require new tools to control the evolution of neoplastic cells. PMID:25567847

  5. Evolutionary routes to stable ownership.

    PubMed

    Hare, D; Reeve, H K; Blossey, B

    2016-06-01

    Ownership can evolve in potentially any species. Drawing on insights from across disciplines, we distinguish between possession and ownership and present species-neutral criteria for ownership, defined as respect for possession. We use a variant of the tug-of-war evolutionary game to demonstrate how ownership can evolve in the form of a new, biologically realistic strategy, Restraint With Retaliation (RWR). In our game, resource holding potential (RHP) is assumed to be equal between interactants, and resource holding asymmetry determines whether ownership is adaptive. RWR will be evolutionarily stable when the ratio of resource holdings between interactants is relatively low, but not when this ratio is sufficiently high. We offer RWR as one evolutionary route to ownership among many, and discuss how ownership unites previously described behavioural phenomena across taxa. We propose that some but not all mechanisms of territory formation and maintenance can be considered ownership, and show that territories are not the only resources that can be owned. We argue that ownership can be a powerful cooperative solution to tragedies of the commons and problems of collective action throughout the biological world. We advance recent scholarship that has begun to investigate the biological importance of ownership, and we call for a comprehensive account of its evolutionary logic and taxonomic distribution. We propose that ownership should be considered a fundamental, unifying biological phenomenon. PMID:26991035

  6. Evolutionary routes to stable ownership.

    PubMed

    Hare, D; Reeve, H K; Blossey, B

    2016-06-01

    Ownership can evolve in potentially any species. Drawing on insights from across disciplines, we distinguish between possession and ownership and present species-neutral criteria for ownership, defined as respect for possession. We use a variant of the tug-of-war evolutionary game to demonstrate how ownership can evolve in the form of a new, biologically realistic strategy, Restraint With Retaliation (RWR). In our game, resource holding potential (RHP) is assumed to be equal between interactants, and resource holding asymmetry determines whether ownership is adaptive. RWR will be evolutionarily stable when the ratio of resource holdings between interactants is relatively low, but not when this ratio is sufficiently high. We offer RWR as one evolutionary route to ownership among many, and discuss how ownership unites previously described behavioural phenomena across taxa. We propose that some but not all mechanisms of territory formation and maintenance can be considered ownership, and show that territories are not the only resources that can be owned. We argue that ownership can be a powerful cooperative solution to tragedies of the commons and problems of collective action throughout the biological world. We advance recent scholarship that has begun to investigate the biological importance of ownership, and we call for a comprehensive account of its evolutionary logic and taxonomic distribution. We propose that ownership should be considered a fundamental, unifying biological phenomenon.

  7. Communication in Natural and Artificial Organisms: Experiments in Evolutionary Robotics

    NASA Astrophysics Data System (ADS)

    Marocco, Davide; Nolfi, Stefano

    In the field of ethological studies many efforts of researchers are devoted to understand how animals communicate and what is the role of communication from an evolutionary and functional point of view. Progress in this area might also have an impact on our understanding of human communication since animal and human communication systems share several features (Hauser, 1996). The social function played by human language, for instance, is one of the first traits that allows us to place language in the same evolutionary field as other animal communication systems. Moreover, recently also the idea of the uniqueness of human language regarding the representational fashion of the knowledge and the compositionality of signals is challenged by new findings in primate research that indicate that, in baboons, knowledge is representational, based on properties that have discrete values and, from a certain point of view, propositional (Seyfarth et al., 2005).

  8. Losing the desire: selection can promote obligate asexuality.

    PubMed

    King, Kayla C; Hurst, Gregory D D

    2010-07-28

    Whilst parthenogenesis has evolved multiple times from sexual invertebrate and vertebrate lineages, the drivers and consequences of the sex-asex transition remain mostly uncertain. A model by Stouthamer et al. recently published in BMC Evolutionary Biology shows a pathway by which obligate asexuality could be selected for following endosymbiont infection. See research article http://www.biomedcentral.com/1471-2148/10/229.

  9. Lethal mutagenesis and evolutionary epidemiology.

    PubMed

    Martin, Guillaume; Gandon, Sylvain

    2010-06-27

    The lethal mutagenesis hypothesis states that within-host populations of pathogens can be driven to extinction when the load of deleterious mutations is artificially increased with a mutagen, and becomes too high for the population to be maintained. Although chemical mutagens have been shown to lead to important reductions in viral titres for a wide variety of RNA viruses, the theoretical underpinnings of this process are still not clearly established. A few recent models sought to describe lethal mutagenesis but they often relied on restrictive assumptions. We extend this earlier work in two novel directions. First, we derive the dynamics of the genetic load in a multivariate Gaussian fitness landscape akin to classical quantitative genetics models. This fitness landscape yields a continuous distribution of mutation effects on fitness, ranging from deleterious to beneficial (i.e. compensatory) mutations. We also include an additional class of lethal mutations. Second, we couple this evolutionary model with an epidemiological model accounting for the within-host dynamics of the pathogen. We derive the epidemiological and evolutionary equilibrium of the system. At this equilibrium, the density of the pathogen is expected to decrease linearly with the genomic mutation rate U. We also provide a simple expression for the critical mutation rate leading to extinction. Stochastic simulations show that these predictions are accurate for a broad range of parameter values. As they depend on a small set of measurable epidemiological and evolutionary parameters, we used available information on several viruses to make quantitative and testable predictions on critical mutation rates. In the light of this model, we discuss the feasibility of lethal mutagenesis as an efficient therapeutic strategy.

  10. Evolutionary Constraints to Viroid Evolution

    PubMed Central

    Elena, Santiago F.; Gómez, Gustavo; Daròs, José-Antonio

    2009-01-01

    We suggest that viroids are trapped into adaptive peaks as the result of adaptive constraints. The first one is imposed by the necessity to fold into packed structures to escape from RNA silencing. This creates antagonistic epistases, which make future adaptive trajectories contingent upon the first mutation and slow down the rate of adaptation. This second constraint can only be surpassed by increasing genetic redundancy or by recombination. Eigen’s paradox imposes a limit to the increase in genome complexity in the absence of mechanisms reducing mutation rate. Therefore, recombination appears as the only possible route to evolutionary innovation in viroids. PMID:21994548

  11. Metabolism at evolutionary optimal States.

    PubMed

    Rabbers, Iraes; van Heerden, Johan H; Nordholt, Niclas; Bachmann, Herwig; Teusink, Bas; Bruggeman, Frank J

    2015-01-01

    Metabolism is generally required for cellular maintenance and for the generation of offspring under conditions that support growth. The rates, yields (efficiencies), adaptation time and robustness of metabolism are therefore key determinants of cellular fitness. For biotechnological applications and our understanding of the evolution of metabolism, it is necessary to figure out how the functional system properties of metabolism can be optimized, via adjustments of the kinetics and expression of enzymes, and by rewiring metabolism. The trade-offs that can occur during such optimizations then indicate fundamental limits to evolutionary innovations and bioengineering. In this paper, we review several theoretical and experimental findings about mechanisms for metabolic optimization. PMID:26042723

  12. Evolutionary shaping of demographic schedules

    PubMed Central

    Wachter, Kenneth W.; Steinsaltz, David; Evans, Steven N.

    2014-01-01

    Evolutionary processes of natural selection may be expected to leave their mark on age patterns of survival and reproduction. Demographic theory includes three main strands—mutation accumulation, stochastic vitality, and optimal life histories. This paper reviews the three strands and, concentrating on mutation accumulation, extends a mathematical result with broad implications concerning the effect of interactions between small age-specific effects of deleterious mutant alleles. Empirical data from genomic sequencing along with prospects for combining strands of theory hold hope for future progress. PMID:25024186

  13. The Evolutionary Biology of Poxviruses

    PubMed Central

    Hughes, Austin L.; Irausquin, Stephanie; Friedman, Robert

    2009-01-01

    The poxviruses (family Poxviridae) are a family of double-stranded viruses including several species that infect humans and their domestic animals, most notably Variola virus (VARV), the causative agent of smallpox. The evolutionary biology of these viruses poses numerous questions, for which we have only partial answers at present. Here we review evidence regarding the origin of poxviruses, the frequency of host transfer in poxvirus history, horizontal transfer of host genes to poxviruses, and the population processes accounting for patterns of nucleotide sequence polymorphism. PMID:19833230

  14. Policy folklists and evolutionary theory

    PubMed Central

    O’Neill, Barry

    2014-01-01

    Policy folklists present a set of alleged historical facts seen as relevant to some social issue. Although the validity of these folklists is dubious, leaders and writers circulate them in the media, variants arise, and the lists continue on, sometimes for decades. Folklists are repeated because their messages are appealing and their users are credible. Because folklists are on the record, we can examine their origins and changes. This report draws an analogy with evolutionary theory and suggests that biological mechanisms of self-repair, boundary maintenance, plasticity, speciation, and predation have significant interpretations for folklists, and clarify how the lists win the credence of otherwise skeptical people. PMID:25024210

  15. Metabolism at Evolutionary Optimal States

    PubMed Central

    Rabbers, Iraes; van Heerden, Johan H.; Nordholt, Niclas; Bachmann, Herwig; Teusink, Bas; Bruggeman, Frank J.

    2015-01-01

    Metabolism is generally required for cellular maintenance and for the generation of offspring under conditions that support growth. The rates, yields (efficiencies), adaptation time and robustness of metabolism are therefore key determinants of cellular fitness. For biotechnological applications and our understanding of the evolution of metabolism, it is necessary to figure out how the functional system properties of metabolism can be optimized, via adjustments of the kinetics and expression of enzymes, and by rewiring metabolism. The trade-offs that can occur during such optimizations then indicate fundamental limits to evolutionary innovations and bioengineering. In this paper, we review several theoretical and experimental findings about mechanisms for metabolic optimization. PMID:26042723

  16. Introduced species as evolutionary traps

    USGS Publications Warehouse

    Schlaepfer, Martin A.; Sherman, P.W.; Blossey, B.; Runge, M.C.

    2005-01-01

    Invasive species can alter environments in such a way that normal behavioural decision-making rules of native species are no longer adaptive. The evolutionary trap concept provides a useful framework for predicting and managing the impact of harmful invasive species. We discuss how native species can respond to changes in their selective regime via evolution or learning. We also propose novel management strategies to promote the long-term co-existence of native and introduced species in cases where the eradication of the latter is either economically or biologically unrealistic.

  17. Historical change and evolutionary theory.

    PubMed

    Masters, Roger D

    2007-09-01

    Despite advances in fields like genetics, evolutionary psychology, and human behavior and evolution--which generally focus on individual or small group behavior from a biological perspective--evolutionary biology has made little impact on studies of political change and social history. Theories of natural selection often seem inapplicable to human history because our social behavior is embedded in language (which makes possible the concepts of time and social identity on which what we call "history" depends). Peter Corning's Holistic Darwinism reconceptualizes evolutionary biology, making it possible to go beyond the barriers separating the social and natural sciences. Corning focuses on two primary processes: "synergy" (complex multivariate interactions at multiple levels between a species and its environment) and "cybernetics" (the information systems permitting communication between individuals and groups over time). Combining this frame of reference with inclusive fitness theory, it is possible to answer the most important (and puzzling) question in human history: How did a species that lived for millennia in hunter-gatherer bands form centralized states governing large populations of non-kin (including multi-ethnic empires as well as modern nation-states)? The fragility and contemporary ethnic violence in Kenya and the Congo should suffice as evidence that these issues need to be taken seriously. To explain the rise and fall of states as well as changes in human laws and customs--the core of historical research--it is essential to show how the provision of collective goods can overcome the challenge of self-interest and free-riding in some instances, yet fail to do so in others. To this end, it is now possible to consider how a state providing public goods can--under circumstances that often include effective leadership--contribute to enhanced inclusive fitness of virtually all its members. Because social behavior needs to adapt to ecology, but ecological

  18. Historical change and evolutionary theory.

    PubMed

    Masters, Roger D

    2007-09-01

    Despite advances in fields like genetics, evolutionary psychology, and human behavior and evolution--which generally focus on individual or small group behavior from a biological perspective--evolutionary biology has made little impact on studies of political change and social history. Theories of natural selection often seem inapplicable to human history because our social behavior is embedded in language (which makes possible the concepts of time and social identity on which what we call "history" depends). Peter Corning's Holistic Darwinism reconceptualizes evolutionary biology, making it possible to go beyond the barriers separating the social and natural sciences. Corning focuses on two primary processes: "synergy" (complex multivariate interactions at multiple levels between a species and its environment) and "cybernetics" (the information systems permitting communication between individuals and groups over time). Combining this frame of reference with inclusive fitness theory, it is possible to answer the most important (and puzzling) question in human history: How did a species that lived for millennia in hunter-gatherer bands form centralized states governing large populations of non-kin (including multi-ethnic empires as well as modern nation-states)? The fragility and contemporary ethnic violence in Kenya and the Congo should suffice as evidence that these issues need to be taken seriously. To explain the rise and fall of states as well as changes in human laws and customs--the core of historical research--it is essential to show how the provision of collective goods can overcome the challenge of self-interest and free-riding in some instances, yet fail to do so in others. To this end, it is now possible to consider how a state providing public goods can--under circumstances that often include effective leadership--contribute to enhanced inclusive fitness of virtually all its members. Because social behavior needs to adapt to ecology, but ecological

  19. Evolutionary dynamics on interdependent populations

    NASA Astrophysics Data System (ADS)

    Gómez-Gardeñes, Jesús; Gracia-Lázaro, Carlos; Floría, Luis Mario; Moreno, Yamir

    2012-11-01

    Although several mechanisms can promote cooperative behavior, there is no general consensus about why cooperation survives when the most profitable action for an individual is to defect, especially when the population is well mixed. Here we show that when a replicator such as evolutionary game dynamics takes place on interdependent networks, cooperative behavior is fixed on the system. Remarkably, we analytically and numerically show that this is even the case for well-mixed populations. Our results open the path to mechanisms able to sustain cooperation and can provide hints for controlling its rise and fall in a variety of biological and social systems.

  20. Conceptual Barriers to Progress Within Evolutionary Biology.

    PubMed

    Laland, Kevin N; Odling-Smee, John; Feldman, Marcus W; Kendal, Jeremy

    2009-08-01

    In spite of its success, Neo-Darwinism is faced with major conceptual barriers to further progress, deriving directly from its metaphysical foundations. Most importantly, neo-Darwinism fails to recognize a fundamental cause of evolutionary change, "niche construction". This failure restricts the generality of evolutionary theory, and introduces inaccuracies. It also hinders the integration of evolutionary biology with neighbouring disciplines, including ecosystem ecology, developmental biology, and the human sciences. Ecology is forced to become a divided discipline, developmental biology is stubbornly difficult to reconcile with evolutionary theory, and the majority of biologists and social scientists are still unhappy with evolutionary accounts of human behaviour. The incorporation of niche construction as both a cause and a product of evolution removes these disciplinary boundaries while greatly generalizing the explanatory power of evolutionary theory.

  1. The Evolving Theory of Evolutionary Radiations.

    PubMed

    Simões, M; Breitkreuz, L; Alvarado, M; Baca, S; Cooper, J C; Heins, L; Herzog, K; Lieberman, B S

    2016-01-01

    Evolutionary radiations have intrigued biologists for more than 100 years, and our understanding of the patterns and processes associated with these radiations continues to grow and evolve. Recently it has been recognized that there are many different types of evolutionary radiation beyond the well-studied adaptive radiations. We focus here on multifarious types of evolutionary radiations, paying special attention to the abiotic factors that might trigger diversification in clades. We integrate concepts such as exaptation, species selection, coevolution, and the turnover-pulse hypothesis (TPH) into the theoretical framework of evolutionary radiations. We also discuss other phenomena that are related to, but distinct from, evolutionary radiations that have relevance for evolutionary biology. PMID:26632984

  2. Language as an evolutionary system

    NASA Astrophysics Data System (ADS)

    Brighton, Henry; Smith, Kenny; Kirby, Simon

    2005-09-01

    John Maynard Smith and Eörs Szathmáry argued that human language signified the eighth major transition in evolution: human language marked a new form of information transmission from one generation to another [Maynard Smith J, Szathmáry E. The major transitions in evolution. Oxford: Oxford Univ. Press; 1995]. According to this view language codes cultural information and as such forms the basis for the evolution of complexity in human culture. In this article we develop the theory that language also codes information in another sense: languages code information on their own structure. As a result, languages themselves provide information that influences their own survival. To understand the consequences of this theory we discuss recent computational models of linguistic evolution. Linguistic evolution is the process by which languages themselves evolve. This article draws together this recent work on linguistic evolution and highlights the significance of this process in understanding the evolution of linguistic complexity. Our conclusions are that: (1) the process of linguistic transmission constitutes the basis for an evolutionary system, and (2), that this evolutionary system is only superficially comparable to the process of biological evolution.

  3. The Evolutionary Puzzle of Suicide

    PubMed Central

    Aubin, Henri-Jean; Berlin, Ivan; Kornreich, Charles

    2013-01-01

    Mechanisms of self-destruction are difficult to reconcile with evolution’s first rule of thumb: survive and reproduce. However, evolutionary success ultimately depends on inclusive fitness. The altruistic suicide hypothesis posits that the presence of low reproductive potential and burdensomeness toward kin can increase the inclusive fitness payoff of self-removal. The bargaining hypothesis assumes that suicide attempts could function as an honest signal of need. The payoff may be positive if the suicidal person has a low reproductive potential. The parasite manipulation hypothesis is founded on the rodent—Toxoplasma gondii host-parasite model, in which the parasite induces a “suicidal” feline attraction that allows the parasite to complete its life cycle. Interestingly, latent infection by T. gondii has been shown to cause behavioral alterations in humans, including increased suicide attempts. Finally, we discuss how suicide risk factors can be understood as nonadaptive byproducts of evolved mechanisms that malfunction. Although most of the mechanisms proposed in this article are largely speculative, the hypotheses that we raise accept self-destructive behavior within the framework of evolutionary theory. PMID:24351787

  4. Evolutionary dynamics on random structures

    SciTech Connect

    Fraser, S.M.; Reidys, C.M. |

    1997-04-01

    In this paper the authors consider the evolutionary dynamics of populations of sequences, under a process of selection at the phenotypic level of structures. They use a simple graph-theoretic representation of structures which captures well the properties of the mapping between RNA sequences and their molecular structure. Each sequence is assigned to a structure by means of a sequence-to-structure mapping. The authors make the basic assumption that every fitness landscape can be factorized through the structures. The set of all sequences that map into a particular random structure can then be modeled as a random graph in sequence space, the so-called neutral network. They analyze in detail how an evolving population searches for new structures, in particular how they switch from one neutral network to another. They verify that transitions occur directly between neutral networks, and study the effects of different population sizes and the influence of the relatedness of the structures on these transitions. In fitness landscapes where several structures exhibit high fitness, the authors then study evolutionary paths on the structural level taken by the population during its search. They present a new way of expressing structural similarities which are shown to have relevant implications for the time evolution of the population.

  5. Exploration dynamics in evolutionary games.

    PubMed

    Traulsen, Arne; Hauert, Christoph; De Silva, Hannelore; Nowak, Martin A; Sigmund, Karl

    2009-01-20

    Evolutionary game theory describes systems where individual success is based on the interaction with others. We consider a system in which players unconditionally imitate more successful strategies but sometimes also explore the available strategies at random. Most research has focused on how strategies spread via genetic reproduction or cultural imitation, but random exploration of the available set of strategies has received less attention so far. In genetic settings, the latter corresponds to mutations in the DNA, whereas in cultural evolution, it describes individuals experimenting with new behaviors. Genetic mutations typically occur with very small probabilities, but random exploration of available strategies in behavioral experiments is common. We term this phenomenon "exploration dynamics" to contrast it with the traditional focus on imitation. As an illustrative example of the emerging evolutionary dynamics, we consider a public goods game with cooperators and defectors and add punishers and the option to abstain from the enterprise in further scenarios. For small mutation rates, cooperation (and punishment) is possible only if interactions are voluntary, whereas moderate mutation rates can lead to high levels of cooperation even in compulsory public goods games. This phenomenon is investigated through numerical simulations and analytical approximations.

  6. Behavior Trees for Evolutionary Robotics.

    PubMed

    Scheper, Kirk Y W; Tijmons, Sjoerd; de Visser, Cornelis C; de Croon, Guido C H E

    2016-01-01

    Evolutionary Robotics allows robots with limited sensors and processing to tackle complex tasks by means of sensory-motor coordination. In this article we show the first application of the Behavior Tree framework on a real robotic platform using the evolutionary robotics methodology. This framework is used to improve the intelligibility of the emergent robotic behavior over that of the traditional neural network formulation. As a result, the behavior is easier to comprehend and manually adapt when crossing the reality gap from simulation to reality. This functionality is shown by performing real-world flight tests with the 20-g DelFly Explorer flapping wing micro air vehicle equipped with a 4-g onboard stereo vision system. The experiments show that the DelFly can fully autonomously search for and fly through a window with only its onboard sensors and processing. The success rate of the optimized behavior in simulation is 88%, and the corresponding real-world performance is 54% after user adaptation. Although this leaves room for improvement, it is higher than the 46% success rate from a tuned user-defined controller. PMID:26606468

  7. Behavior Trees for Evolutionary Robotics.

    PubMed

    Scheper, Kirk Y W; Tijmons, Sjoerd; de Visser, Cornelis C; de Croon, Guido C H E

    2016-01-01

    Evolutionary Robotics allows robots with limited sensors and processing to tackle complex tasks by means of sensory-motor coordination. In this article we show the first application of the Behavior Tree framework on a real robotic platform using the evolutionary robotics methodology. This framework is used to improve the intelligibility of the emergent robotic behavior over that of the traditional neural network formulation. As a result, the behavior is easier to comprehend and manually adapt when crossing the reality gap from simulation to reality. This functionality is shown by performing real-world flight tests with the 20-g DelFly Explorer flapping wing micro air vehicle equipped with a 4-g onboard stereo vision system. The experiments show that the DelFly can fully autonomously search for and fly through a window with only its onboard sensors and processing. The success rate of the optimized behavior in simulation is 88%, and the corresponding real-world performance is 54% after user adaptation. Although this leaves room for improvement, it is higher than the 46% success rate from a tuned user-defined controller.

  8. Physical foundations of evolutionary theory

    NASA Astrophysics Data System (ADS)

    Annila, Arto; Salthe, Stanley

    2010-10-01

    The theory of evolution by natural selection is herein subsumed by the 2nd law of thermodynamics. The mathematical form of evolutionary theory is based on a re-examination of the probability concept that underlies statistical physics. Probability regarded as physical must include, in addition to isoenergic combinatorial configurations, also energy in conditional circumstances. Consequently, entropy as an additive logarithmic probability measure is found to be a function of the free energy, and the process toward the maximum entropy state is found equivalent to evolution toward the free energy minimum in accordance with the basic maxim of chemical thermodynamics. The principle of increasing entropy when given as an equation of motion reveals that expansion, proliferation, differentiation, diversification, and catalysis are all ways for a system to evolve toward the stationary state in its respective surroundings. Intriguingly, the equation of evolution cannot be solved when there remain degrees of freedom to consume the free energy, and hence evolutionary trajectories of a non-Hamiltonian system remain intractable. Finally, when to-and-from flows of energy are balanced between a system and its surroundings, the system is at the Lyapunov-stable stationary state. The principle of maximal energy dispersal, equivalent to the maximal rate of entropy production, gives rise to the ubiquitous characteristics, conventions, and regularities found in nature, where thermodynamics makes no demarcation line between animate and inanimate.

  9. Evolutionary expansion of the Monogenea.

    PubMed

    Kearn, G C

    1994-12-01

    The evolutionary expansion of the monogeneans has taken place in parallel with the diversification of the fish-like vertebrates. In this article the main trends in monogenean evolution are traced from a hypothetical skin-parasitic ancestor on early vertebrates. Special consideration is given to the following topics: early divergence between skin feeders and blood feeders; diversification and specialization of the haptor for attachment to skin; transfer from host to host, viviparity and the success of the gyrodactylids; predation on skin parasites and camouflage; colonization of the buccal and branchial cavities; diversification and specialization of the haptor for attachment to the gills; phoresy in gill parasites; the development of endoparasitism and the origin of the cestodes; the success of dactylogyroidean gill parasites; the uniqueness of the polyopisthocotyleans; ovoviviparity and the colonization of the tetrapods. Host specificity has been the guiding force of coevolution between monogeneans and their vertebrate hosts, but the establishment of monogeneans on unrelated hosts sharing the same environment (host-switching) may have been underestimated. Host-switching has provided significant opportunities for evolutionary change of direction and is probably responsible for the establishment of monogeneans on cephalopod molluscs, on the hippopotamus and possibly on chelonians. There are indications that host-switching may be more common in monogeneans that spread by direct transfer of adults/juveniles from host to host. A limitation on the further expansion of monogeneans is the need for water for the dispersal of the infective larva (oncomiracidium).

  10. Measuring Evolutionary Isolation for Conservation.

    PubMed

    Redding, David W; Mazel, Florent; Mooers, Arne Ø

    2014-01-01

    Conservation planning needs to account for limited resources when choosing those species on which to focus attention and resources. Currently, funding is biased to small sections of the tree of life, such as raptors and carnivores. One new approach for increasing the diversity of species under consideration considers how many close relatives a species has in its evolutionary tree. At least eleven different ways to measure this characteristic on phylogenies for the purposes of setting species-specific priorities for conservation have been proposed. We find that there is much redundancy within the current set, with three pairs of metrics being essentially identical. Non-redundant metrics represent different trade-offs between the unique evolutionary history represented by a species verses its average distance to all other species. Depending on which metric is used, species priority lists can differ as much as 85% for the top 100 species. We call for some consensus on the theory behind these metrics and suggest that all future developments are compared to the current published set, and offer scripts to aid such comparisons.

  11. Evolutionary potential games on lattices

    NASA Astrophysics Data System (ADS)

    Szabó, György; Borsos, István

    2016-04-01

    Game theory provides a general mathematical background to study the effect of pair interactions and evolutionary rules on the macroscopic behavior of multi-player games where players with a finite number of strategies may represent a wide scale of biological objects, human individuals, or even their associations. In these systems the interactions are characterized by matrices that can be decomposed into elementary matrices (games) and classified into four types. The concept of decomposition helps the identification of potential games and also the evaluation of the potential that plays a crucial role in the determination of the preferred Nash equilibrium, and defines the Boltzmann distribution towards which these systems evolve for suitable types of dynamical rules. This survey draws parallel between the potential games and the kinetic Ising type models which are investigated for a wide scale of connectivity structures. We discuss briefly the applicability of the tools and concepts of statistical physics and thermodynamics. Additionally the general features of ordering phenomena, phase transitions and slow relaxations are outlined and applied to evolutionary games. The discussion extends to games with three or more strategies. Finally we discuss what happens when the system is weakly driven out of the "equilibrium state" by adding non-potential components representing games of cyclic dominance.

  12. [Evolutionary endocrinology: a pending matter].

    PubMed

    Zafón, Carles

    2012-01-01

    Twenty years have passed since the foundational article of what is now known as evolutionary medicine (EM) was published. This young medical discipline examines, following Darwinian principles, susceptibility to certain diseases and how we react to them. In short, EM analyzes the final cause of the disease from a historical perspective. Over the years, EM has been introduced in various medical areas in very different ways. While it has found a role in some fields such as infectious diseases and oncology, its contribution in other areas has been quite limited. In endocrinology, EM has only gained prominence as a basis for the so-called "diseases of civilization", including diabetes mellitus and obesity. However, many experts suggest that it may have a much higher potential. The aim of this paper is to provide a view about what evolutionary medicine is. Some examples of how EM may contribute to progress of our specialty are also given. There is no doubt that evolution enriches medicine, but medicine also offers knowledge to evolution. PMID:22113050

  13. Evolutionary development of tensegrity structures.

    PubMed

    Lobo, Daniel; Vico, Francisco J

    2010-09-01

    Contributions from the emerging fields of molecular genetics and evo-devo (evolutionary developmental biology) are greatly benefiting the field of evolutionary computation, initiating a promise of renewal in the traditional methodology. While direct encoding has constituted a dominant paradigm, indirect ways to encode the solutions have been reported, yet little attention has been paid to the benefits of the proposed methods to real problems. In this work, we study the biological properties that emerge by means of using indirect encodings in the context of form-finding problems. A novel indirect encoding model for artificial development has been defined and applied to an engineering structural-design problem, specifically to the discovery of tensegrity structures. This model has been compared with a direct encoding scheme. While the direct encoding performs similarly well to the proposed method, indirect-based results typically outperform the direct-based results in aspects not directly linked to the nature of the problem itself, but to the emergence of properties found in biological organisms, like organicity, generalization capacity, or modularity aspects which are highly valuable in engineering. PMID:20619314

  14. The evolutionary puzzle of suicide.

    PubMed

    Aubin, Henri-Jean; Berlin, Ivan; Kornreich, Charles

    2013-12-09

    Mechanisms of self-destruction are difficult to reconcile with evolution's first rule of thumb: survive and reproduce. However, evolutionary success ultimately depends on inclusive fitness. The altruistic suicide hypothesis posits that the presence of low reproductive potential and burdensomeness toward kin can increase the inclusive fitness payoff of self-removal. The bargaining hypothesis assumes that suicide attempts could function as an honest signal of need. The payoff may be positive if the suicidal person has a low reproductive potential. The parasite manipulation hypothesis is founded on the rodent-Toxoplasma gondii host-parasite model, in which the parasite induces a "suicidal" feline attraction that allows the parasite to complete its life cycle. Interestingly, latent infection by T. gondii has been shown to cause behavioral alterations in humans, including increased suicide attempts. Finally, we discuss how suicide risk factors can be understood as nonadaptive byproducts of evolved mechanisms that malfunction. Although most of the mechanisms proposed in this article are largely speculative, the hypotheses that we raise accept self-destructive behavior within the framework of evolutionary theory.

  15. Exploration dynamics in evolutionary games.

    PubMed

    Traulsen, Arne; Hauert, Christoph; De Silva, Hannelore; Nowak, Martin A; Sigmund, Karl

    2009-01-20

    Evolutionary game theory describes systems where individual success is based on the interaction with others. We consider a system in which players unconditionally imitate more successful strategies but sometimes also explore the available strategies at random. Most research has focused on how strategies spread via genetic reproduction or cultural imitation, but random exploration of the available set of strategies has received less attention so far. In genetic settings, the latter corresponds to mutations in the DNA, whereas in cultural evolution, it describes individuals experimenting with new behaviors. Genetic mutations typically occur with very small probabilities, but random exploration of available strategies in behavioral experiments is common. We term this phenomenon "exploration dynamics" to contrast it with the traditional focus on imitation. As an illustrative example of the emerging evolutionary dynamics, we consider a public goods game with cooperators and defectors and add punishers and the option to abstain from the enterprise in further scenarios. For small mutation rates, cooperation (and punishment) is possible only if interactions are voluntary, whereas moderate mutation rates can lead to high levels of cooperation even in compulsory public goods games. This phenomenon is investigated through numerical simulations and analytical approximations. PMID:19124771

  16. Major evolutionary transitions in individuality

    PubMed Central

    West, Stuart A.; Fisher, Roberta M.; Gardner, Andy; Kiers, E. Toby

    2015-01-01

    The evolution of life on earth has been driven by a small number of major evolutionary transitions. These transitions have been characterized by individuals that could previously replicate independently, cooperating to form a new, more complex life form. For example, archaea and eubacteria formed eukaryotic cells, and cells formed multicellular organisms. However, not all cooperative groups are en route to major transitions. How can we explain why major evolutionary transitions have or haven’t taken place on different branches of the tree of life? We break down major transitions into two steps: the formation of a cooperative group and the transformation of that group into an integrated entity. We show how these steps require cooperation, division of labor, communication, mutual dependence, and negligible within-group conflict. We find that certain ecological conditions and the ways in which groups form have played recurrent roles in driving multiple transitions. In contrast, we find that other factors have played relatively minor roles at many key points, such as within-group kin discrimination and mechanisms to actively repress competition. More generally, by identifying the small number of factors that have driven major transitions, we provide a simpler and more unified description of how life on earth has evolved. PMID:25964342

  17. DED: Database of Evolutionary Distances.

    PubMed

    Veeramachaneni, Vamsi; Makalowski, Wojciech

    2005-01-01

    A large database of homologous sequence alignments with good estimates of evolutionary distances can be a valuable resource for molecular evolutionary studies and phylogenetic research in particular. We recently created a database containing 159,921 transcripts from human, mouse, rat, zebrafish and fugu species. Approximately 1,000 homology groups were identified with the help of Ensembl homology evidence. At the macro-level, the database allows us to answer queries of the form: 1. What is the average k-distance between 5' untranslated regions of human and mouse? 2. List the 10 groups with the highest K(a)/K(s) ratio between mouse and rat. 3. List all identical proteins between human and rat. Researchers interested in specific proteins can use a simple web interface to retrieve the homology groups of interest, examine all pairwise distances between members of the group and study the conservation of exon-intron gene structures using a graphical interface. The database is available at http://warta.bio.psu.edu/DED/.

  18. Evolutionary development of tensegrity structures.

    PubMed

    Lobo, Daniel; Vico, Francisco J

    2010-09-01

    Contributions from the emerging fields of molecular genetics and evo-devo (evolutionary developmental biology) are greatly benefiting the field of evolutionary computation, initiating a promise of renewal in the traditional methodology. While direct encoding has constituted a dominant paradigm, indirect ways to encode the solutions have been reported, yet little attention has been paid to the benefits of the proposed methods to real problems. In this work, we study the biological properties that emerge by means of using indirect encodings in the context of form-finding problems. A novel indirect encoding model for artificial development has been defined and applied to an engineering structural-design problem, specifically to the discovery of tensegrity structures. This model has been compared with a direct encoding scheme. While the direct encoding performs similarly well to the proposed method, indirect-based results typically outperform the direct-based results in aspects not directly linked to the nature of the problem itself, but to the emergence of properties found in biological organisms, like organicity, generalization capacity, or modularity aspects which are highly valuable in engineering.

  19. An introduction to evolutionary developmental psychology.

    PubMed

    Machluf, Karin; Liddle, James R; Bjorklund, David F

    2014-04-29

    Evolutionary developmental psychology represents a synthesis of modern evolutionary theory and developmental psychology. Here we introduce the special issue on evolutionary developmental psychology by briefly discussing the history of this field and then summarizing the variety of topics that are covered. In this special issue, leading researchers provide a collection of theoretical and empirical articles that highlight recent findings and propose promising areas for future research.

  20. Evolutionary psychology: its programs, prospects, and pitfalls.

    PubMed

    Neher, Andrew

    2006-01-01

    The emerging specialty of evolutionary psychology presents a challenge to mainstream psychology. It proposes that cognitive, notjust more fundamental, traits in humans are grounded in dedicated evolutionary programs. Specifically, it maintains that the common assumption in psychology-that the complexities of our psyches have been largely freed from evolutionary constraints and are instead based in a general learning capacity-is mistaken. The major premises of evolutionary psychology are examined in light of arguments and evidence presented by both supporters and detractors. Although some of these premises are well grounded, others are questionable and limit the development of the specialty and its integration into mainstream psychology.

  1. An introduction to comparative evolutionary psychology.

    PubMed

    Vonk, Jennifer; Shackelford, Todd K

    2013-07-18

    Previously we (Vonk and Shackelford, 2012, in press) proposed an integration of comparative psychology and evolutionary psychology into a new field of "comparative evolutionary psychology." This integrative discipline incorporates principles from ethology, ecology, biology, anthropology, and psychology, broadly defined. We present in this special issue a collection of original empirical and theoretical review articles in which leading researchers propose ways to successfully integrate comparative and evolutionary approaches within their particular areas of study. We showcase the key contributions of these articles and highlight several empirical and theoretical challenges, as well as key future directions, for comparative evolutionary psychology.

  2. Child murder by parents and evolutionary psychology.

    PubMed

    Friedman, Susan Hatters; Cavney, James; Resnick, Phillip J

    2012-12-01

    This article explores the contribution of evolutionary theory to the understanding of causation and motive in filicide cases and also reviews special issues in the forensic evaluation of alleged perpetrators of filicide. Evolutionary social psychology seeks to understand the context in which our brains evolved, to understand human behaviors. The authors propose evolutionary theory as a framework theory to meaningfully appreciate research about filicide. Using evolutionary psychology as a theoretical lens, this article reviews the research on filicide over the past 40 years, and describes epidemiologic and typologic studies of filicide, and theoretical analyses from a range of disciplines.

  3. Child murder by parents and evolutionary psychology.

    PubMed

    Friedman, Susan Hatters; Cavney, James; Resnick, Phillip J

    2012-12-01

    This article explores the contribution of evolutionary theory to the understanding of causation and motive in filicide cases and also reviews special issues in the forensic evaluation of alleged perpetrators of filicide. Evolutionary social psychology seeks to understand the context in which our brains evolved, to understand human behaviors. The authors propose evolutionary theory as a framework theory to meaningfully appreciate research about filicide. Using evolutionary psychology as a theoretical lens, this article reviews the research on filicide over the past 40 years, and describes epidemiologic and typologic studies of filicide, and theoretical analyses from a range of disciplines. PMID:23107563

  4. Evolutionary triangulation: informing genetic association studies with evolutionary evidence.

    PubMed

    Huang, Minjun; Graham, Britney E; Zhang, Ge; Harder, Reed; Kodaman, Nuri; Moore, Jason H; Muglia, Louis; Williams, Scott M

    2016-01-01

    Genetic studies of human diseases have identified many variants associated with pathogenesis and severity. However, most studies have used only statistical association to assess putative relationships to disease, and ignored other factors for evaluation. For example, evolution is a factor that has shaped disease risk, changing allele frequencies as human populations migrated into and inhabited new environments. Since many common variants differ among populations in frequency, as does disease prevalence, we hypothesized that patterns of disease and population structure, taken together, will inform association studies. Thus, the population distributions of allelic risk variants should reflect the distributions of their associated diseases. Evolutionary Triangulation (ET) exploits this evolutionary differentiation by comparing population structure among three populations with variable patterns of disease prevalence. By selecting populations based on patterns where two have similar rates of disease that differ substantially from a third, we performed a proof of principle analysis for this method. We examined three disease phenotypes, lactase persistence, melanoma, and Type 2 diabetes mellitus. We show that for lactase persistence, a phenotype with a simple genetic architecture, ET identifies the key gene, lactase. For melanoma, ET identifies several genes associated with this disease and/or phenotypes related to it, such as skin color genes. ET was less obviously successful for Type 2 diabetes mellitus, perhaps because of the small effect sizes in known risk loci and recent environmental changes that have altered disease risk. Alternatively, ET may have revealed new genes involved in conferring disease risk for diabetes that did not meet nominal GWAS significance thresholds. We also compared ET to another method used to filter for phenotype associated genes, population branch statistic (PBS), and show that ET performs better in identifying genes known to associate with

  5. Evolutionary triangulation: informing genetic association studies with evolutionary evidence.

    PubMed

    Huang, Minjun; Graham, Britney E; Zhang, Ge; Harder, Reed; Kodaman, Nuri; Moore, Jason H; Muglia, Louis; Williams, Scott M

    2016-01-01

    Genetic studies of human diseases have identified many variants associated with pathogenesis and severity. However, most studies have used only statistical association to assess putative relationships to disease, and ignored other factors for evaluation. For example, evolution is a factor that has shaped disease risk, changing allele frequencies as human populations migrated into and inhabited new environments. Since many common variants differ among populations in frequency, as does disease prevalence, we hypothesized that patterns of disease and population structure, taken together, will inform association studies. Thus, the population distributions of allelic risk variants should reflect the distributions of their associated diseases. Evolutionary Triangulation (ET) exploits this evolutionary differentiation by comparing population structure among three populations with variable patterns of disease prevalence. By selecting populations based on patterns where two have similar rates of disease that differ substantially from a third, we performed a proof of principle analysis for this method. We examined three disease phenotypes, lactase persistence, melanoma, and Type 2 diabetes mellitus. We show that for lactase persistence, a phenotype with a simple genetic architecture, ET identifies the key gene, lactase. For melanoma, ET identifies several genes associated with this disease and/or phenotypes related to it, such as skin color genes. ET was less obviously successful for Type 2 diabetes mellitus, perhaps because of the small effect sizes in known risk loci and recent environmental changes that have altered disease risk. Alternatively, ET may have revealed new genes involved in conferring disease risk for diabetes that did not meet nominal GWAS significance thresholds. We also compared ET to another method used to filter for phenotype associated genes, population branch statistic (PBS), and show that ET performs better in identifying genes known to associate with

  6. Anticipatory Mechanisms in Evolutionary Living Systems

    NASA Astrophysics Data System (ADS)

    Dubois, Daniel M.; Holmberg, Stig C.

    2010-11-01

    This paper deals firstly with a revisiting of Darwin's theory of Natural Selection. Darwin in his book never uses the word "evolution", but shows a clear position about mutability of species. Darwin's Natural Selection was mainly inspired by the anticipatory Artificial Selection by humans in domestication, and the Malthus struggle for existence. Darwin showed that the struggle for existence leads to the preservation of the most divergent offspring of any one species. He cited several times the canon of "Natura non facit saltum". He spoke about the origin of life from some one primordial form, into which life was first breathed. Finally, Darwin made anticipation about the future researches in psychology. This paper cites the work of Ernst Mayr who was the first, after 90 years of an intense scientific debate, to present a new and stable Darwinian paradigm as the "Evolutionary Synthesis" in 1942. To explain what is life, the Living Systems Theory (LST) by J. G. Miller is presented. It is showed that the Autopoietic Systems Theory of Varela et al is also a fundamental component of living systems. In agreement with Darwin, the natural selection is a necessary condition for transformation of biological systems, but is not a sufficient condition. Thus, in this paper we conjecture that an anticipatory evolutionary mechanism exists with the genetic code that is a self-replicating and self-modifying anticipatory program. As demonstrated by Nobel laureate McClintock, evolution in genomes is programmed. The word "program" comes from "pro-gram" meaning to write before, by anticipation, and means a plan for the programming of a mechanism, or a sequence of coded instructions that can be inserted into a mechanism, or a sequence of coded instructions, as genes of behavioural responses, that is part of an organism. For example, cell death may be programmed by what is called the apoptosis. This definitively is a great breakthrough in our understanding of biological evolution. Hence

  7. 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

  8. 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

  9. Al Composites

    NASA Astrophysics Data System (ADS)

    Chandanayaka, Tharaka; Azarmi, Fardad

    2014-05-01

    In the present study, cold spraying technique was used to fabricate a metal matrix composite (MMC) that consists of Ni matrix and 20 vol.% Ni3Al particles at two different particle sizes as reinforcement. This study intends to investigate the effect of reinforcement particle size on microstructural and mechanical properties of cold sprayed MMCs. Two different Ni3Al powders with nominal particle size of -45 to +5 and +45 to 100 μm were used as reinforcement in this study. Cold sprayed Ni-Ni3Al samples were subjected to the microstructural observation and characterization prior to any mechanical testing. Then, samples were tested using nano-indentation, Knoop hardness, Vickers hardness, and Resonance frequency to evaluate their mechanical properties. No significant changes were observed in microstructural characteristics due to different particle sizes. The results obtained from a variety of mechanical testings indicated that the increasing reinforcement particle size resulted in the slight reduction of mechanical properties such as elastic modulus and hardness in cold sprayed MMCs. The mechanical interlock between deposited particles defines the bonding strength in cold sprayed samples. Small size particles have a higher velocity and impact resulting in stronger interlock between deformed particles.

  10. Evolutionary Adaptations to Dietary Changes

    PubMed Central

    Luca, F.; Perry, G.H.; Di Rienzo, A.

    2014-01-01

    Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area. PMID:20420525

  11. Alcoholism's evolutionary and cultural origins.

    PubMed

    Abel, Ernest L

    2010-12-01

    Alcoholism's heritability has been convincingly documented but the question of why a disorder that is so damaging to the individual and to society should continue to persist is still baffling. A widely held assumption is that whatever genotype is involved, its components must originally have conferred survival value else it would never have evolved. The corollary to that assumption is that when conditions favoring that genotype changed, the former advantages became detrimental. However, the genotype has persisted because it does not affect sexual function, if at all, until after peak productive years. An appreciation of the evolutionary biology and the historical-cultural context associated with alcohol consumption may lead not only to a better understanding of this disorder but to treatment alternatives based on that understanding.

  12. The evolutionary origins of friendship.

    PubMed

    Seyfarth, Robert M; Cheney, Dorothy L

    2012-01-01

    Convergent evidence from many species reveals the evolutionary origins of human friendship. In horses, elephants, hyenas, dolphins, monkeys, and chimpanzees, some individuals form friendships that last for years. Bonds occur among females, among males, or between males and females. Genetic relatedness affects friendships. In species where males disperse, friendships are more likely among females. If females disperse, friendships are more likely among males. Not all friendships, however, depend on kinship; many are formed between unrelated individuals. Friendships often involve cooperative interactions that are separated in time. They depend, at least in part, on the memory and emotions associated with past interactions. Applying the term "friendship" to animals is not anthropomorphic: Many studies have shown that the animals themselves recognize others' relationships. Friendships are adaptive. Male allies have superior competitive ability and improved reproductive success; females with the strongest, most enduring friendships experience less stress, higher infant survival, and live longer. PMID:21740224

  13. Evolutionary Industrial Physical Model Generation

    NASA Astrophysics Data System (ADS)

    Carrascal, Alberto; Alberdi, Amaia

    Both complexity and lack of knowledge associated to physical processes makes physical models design an arduous task. Frequently, the only available information about the physical processes are the heuristic data obtained from experiments or at best a rough idea on what are the physical principles and laws that underlie considered physical processes. Then the problem is converted to find a mathematical expression which fits data. There exist traditional approaches to tackle the inductive model search process from data, such as regression, interpolation, finite element method, etc. Nevertheless, these methods either are only able to solve a reduced number of simple model typologies, or the given black-box solution does not contribute to clarify the analyzed physical process. In this paper a hybrid evolutionary approach to search complex physical models is proposed. Tests carried out on a real-world industrial physical process (abrasive water jet machining) demonstrate the validity of this approach.

  14. Bacterial Actins? An Evolutionary Perspective

    NASA Technical Reports Server (NTRS)

    Doolittle, Russell F.; York, Amanda L.

    2003-01-01

    According to the conventional wisdom, the existence of a cytoskeleton in eukaryotes and its absence in prokaryotes constitute a fundamental divide between the two domains of life. An integral part of the dogma is that a cytoskeleton enabled an early eukaryote to feed upon prokaryotes, a consequence of which was the occasional endosymbiosis and the eventual evolution of organelles. Two recent papers present compelling evidence that actin, one of the principal components of a cytoskeleton, has a homolog in Bacteria that behaves in many ways like eukaryotic actin. Sequence comparisons reveml that eukaryotic actin and the bacterial homolog (mreB protein), unlike many other proteins common to eukaryotes and Bacteria, have very different and more highly extended evolutionary histories.

  15. Genomic clocks and evolutionary timescales

    NASA Technical Reports Server (NTRS)

    Blair Hedges, S.; Kumar, Sudhir

    2003-01-01

    For decades, molecular clocks have helped to illuminate the evolutionary timescale of life, but now genomic data pose a challenge for time estimation methods. It is unclear how to integrate data from many genes, each potentially evolving under a different model of substitution and at a different rate. Current methods can be grouped by the way the data are handled (genes considered separately or combined into a 'supergene') and the way gene-specific rate models are applied (global versus local clock). There are advantages and disadvantages to each of these approaches, and the optimal method has not yet emerged. Fortunately, time estimates inferred using many genes or proteins have greater precision and appear to be robust to different approaches.

  16. EPR: an Advanced Evolutionary Design

    SciTech Connect

    Czech, Juergen; Bouteille, Francois; Hudson, Greg

    2004-07-01

    This paper presents the main features of the EPR, an evolutionary design product that builds on French N4 plants (Chooz and Civaux) and Konvoi, the most recent reactor series built in Germany. This Franco-German project was driven by a common French and German desire to cooperate in several areas. In January 2001, Framatome SA and Siemens AG merged their nuclear activities to form Framatome ANP with three regional entities in France, Germany and the USA. The recent decision of Teollisuuden Voima Oy (TVO) to select the EPR for construction in Olkiluoto of the fifth Nuclear Power Plant in Finland gave a new impetus to the project. Framatome ANP is committed to put the FOAK EPR in commercial operation on May 1, 2009. This challenging time schedule will set a new reference for 'Generation III +' LWR's. (authors)

  17. Evolutionary adaptations to dietary changes.

    PubMed

    Luca, F; Perry, G H; Di Rienzo, A

    2010-08-21

    Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area. PMID:20420525

  18. Evolutionary genomics of dog domestication.

    PubMed

    Wayne, Robert K; vonHoldt, Bridgett M

    2012-02-01

    We review the underlying principles and tools used in genomic studies of domestic dogs aimed at understanding the genetic changes that have occurred during domestication. We show that there are two principle modes of evolution within dogs. One primary mode that accounts for much of the remarkable diversity of dog breeds is the fixation of discrete mutations of large effect in individual lineages that are then crossed to various breed groupings. This transfer of mutations across the dog evolutionary tree leads to the appearance of high phenotypic diversity that in actuality reflects a small number of major genes. A second mechanism causing diversification involves the selective breeding of dogs within distinct phenotypic or functional groups, which enhances specific group attributes such as heading or tracking. Such progressive selection leads to a distinct genetic structure in evolutionary trees such that functional and phenotypic groups cluster genetically. We trace the origin of the nuclear genome in dogs based on haplotype-sharing analyses between dogs and gray wolves and show that contrary to previous mtDNA analyses, the nuclear genome of dogs derives primarily from Middle Eastern or European wolves, a result more consistent with the archeological record. Sequencing analysis of the IGF1 gene, which has been the target of size selection in small breeds, further supports this conclusion. Finally, we discuss how a black coat color mutation that evolved in dogs has transformed North American gray wolf populations, providing a first example of a mutation that appeared under domestication and selectively swept through a wild relative. PMID:22270221

  19. Evolutionary History of Tissue Kallikreins

    PubMed Central

    Pavlopoulou, Athanasia; Pampalakis, Georgios; Michalopoulos, Ioannis; Sotiropoulou, Georgia

    2010-01-01

    The gene family of human kallikrein-related peptidases (KLKs) encodes proteins with diverse and pleiotropic functions in normal physiology as well as in disease states. Currently, the most widely known KLK is KLK3 or prostate-specific antigen (PSA) that has applications in clinical diagnosis and monitoring of prostate cancer. The KLK gene family encompasses the largest contiguous cluster of serine proteases in humans which is not interrupted by non-KLK genes. This exceptional and unique characteristic of KLKs makes them ideal for evolutionary studies aiming to infer the direction and timing of gene duplication events. Previous studies on the evolution of KLKs were restricted to mammals and the emergence of KLKs was suggested about 150 million years ago (mya). In order to elucidate the evolutionary history of KLKs, we performed comprehensive phylogenetic analyses of KLK homologous proteins in multiple genomes including those that have been completed recently. Interestingly, we were able to identify novel reptilian, avian and amphibian KLK members which allowed us to trace the emergence of KLKs 330 mya. We suggest that a series of duplication and mutation events gave rise to the KLK gene family. The prominent feature of the KLK family is that it consists of tandemly and uninterruptedly arrayed genes in all species under investigation. The chromosomal co-localization in a single cluster distinguishes KLKs from trypsin and other trypsin-like proteases which are spread in different genetic loci. All the defining features of the KLKs were further found to be conserved in the novel KLK protein sequences. The study of this unique family will further assist in selecting new model organisms for functional studies of proteolytic pathways involving KLKs. PMID:21072173

  20. Evolutionary history of exon shuffling.

    PubMed

    França, Gustavo S; Cancherini, Douglas V; de Souza, Sandro J

    2012-06-01

    Exon shuffling has been characterized as one of the major evolutionary forces shaping both the genome and the proteome of eukaryotes. This mechanism was particularly important in the creation of multidomain proteins during animal evolution, bringing a number of functional genetic novelties. Here, genome information from a variety of eukaryotic species was used to address several issues related to the evolutionary history of exon shuffling. By comparing all protein sequences within each species, we were able to characterize exon shuffling signatures throughout metazoans. Intron phase (the position of the intron regarding the codon) and exon symmetry (the pattern of flanking introns for a given exon or block of adjacent exons) were features used to evaluate exon shuffling. We confirmed previous observations that exon shuffling mediated by phase 1 introns (1-1 exon shuffling) is the predominant kind in multicellular animals. Evidence is provided that such pattern was achieved since the early steps of animal evolution, supported by a detectable presence of 1-1 shuffling units in Trichoplax adhaerens and a considerable prevalence of them in Nematostella vectensis. In contrast, Monosiga brevicollis, one of the closest relatives of metazoans, and Arabidopsis thaliana, showed no evidence of 1-1 exon or domain shuffling above what it would be expected by chance. Instead, exon shuffling events are less abundant and predominantly mediated by phase 0 introns (0-0 exon shuffling) in those non-metazoan species. Moreover, an intermediate pattern of 1-1 and 0-0 exon shuffling was observed for the placozoan T. adhaerens, a primitive animal. Finally, characterization of flanking intron phases around domain borders allowed us to identify a common set of symmetric 1-1 domains that have been shuffled throughout the metazoan lineage.

  1. 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

  2. Toward a unifying framework for evolutionary processes

    PubMed Central

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

    2015-01-01

    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. PMID:26215686

  3. Evolutionary Biology in the Medical School Curriculum.

    ERIC Educational Resources Information Center

    Neese, Randolph M.; Schiffman, Joshua D.

    2003-01-01

    Presents a study in which a questionnaire was given to deans at North American medical schools to determine which aspects of evolutionary biology are included in the curricula and the factors that influence this. Suggests that most future physicians should learn evolutionary biology as undergraduates if they are to learn it at all. (Author/NB)

  4. Algorithmic Mechanism Design of Evolutionary Computation

    PubMed Central

    Pei, Yan

    2015-01-01

    We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm. PMID:26257777

  5. 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.

  6. Evolutionary Genomics of Life in (and from) the Sea

    SciTech Connect

    Boore, Jeffrey L.; Dehal, Paramvir; Fuerstenberg, Susan I.

    2006-01-09

    High throughput genome sequencing centers that were originally built for the Human Genome Project (Lander et al., 2001; Venter et al., 2001) have now become an engine for comparative genomics. The six largest centers alone are now producing over 150 billion nucleotides per year, more than 50 times the amount of DNA in the human genome, and nearly all of this is directed at projects that promise great insights into the pattern and processes of evolution. Unfortunately, this data is being produced at a pace far exceeding the capacity of the scientific community to provide insightful analysis, and few scientists with training and experience in evolutionary biology have played prominent roles to date. One of the consequences is that poor quality analyses are typical; for example, orthology among genes is generally determined by simple measures of sequence similarity, when this has been discredited by molecular evolutionary biologists decades ago. Here we discuss the how genomes are chosen for sequencing and how the scientific community can have input. We describe the PhIGs database and web tools (Dehal and Boore 2005a; http://PhIGs.org), which provide phylogenetic analysis of all gene families for all completely sequenced genomes and the associated 'Synteny Viewer', which allows comparisons of the relative positions of orthologous genes. This is the best tool available for inferring gene function across multiple genomes. We also describe how we have used the PhIGs methods with the whole genome sequences of a tunicate, fish, mouse, and human to conclusively demonstrate that two rounds of whole genome duplication occurred at the base of vertebrates (Dehal and Boore 2005b). This evidence is found in the large scale structure of the positions of paralogous genes that arose from duplications inferred by evolutionary analysis to have occurred at the base of vertebrates.

  7. Evolutionary theory in letters to the editor.

    PubMed

    Silva, Eric Orion; Lowe, Clayton Cory

    2015-05-01

    This research note presents the results of a content analysis of 234 letters to the editors that discuss evolutionary theory and were published in American newspapers. We find that letters to the editor both support and hinder the cause of teaching evolutionary theory in American secondary schools. On the one hand, anti-evolutionary theory messages are marginalized in the letters section. This marginalization signals a low level of legitimacy for creationism. It might also contribute to the sense of tension that sustains creationist identities. On the other hand, relatively few letters explicitly note the fact that scientists or the scientific community accept evolution. Interestingly, the obscuration of the scientific community's support for evolutionary theory occurs both in letters supporting and opposing evolutionary theory.

  8. Evolutionary theory in letters to the editor.

    PubMed

    Silva, Eric Orion; Lowe, Clayton Cory

    2015-05-01

    This research note presents the results of a content analysis of 234 letters to the editors that discuss evolutionary theory and were published in American newspapers. We find that letters to the editor both support and hinder the cause of teaching evolutionary theory in American secondary schools. On the one hand, anti-evolutionary theory messages are marginalized in the letters section. This marginalization signals a low level of legitimacy for creationism. It might also contribute to the sense of tension that sustains creationist identities. On the other hand, relatively few letters explicitly note the fact that scientists or the scientific community accept evolution. Interestingly, the obscuration of the scientific community's support for evolutionary theory occurs both in letters supporting and opposing evolutionary theory. PMID:25540333

  9. Evolutionary rescue in a changing world.

    PubMed

    Carlson, Stephanie M; Cunningham, Curry J; Westley, Peter A H

    2014-09-01

    Evolutionary rescue occurs when adaptive evolutionary change restores positive growth to declining populations and prevents extinction. Here we outline the diagnostic features of evolutionary rescue and distinguish this phenomenon from demographic and genetic rescue. We then synthesize the rapidly accumulating theoretical and experimental studies of evolutionary rescue, highlighting the demographic, genetic, and extrinsic factors that affect the probability of rescue. By doing so, we clarify the factors to target through management and conservation. Additionally, we identify several putative cases of evolutionary rescue in nature, but conclude that compelling evidence remains elusive. We conclude with a horizon scan of where the field might develop, highlighting areas of potential application, and suggest areas where experimental evaluation will help to evaluate theoretical predictions. PMID:25038023

  10. The emergence of an `evolutionary geomorphology'?

    NASA Astrophysics Data System (ADS)

    Steiger, Johannes; Corenblit, Dov

    2012-09-01

    Earth surface processes and landforms are modified through the actions of many microorganisms, plants and animals. As organism-driven landform modifications are sometimes to the advantage of the organism, some of these landform features have become adaptive functional components of ecosystems, concurrently affecting and responding to ecological and evolutionary processes. These recent eco-evolutionary insights, focused on feedback among geomorphologic, ecological and evolutionary processes, are currently leading to the emergence of what has been called an `evolutionary geomorphology', with explicit consideration of feedbacks among the evolution of organisms, ecosystem structure and function and landform organization at the Earth surface. Here we provide an overview in the form of a commentary of this emerging sub-discipline in geosciences and ask whether the use of the term `evolutionary geomorphology' is appropriate or rather misleading.

  11. Evolutionary psychology. Controversies, questions, prospects, and limitations.

    PubMed

    Confer, Jaime C; Easton, Judith A; Fleischman, Diana S; Goetz, Cari D; Lewis, David M G; Perilloux, Carin; Buss, David M

    2010-01-01

    Evolutionary psychology has emerged over the past 15 years as a major theoretical perspective, generating an increasing volume of empirical studies and assuming a larger presence within psychological science. At the same time, it has generated critiques and remains controversial among some psychologists. Some of the controversy stems from hypotheses that go against traditional psychological theories; some from empirical findings that may have disturbing implications; some from misunderstandings about the logic of evolutionary psychology; and some from reasonable scientific concerns about its underlying framework. This article identifies some of the most common concerns and attempts to elucidate evolutionary psychology's stance pertaining to them. These include issues of testability and falsifiability; the domain specificity versus domain generality of psychological mechanisms; the role of novel environments as they interact with evolved psychological circuits; the role of genes in the conceptual structure of evolutionary psychology; the roles of learning, socialization, and culture in evolutionary psychology; and the practical value of applied evolutionary psychology. The article concludes with a discussion of the limitations of current evolutionary psychology.

  12. Maximum likelihood inference of reticulate evolutionary histories.

    PubMed

    Yu, Yun; Dong, Jianrong; Liu, Kevin J; Nakhleh, Luay

    2014-11-18

    Hybridization plays an important role in the evolution of certain groups of organisms, adaptation to their environments, and diversification of their genomes. The evolutionary histories of such groups are reticulate, and methods for reconstructing them are still in their infancy and have limited applicability. We present a maximum likelihood method for inferring reticulate evolutionary histories while accounting simultaneously for incomplete lineage sorting. Additionally, we propose methods for assessing confidence in the amount of reticulation and the topology of the inferred evolutionary history. Our method obtains accurate estimates of reticulate evolutionary histories on simulated datasets. Furthermore, our method provides support for a hypothesis of a reticulate evolutionary history inferred from a set of house mouse (Mus musculus) genomes. As evidence of hybridization in eukaryotic groups accumulates, it is essential to have methods that infer reticulate evolutionary histories. The work we present here allows for such inference and provides a significant step toward putting phylogenetic networks on par with phylogenetic trees as a model of capturing evolutionary relationships. PMID:25368173

  13. Evolutionary indirect effects of biological invasions.

    PubMed

    Lau, Jennifer A

    2012-09-01

    Just as ecological indirect effects can have a wide range of consequences for community structure and ecosystem function, theory suggests that evolutionary indirect effects can also influence community dynamics and the outcome of species interactions. There is little empirical evidence documenting such effects, however. Here, I use a multi-generation selection experiment in the field to investigate: (1) how the exotic plant Medicago polymorpha and the exotic insect herbivore Hypera brunneipennis affect the evolution of anti-herbivore resistance traits in the native plant Lotus wrangelianus and (2) how observed Lotus evolutionary responses to Hypera alter interactions between Lotus and other members of the herbivore community. In one of two study populations, I document rapid evolutionary changes in Lotus resistance to Hypera in response to insecticide treatments that experimentally reduced Hypera abundance, and in response to Medicago-removal treatments that also reduced Hypera abundance. These evolutionary changes in response to Hypera result in reduced attack by aphids. Thus, an evolutionary change caused by one herbivore species alters interactions with other herbivore taxa, an example of an eco-evolutionary feedback. Given that many traits mediate interactions with multiple species, the effects of evolutionary changes in response to one key biotic selective agent may often cascade through interaction webs to influence additional community members.

  14. The Evolutionary Origins of Hierarchy.

    PubMed

    Mengistu, Henok; Huizinga, Joost; Mouret, Jean-Baptiste; Clune, Jeff

    2016-06-01

    Hierarchical organization-the recursive composition of sub-modules-is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments). Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force-the cost of connections-promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics. PMID:27280881

  15. The Evolutionary Origins of Hierarchy.

    PubMed

    Mengistu, Henok; Huizinga, Joost; Mouret, Jean-Baptiste; Clune, Jeff

    2016-06-01

    Hierarchical organization-the recursive composition of sub-modules-is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments). Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force-the cost of connections-promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics.

  16. The Evolutionary Origins of Hierarchy

    PubMed Central

    Huizinga, Joost; Clune, Jeff

    2016-01-01

    Hierarchical organization—the recursive composition of sub-modules—is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments). Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force–the cost of connections–promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics. PMID:27280881

  17. Natural pedagogy as evolutionary adaptation

    PubMed Central

    Csibra, Gergely; Gergely, György

    2011-01-01

    We propose that the cognitive mechanisms that enable the transmission of cultural knowledge by communication between individuals constitute a system of ‘natural pedagogy’ in humans, and represent an evolutionary adaptation along the hominin lineage. We discuss three kinds of arguments that support this hypothesis. First, natural pedagogy is likely to be human-specific: while social learning and communication are both widespread in non-human animals, we know of no example of social learning by communication in any other species apart from humans. Second, natural pedagogy is universal: despite the huge variability in child-rearing practices, all human cultures rely on communication to transmit to novices a variety of different types of cultural knowledge, including information about artefact kinds, conventional behaviours, arbitrary referential symbols, cognitively opaque skills and know-how embedded in means-end actions. Third, the data available on early hominin technological culture are more compatible with the assumption that natural pedagogy was an independently selected adaptive cognitive system than considering it as a by-product of some other human-specific adaptation, such as language. By providing a qualitatively new type of social learning mechanism, natural pedagogy is not only the product but also one of the sources of the rich cultural heritage of our species. PMID:21357237

  18. The Year in Evolutionary Biology

    PubMed Central

    Bataillon, Thomas; Bailey, Susan F

    2014-01-01

    The rates and properties of new mutations affecting fitness have implications for a number of outstanding questions in evolutionary biology. Obtaining estimates of mutation rates and effects has historically been challenging, and little theory has been available for predicting the distribution of fitness effects (DFE); however, there have been recent advances on both fronts. Extreme-value theory predicts the DFE of beneficial mutations in well-adapted populations, while phenotypic fitness landscape models make predictions for the DFE of all mutations as a function of the initial level of adaptation and the strength of stabilizing selection on traits underlying fitness. Direct experimental evidence confirms predictions on the DFE of beneficial mutations and favors distributions that are roughly exponential but bounded on the right. A growing number of studies infer the DFE using genomic patterns of polymorphism and divergence, recovering a wide range of DFE. Future work should be aimed at identifying factors driving the observed variation in the DFE. We emphasize the need for further theory explicitly incorporating the effects of partial pleiotropy and heterogeneity in the environment on the expected DFE. PMID:24891070

  19. 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.

  20. 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

  1. Evolutionary optimization of protein folding.

    PubMed

    Debès, Cédric; Wang, Minglei; Caetano-Anollés, Gustavo; Gräter, Frauke

    2013-01-01

    Nature has shaped the make up of proteins since their appearance, [Formula: see text]3.8 billion years ago. However, the fundamental drivers of structural change responsible for the extraordinary diversity of proteins have yet to be elucidated. Here we explore if protein evolution affects folding speed. We estimated folding times for the present-day catalog of protein domains directly from their size-modified contact order. These values were mapped onto an evolutionary timeline of domain appearance derived from a phylogenomic analysis of protein domains in 989 fully-sequenced genomes. Our results show a clear overall increase of folding speed during evolution, with known ultra-fast downhill folders appearing rather late in the timeline. Remarkably, folding optimization depends on secondary structure. While alpha-folds showed a tendency to fold faster throughout evolution, beta-folds exhibited a trend of folding time increase during the last [Formula: see text]1.5 billion years that began during the "big bang" of domain combinations. As a consequence, these domain structures are on average slow folders today. Our results suggest that fast and efficient folding of domains shaped the universe of protein structure. This finding supports the hypothesis that optimization of the kinetic and thermodynamic accessibility of the native fold reduces protein aggregation propensities that hamper cellular functions. PMID:23341762

  2. Evolutionary advantages of adaptive rewarding

    NASA Astrophysics Data System (ADS)

    Szolnoki, Attila; Perc, Matjaž

    2012-09-01

    Our well-being depends on both our personal success and the success of our society. The realization of this fact makes cooperation an essential trait. Experiments have shown that rewards can elevate our readiness to cooperate, but since giving a reward inevitably entails paying a cost for it, the emergence and stability of such behavior remains elusive. Here we show that allowing for the act of rewarding to self-organize in dependence on the success of cooperation creates several evolutionary advantages that instill new ways through which collaborative efforts are promoted. Ranging from indirect territorial battle to the spontaneous emergence and destruction of coexistence, phase diagrams and the underlying spatial patterns reveal fascinatingly rich social dynamics that explain why this costly behavior has evolved and persevered. Comparisons with adaptive punishment, however, uncover an Achilles heel of adaptive rewarding, coming from over-aggression, which in turn hinders optimal utilization of network reciprocity. This may explain why, despite its success, rewarding is not as firmly embedded into our societal organization as punishment.

  3. Evolutionary dynamics of taxonomic structure

    PubMed Central

    Foote, Michael

    2012-01-01

    The distribution of species among genera and higher taxa has largely untapped potential to reveal among-clade variation in rates of origination and extinction. The probability distribution of the number of species within a genus is modelled with a stochastic, time-homogeneous birth–death model having two parameters: the rate of species extinction, μ, and the rate of genus origination, γ, each scaled as a multiple of the rate of within-genus speciation, λ. The distribution is more sensitive to γ than to μ, although μ affects the size of the largest genera. The species : genus ratio depends strongly on both γ and μ, and so is not a good diagnostic of evolutionary dynamics. The proportion of monotypic genera, however, depends mainly on γ, and so may provide an index of the genus origination rate. Application to living marine molluscs of New Zealand shows that bivalves have a higher relative rate of genus origination than gastropods. This is supported by the analysis of palaeontological data. This concordance suggests that analysis of living taxonomic distributions may allow inference of macroevolutionary dynamics even without a fossil record. PMID:21865239

  4. 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. PMID:20212124

  5. Computational and evolutionary aspects of language.

    PubMed

    Nowak, Martin A; Komarova, Natalia L; Niyogi, Partha

    2002-06-01

    Language is our legacy. It is the main evolutionary contribution of humans, and perhaps the most interesting trait that has emerged in the past 500 million years. Understanding how darwinian evolution gives rise to human language requires the integration of formal language theory, learning theory and evolutionary dynamics. Formal language theory provides a mathematical description of language and grammar. Learning theory formalizes the task of language acquisition it can be shown that no procedure can learn an unrestricted set of languages. Universal grammar specifies the restricted set of languages learnable by the human brain. Evolutionary dynamics can be formulated to describe the cultural evolution of language and the biological evolution of universal grammar.

  6. How mutation affects evolutionary games on graphs.

    PubMed

    Allen, Benjamin; Traulsen, Arne; Tarnita, Corina E; Nowak, Martin A

    2012-04-21

    Evolutionary dynamics are affected by population structure, mutation rates and update rules. Spatial or network structure facilitates the clustering of strategies, which represents a mechanism for the evolution of cooperation. Mutation dilutes this effect. Here we analyze how mutation influences evolutionary clustering on graphs. We introduce new mathematical methods to evolutionary game theory, specifically the analysis of coalescing random walks via generating functions. These techniques allow us to derive exact identity-by-descent (IBD) probabilities, which characterize spatial assortment on lattices and Cayley trees. From these IBD probabilities we obtain exact conditions for the evolution of cooperation and other game strategies, showing the dual effects of graph topology and mutation rate. High mutation rates diminish the clustering of cooperators, hindering their evolutionary success. Our model can represent either genetic evolution with mutation, or social imitation processes with random strategy exploration.

  7. [Evolutionary medicine: an emergent basic science].

    PubMed

    Spotorno, Angel E

    2005-02-01

    Evolutionary Medicine is an emergent basic science that offers new and varied perspectives to the comprehension of human health. The application of classic evolutionary theories (descent with modification, and natural selection) to the human organism, to its pathogens, and their mutual co-evolution, provides new explanations about why we get sick, how we can prevent this, and how we can heal. Medicine has focused mainly on the proximate or immediate causes of diseases and the treatment of symptoms, and very little on its evolutionary or mediate causes. For instance, the present human genome and phenotypes are essentially paleolithic ones: they are not adapted to modern life style, thus favoring the so-called diseases of civilization (ie: ateroesclerosis, senescence, myopia, phobias, panic attacks, stress, reproductive cancers). With the evolutionary approach, post-modern medicine is detecting better the vulnerabilities, restrictions, biases, adaptations and maladaptations of human body, its actual diseases, and its preventions.

  8. Evolutionary fire ecology: lessons learned from pines.

    PubMed

    Pausas, Juli G

    2015-05-01

    Macroevolutionary studies of the genus Pinus provide the oldest current evidence of fire as an evolutionary pressure on plants and date back to ca. 125 million years ago (Ma). Microevolutionary studies show that fire traits are variable within and among populations, especially among those subject to different fire regimes. In addition, there is increasing evidence of an inherited genetic basis to variability in fire traits. Added together, pines provide compelling evidence that fire can exert an evolutionary pressure on plants and, thus, shape biodiversity. In addition, evolutionary fire ecology is providing insights to improve the management of pine forests under changing conditions. The lessons learned from pines may guide research on the evolutionary ecology of other taxa.

  9. Teaching Evolutionary Theory as General Education.

    ERIC Educational Resources Information Center

    Todd, Paul

    1984-01-01

    Provides a rationale for including evolution as part of a college general education curriculum, discussing the content of evolutionary theory, instructional principles, Darwin's contributions, evolution and religion, and the relationship of evolution with current events. (DMM)

  10. A Philosophical Perspective on Evolutionary Systems Biology

    PubMed Central

    Soyer, Orkun S.; Siegal, Mark L.

    2015-01-01

    Evolutionary systems biology (ESB) is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these discussions in the context of long-running philosophical deliberations on explanation, modeling, and theoretical synthesis. We show how many of the issues central to ESB’s progress can be understood as general philosophical problems. The benefits of addressing these philosophical issues feed back into philosophy too, because ESB provides excellent examples of scientific practice for the development of philosophy of science and philosophy of biology. PMID:26085823

  11. Variant evolutionary trees under phenotypic variance.

    PubMed

    Nishimura, Kinya; Isoda, Yutaka

    2004-01-01

    Evolutionary branching, which is a coevolutionary phenomenon of the development of two or more distinctive traits from a single trait in a population, is the issue of recent studies on adaptive dynamics. In previous studies, it was revealed that trait variance is a minimum requirement for evolutionary branching, and that it does not play an important role in the formation of an evolutionary pattern of branching. Here we demonstrate that the trait evolution exhibits various evolutionary branching paths starting from an identical initial trait to different evolutional terminus traits as determined by only changing the assumption of trait variance. The key feature of this phenomenon is the topological configuration of equilibria and the initial point in the manifold of dimorphism from which dimorphic branches develop. This suggests that the existing monomorphic or polymorphic set in a population is not an unique inevitable consequence of an identical initial phenotype.

  12. Evolutionary origins of leadership and followership.

    PubMed

    Van Vugt, Mark

    2006-01-01

    Drawing upon evolutionary logic, leadership is reconceptualized in terms of the outcome of strategic interactions among individuals who are following different, yet complementary, decision rules to solve recurrent coordination problems. This article uses the vast psychological literature on leadership as a database to test several evolutionary hypotheses about the origins of leadership and followership in humans. As expected, leadership correlates with initiative taking, trait measures of intelligence, specific task competencies, and several indicators of generosity. The review finds no link between leadership and dominance. The evolutionary analysis accounts for reliable age, health, and sex differences in leadership emergence. In general, evolutionary theory provides a useful, integrative framework for studying leader-follower relationships and generates various novel research hypotheses.

  13. Evolutionary interaction networks of insect pathogenic fungi.

    PubMed

    Boomsma, Jacobus J; Jensen, Annette B; Meyling, Nicolai V; Eilenberg, Jørgen

    2014-01-01

    Lineages of insect pathogenic fungi are concentrated in three major clades: Hypocreales (several genera), Entomophthoromycota (orders Entomophthorales and Neozygitales), and Onygenales (genus Ascosphaera). Our review focuses on aspects of the evolutionary biology of these fungi that have remained underemphasized in previous reviews. To ensure integration with the better-known domains of insect pathology research, we followed a conceptual framework formulated by Tinbergen, asking complementary questions on mechanism, ontogeny, phylogeny, and adaptation. We aim to provide an introduction to the merits of evolutionary approaches for readers with a background in invertebrate pathology research and to make the insect pathogenic fungi more accessible as model systems for evolutionary biologists. We identify a number of questions in which fundamental research can offer novel insights into the evolutionary forces that have shaped host specialization and life-history traits such as spore number and size, somatic growth rate, toxin production, and interactions with host immune systems.

  14. How Evolutionary Biologists Reconstruct History: Patterns & Processes

    ERIC Educational Resources Information Center

    Cooper, Robert A.

    2004-01-01

    Focusing on specific modes of evolutionally inquiry is important for students to achieve a mature understanding about evolutionary biology. Presenting evolution as rhetoric of conclusions would only confuse the minds of students.

  15. Scheduling Earth Observing Satellites with Evolutionary Algorithms

    NASA Technical Reports Server (NTRS)

    Globus, Al; Crawford, James; Lohn, Jason; Pryor, Anna

    2003-01-01

    We hypothesize that evolutionary algorithms can effectively schedule coordinated fleets of Earth observing satellites. The constraints are complex and the bottlenecks are not well understood, a condition where evolutionary algorithms are often effective. This is, in part, because evolutionary algorithms require only that one can represent solutions, modify solutions, and evaluate solution fitness. To test the hypothesis we have developed a representative set of problems, produced optimization software (in Java) to solve them, and run experiments comparing techniques. This paper presents initial results of a comparison of several evolutionary and other optimization techniques; namely the genetic algorithm, simulated annealing, squeaky wheel optimization, and stochastic hill climbing. We also compare separate satellite vs. integrated scheduling of a two satellite constellation. While the results are not definitive, tests to date suggest that simulated annealing is the best search technique and integrated scheduling is superior.

  16. Evolutionary medicine: its scope, interest and potential

    PubMed Central

    Stearns, Stephen C.

    2012-01-01

    This review is aimed at readers seeking an introductory overview, teaching courses and interested in visionary ideas. It first describes the range of topics covered by evolutionary medicine, which include human genetic variation, mismatches to modernity, reproductive medicine, degenerative disease, host–pathogen interactions and insights from comparisons with other species. It then discusses priorities for translational research, basic research and health management. Its conclusions are that evolutionary thinking should not displace other approaches to medical science, such as molecular medicine and cell and developmental biology, but that evolutionary insights can combine with and complement established approaches to reduce suffering and save lives. Because we are on the cusp of so much new research and innovative insights, it is hard to estimate how much impact evolutionary thinking will have on medicine, but it is already clear that its potential is enormous. PMID:22933370

  17. Evolutionary contingency and SETI revisited

    NASA Astrophysics Data System (ADS)

    Cirkovic, Milan M.

    2014-07-01

    The well-known argument against the Search for ExtraTerrestrial Intelligence (SETI) due to George Gaylord Simpson is re-analyzed almost half a century later, in the light of our improved understanding of preconditions for the emergence of life and intelligence brought about by the ongoing "astrobiological revolution". Simpson's argument has been enormously influential, in particular in biological circles, and it arguably fueled the most serious opposition to SETI programmes and their funding. I argue that both proponents and opponents of Simpson's argument have occasionally mispresented its core content. Proponents often oversimplify it as just another consequence of biological contingency, thus leaving their position open to general arguments limiting the scope of contingency in evolution (such as the recent argument of Geerat Vermeij based on selection effects in the fossil record). They also tend to neglect that the argument has been presented as essentially atemporal, while referring to entities and processes that are likely to change over time; this has become even less justifiable as our astrobiological knowledge increased in recent years. Opponents have failed to see that the weaknesses in Simpson's position could be removed by restructuring of the argument; I suggest one way of such restructuring, envisioned long ago in the fictional context by Stanislaw Lem. While no firm consensus has emerged on the validity of Simpson's argument so far, I suggest that, contrary to the original motivation, today it is less an anti-SETI argument, and more an astrobiological research programme. In this research programme, SETI could be generalized into a platform for testing some of the deepest assumptions about evolutionary continuity and the relative role of contingency versus convergence on unprecedented spatial and temporal scales.

  18. Wolbachia versus dengue: Evolutionary forecasts.

    PubMed

    Bull, James J; Turelli, Michael

    2013-01-01

    A novel form of biological control is being applied to the dengue virus. The agent is the maternally transmitted bacterium Wolbachia, naturally absent from the main dengue vector, the mosquito Aedes aegypti. Three Wolbachia-based control strategies have been proposed. One is suppression of mosquito populations by large-scale releases of males incompatible with native females; this intervention requires ongoing releases. The other interventions transform wild mosquito populations with Wolbachia that spread via the frequency-dependent fitness advantage of Wolbachia-infected females; those interventions potentially require just a single, local release for area-wide disease control. One of these latter strategies uses Wolbachia that shortens mosquito life, indirectly preventing viral maturation/transmission. The other strategy uses Wolbachia that block viral transmission. All interventions can be undermined by viral, bacterial or mosquito evolution; viral virulence in humans may also evolve. We examine existing theory, experiments and comparative evidence to motivate predictions about evolutionary outcomes. (i) The life-shortening strategy seems the most likely to be thwarted by evolution. (ii) Mosquito suppression has a reasonable chance of working locally, at least in the short term, but long-term success over large areas is challenging. (iii) Dengue blocking faces strong selection for viral resistance but may well persist indefinitely at some level. Virulence evolution is not mathematically predictable, but comparative data provide no precedent for Wolbachia increasing dengue virulence. On balance, our analysis suggests that the considerable possible benefits of these technologies outweigh the known negatives, but the actual risk is largely unknown. PMID:24481199

  19. Evolutionary transgenomics: prospects and challenges

    PubMed Central

    Correa, Raul; Baum, David A.

    2015-01-01

    Many advances in our understanding of the genetic basis of species differences have arisen from transformation experiments, which allow us to study the effect of genes from one species (the donor) when placed in the genetic background of another species (the recipient). Such interspecies transformation experiments are usually focused on candidate genes – genes that, based on work in model systems, are suspected to be responsible for certain phenotypic differences between the donor and recipient species. We suggest that the high efficiency of transformation in a few plant species, most notably Arabidopsis thaliana, combined with the small size of typical plant genes and their cis-regulatory regions allow implementation of a screening strategy that does not depend upon a priori candidate gene identification. This approach, transgenomics, entails moving many large genomic inserts of a donor species into the wild type background of a recipient species and then screening for dominant phenotypic effects. As a proof of concept, we recently conducted a transgenomic screen that analyzed more than 1100 random, large genomic inserts of the Alabama gladecress Leavenworthia alabamica for dominant phenotypic effects in the A. thaliana background. This screen identified one insert that shortens fruit and decreases A. thaliana fertility. In this paper we discuss the principles of transgenomic screens and suggest methods to help minimize the frequencies of false positive and false negative results. We argue that, because transgenomics avoids committing in advance to candidate genes it has the potential to help us identify truly novel genes or cryptic functions of known genes. Given the valuable knowledge that is likely to be gained, we believe the time is ripe for the plant evolutionary community to invest in transgenomic screens, at least in the mustard family Brassicaceae where many species are amenable to efficient transformation. PMID:26579137

  20. Evolutionary Design of Controlled Structures

    NASA Technical Reports Server (NTRS)

    Masters, Brett P.; Crawley, Edward F.

    1997-01-01

    Basic physical concepts of structural delay and transmissibility are provided for simple rod and beam structures. Investigations show the sensitivity of these concepts to differing controlled-structures variables, and to rational system modeling effects. An evolutionary controls/structures design method is developed. The basis of the method is an accurate model formulation for dynamic compensator optimization and Genetic Algorithm based updating of sensor/actuator placement and structural attributes. One and three dimensional examples from the literature are used to validate the method. Frequency domain interpretation of these controlled structure systems provide physical insight as to how the objective is optimized and consequently what is important in the objective. Several disturbance rejection type controls-structures systems are optimized for a stellar interferometer spacecraft application. The interferometric designs include closed loop tracking optics. Designs are generated for differing structural aspect ratios, differing disturbance attributes, and differing sensor selections. Physical limitations in achieving performance are given in terms of average system transfer function gains and system phase loss. A spacecraft-like optical interferometry system is investigated experimentally over several different optimized controlled structures configurations. Configurations represent common and not-so-common approaches to mitigating pathlength errors induced by disturbances of two different spectra. Results show that an optimized controlled structure for low frequency broadband disturbances achieves modest performance gains over a mass equivalent regular structure, while an optimized structure for high frequency narrow band disturbances is four times better in terms of root-mean-square pathlength. These results are predictable given the nature of the physical system and the optimization design variables. Fundamental limits on controlled performance are discussed

  1. Humanism and multiculturalism: an evolutionary alliance.

    PubMed

    Comas-Diaz, Lillian

    2012-12-01

    Humanism and multiculturalism are partners in an evolutionary alliance. Humanistic and multicultural psychotherapies have historically influenced each other. Humanism represents the third force in psychotherapy, while multiculturalism embodies the fourth developmental stage. Multiculturalism embraces humanistic values grounded in collective and social justice contexts. Examples of multicultural humanistic constructs include contextualism, holism, and liberation. Certainly, the multicultural-humanistic connection is a necessary shift in the evolution of psychotherapy. Humanism and multiculturalism participate in the development of an inclusive and evolutionary psychotherapy. PMID:23205825

  2. Evolutionary Game Theory Analysis of Tumor Progression

    NASA Astrophysics Data System (ADS)

    Wu, Amy; Liao, David; Sturm, James; Austin, Robert

    2014-03-01

    Evolutionary game theory applied to two interacting cell populations can yield quantitative prediction of the future densities of the two cell populations based on the initial interaction terms. We will discuss how in a complex ecology that evolutionary game theory successfully predicts the future densities of strains of stromal and cancer cells (multiple myeloma), and discuss the possible clinical use of such analysis for predicting cancer progression. Supported by the National Science Foundation and the National Cancer Institute.

  3. Ecological aspects of the evolutionary processes.

    PubMed

    Bock, Walter J

    2003-03-01

    Darwin in his On the Origin of species made it clear that evolutionary change depends on the combined action of two different causes, the first being the origin of genetically based phenotypic variation in the individual organisms comprising the population and the second being the action of selective agents of the external environment placing demands on the individual organisms. For over a century following Darwin, most evolutionists focused on the origin of inherited variation and its transmission; many workers continue to regard genetics to be the core of evolutionary theory. Far less attention has been given to the exact nature of the selective agents with most evolutionists still treating this cause imprecisely to the detriment of our understanding of both nomological and historical evolutionary theory. Darwin was vague in the meaning of his new concept of "Natural Selection," using it interchangeably as one of the causes for evolutionary change and as the final outcome (= evolutionary change). In 1930, natural selection was defined clearly as "non-random, differential reproduction of genes" by R. Fisher and J.B.S. Haldane which is a statement of the outcome of evolutionary process and which omits mention of the causes bringing about this change. Evolutionists quickly accepted this outcome definition of natural selection, and have used interchangeably selection both as a cause and as the result of evolutionary change, causing great confusion. Herein, the details will be discussed of how the external environment (i.e., the environment-phenotype interaction) serves as selective agents and exerts demands on the phenotypic organisms. Included are the concepts of fitness and of the components of fitness (= adaptations) which are respectively (a) survival, (b) direct reproductive and (c) indirect reproductive features. Finally, it will be argued that historical-narrative analyses of organisms, including classification and phylogenetic history, are possible only with

  4. Humanism and multiculturalism: an evolutionary alliance.

    PubMed

    Comas-Diaz, Lillian

    2012-12-01

    Humanism and multiculturalism are partners in an evolutionary alliance. Humanistic and multicultural psychotherapies have historically influenced each other. Humanism represents the third force in psychotherapy, while multiculturalism embodies the fourth developmental stage. Multiculturalism embraces humanistic values grounded in collective and social justice contexts. Examples of multicultural humanistic constructs include contextualism, holism, and liberation. Certainly, the multicultural-humanistic connection is a necessary shift in the evolution of psychotherapy. Humanism and multiculturalism participate in the development of an inclusive and evolutionary psychotherapy.

  5. Evolutionary game theory and leadership.

    PubMed

    Guastello, Stephen J

    2009-01-01

    Comments on the article Leadership, followership, and evolution: Some lessons from the past by Van Vugt, Hogan, and Kaiser. This article offers a fresh perspective on leaders, followers, and their possible origins in nonhuman and primitive human behavior patterns. The connections between group coordination, leadership, and game theory have some prior history (Guastello, 2002; Guastello, Bock, Caldwell, & Bond, 2005; Guastello & Bond, 2004, 2007; Guastello & Guastello, 1998), however, that suggests that some points made by Van Vugt et al. could have been more accurate. The current author provides some suggetions to the author to improve on the accuracy of this article.

  6. Characterizing behavioural 'characters': an evolutionary framework.

    PubMed

    Araya-Ajoy, Yimen G; Dingemanse, Niels J

    2014-02-01

    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.

  7. Evolutionary cell biology: two origins, one objective.

    PubMed

    Lynch, Michael; Field, Mark C; Goodson, Holly V; Malik, Harmit S; Pereira-Leal, José B; Roos, David S; Turkewitz, Aaron P; Sazer, Shelley

    2014-12-01

    All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology.

  8. Extinction as the loss of evolutionary history

    PubMed Central

    Erwin, Douglas H.

    2008-01-01

    Current plant and animal diversity preserves at most 1–2% of the species that have existed over the past 600 million years. But understanding the evolutionary impact of these extinctions requires a variety of metrics. The traditional measurement is loss of taxa (species or a higher category) but in the absence of phylogenetic information it is difficult to distinguish the evolutionary depth of different patterns of extinction: the same species loss can encompass very different losses of evolutionary history. Furthermore, both taxic and phylogenetic measures are poor metrics of morphologic disparity. Other measures of lost diversity include: functional diversity, architectural components, behavioral and social repertoires, and developmental strategies. The canonical five mass extinctions of the Phanerozoic reveals the loss of different, albeit sometimes overlapping, aspects of loss of evolutionary history. The end-Permian mass extinction (252 Ma) reduced all measures of diversity. The same was not true of other episodes, differences that may reflect their duration and structure. The construction of biodiversity reflects similarly uneven contributions to each of these metrics. Unraveling these contributions requires greater attention to feedbacks on biodiversity and the temporal variability in their contribution to evolutionary history. Taxic diversity increases after mass extinctions, but the response by other aspects of evolutionary history is less well studied. Earlier views of postextinction biotic recovery as the refilling of empty ecospace fail to capture the dynamics of this diversity increase. PMID:18695248

  9. Evolutionary theories of aging and longevity.

    PubMed

    Gavrilov, Leonid A; Gavrilova, Natalia S

    2002-02-01

    The purpose of this article is to provide students and researchers entering the field of aging studies with an introduction to the evolutionary theories of aging, as well as to orient them in the abundant modern scientific literature on evolutionary gerontology. The following three major evolutionary theories of aging are discussed: 1) the theory of programmed death suggested by August Weismann, 2) the mutation accumulation theory of aging suggested by Peter Medawar, and 3) the antagonistic pleiotropy theory of aging suggested by George Williams. We also discuss a special case of the antagonistic pleiotropy theory, the disposable soma theory developed by Tom Kirkwood and Robin Holliday. The theories are compared with each other as well as with recent experimental findings. At present the most viable evolutionary theories are the mutation accumulation theory and the antagonistic pleiotropy theory; these theories are not mutually exclusive, and they both may become a part of a future unifying theory of aging. Evolutionary theories of aging are useful because they open new opportunities for further research by suggesting testable predictions, but they have also been harmful in the past when they were used to impose limitations on aging studies. At this time, the evolutionary theories of aging are not ultimate completed theories, but rather a set of ideas that themselves require further elaboration and validation. This theoretical review article is written for a wide readership. PMID:12806021

  10. Assessment of student conceptions of evolutionary trees

    NASA Astrophysics Data System (ADS)

    Blacquiere, Luke

    Biologists use evolutionary trees to depict hypotheses about the relationships among taxa. Trees possess lines that represent lineages, internal nodes that represent where lineages become evolutionarily isolated from one another and terminal nodes that represent the taxa under consideration. Interpreting a tree (i.e., "tree-thinking") is an important skill for biologists yet many students struggle when reading evolutionary trees. Common documented misconceptions include using morphological similarity, internal node counting or terminal node proximity, instead of identifying the internal node that represents a most recent common ancestor (MRCA), to determine relationships among taxa. I developed an instrument to assess whether students were using common ancestry or another, non-scientific, strategy to determine relationships among taxa. The study is the first to explicitly test hypotheses about how students approach reading evolutionary trees. To test the hypotheses an instrument was developed. The instrument is the first reliable and valid assessment testing student understanding of how to use most recent common ancestor to interpret evolutionary relationships in tree diagrams. Instructors can use the instrument as a diagnostic tool enabling them to help students learn this challenging concept. This study shows that, contrary to the assertion that students hold misconceptions about evolutionary trees made in the literature, students do not consistently use erroneous strategies when interpreting trees. This study suggests that a constructivist perspective of cognitive structure describes students' conception of evolutionary trees more closely than a misconception perspective.

  11. Evolutionary Biology Instruction: What Students Gain from Learning through Inquiry.

    ERIC Educational Resources Information Center

    Dremock, Fae, Ed.

    2002-01-01

    This bulletin features articles on real world evolutionary biology, revolutionary classroom science, a review of new curricula in evolutionary biology, and the use of case studies to illustrate points in evolutionary biology. The articles are: (1) "'Real World' Evolutionary Biology: A Pragmatic Quest. Interview with BioQUEST's John Jungck" (Harvey…

  12. Evolving Science in Adolescence: Comment on Ellis et al. (2012)

    ERIC Educational Resources Information Center

    Dodge, Kenneth A.; Albert, Dustin

    2012-01-01

    Ellis et al. (2012) bring an evolutionary perspective to bear on adolescent risky behavioral development, clinical practice, and public policy. The authors offer important insights that (a) some risky behaviors may be adaptive for the individual and the species by being hard-wired due to fitness benefits and (b) interventions might be more…

  13. Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis.

    PubMed

    Wen, Dingqiao; Yu, Yun; Hahn, Matthew W; Nakhleh, Luay

    2016-06-01

    The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of 'network thinking' and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence. PMID:26808290

  14. Transmissible cancers in an evolutionary context.

    PubMed

    Ujvari, Beata; Papenfuss, Anthony T; Belov, Katherine

    2016-07-01

    Cancer is an evolutionary and ecological process in which complex interactions between tumour cells and their environment share many similarities with organismal evolution. Tumour cells with highest adaptive potential have a selective advantage over less fit cells. Naturally occurring transmissible cancers provide an ideal model system for investigating the evolutionary arms race between cancer cells and their surrounding micro-environment and macro-environment. However, the evolutionary landscapes in which contagious cancers reside have not been subjected to comprehensive investigation. Here, we provide a multifocal analysis of transmissible tumour progression and discuss the selection forces that shape it. We demonstrate that transmissible cancers adapt to both their micro-environment and macro-environment, and evolutionary theories applied to organisms are also relevant to these unique diseases. The three naturally occurring transmissible cancers, canine transmissible venereal tumour (CTVT) and Tasmanian devil facial tumour disease (DFTD) and the recently discovered clam leukaemia, exhibit different evolutionary phases: (i) CTVT, the oldest naturally occurring cell line is remarkably stable; (ii) DFTD exhibits the signs of stepwise cancer evolution; and (iii) clam leukaemia shows genetic instability. While all three contagious cancers carry the signature of ongoing and fairly recent adaptations to selective forces, CTVT appears to have reached an evolutionary stalemate with its host, while DFTD and the clam leukaemia appear to be still at a more dynamic phase of their evolution. Parallel investigation of contagious cancer genomes and transcriptomes and of their micro-environment and macro-environment could shed light on the selective forces shaping tumour development at different time points: during the progressive phase and at the endpoint. A greater understanding of transmissible cancers from an evolutionary ecology perspective will provide novel avenues for

  15. EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data.

    PubMed

    Linard, Benjamin; Nguyen, Ngoc Hoan; Prosdocimi, Francisco; Poch, Olivier; Thompson, Julie D

    2012-01-01

    Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.

  16. Studying Evolutionary Dynamics of Gene Families Encoding SUMO-Activating Enzymes with SeaView and ProtTest.

    PubMed

    Carretero-Paulet, Lorenzo; Albert, Victor A

    2016-01-01

    Molecular evolutionary analysis of gene families commonly involves a sequence of steps including multiple sequence alignment (MSA) and reconstructing phylogenetic trees, using any of the multiple algorithms available. SeaView is a multiplatform program that integrates different methods for performing the above tasks, and others, within a friendly and simple-to-use graphical user interface (Gouy et al. Mol Biol Evol 27(2):221-224, 2010). By using SeaView, we will investigate the evolutionary relationships among SAE1 genes in Brassicaceae species by means of two alternative methods of phylogenetic reconstruction: Maximum Likelihood (ML) and Neighbor-Joining (NJ). Prior to ML phylogenetic analysis (Guindon and Gascuel. Syst Biol 52(5):696-704, 2003), we will use ProtTest to select the best-fit evolutionary model of amino acid substitution for the MSA of SAE1 proteins (Abascal et al. Bioinformatics 21(9):2104-2105, 2005). PMID:27424762

  17. Exploring evolutionary constraints is a task for an integrative evolutionary biology.

    PubMed

    Brakefield, P M; Roskam, J C

    2006-12-01

    Judging by the volume of writings about evolutionary constraints, they are an important topic in evolutionary biology. However, their involvement in shaping patterns of evolutionary change from morphological stasis to adaptive radiation remains contentious. This is at least in part because of the paucity of robust analyses of potential examples of constraints, whether of a more absolute or a relative nature. Here, we argue that what is needed to explore the type of constraints and bias on evolutionary change that may emerge from the way in which phenotypic variation is generated is an integrative approach applied to systems that can be tackled at different levels of biological organization. This is illustrated using research on the evolution of patterns in butterfly wing eyespots that has applied a combination of evolutionary genetics and evo-devo to an emerging model species with the beginnings of a comparative approach to describe patterns of variability among the extant taxa of two species-rich genera. PMID:17109328

  18. Exploring evolutionary constraints is a task for an integrative evolutionary biology.

    PubMed

    Brakefield, P M; Roskam, J C

    2006-12-01

    Judging by the volume of writings about evolutionary constraints, they are an important topic in evolutionary biology. However, their involvement in shaping patterns of evolutionary change from morphological stasis to adaptive radiation remains contentious. This is at least in part because of the paucity of robust analyses of potential examples of constraints, whether of a more absolute or a relative nature. Here, we argue that what is needed to explore the type of constraints and bias on evolutionary change that may emerge from the way in which phenotypic variation is generated is an integrative approach applied to systems that can be tackled at different levels of biological organization. This is illustrated using research on the evolution of patterns in butterfly wing eyespots that has applied a combination of evolutionary genetics and evo-devo to an emerging model species with the beginnings of a comparative approach to describe patterns of variability among the extant taxa of two species-rich genera.

  19. Evolutionary-thinking in agricultural weed management.

    PubMed

    Neve, Paul; Vila-Aiub, Martin; Roux, Fabrice

    2009-12-01

    Agricultural weeds evolve in response to crop cultivation. Nevertheless, the central importance of evolutionary ecology for understanding weed invasion, persistence and management in agroecosystems is not widely acknowledged. This paper calls for more evolutionarily-enlightened weed management, in which management principles are informed by evolutionary biology to prevent or minimize weed adaptation and spread. As a first step, a greater knowledge of the extent, structure and significance of genetic variation within and between weed populations is required to fully assess the potential for weed adaptation. The evolution of resistance to herbicides is a classic example of weed adaptation. Even here, most research focuses on describing the physiological and molecular basis of resistance, rather than conducting studies to better understand the evolutionary dynamics of selection for resistance. We suggest approaches to increase the application of evolutionary-thinking to herbicide resistance research. Weed population dynamics models are increasingly important tools in weed management, yet these models often ignore intrapopulation and interpopulation variability, neglecting the potential for weed adaptation in response to management. Future agricultural weed management can benefit from greater integration of ecological and evolutionary principles to predict the long-term responses of weed populations to changing weed management, agricultural environments and global climate.

  20. Three Laws in Darwinian Evolutionary Theory

    NASA Astrophysics Data System (ADS)

    Ao, Ping

    2006-03-01

    Recent works to formulate laws in Darwinian evolutionary dynamics will be discussed. Specifically, three laws which form a consistent mathematical framework for the evolutionary dynamics in biology will be spelt out. The second law is most quantitative and is explicitly expressed in the unique form of a stochastic differential equation. Salient features of Darwinian evolutionary dynamics are captured by this law: the probabilistic nature of evolution, ascendancy, and the adaptive landscape. Four dynamical elements are introduced in this formulation: the ascendant matrix, the transverse matrix, the Wright evolutionary potential, and the stochastic drive. The first law may be regarded as a special case of the second law. It gives the reference point to discuss the evolutionary dynamics. The third law describes the relationship between the focused level of description to its lower and higher ones, and defines the dichotomy of deterministic and stochastic drives. It is an acknowledgement of the hierarchical structure in biology. A new interpretation of Fisher's fundamental theorem of natural selection is provided in terms of the F-Theorem. Ref. P. Ao, Physics of Life Reviews 2 (2005) 117-156.

  1. Evolutionary accounts of human behavioural diversity

    PubMed Central

    Brown, Gillian R.; Dickins, Thomas E.; Sear, Rebecca; Laland, Kevin N.

    2011-01-01

    Human beings persist in an extraordinary range of ecological settings, in the process exhibiting enormous behavioural diversity, both within and between populations. People vary in their social, mating and parental behaviour and have diverse and elaborate beliefs, traditions, norms and institutions. The aim of this theme issue is to ask whether, and how, evolutionary theory can help us to understand this diversity. In this introductory article, we provide a background to the debate surrounding how best to understand behavioural diversity using evolutionary models of human behaviour. In particular, we examine how diversity has been viewed by the main subdisciplines within the human evolutionary behavioural sciences, focusing in particular on the human behavioural ecology, evolutionary psychology and cultural evolution approaches. In addition to differences in focus and methodology, these subdisciplines have traditionally varied in the emphasis placed on human universals, ecological factors and socially learned behaviour, and on how they have addressed the issue of genetic variation. We reaffirm that evolutionary theory provides an essential framework for understanding behavioural diversity within and between human populations, but argue that greater integration between the subfields is critical to developing a satisfactory understanding of diversity. PMID:21199836

  2. Comparative evolutionary psychology of sperm competition.

    PubMed

    Shackelford, Todd K; Goetz, Aaron T

    2006-05-01

    A comparative evolutionary psychological perspective predicts that species that recurrently faced similar adaptive problems may have evolved similar psychological mechanisms to solve these problems. Sperm competition provides an arena in which to assess the heuristic value of such a comparative evolutionary perspective. The sperm competition that results from female infidelity and polyandry presents a similar class of adaptive problems for individuals across many species. The authors first describe mechanisms of sperm competition in insects and in birds. They suggest that the adaptive problems and evolved solutions in these species provide insight into human anatomy, physiology, psychology, and behavior. The authors then review recent theoretical and empirical arguments for the existence of sperm competition in humans and discuss proposed adaptations in humans that have analogs in insects or birds. The authors conclude by highlighting the heuristic value of a comparative evolutionary psychological approach in this field.

  3. Evolutionary psychology: the emperor's new paradigm.

    PubMed

    Buller, David J

    2005-06-01

    For some evolutionary psychology is merely a field of inquiry, but for others it is a robust paradigm involving specific theories about the nature and evolution of the human mind. Proponents of this paradigm claim to have made several important discoveries regarding the evolved architecture of the mind. Highly publicized discoveries include a cheater-detection module, a psychological sex difference in jealousy, and motivational mechanisms underlying parental love and its lapses, which purportedly result in child maltreatment. In this article, I argue that the empirical evidence for these "discoveries" is inconclusive, at best. I suggest that, as the reigning paradigm in evolutionary psychology has produced questionable results, the evolutionary study of human psychology is still in need of a guiding paradigm.

  4. Towards a postmodern synthesis of evolutionary biology.

    PubMed

    Koonin, Eugene V

    2009-03-15

    In 2009, we are celebrating the 200th anniversary of Charles Darwin and the 150th jubilee of his masterpiece, the Origin of Species. Darwin developed the first coherent and compelling narrative of biological evolution and thus founded evolutionary biology-and modern biology in general, remembering the famous dictum of Dobzhansky. It is, however, counter-productive, and ultimately, a disservice to Darwin's legacy, to define modern evolutionary biology as neo-Darwinism. The current picture of evolution, informed, in particular, by results of comparative genomics and systems biology, is by far more complex than that presented in the Origin of Species, so that Darwinian principles, including natural selection, are incorporated into the evolving new synthesis as important but certainly not all-embracing tenets. This expansion of evolutionary biology does not denigrate Darwin in the least but rather emphasizes the fertility of his ideas. PMID:19242109

  5. Incorporating evolutionary processes into population viability models.

    PubMed

    Pierson, Jennifer C; Beissinger, Steven R; Bragg, Jason G; Coates, David J; Oostermeijer, J Gerard B; Sunnucks, Paul; Schumaker, Nathan H; Trotter, Meredith V; Young, Andrew G

    2015-06-01

    We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand the influence of evolutionary processes on population persistence. We developed the mechanistic basis of an eco-evo PVA using individual-based models with individual-level genotype tracking and dynamic genotype-phenotype mapping to model emergent population-level effects, such as local adaptation and genetic rescue. We then outline how genomics can allow or improve parameter estimation for PVA models by providing genotypic information at large numbers of loci for neutral and functional genome regions. As climate change and other threatening processes increase in rate and scale, eco-evo PVAs will become essential research tools to evaluate the effects of adaptive potential, evolutionary rescue, and locally adapted traits on persistence.

  6. Atavisms: medical, genetic, and evolutionary implications.

    PubMed

    Tomić, Nenad; Meyer-Rochow, Victor Benno

    2011-01-01

    Traits expected to be lost in the evolutionary history of a species occasionally reappear apparently out of the blue. Such traits as extra nipples or tails in humans, hind limbs in whales, teeth in birds, or wings in wingless stick insects remind us that certain genetic information is not completely lost, but can be reactivated. Atavisms seem to violate one of the central evolutionary principles, known as Dollo's law, that "an organism is unable to return, even partially, to a previous stage already realized in the ranks of its ancestors." Although it is still not clear what triggers and controls the reactivation of dormant traits, atavisms are a challenge to evolutionary biologists and geneticists. This article presents some of the more striking examples of atavisms, discusses some of the currently controversial issues like human quadrupedalism, and reviews the progress made in explaining some of the mechanisms that can lead to atavistic features. PMID:21857125

  7. Modeling the evolutionary demographic processes for geomedicine

    NASA Astrophysics Data System (ADS)

    Lushnikov, A. A.; Kagan, A. I.; Gvishiani, A. D.; Lyubovtseva, Yu. S.

    2014-12-01

    We describe the principles for constructing evolutionary demographic models for geomedical statistics. Several variants of evolutionary models are proposed: (1) a model of the evolution of a closed population taking into account distribution by age, (2) a model that takes into account the morbidity and difference in mortality for groups of patients and healthy individuals, (3) a model that takes into account the distribution of different age groups by fertile ability, (4) a migration model that takes into account the population exchange between several localities, and (5) a model of the propagation of infectious diseases. Each model depends on a group of parameters determined from the medical and demographic state of the population. We discuss the possible application of the proposed evolutionary models to geomedical statistics.

  8. Do we need an extended evolutionary synthesis?

    PubMed

    Pigliucci, Massimo

    2007-12-01

    The Modern Synthesis (MS) is the current paradigm in evolutionary biology. It was actually built by expanding on the conceptual foundations laid out by its predecessors, Darwinism and neo-Darwinism. For sometime now there has been talk of a new Extended Evolutionary Synthesis (EES), and this article begins to outline why we may need such an extension, and how it may come about. As philosopher Karl Popper has noticed, the current evolutionary theory is a theory of genes, and we still lack a theory of forms. The field began, in fact, as a theory of forms in Darwin's days, and the major goal that an EES will aim for is a unification of our theories of genes and of forms. This may be achieved through an organic grafting of novel concepts onto the foundational structure of the MS, particularly evolvability, phenotypic plasticity, epigenetic inheritance, complexity theory, and the theory of evolution in highly dimensional adaptive landscapes. PMID:17924956

  9. Neurocontroller analysis via evolutionary network minimization.

    PubMed

    Ganon, Zohar; Keinan, Alon; Ruppin, Eytan

    2006-01-01

    This study presents a new evolutionary network minimization (ENM) algorithm. Neurocontroller minimization is beneficial for finding small parsimonious networks that permit a better understanding of their workings. The ENM algorithm is specifically geared to an evolutionary agents setup, as it does not require any explicit supervised training error, and is very easily incorporated in current evolutionary algorithms. ENM is based on a standard genetic algorithm with an additional step during reproduction in which synaptic connections are irreversibly eliminated. It receives as input a successfully evolved neurocontroller and aims to output a pruned neurocontroller, while maintaining the original fitness level. The small neurocontrollers produced by ENM provide upper bounds on the neurocontroller size needed to perform a given task successfully, and can provide for more effcient hardware implementations. PMID:16859448

  10. Towards a postmodern synthesis of evolutionary biology

    PubMed Central

    Koonin, Eugene V.

    2012-01-01

    In 2009, we are celebrating the 200th anniversary of Charles Darwin and the 150th jubilee of his masterpiece, the Origin of Species. Darwin developed the first coherent and compelling narrative of biological evolution and thus founded evolutionary biology—and modern biology in general, remembering the famous dictum of Dobzhansky. It is, however, counter-productive, and ultimately, a disservice to Darwin’s legacy, to define modern evolutionary biology as neo-Darwinism. The current picture of evolution, informed, in particular, by results of comparative genomics and systems biology, is by far more complex than that presented in the Origin of Species, so that Darwinian principles, including natural selection, are incorporated into the evolving new synthesis as important but certainly not all-embracing tenets. This expansion of evolutionary biology does not denigrate Darwin in the least but rather emphasizes the fertility of his ideas. PMID:19242109

  11. Towards a postmodern synthesis of evolutionary biology.

    PubMed

    Koonin, Eugene V

    2009-03-15

    In 2009, we are celebrating the 200th anniversary of Charles Darwin and the 150th jubilee of his masterpiece, the Origin of Species. Darwin developed the first coherent and compelling narrative of biological evolution and thus founded evolutionary biology-and modern biology in general, remembering the famous dictum of Dobzhansky. It is, however, counter-productive, and ultimately, a disservice to Darwin's legacy, to define modern evolutionary biology as neo-Darwinism. The current picture of evolution, informed, in particular, by results of comparative genomics and systems biology, is by far more complex than that presented in the Origin of Species, so that Darwinian principles, including natural selection, are incorporated into the evolving new synthesis as important but certainly not all-embracing tenets. This expansion of evolutionary biology does not denigrate Darwin in the least but rather emphasizes the fertility of his ideas.

  12. Do we need an extended evolutionary synthesis?

    PubMed

    Pigliucci, Massimo

    2007-12-01

    The Modern Synthesis (MS) is the current paradigm in evolutionary biology. It was actually built by expanding on the conceptual foundations laid out by its predecessors, Darwinism and neo-Darwinism. For sometime now there has been talk of a new Extended Evolutionary Synthesis (EES), and this article begins to outline why we may need such an extension, and how it may come about. As philosopher Karl Popper has noticed, the current evolutionary theory is a theory of genes, and we still lack a theory of forms. The field began, in fact, as a theory of forms in Darwin's days, and the major goal that an EES will aim for is a unification of our theories of genes and of forms. This may be achieved through an organic grafting of novel concepts onto the foundational structure of the MS, particularly evolvability, phenotypic plasticity, epigenetic inheritance, complexity theory, and the theory of evolution in highly dimensional adaptive landscapes.

  13. Inferring evolutionary trees from ordinal data

    SciTech Connect

    Kearney, P.E.; Hayward, R.B.; Meijer, H.

    1997-06-01

    In this paper we present four results on the inference of evolutionary trees from ordinal information. An evolutionary tree T, or phylogeny, is an ordinal representation of a distance matrix , for all species a, b, c and d under consideration. In particular, we show that (1) Ordinal representations of distance matrices can be found in O(n{sup 2}log{sup 2} n) time where n is the number of species. Ordinal representations are shown to be unique, when they exist. (3) Determining if there is an ordinal representation for an incomplete distance matrix, a situation which arises in evolutionary studies, is NP-complete. (3) Finding a phylogeny that best fits a distance matrix containing ordinal errors is NP-complete. (4) Under reasonable conditions, a weighted ordinal representation of a distance matrix can be obtained in polynomial time.

  14. Computational and evolutionary aspects of language

    NASA Astrophysics Data System (ADS)

    Nowak, Martin A.; Komarova, Natalia L.; Niyogi, Partha

    2002-06-01

    Language is our legacy. It is the main evolutionary contribution of humans, and perhaps the most interesting trait that has emerged in the past 500 million years. Understanding how darwinian evolution gives rise to human language requires the integration of formal language theory, learning theory and evolutionary dynamics. Formal language theory provides a mathematical description of language and grammar. Learning theory formalizes the task of language acquisition-it can be shown that no procedure can learn an unrestricted set of languages. Universal grammar specifies the restricted set of languages learnable by the human brain. Evolutionary dynamics can be formulated to describe the cultural evolution of language and the biological evolution of universal grammar.

  15. Aerodynamic Shape Optimization using an Evolutionary Algorithm

    NASA Technical Reports Server (NTRS)

    Hoist, Terry L.; Pulliam, Thomas H.

    2003-01-01

    A method for aerodynamic shape optimization based on an evolutionary algorithm approach is presented and demonstrated. Results are presented for a number of model problems to access the effect of algorithm parameters on convergence efficiency and reliability. A transonic viscous airfoil optimization problem-both single and two-objective variations is used as the basis for a preliminary comparison with an adjoint-gradient optimizer. The evolutionary algorithm is coupled with a transonic full potential flow solver and is used to optimize the inviscid flow about transonic wings including multi-objective and multi-discipline solutions that lead to the generation of pareto fronts. The results indicate that the evolutionary algorithm approach is easy to implement, flexible in application and extremely reliable.

  16. Aerodynamic Shape Optimization using an Evolutionary Algorithm

    NASA Technical Reports Server (NTRS)

    Holst, Terry L.; Pulliam, Thomas H.; Kwak, Dochan (Technical Monitor)

    2003-01-01

    A method for aerodynamic shape optimization based on an evolutionary algorithm approach is presented and demonstrated. Results are presented for a number of model problems to access the effect of algorithm parameters on convergence efficiency and reliability. A transonic viscous airfoil optimization problem, both single and two-objective variations, is used as the basis for a preliminary comparison with an adjoint-gradient optimizer. The evolutionary algorithm is coupled with a transonic full potential flow solver and is used to optimize the inviscid flow about transonic wings including multi-objective and multi-discipline solutions that lead to the generation of pareto fronts. The results indicate that the evolutionary algorithm approach is easy to implement, flexible in application and extremely reliable.

  17. From computers to cultivation: reconceptualizing evolutionary psychology.

    PubMed

    Barrett, Louise; Pollet, Thomas V; Stulp, Gert

    2014-01-01

    Does evolutionary theorizing have a role in psychology? This is a more contentious issue than one might imagine, given that, as evolved creatures, the answer must surely be yes. The contested nature of evolutionary psychology lies not in our status as evolved beings, but in the extent to which evolutionary ideas add value to studies of human behavior, and the rigor with which these ideas are tested. This, in turn, is linked to the framework in which particular evolutionary ideas are situated. While the framing of the current research topic places the brain-as-computer metaphor in opposition to evolutionary psychology, the most prominent school of thought in this field (born out of cognitive psychology, and often known as the Santa Barbara school) is entirely wedded to the computational theory of mind as an explanatory framework. Its unique aspect is to argue that the mind consists of a large number of functionally specialized (i.e., domain-specific) computational mechanisms, or modules (the massive modularity hypothesis). Far from offering an alternative to, or an improvement on, the current perspective, we argue that evolutionary psychology is a mainstream computational theory, and that its arguments for domain-specificity often rest on shaky premises. We then go on to suggest that the various forms of e-cognition (i.e., embodied, embedded, enactive) represent a true alternative to standard computational approaches, with an emphasis on "cognitive integration" or the "extended mind hypothesis" in particular. We feel this offers the most promise for human psychology because it incorporates the social and historical processes that are crucial to human "mind-making" within an evolutionarily informed framework. In addition to linking to other research areas in psychology, this approach is more likely to form productive links to other disciplines within the social sciences, not least by encouraging a healthy pluralism in approach.

  18. A framework for evolutionary systems biology

    PubMed Central

    Loewe, Laurence

    2009-01-01

    Background Many difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often simple to predict. Current systems biology has accumulated much data on mutations with large effects and can predict the properties of knockout mutants in some systems. However experimental methods are too insensitive to observe small effects. Results Here I propose a novel framework that brings together evolutionary theory and current systems biology approaches in order to quantify small effects of mutations and their epistatic interactions in silico. Central to this approach is the definition of fitness correlates that can be computed in some current systems biology models employing the rigorous algorithms that are at the core of much work in computational systems biology. The framework exploits synergies between the realism of such models and the need to understand real systems in evolutionary theory. This framework can address many longstanding topics in evolutionary biology by defining various 'levels' of the adaptive landscape. Addressed topics include the distribution of mutational effects on fitness, as well as the nature of advantageous mutations, epistasis and robustness. Combining corresponding parameter estimates with population genetics models raises the possibility of testing evolutionary hypotheses at a new level of realism. Conclusion EvoSysBio is expected to lead to a more detailed understanding of the fundamental principles of life by combining knowledge about well-known biological systems from several disciplines. This will benefit both evolutionary theory and current systems biology. Understanding robustness by analysing distributions of mutational effects and epistasis is pivotal for drug design, cancer research, responsible genetic engineering in synthetic biology and many other practical applications. PMID:19239699

  19. From computers to cultivation: reconceptualizing evolutionary psychology

    PubMed Central

    Barrett, Louise; Pollet, Thomas V.; Stulp, Gert

    2014-01-01

    Does evolutionary theorizing have a role in psychology? This is a more contentious issue than one might imagine, given that, as evolved creatures, the answer must surely be yes. The contested nature of evolutionary psychology lies not in our status as evolved beings, but in the extent to which evolutionary ideas add value to studies of human behavior, and the rigor with which these ideas are tested. This, in turn, is linked to the framework in which particular evolutionary ideas are situated. While the framing of the current research topic places the brain-as-computer metaphor in opposition to evolutionary psychology, the most prominent school of thought in this field (born out of cognitive psychology, and often known as the Santa Barbara school) is entirely wedded to the computational theory of mind as an explanatory framework. Its unique aspect is to argue that the mind consists of a large number of functionally specialized (i.e., domain-specific) computational mechanisms, or modules (the massive modularity hypothesis). Far from offering an alternative to, or an improvement on, the current perspective, we argue that evolutionary psychology is a mainstream computational theory, and that its arguments for domain-specificity often rest on shaky premises. We then go on to suggest that the various forms of e-cognition (i.e., embodied, embedded, enactive) represent a true alternative to standard computational approaches, with an emphasis on “cognitive integration” or the “extended mind hypothesis” in particular. We feel this offers the most promise for human psychology because it incorporates the social and historical processes that are crucial to human “mind-making” within an evolutionarily informed framework. In addition to linking to other research areas in psychology, this approach is more likely to form productive links to other disciplines within the social sciences, not least by encouraging a healthy pluralism in approach. PMID:25161633

  20. ECOD: An Evolutionary Classification of Protein Domains

    PubMed Central

    Kinch, Lisa N.; Pei, Jimin; Shi, Shuoyong; Kim, Bong-Hyun; Grishin, Nick V.

    2014-01-01

    Understanding the evolution of a protein, including both close and distant relationships, often reveals insight into its structure and function. Fast and easy access to such up-to-date information facilitates research. We have developed a hierarchical evolutionary classification of all proteins with experimentally determined spatial structures, and presented it as an interactive and updatable online database. ECOD (Evolutionary Classification of protein Domains) is distinct from other structural classifications in that it groups domains primarily by evolutionary relationships (homology), rather than topology (or “fold”). This distinction highlights cases of homology between domains of differing topology to aid in understanding of protein structure evolution. ECOD uniquely emphasizes distantly related homologs that are difficult to detect, and thus catalogs the largest number of evolutionary links among structural domain classifications. Placing distant homologs together underscores the ancestral similarities of these proteins and draws attention to the most important regions of sequence and structure, as well as conserved functional sites. ECOD also recognizes closer sequence-based relationships between protein domains. Currently, approximately 100,000 protein structures are classified in ECOD into 9,000 sequence families clustered into close to 2,000 evolutionary groups. The classification is assisted by an automated pipeline that quickly and consistently classifies weekly releases of PDB structures and allows for continual updates. This synchronization with PDB uniquely distinguishes ECOD among all protein classifications. Finally, we present several case studies of homologous proteins not recorded in other classifications, illustrating the potential of how ECOD can be used to further biological and evolutionary studies. PMID:25474468

  1. Evolutionary Phase Transitions in Random Environments.

    PubMed

    Skanata, Antun; Kussell, Edo

    2016-07-15

    We present analytical results for long-term growth rates of structured populations in randomly fluctuating environments, which we apply to predict how cellular response networks evolve. We show that networks which respond rapidly to a stimulus will evolve phenotypic memory exclusively under random (i.e., nonperiodic) environments. We identify the evolutionary phase diagram for simple response networks, which we show can exhibit both continuous and discontinuous transitions. Our approach enables exact analysis of diverse evolutionary systems, from viral epidemics to emergence of drug resistance. PMID:27472146

  2. Evolutionary genetics of insect innate immunity

    PubMed Central

    2015-01-01

    Patterns of evolution in immune defense genes help to understand the evolutionary dynamics between hosts and pathogens. Multiple insect genomes have been sequenced, with many of them having annotated immune genes, which paves the way for a comparative genomic analysis of insect immunity. In this review, I summarize the current state of comparative and evolutionary genomics of insect innate immune defense. The focus is on the conserved and divergent components of immunity with an emphasis on gene family evolution and evolution at the sequence level; both population genetics and molecular evolution frameworks are considered. PMID:25750410

  3. Genomes, Phylogeny, and Evolutionary Systems Biology

    SciTech Connect

    Medina, Monica

    2005-03-25

    With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

  4. Langley's CSI evolutionary model: Phase O

    NASA Technical Reports Server (NTRS)

    Belvin, W. Keith; Elliott, Kenny B.; Horta, Lucas G.; Bailey, Jim P.; Bruner, Anne M.; Sulla, Jeffrey L.; Won, John; Ugoletti, Roberto M.

    1991-01-01

    A testbed for the development of Controls Structures Interaction (CSI) technology to improve space science platform pointing is described. The evolutionary nature of the testbed will permit the study of global line-of-sight pointing in phases 0 and 1, whereas, multipayload pointing systems will be studied beginning with phase 2. The design, capabilities, and typical dynamic behavior of the phase 0 version of the CSI evolutionary model (CEM) is documented for investigator both internal and external to NASA. The model description includes line-of-sight pointing measurement, testbed structure, actuators, sensors, and real time computers, as well as finite element and state space models of major components.

  5. The evolutionary origin of cooperators and defectors.

    PubMed

    Doebeli, Michael; Hauert, Christoph; Killingback, Timothy

    2004-10-29

    Coexistence of cooperators and defectors is common in nature, yet the evolutionary origin of such social diversification is unclear. Many models have been studied on the basis of the assumption that benefits of cooperative acts only accrue to others. Here, we analyze the continuous snowdrift game, in which cooperative investments are costly but yield benefits to others as well as to the cooperator. Adaptive dynamics of investment levels often result in evolutionary diversification from initially uniform populations to a stable state in which cooperators making large investments coexist with defectors who invest very little. Thus, when individuals benefit from their own actions, large asymmetries in cooperative investments can evolve.

  6. Evolutionary strategy for achieving autonomous navigation

    NASA Astrophysics Data System (ADS)

    Gage, Douglas W.

    1999-01-01

    An approach is presented for the evolutionary development of supervised autonomous navigation capabilities for small 'backpackable' ground robots, in the context of a DARPA- sponsored program to provide robotic support to small units of dismounted warfighters. This development approach relies on the implementation of a baseline visual serving navigation capability, including tools to support operator oversight and override, which is then enhanced with semantically referenced commands and a mission scripting structure. As current and future machine perception techniques are able to automatically designate visual serving goal points, this approach should provide a natural evolutionary pathway to higher levels of autonomous operation and reduced requirements for operator intervention.

  7. Evolutionary Phase Transitions in Random Environments

    NASA Astrophysics Data System (ADS)

    Skanata, Antun; Kussell, Edo

    2016-07-01

    We present analytical results for long-term growth rates of structured populations in randomly fluctuating environments, which we apply to predict how cellular response networks evolve. We show that networks which respond rapidly to a stimulus will evolve phenotypic memory exclusively under random (i.e., nonperiodic) environments. We identify the evolutionary phase diagram for simple response networks, which we show can exhibit both continuous and discontinuous transitions. Our approach enables exact analysis of diverse evolutionary systems, from viral epidemics to emergence of drug resistance.

  8. Evolutionary thinking: "A conversation with Carter Phipps about the role of evolutionary thinking in modern culture".

    PubMed

    Hunt, Tam

    2014-12-01

    Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution-both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place-has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps' book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging "integral" or "evolutionary" cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps.

  9. Evolutionary Psychology: Controversies, Questions, Prospects, and Limitations

    ERIC Educational Resources Information Center

    Confer, Jaime C.; Easton, Judith A.; Fleischman, Diana S.; Goetz, Cari D.; Lewis, David M. G.; Perilloux, Carin; Buss, David M.

    2010-01-01

    Evolutionary psychology has emerged over the past 15 years as a major theoretical perspective, generating an increasing volume of empirical studies and assuming a larger presence within psychological science. At the same time, it has generated critiques and remains controversial among some psychologists. Some of the controversy stems from…

  10. Evolutionary Dynamics of Digitized Organizational Routines

    ERIC Educational Resources Information Center

    Liu, Peng

    2013-01-01

    This dissertation explores the effects of increased digitization on the evolutionary dynamics of organizational routines. Do routines become more flexible, or more rigid, as the mix of digital technologies and human actors changes? What are the mechanisms that govern the evolution of routines? The dissertation theorizes about the effects of…

  11. Compassion: An Evolutionary Analysis and Empirical Review

    ERIC Educational Resources Information Center

    Goetz, Jennifer L.; Keltner, Dacher; Simon-Thomas, Emiliana

    2010-01-01

    What is compassion? And how did it evolve? In this review, we integrate 3 evolutionary arguments that converge on the hypothesis that compassion evolved as a distinct affective experience whose primary function is to facilitate cooperation and protection of the weak and those who suffer. Our empirical review reveals compassion to have distinct…

  12. Evo-Devo: evolutionary developmental mechanisms.

    PubMed

    Hall, Brian K

    2003-01-01

    Evolutionary developmental biology (Evo-Devo) as a discipline is concerned, among other things, with discovering and understanding the role of changes in developmental mechanisms in the evolutionary origin of aspects of the phenotype. In a very real sense, Evo-Devo opens the black box between genotype and phenotype, or more properly, phenotypes as multiple life history stages arise in many organisms from a single genotype. Changes in the timing or positioning of an aspect of development in a descendant relative to an ancestor (heterochrony and heterotopy) were two evolutionary developmental mechanisms identified by Ernst Haeckel in the 1870s. Many more have since been identified, in large part because of our enhanced understanding of development and because new mechanisms emerge as development proceeds: the transfer from maternal to zygotic genomic control; cell-to-cell interactions; cell differentiation and cell migration; embryonic inductions; functional interactions at the tissue and organ levels; growth. Within these emergent processes, gene networks and gene cascades (genetic modules) link the genotype with morphogenetic units (cellular modules, namely germ layers, embryonic fields or cellular condensations), while epigenetic processes such as embryonic inductions, tissue interactions and functional integration, link morphogenetic units to the phenotype. Evolutionary developmental mechanisms also include interactions between individuals of the same species, individuals of different species, and species and their biotic and/or abiotic environment. Such interactions link ecological communities. Importantly, there is little to distinguish the causality that underlies these interactions from that which underlies inductive interactions within embryos. PMID:14756324

  13. Haplogroups as Evolutionary Markers of Cognitive Ability

    ERIC Educational Resources Information Center

    Rindermann, Heiner; Woodley, Michael A.; Stratford, James

    2012-01-01

    Studies investigating evolutionary theories on the origins of national differences in intelligence have been criticized on the basis that both national cognitive ability measures and supposedly evolutionarily informative proxies (such as latitude and climate) are confounded with general developmental status. In this study 14 Y chromosomal…

  14. Climate as a driver of evolutionary change.

    PubMed

    Erwin, Douglas H

    2009-07-28

    The link between biodiversity and climate has been obvious to biologists since the work of von Humboldt in the early 1800s, but establishing the relationship of climate to ecological and evolutionary patterns is more difficult. On evolutionary timescales, climate can affect supply of energy by biotic and abiotic effects. Some of the best evidence for a link between biodiversity and climate comes from latitudinal gradients in diversity, which provide an avenue to explore the more general relationship between climate and evolution. Among the wide range of biotic hypotheses, those with the greatest empirical support indicate that warmer climates have provided the energetic foundation for increased biodiversity by fostering greater population size and thus increased extinction resistance; have increased metabolic scope; have allowed more species to exploit specialized niches as a result of greater available energy; and generated faster speciation and/or lower extinction rates. In combination with geologic evidence for carbon dioxide levels and changing areas of tropical seas, these observations provide the basis for a simple, first-order model of the relationship between climate through the Phanerozoic and evolutionary patterns and diversity. Such a model suggests that we should expect greatest marine diversity during globally warm intervals with dispersed continents, broad shelves and moderately extensive continental seas. Demonstrating a significant evolutionary response to either climate or climatic change is challenging, however, because of continuing uncertainties over patterns of Phanerozoic marine diversity and the variety of factors beyond climate that influence evolution. PMID:19640496

  15. The Evolutionary Development of CAI Evaluation Approaches.

    ERIC Educational Resources Information Center

    Avner, R. A.

    The role of evaluation in the development of evolutionary procedures is briefly described and highlighted. Four aspects of evaluation technique which distinguish efficient from inefficient CAI programs are identified. Evaluation of products is also characterized. Findings of a continuing survey of students via questionnaire as to the value of…

  16. Climate as a driver of evolutionary change.

    PubMed

    Erwin, Douglas H

    2009-07-28

    The link between biodiversity and climate has been obvious to biologists since the work of von Humboldt in the early 1800s, but establishing the relationship of climate to ecological and evolutionary patterns is more difficult. On evolutionary timescales, climate can affect supply of energy by biotic and abiotic effects. Some of the best evidence for a link between biodiversity and climate comes from latitudinal gradients in diversity, which provide an avenue to explore the more general relationship between climate and evolution. Among the wide range of biotic hypotheses, those with the greatest empirical support indicate that warmer climates have provided the energetic foundation for increased biodiversity by fostering greater population size and thus increased extinction resistance; have increased metabolic scope; have allowed more species to exploit specialized niches as a result of greater available energy; and generated faster speciation and/or lower extinction rates. In combination with geologic evidence for carbon dioxide levels and changing areas of tropical seas, these observations provide the basis for a simple, first-order model of the relationship between climate through the Phanerozoic and evolutionary patterns and diversity. Such a model suggests that we should expect greatest marine diversity during globally warm intervals with dispersed continents, broad shelves and moderately extensive continental seas. Demonstrating a significant evolutionary response to either climate or climatic change is challenging, however, because of continuing uncertainties over patterns of Phanerozoic marine diversity and the variety of factors beyond climate that influence evolution.

  17. Telling Tales at Work: An Evolutionary Explanation

    ERIC Educational Resources Information Center

    Yang, Chulguen

    2013-01-01

    This article explores the adaptive functions of storytelling in the workplace from an evolutionary perspective. Based on the analysis of ethnographic studies on hunter-gatherer and modern work organizations, this article claims that storytelling, as an adapted cognitive device, was selectively retained by natural and sexual selection, because of…

  18. Molecular selection in a unified evolutionary sequence

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1986-01-01

    With guidance from experiments and observations that indicate internally limited phenomena, an outline of unified evolutionary sequence is inferred. Such unification is not visible for a context of random matrix and random mutation. The sequence proceeds from Big Bang through prebiotic matter, protocells, through the evolving cell via molecular and natural selection, to mind, behavior, and society.

  19. The Finches' Beaks: Introducing Evolutionary Concepts

    ERIC Educational Resources Information Center

    Kampourakis, Kostas

    2006-01-01

    Many secondary students hold misconceptions about evolution, even after instruction, that are often inconsistent with what is accepted by evolutionary biologists. Understanding evolution is difficult due to major conceptual difficulties concerning variation, differential survival, adaptation, and natural selection. In this article, the author…

  20. College Students' Misconceptions about Evolutionary Trees

    ERIC Educational Resources Information Center

    Meir, Eli; Perry, Judy; Herron, Jon C.; Kingsolver, Joel

    2007-01-01

    Evolution is at the center of the biological sciences and is therefore a required topic for virtually every college biology student. Over the past year, the authors have been building a new simulation software package called EvoBeaker to teach college-level evolutionary biology through simulated experiments. They have built both micro and…

  1. Testing for Independence between Evolutionary Processes.

    PubMed

    Behdenna, Abdelkader; Pothier, Joël; Abby, Sophie S; Lambert, Amaury; Achaz, Guillaume

    2016-09-01

    Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for the larger diversity of possible relative positions of events in a tree. Here we propose a method to quantify to what extent two or more evolutionary events are associated on a phylogenetic tree. The method is applicable to any discrete character, like substitutions within a coding sequence or gains/losses of a biological function. Our method uses a general approach to statistically test for significant associations between events along the tree, which encompasses both events inseparable on the same branch, and events genealogically ordered on different branches. It assumes that the phylogeny and themapping of branches is known without errors. We address this problem from the statistical viewpoint by a linear algebra representation of the localization of the evolutionary events on the tree.We compute the full probability distribution of the number of paired events occurring in the same branch or in different branches of the tree, under a null model of independence where each type of event occurs at a constant rate uniformly inthephylogenetic tree. The strengths andweaknesses of themethodare assessed via simulations;we then apply the method to explore the loss of cell motility in intracellular pathogens. PMID:27208890

  2. Phylogeny and the inference of evolutionary trajectories.

    PubMed

    Hancock, Lillian; Edwards, Erika J

    2014-07-01

    Most important organismal adaptations are not actually single traits, but complex trait syndromes that are evolutionarily integrated into a single emergent phenotype. Two alternative photosynthetic pathways, C4 photosynthesis and crassulacean acid metabolism (CAM), are primary plant adaptations of this sort, each requiring multiple biochemical and anatomical modifications. Phylogenetic methods are a promising approach for teasing apart the order of character acquisition during the evolution of complex traits, and the phylogenetic placement of intermediate phenotypes as sister taxa to fully optimized syndromes has been taken as good evidence of an 'ordered' evolutionary trajectory. But how much power does the phylogenetic approach have to detect ordered evolution? This study simulated ordered and unordered character evolution across a diverse set of phylogenetic trees to understand how tree size, models of evolution, and sampling efforts influence the ability to detect an evolutionary trajectory. The simulations show that small trees (15 taxa) do not contain enough information to correctly infer either an ordered or unordered trajectory, although inference improves as tree size and sampling increases. However, even when working with a 1000-taxon tree, the possibility of inferring the incorrect evolutionary model (type I/type II error) remains. Caution is needed when interpreting the phylogenetic placement of intermediate phenotypes, especially in small lineages. Such phylogenetic patterns can provide a line of evidence for the existence of a particular evolutionary trajectory, but they should be coupled with other types of data to infer the stepwise evolution of a complex character trait.

  3. Testing for Independence between Evolutionary Processes.

    PubMed

    Behdenna, Abdelkader; Pothier, Joël; Abby, Sophie S; Lambert, Amaury; Achaz, Guillaume

    2016-09-01

    Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for the larger diversity of possible relative positions of events in a tree. Here we propose a method to quantify to what extent two or more evolutionary events are associated on a phylogenetic tree. The method is applicable to any discrete character, like substitutions within a coding sequence or gains/losses of a biological function. Our method uses a general approach to statistically test for significant associations between events along the tree, which encompasses both events inseparable on the same branch, and events genealogically ordered on different branches. It assumes that the phylogeny and themapping of branches is known without errors. We address this problem from the statistical viewpoint by a linear algebra representation of the localization of the evolutionary events on the tree.We compute the full probability distribution of the number of paired events occurring in the same branch or in different branches of the tree, under a null model of independence where each type of event occurs at a constant rate uniformly inthephylogenetic tree. The strengths andweaknesses of themethodare assessed via simulations;we then apply the method to explore the loss of cell motility in intracellular pathogens.

  4. Eco-evolutionary dynamics of social dilemmas.

    PubMed

    Gokhale, Chaitanya S; Hauert, Christoph

    2016-10-01

    Social dilemmas are an integral part of social interactions. Cooperative actions, ranging from secreting extra-cellular products in microbial populations to donating blood in humans, are costly to the actor and hence create an incentive to shirk and avoid the costs. Nevertheless, cooperation is ubiquitous in nature. Both costs and benefits often depend non-linearly on the number and types of individuals involved-as captured by idioms such as 'too many cooks spoil the broth' where additional contributions are discounted, or 'two heads are better than one' where cooperators synergistically enhance the group benefit. Interaction group sizes may depend on the size of the population and hence on ecological processes. This results in feedback mechanisms between ecological and evolutionary processes, which jointly affect and determine the evolutionary trajectory. Only recently combined eco-evolutionary processes became experimentally tractable in microbial social dilemmas. Here we analyse the evolutionary dynamics of non-linear social dilemmas in settings where the population fluctuates in size and the environment changes over time. In particular, cooperation is often supported and maintained at high densities through ecological fluctuations. Moreover, we find that the combination of the two processes routinely reveals highly complex dynamics, which suggests common occurrence in nature. PMID:27256794

  5. Knowledge Guided Evolutionary Algorithms in Financial Investing

    ERIC Educational Resources Information Center

    Wimmer, Hayden

    2013-01-01

    A large body of literature exists on evolutionary computing, genetic algorithms, decision trees, codified knowledge, and knowledge management systems; however, the intersection of these computing topics has not been widely researched. Moving through the set of all possible solutions--or traversing the search space--at random exhibits no control…

  6. 2004 Structural, Function and Evolutionary Genomics

    SciTech Connect

    Douglas L. Brutlag Nancy Ryan Gray

    2005-03-23

    This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

  7. Teaching about Adaptation: Why Evolutionary History Matters

    ERIC Educational Resources Information Center

    Kampourakis, Kostas

    2013-01-01

    Adaptation is one of the central concepts in evolutionary theory, which nonetheless has been given different definitions. Some scholars support a historical definition of adaptation, considering it as a trait that is the outcome of natural selection, whereas others support an ahistorical definition, considering it as a trait that contributes to…

  8. Teaching evolutionary processes to skeptical students

    NASA Astrophysics Data System (ADS)

    Bobrowsky, Matthew

    2000-12-01

    This article draws on current information from scientific and educational sources to provide an extremely useful summary of problems and solutions when teaching about evolutionary processes in physics and astronomy. The article addresses the process of science as described in position statements from professional organizations and actual experiences of instructors in the classroom as described at an AAS panel discussion.

  9. Investigating Evolutionary Dynamics of RHA1 Operons

    PubMed Central

    Chen, Yong; Geng, Dandan; Ehrhardt, Kristina; Zhang, Shaoqiang

    2016-01-01

    Grouping genes as operons is an important genomic feature of prokaryotic organisms. The comprehensive understanding of the operon organizations would be helpful to decipher transcriptional mechanisms, cellular pathways, and the evolutionary landscape of prokaryotic genomes. Although thousands of prokaryotes have been sequenced, genome-wide investigation of the evolutionary dynamics (division and recombination) of operons among these genomes remains unexplored. Here, we systematically analyzed the operon dynamics of Rhodococcus jostii RHA1 (RHA1), an oleaginous bacterium with high potential applications in biofuel, by comparing 340 prokaryotic genomes that were carefully selected from different genera. Interestingly, 99% of RHA1 operons were observed to exhibit evolutionary events of division and recombination among the 340 compared genomes. An operon that encodes all enzymes related to histidine biosynthesis in RHA1 (His-operon) was found to be segmented into smaller gene groups (sub-operons) in diverse genomes. These sub-operons were further reorganized with different functional genes as novel operons that are related to different biochemical processes. Comparatively, the operons involved in the functional categories of lipid transport and metabolism are relatively conserved among the 340 compared genomes. At the pathway level, RHA1 operons found to be significantly conserved were involved in ribosome synthesis, oxidative phosphorylation, and fatty acid synthesis. These analyses provide evolutionary insights of operon organization and the dynamic associations of various biochemical pathways in different prokaryotes. PMID:27398020

  10. The population genetics of evolutionary rescue.

    PubMed

    Orr, H Allen; Unckless, Robert L

    2014-08-01

    Evolutionary rescue occurs when a population that is threatened with extinction by an environmental change adapts to the change sufficiently rapidly to survive. Here we extend the mathematical theory of evolutionary rescue. In particular, we model evolutionary rescue to a sudden environmental change when adaptation involves evolution at a single locus. We consider adaptation using either new mutations or alleles from the standing genetic variation that begin rare. We obtain several results: i) the total probability of evolutionary rescue from either new mutation or standing variation; ii) the conditions under which rescue is more likely to involve a new mutation versus an allele from the standing genetic variation; iii) a mathematical description of the U-shaped curve of total population size through time, conditional on rescue; and iv) the time until the average population size begins to rebound as well as the minimal expected population size experienced by a rescued population. Our analysis requires taking into account a subtle population-genetic effect (familiar from the theory of genetic hitchhiking) that involves "oversampling" of those lucky alleles that ultimately sweep to high frequency. Our results are relevant to conservation biology, experimental microbial evolution, and medicine (e.g., the dynamics of antibiotic resistance).

  11. On the Evolutionary Bases of Consumer Reinforcement

    ERIC Educational Resources Information Center

    Nicholson, Michael; Xiao, Sarah Hong

    2010-01-01

    This article locates consumer behavior analysis within the modern neo-Darwinian synthesis, seeking to establish an interface between the ultimate-level theorizing of human evolutionary psychology and the proximate level of inquiry typically favored by operant learning theorists. Following an initial overview of the central tenets of neo-Darwinism,…

  12. 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)

  13. Evolutionary Stability in the Traveler's Dilemma

    ERIC Educational Resources Information Center

    Barker, Andrew T.

    2009-01-01

    The traveler's dilemma is a generalization of the prisoner's dilemma which shows clearly a paradox of game theory. In the traveler's dilemma, the strategy chosen by analysis and theory seems obviously wrong intuitively. Here we develop a measure of evolutionary stability and show that the evolutionarily stable equilibrium is in some sense not very…

  14. Evolutionary Biology: Its Value to Society

    ERIC Educational Resources Information Center

    Carson, Hampton L.

    1972-01-01

    Cites examples of the contribution of basic research in evolutionary biology to the solution of problems facing society (1) by dispelling myths about human origins, the nature of the individual, and the nature of race (2) by providing basic data concerning the effects of overpopulation, the production of improved sources of food, resistance of…

  15. Static and evolutionary quantum public goods games

    NASA Astrophysics Data System (ADS)

    Liao, Zeyang; Qin, Gan; Hu, Lingzhi; Li, Songjian; Xu, Nanyang; Du, Jiangfeng

    2008-05-01

    We apply the continuous-variable quantization scheme to quantize public goods game and find that new pure strategy Nash equilibria emerge in the static case. Furthermore, in the evolutionary public goods game, entanglement can also contribute to the persistence of cooperation under various population structures without altruism, voluntary participation, and punishment.

  16. Intervals in evolutionary algorithms for global optimization

    SciTech Connect

    Patil, R.B.

    1995-05-01

    Optimization is of central concern to a number of disciplines. Interval Arithmetic methods for global optimization provide us with (guaranteed) verified results. These methods are mainly restricted to the classes of objective functions that are twice differentiable and use a simple strategy of eliminating a splitting larger regions of search space in the global optimization process. An efficient approach that combines the efficient strategy from Interval Global Optimization Methods and robustness of the Evolutionary Algorithms is proposed. In the proposed approach, search begins with randomly created interval vectors with interval widths equal to the whole domain. Before the beginning of the evolutionary process, fitness of these interval parameter vectors is defined by evaluating the objective function at the center of the initial interval vectors. In the subsequent evolutionary process the local optimization process returns an estimate of the bounds of the objective function over the interval vectors. Though these bounds may not be correct at the beginning due to large interval widths and complicated function properties, the process of reducing interval widths over time and a selection approach similar to simulated annealing helps in estimating reasonably correct bounds as the population evolves. The interval parameter vectors at these estimated bounds (local optima) are then subjected to crossover and mutation operators. This evolutionary process continues for predetermined number of generations in the search of the global optimum.

  17. Using Human Evolution to Teach Evolutionary Theory

    ERIC Educational Resources Information Center

    Besterman, Hugo; La Velle, Linda Baggott

    2007-01-01

    This paper discusses some traditional approaches to the teaching of evolutionary theory at pre-university level, criticising in particular some of the more commonly used models and exemplars. Curricular demands are described and an alternative approach is suggested, using the emerging story of human evolution. Recent discoveries help to illustrate…

  18. Indoor Thermal Comfort, an Evolutionary Biology Perspective

    SciTech Connect

    Stoops, John L.

    2006-04-15

    As is becoming increasingly clear, the human species evolvedin the East African savannah. Details of the precise evolutionary chainremain unresolved however it appears that the process lasted severalmillion years, culminating with the emergence of modern Homo sapiensroughly 200,000 years ago. Following that final evolutionary developmentmodern Homo sapiens relatively quickly populated the entire world.Clearly modern Homo sapiens is a successful, resourceful and adaptablespecies. In the developed societies, modern humans live an existence farremoved from our evolutionary ancestors. As we have learned over the lastcentury, this "new" lifestyle can often result in unintendedconsequences. Clearly, our modern access to food, shelter, transportationand healthcare has resulted in greatly expanded expected lifespan butthis new lifestyle can also result in the emergence of different kinds ofdiseases and health problems. The environment in modern buildings haslittle resemblance to the environment of the savannah. We strive tocreate environments with little temperature, air movement and lightvariation. Building occupants often express great dissatisfaction withthese modern created environments and a significant fraction even developsomething akin to allergies to specific buildings (sick buildingsyndrome). Are the indoor environments we are creating fundamentallyunhealthy -- when examined from an evolutionary perspective?

  19. Evolutionary software for autonomous path planning

    SciTech Connect

    Couture, S; Hage, M

    1999-02-10

    This research project demonstrated the effectiveness of using evolutionary software techniques in the development of path-planning algorithms and control programs for mobile vehicles in radioactive environments. The goal was to take maximum advantage of the programmer's intelligence by tasking the programmer with encoding the measures of success for a path-planning algorithm, rather than developing the path-planning algorithms themselves. Evolutionary software development techniques could then be used to develop algorithms most suitable to the particular environments of interest. The measures of path-planning success were encoded in the form of a fitness function for an evolutionary software development engine. The task for the evolutionary software development engine was to evaluate the performance of individual algorithms, select the best performers for the population based on the fitness function, and breed them to evolve the next generation of algorithms. The process continued for a set number of generations or until the algorithm converged to an optimal solution. The task environment was the navigation of a rover from an initial location to a goal, then to a processing point, in an environment containing physical and radioactive obstacles. Genetic algorithms were developed for a variety of environmental configurations. Algorithms were simple and non-robust strings of behaviors, but they could be evolved to be nearly optimal for a given environment. In addition, a genetic program was evolved in the form of a control algorithm that operates at every motion of the robot. Programs were more complex than algorithms and less optimal in a given environment. However, after training in a variety of different environments, they were more robust and could perform acceptably in environments they were not trained in. This paper describes the evolutionary software development engine and the performance of algorithms and programs evolved by it for the chosen task.

  20. Automated Antenna Design with Evolutionary Algorithms

    NASA Technical Reports Server (NTRS)

    Linden, Derek; Hornby, Greg; Lohn, Jason; Globus, Al; Krishunkumor, K.

    2006-01-01

    Current methods of designing and optimizing antennas by hand are time and labor intensive, and limit complexity. Evolutionary design techniques can overcome these limitations by searching the design space and automatically finding effective solutions. In recent years, evolutionary algorithms have shown great promise in finding practical solutions in large, poorly understood design spaces. In particular, spacecraft antenna design has proven tractable to evolutionary design techniques. Researchers have been investigating evolutionary antenna design and optimization since the early 1990s, and the field has grown in recent years as computer speed has increased and electromagnetic simulators have improved. Two requirements-compliant antennas, one for ST5 and another for TDRS-C, have been automatically designed by evolutionary algorithms. The ST5 antenna is slated to fly this year, and a TDRS-C phased array element has been fabricated and tested. Such automated evolutionary design is enabled by medium-to-high quality simulators and fast modern computers to evaluate computer-generated designs. Evolutionary algorithms automate cut-and-try engineering, substituting automated search though millions of potential designs for intelligent search by engineers through a much smaller number of designs. For evolutionary design, the engineer chooses the evolutionary technique, parameters and the basic form of the antenna, e.g., single wire for ST5 and crossed-element Yagi for TDRS-C. Evolutionary algorithms then search for optimal configurations in the space defined by the engineer. NASA's Space Technology 5 (ST5) mission will launch three small spacecraft to test innovative concepts and technologies. Advanced evolutionary algorithms were used to automatically design antennas for ST5. The combination of wide beamwidth for a circularly-polarized wave and wide impedance bandwidth made for a challenging antenna design problem. From past experience in designing wire antennas, we chose to

  1. Inferring the determinants of protein evolutionary rates in mammals.

    PubMed

    Zou, Yang; Shao, Xiaojian; Dong, Dong

    2016-06-15

    Understanding the determinants of protein evolutionary rates is one of the most fundamental evolutionary questions. Previous studies have revealed that many biological variables are tightly associated with protein evolutionary rates in mammals. However, the dominant role of these biological variables and their combinatorial effects to evolutionary rates of mammalian proteins are still less understood. In this work, we derived a quantitative model to correlate protein evolutionary rates with the levels of these variables. The result showed that only a small number of variables are necessary to accurately predict protein evolutionary rates, among which miRNA regulation plays the most important role. Our result suggested that biological variables are extensively interrelated and suffer from hidden redundancies in determining protein evolutionary rates. Various variables should be considered in a natural ensemble to comprehensively assess the determinants of protein evolutionary rate.

  2. Advanced evolutionary phases in globular clusters. . Empirical and theoretical constraints

    NASA Astrophysics Data System (ADS)

    Bono, G.

    We present empirical and theoretical constraints for advanced evolutionary phases in Globular Clusters. In particular, we focus our attention on the central helium burning phases (Horizontal Branch) and on the white dwarf cooling sequence. We introduce the canonical evolutionary scenario and discuss new possible routes which can provide firm constraints on several open problems. Finally, we briefly outline new predicted near-infrared evolutionary features of the white dwarf cooling sequences which can be adopted to constrain their evolutionary properties.

  3. Evolutionary psychiatry: a new College special interest group

    PubMed Central

    Abed, Riadh; St John-Smith, Paul

    2016-01-01

    Evolutionary science remains an overlooked area in psychiatry and medicine. The newly established Royal College of Psychiatrists' Evolutionary Psychiatry Special Interest Group aims to reverse this trend by raising the profile of evolutionary thinking among College members and others further afield. Here we provide a brief outline of the importance of the evolutionary approach to both the theory and practice of psychiatry and for future research. PMID:27752339

  4. Gender Inequality in Interaction--An Evolutionary Account

    ERIC Educational Resources Information Center

    Hopcroft, Rosemary L.

    2009-01-01

    In this article I argue that evolutionary theorizing can help sociologists and feminists better understand gender inequality. Evolutionary theory explains why control of the sexuality of young women is a priority across most human societies both past and present. Evolutionary psychology has extended our understanding of male violence against…

  5. Microscopic Approach to Species Coexistence Based on Evolutionary Game Dynamics

    NASA Astrophysics Data System (ADS)

    Grebogi, Celso; Lai, Ying-Cheng; Wang, Wen-Xu

    2014-12-01

    An outstanding problem in complex systems and mathematical biology is to explore and understand the fundamental mechanisms of species coexistence. Existing approaches are based on niche partitioning, dispersal, chaotic evolutionary dynamics, and more recently, evolutionary games. Here we briefly review a number of fundamental issues associated with the coexistence of mobile species under cyclic competitions in the framework of evolutionary games.

  6. Conservation: evolutionary values for all 10,000 birds.

    PubMed

    Lovette, Irby J

    2014-05-19

    Many biologists and conservation practitioners believe that preserving evolutionary diversity should be a priority. An innovative new study measures the evolutionary distinctness of all the world's birds and identifies the species and locations that capture the highest fraction of avian evolutionary history.

  7. Interpreting Evolutionary Diagrams: When Topology and Process Conflict

    ERIC Educational Resources Information Center

    Catley, Kefyn M.; Novick, Laura R.; Shade, Courtney K.

    2010-01-01

    The authors argue that some diagrams in biology textbooks and the popular press presented as depicting evolutionary relationships suggest an inappropriate (anagenic) conception of evolutionary history. The goal of this research was to provide baseline data that begin to document how college students conceptualize the evolutionary relationships…

  8. A Note on Evolutionary Algorithms and Its Applications

    ERIC Educational Resources Information Center

    Bhargava, Shifali

    2013-01-01

    This paper introduces evolutionary algorithms with its applications in multi-objective optimization. Here elitist and non-elitist multiobjective evolutionary algorithms are discussed with their advantages and disadvantages. We also discuss constrained multiobjective evolutionary algorithms and their applications in various areas.

  9. Evolutionary contributions to solving the "matrilineal puzzle": a test of Holden, Sear, and Mace's model.

    PubMed

    Mattison, Siobhán M

    2011-07-01

    Matriliny has long been debated by anthropologists positing either its primitive or its puzzling nature. More recently, evolutionary anthropologists have attempted to recast matriliny as an adaptive solution to modern social and ecological environments, tying together much of what was known to be associated with matriliny. This paper briefly reviews the major anthropological currents in studies of matriliny and discusses the contribution of evolutionary anthropology to this body of literature. It discusses the utility of an evolutionary framework in the context of the first independent test of Holden et al.'s 2003 model of matriliny as daughter-biased investment. It finds that historical daughter-biased transmission of land among the Mosuo is consistent with the model, whereas current income transmission is not. In both cases, resources had equivalent impacts on male and female reproduction, a result which predicts daughter-biased resource transmission given any nonzero level of paternity uncertainty. However, whereas land was transmitted traditionally to daughters, income today is invested in both sexes. Possible reasons for this discrepancy are discussed. PMID:22388801

  10. Were there evolutionary advantages to premenstrual syndrome?

    PubMed

    Gillings, Michael R

    2014-09-01

    Premenstrual syndrome (PMS) affects up to 80% of women, often leading to significant personal, social and economic costs. When apparently maladaptive states are widespread, they sometimes confer a hidden advantage, or did so in our evolutionary past. We suggest that PMS had a selective advantage because it increased the chance that infertile pair bonds would dissolve, thus improving the reproductive outcomes of women in such partnerships. We confirm predictions arising from the hypothesis: PMS has high heritability; gene variants associated with PMS can be identified; animosity exhibited during PMS is preferentially directed at current partners; and behaviours exhibited during PMS may increase the chance of finding a new partner. Under this view, the prevalence of PMS might result from genes and behaviours that are adaptive in some societies, but are potentially less appropriate in modern cultures. Understanding this evolutionary mismatch might help depathologize PMS, and suggests solutions, including the choice to use cycle-stopping contraception.

  11. Evolutionary ethics from Darwin to Moore.

    PubMed

    Allhoff, Fritz

    2003-01-01

    Evolutionary ethics has a long history, dating all the way back to Charles Darwin. Almost immediately after the publication of the Origin, an immense interest arose in the moral implications of Darwinism and whether the truth of Darwinism would undermine traditional ethics. Though the biological thesis was certainly exciting, nobody suspected that the impact of the Origin would be confined to the scientific arena. As one historian wrote, 'whether or not ancient populations of armadillos were transformed into the species that currently inhabit the new world was certainly a topic about which zoologists could disagree. But it was in discussing the broader implications of the theory...that tempers flared and statements were made which could transform what otherwise would have been a quiet scholarly meeting into a social scandal' (Farber 1994, 22). Some resistance to the biological thesis of Darwinism sprung from the thought that it was incompatible with traditional morality and, since one of them had to go, many thought that Darwinism should be rejected. However, some people did realize that a secular ethics was possible so, even if Darwinism did undermine traditional religious beliefs, it need not have any effects on moral thought. Before I begin my discussion of evolutionary ethics from Darwin to Moore, I would like to make some more general remarks about its development. There are three key events during this history of evolutionary ethics. First, Charles Darwin published On the Origin of the Species (Darwin 1859). Since one did not have a fully developed theory of evolution until 1859, there exists little work on evolutionary ethics until then. Shortly thereafter, Herbert Spencer (1898) penned the first systematic theory of evolutionary ethics, which was promptly attacked by T.H. Huxley (Huxley 1894). Second, at about the turn of the century, moral philosophers entered the fray and attempted to demonstrate logical errors in Spencer's work; such errors were alluded

  12. Evolutionary preservation of redundant duplicated genes.

    PubMed

    Krakauer, D C; Nowak, M A

    1999-10-01

    Gene duplication events produce both perfect and imperfect copies of genes. Perfect copies are said to be functionally redundant when knockout of one gene produces no 'scoreable', phenotypic effects. Preserving identical, duplicate copies of genes is problematic as all copies are prone to accumulate neutral mutations as pseudogenes, or more rarely, evolve into new genes with novel functions. We summarise theoretical treatments for the invasion and subsequent evolutionary modification of functionally redundant genes. We then consider the preservation of functionally identical copies of a gene over evolutionary time. We present several models for conserving redundancy: asymmetric mutation, asymmetric efficacy, pleiotropy, developmental buffering, allelic competition and regulatory asymmetries. In all cases, some form of symmetry breaking is required to maintain functional redundancy indefinitely.

  13. Were there evolutionary advantages to premenstrual syndrome?

    PubMed Central

    Gillings, Michael R

    2014-01-01

    Premenstrual syndrome (PMS) affects up to 80% of women, often leading to significant personal, social and economic costs. When apparently maladaptive states are widespread, they sometimes confer a hidden advantage, or did so in our evolutionary past. We suggest that PMS had a selective advantage because it increased the chance that infertile pair bonds would dissolve, thus improving the reproductive outcomes of women in such partnerships. We confirm predictions arising from the hypothesis: PMS has high heritability; gene variants associated with PMS can be identified; animosity exhibited during PMS is preferentially directed at current partners; and behaviours exhibited during PMS may increase the chance of finding a new partner. Under this view, the prevalence of PMS might result from genes and behaviours that are adaptive in some societies, but are potentially less appropriate in modern cultures. Understanding this evolutionary mismatch might help depathologize PMS, and suggests solutions, including the choice to use cycle-stopping contraception. PMID:25469168

  14. The Ancient Evolutionary History of Polyomaviruses.

    PubMed

    Buck, Christopher B; Van Doorslaer, Koenraad; Peretti, Alberto; Geoghegan, Eileen M; Tisza, Michael J; An, Ping; Katz, Joshua P; Pipas, James M; McBride, Alison A; Camus, Alvin C; McDermott, Alexa J; Dill, Jennifer A; Delwart, Eric; Ng, Terry F F; Farkas, Kata; Austin, Charlotte; Kraberger, Simona; Davison, William; Pastrana, Diana V; Varsani, Arvind

    2016-04-01

    Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae. PMID:27093155

  15. The evolutionary sequence of Fermi blazars

    NASA Astrophysics Data System (ADS)

    Cha, Yongjuan; Zhang, Haojing; Zhang, Xiong; Xiong, Dingrong; Li, Bijun; Dong, Xia; Li, Jin

    2014-02-01

    Using γ-ray data ( α γ , F γ ) detected by Fermi Large Area Telescope (LAT) and black hole mass which has been compiled from literatures for 116 Fermi blazars, we calculated intrinsic γ-ray luminosity, intrinsic bolometric luminosity, intrinsic Eddington ratio and studied the relationships between all above parameters and redshift, between α γ and L γ . Furthermore, we obtained the histograms of key parameters. Our results are the following: (1) The main reason for the evolutionary sequence of three subclasses (HBLs, LBLs, FSRQs) may be Eddington ratio rather than black hole mass; (2) FSRQs occupy in the earlier, high-luminosity, high Eddington ratio, violent phase of the galactic evolution sequence, while BL Lac objects occur in the low luminosity, low Eddington ratio, late phase of the galactic evolution sequence; (3) These results imply that the evolutionary track of Fermi blazars is FSRQs ⟶ LBLs ⟶ HBLs.

  16. Human nature, cultural diversity and evolutionary theory

    PubMed Central

    Plotkin, Henry

    2011-01-01

    Incorporating culture into an expanded theory of evolution will provide the foundation for a universal account of human diversity. Two requirements must be met. The first is to see learning as an extension of the processes of evolution. The second is to understand that there are specific components of human culture, viz. higher order knowledge structures and social constructions, which give rise to culture as invented knowledge. These components, which are products of psychological processes and mechanisms, make human culture different from the forms of shared knowledge observed in other species. One serious difficulty for such an expanded theory is that social constructions may not add to the fitness of all humans exposed to them. This may be because human culture has existed for only a relatively short time in evolutionary terms. Or it may be that, as some maintain, adaptation is a limited, even a flawed, aspect of evolutionary theory. PMID:21199849

  17. Ecological and evolutionary consequences of biotic homogenization.

    PubMed

    Olden, Julian D; Leroy Poff, N; Douglas, Marlis R; Douglas, Michael E; Fausch, Kurt D

    2004-01-01

    Biotic homogenization, the gradual replacement of native biotas by locally expanding non-natives, is a global process that diminishes floral and faunal distinctions among regions. Although patterns of homogenization have been well studied, their specific ecological and evolutionary consequences remain unexplored. We argue that our current perspective on biotic homogenization should be expanded beyond a simple recognition of species diversity loss, towards a synthesis of higher order effects. Here, we explore three distinct forms of homogenization (genetic, taxonomic and functional), and discuss their immediate and future impacts on ecological and evolutionary processes. Our goal is to initiate future research that investigates the broader conservation implications of homogenization and to promote a proactive style of adaptive management that engages the human component of the anthropogenic blender that is currently mixing the biota on Earth. PMID:16701221

  18. Evolutionary approach to image reconstruction from projections

    NASA Astrophysics Data System (ADS)

    Nakao, Zensho; Ali, Fathelalem F.; Takashibu, Midori; Chen, Yen-Wei

    1997-10-01

    We present an evolutionary approach for reconstructing CT images; the algorithm reconstructs two-dimensional unknown images from four one-dimensional projections. A genetic algorithm works on a randomly generated population of strings each of which contains encodings of an image. The traditional, as well as new, genetic operators are applied on each generation. The mean square error between the projection data of the image encoded into a string and original projection data is used to estimate the string fitness. A Laplacian constraint term is included in the fitness function of the genetic algorithm for handling smooth images. Two new modified versions of the original genetic algorithm are presented. Results obtained by the original algorithm and the modified versions are compared to those obtained by the well-known algebraic reconstruction technique (ART), and it was found that the evolutionary method is more effective than ART in the particular case of limiting projection directions to four.

  19. The Ancient Evolutionary History of Polyomaviruses

    PubMed Central

    Buck, Christopher B.; Van Doorslaer, Koenraad; Peretti, Alberto; Geoghegan, Eileen M.; Tisza, Michael J.; An, Ping; Katz, Joshua P.; Pipas, James M.; McBride, Alison A.; Camus, Alvin C.; McDermott, Alexa J.; Dill, Jennifer A.; Delwart, Eric; Ng, Terry F. F.; Farkas, Kata; Austin, Charlotte; Kraberger, Simona; Davison, William; Pastrana, Diana V.; Varsani, Arvind

    2016-01-01

    Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae. PMID:27093155

  20. Evolutionary stability in Lotka-Volterra systems.

    PubMed

    Cressman, Ross; Garay, József

    2003-05-21

    The Lotka-Volterra model of population ecology, which assumes all individuals in each species behave identically, is combined with the behavioral evolution model of evolutionary game theory. In the resultant monomorphic situation, conditions for the stability of the resident Lotka-Volterra system, when perturbed by a mutant phenotype in each species, are analysed. We develop an evolutionary ecology stability concept, called a monomorphic evolutionarily stable ecological equilibrium, which contains as a special case the original definition by Maynard Smith of an evolutionarily stable strategy for a single species. Heuristically, the concept asserts that the resident ecological system must be stable as well as the phenotypic evolution on the "stationary density surface". The conditions are also shown to be central to analyse stability issues in the polymorphic model that allows arbitrarily many phenotypes in each species, especially when the number of species is small. The mathematical techniques are from the theory of dynamical systems, including linearization, centre manifolds and Molchanov's Theorem.

  1. Applying evolutionary biology to address global challenges

    PubMed Central

    Carroll, Scott P.; Jørgensen, Peter Søgaard; Kinnison, Michael T.; Bergstrom, Carl T.; Denison, R. Ford; Gluckman, Peter; Smith, Thomas B.; Strauss, Sharon Y.; Tabashnik, Bruce E.

    2014-01-01

    Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens and pests that evolve too quickly, and the second from the inability of many valued species to adapt quickly enough. Applied evolutionary biology provides a suite of strategies to address these global challenges that threaten human health, food security, and biodiversity. This review highlights both progress and gaps in genetic, developmental and environmental manipulations across the life sciences that either target the rate and direction of evolution, or reduce the mismatch between organisms and human-altered environments. Increased development and application of these underused tools will be vital in meeting current and future targets for sustainable development. PMID:25213376

  2. Product Mix Selection Using AN Evolutionary Technique

    NASA Astrophysics Data System (ADS)

    Tsoulos, Ioannis G.; Vasant, Pandian

    2009-08-01

    This paper proposes an evolutionary technique for the solution of a real—life industrial problem and particular for the product mix selection problem. The evolutionary technique is a combination of a genetic algorithm that preserves the feasibility of the trial solutions with penalties and some local optimization method. The goal of this paper has been achieved in finding the best near optimal solution for the profit fitness function respect to vagueness factor and level of satisfaction. The findings of the profit values will be very useful for the decision makers in the industrial engineering sector for the implementation purpose. It's possible to improve the solutions obtained in this study by employing other meta-heuristic methods such as simulated annealing, tabu Search, ant colony optimization, particle swarm optimization and artificial immune systems.

  3. Teaching About Adaptation: Why Evolutionary History Matters

    NASA Astrophysics Data System (ADS)

    Kampourakis, Kostas

    2013-02-01

    Adaptation is one of the central concepts in evolutionary theory, which nonetheless has been given different definitions. Some scholars support a historical definition of adaptation, considering it as a trait that is the outcome of natural selection, whereas others support an ahistorical definition, considering it as a trait that contributes to the survival and reproduction of its possessors. Finally, adaptation has been defined as a process, as well. Consequently, two questions arise: the first is a philosophical one and focuses on what adaptation actually is; the second is a pedagogical one and focuses on what science teachers and educators should teach about it. In this article, the various definitions of adaptation are discussed and their uses in some textbooks are presented. It is suggested that, given elementary students' intuitions about purpose and design in nature and secondary students' teleological explanations for the origin of adaptations, any definition of adaptation as a trait should include some information about its evolutionary history.

  4. Phylomemetics—Evolutionary Analysis beyond the Gene

    PubMed Central

    Howe, Christopher J.; Windram, Heather F.

    2011-01-01

    Genes are propagated by error-prone copying, and the resulting variation provides the basis for phylogenetic reconstruction of evolutionary relationships. Horizontal gene transfer may be superimposed on a tree-like evolutionary pattern, with some relationships better depicted as networks. The copying of manuscripts by scribes is very similar to the replication of genes, and phylogenetic inference programs can be used directly for reconstructing the copying history of different versions of a manuscript text. Phylogenetic methods have also been used for some time to analyse the evolution of languages and the development of physical cultural artefacts. These studies can help to answer a range of anthropological questions. We propose the adoption of the term “phylomemetics” for phylogenetic analysis of reproducing non-genetic elements. PMID:21655311

  5. Evolutionary Games with Randomly Changing Payoff Matrices

    NASA Astrophysics Data System (ADS)

    Yakushkina, Tatiana; Saakian, David B.; Bratus, Alexander; Hu, Chin-Kun

    2015-06-01

    Evolutionary games are used in various fields stretching from economics to biology. In most of these games a constant payoff matrix is assumed, although some works also consider dynamic payoff matrices. In this article we assume a possibility of switching the system between two regimes with different sets of payoff matrices. Potentially such a model can qualitatively describe the development of bacterial or cancer cells with a mutator gene present. A finite population evolutionary game is studied. The model describes the simplest version of annealed disorder in the payoff matrix and is exactly solvable at the large population limit. We analyze the dynamics of the model, and derive the equations for both the maximum and the variance of the distribution using the Hamilton-Jacobi equation formalism.

  6. Evolutionary algorithms and multi-agent systems

    NASA Astrophysics Data System (ADS)

    Oh, Jae C.

    2006-05-01

    This paper discusses how evolutionary algorithms are related to multi-agent systems and the possibility of military applications using the two disciplines. In particular, we present a game theoretic model for multi-agent resource distribution and allocation where agents in the environment must help each other to survive. Each agent maintains a set of variables representing actual friendship and perceived friendship. The model directly addresses problems in reputation management schemes in multi-agent systems and Peer-to-Peer distributed systems. We present algorithms based on evolutionary game process for maintaining the friendship values as well as a utility equation used in each agent's decision making. For an application problem, we adapted our formal model to the military coalition support problem in peace-keeping missions. Simulation results show that efficient resource allocation and sharing with minimum communication cost is achieved without centralized control.

  7. The Ancient Evolutionary History of Polyomaviruses.

    PubMed

    Buck, Christopher B; Van Doorslaer, Koenraad; Peretti, Alberto; Geoghegan, Eileen M; Tisza, Michael J; An, Ping; Katz, Joshua P; Pipas, James M; McBride, Alison A; Camus, Alvin C; McDermott, Alexa J; Dill, Jennifer A; Delwart, Eric; Ng, Terry F F; Farkas, Kata; Austin, Charlotte; Kraberger, Simona; Davison, William; Pastrana, Diana V; Varsani, Arvind

    2016-04-01

    Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae.

  8. Applying evolutionary biology to address global challenges.

    PubMed

    Carroll, Scott P; Jørgensen, Peter Søgaard; Kinnison, Michael T; Bergstrom, Carl T; Denison, R Ford; Gluckman, Peter; Smith, Thomas B; Strauss, Sharon Y; Tabashnik, Bruce E

    2014-10-17

    Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens, and pests that evolve too quickly and the second, from the inability of many valued species to adapt quickly enough. Applied evolutionary biology provides a suite of strategies to address these global challenges that threaten human health, food security, and biodiversity. This Review highlights both progress and gaps in genetic, developmental, and environmental manipulations across the life sciences that either target the rate and direction of evolution or reduce the mismatch between organisms and human-altered environments. Increased development and application of these underused tools will be vital in meeting current and future targets for sustainable development.

  9. Evolutionary development of path planning algorithms

    SciTech Connect

    Hage, M

    1998-09-01

    This paper describes the use of evolutionary software techniques for developing both genetic algorithms and genetic programs. Genetic algorithms are evolved to solve a specific problem within a fixed and known environment. While genetic algorithms can evolve to become very optimized for their task, they often are very specialized and perform poorly if the environment changes. Genetic programs are evolved through simultaneous training in a variety of environments to develop a more general controller behavior that operates in unknown environments. Performance of genetic programs is less optimal than a specially bred algorithm for an individual environment, but the controller performs acceptably under a wider variety of circumstances. The example problem addressed in this paper is evolutionary development of algorithms and programs for path planning in nuclear environments, such as Chernobyl.

  10. Applying Evolutionary Genetics to Schistosome Epidemiology

    PubMed Central

    Steinauer, Michelle L.; Blouin, Michael S.; Criscione, Charles D.

    2010-01-01

    We review how molecular markers and evolutionary analysis have been applied to the study of schistosome parasites, important pathogens that infect over 200 million people worldwide. Topics reviewed include phylogenetics and biogeography, hybridization, infection within snails, mating systems, and genetic structure. Some interesting generalizations include that schistosome species hybridize frequently and have switched definitive hosts repeatedly in evolutionary time. We show that molecular markers can be used to infer epidemiologically-relevant processes such as spatial variation in transmission, or to reveal complex patterns of mate choice. Analysis of genetic structure data shows that transmission foci can be structured by watershed boundaries, habitat types, and host species. We also discuss sampling and analytical problems that arise when using larvae to estimate genetic parameters of adult schistosome populations. Finally, we review pitfalls in methodologies such as genotyping very small individuals, statistical methods for identifying clonemates or for identifying sibling groups, and estimating allele frequencies from pooled egg samples. PMID:20176142

  11. The evolutionary conservation of DNA polymerase. alpha

    SciTech Connect

    Miller, M.A.; Korn, D.; Wang, T.S.F. )

    1988-08-25

    The evolutionary conservation of DNA polymerase {alpha} was assessed by immunological and molecular genetic approaches. Four anti-human KB cell DNA polymerase {alpha} monoclonal antibodies were tested for their ability to recognize a phylogenetically broad array of eukaryotic DNA polymerases. While the single non-neutralizing antibody used in this study recognizes higher mammalian (human, simian, canine, and bovine) polymerases only, three neutralizing antibodies exhibit greater, but variable, extents of cross-reactivity among vertebrate species. Genomic Southern hybridization studies with the cDNA of the human DNA polymerase {alpha} catalytic polypeptide identify the existence of many consensus DNA sequences within the DNA polymerase genes of vertebrate, invertebrate, plant and unicellular organisms. These findings illustrate the differential evolutionary conservation of four unique epitopes on DNA sequences, presumably reflective of critical functional domains, in the DNA polymerase genes from a broad diversity of living forms.

  12. The karyomastigont as an evolutionary seme.

    PubMed

    Chapman, Michael; Alliegro, Mark C

    2012-12-01

    The problem of eukaryogenesis--the evolutionary mechanism whereby eukaryotic cells evolved from prokaryotes--remains one of the great unsolved mysteries of cell biology, possibly due to the reductionist tendency of most scientists to work only within their subdisciplines. Communication between biologists who conduct research on the nucleus and those working on the cytoskeleton or endomembrane system are sometimes wanting, and yet, all of these quintessentially eukaryotic elements of the cell are interdependent, and are physically associated in many protists as the karyomastigont organellar system: nucleus, one or more basal bodies and flagella, nuclear connector, and Golgi apparatus. Here we suggest a more holistic view of the karyomastigont as not simply an organellar system, but an evolutionary seme, the archaic state of the eukaryotic cell. We also present a scheme whereby the karyomastigont may have dissociated, giving rise in more derived cells to one or more free nuclei and discrete flagellar apparati (akaryomastigonts).

  13. Prefrontal cortical dopamine from an evolutionary perspective.

    PubMed

    Lee, Young-A; Goto, Yukiori

    2015-04-01

    In this article, we propose the hypothesis that the prefrontal cortex (PFC) acquired neotenic development as a consequence of mesocortical dopamine (DA) innervation, which in turn drove evolution of the PFC into becoming a complex functional system. Accordingly, from the evolutionary perspective, decreased DA signaling in the PFC associated with such adverse conditions as chronic stress may be considered as an environmental adaptation strategy. Psychiatric disorders such as schizophrenia and attention deficit/hyperactivity disorder may also be understood as environmental adaptation or a by-product of such a process that has emerged through evolution in humans. To investigate the evolutionary perspective of DA signaling in the PFC, domestic animals such as dogs may be a useful model. PMID:25617024

  14. Toward an evolutionary definition of cheating.

    PubMed

    Ghoul, Melanie; Griffin, Ashleigh S; West, Stuart A

    2014-02-01

    The term "cheating" is used in the evolutionary and ecological literature to describe a wide range of exploitative or deceitful traits. Although many find this a useful short hand, others have suggested that it implies cognitive intent in a misleading way, and is used inconsistently. We provide a formal justification of the use of the term "cheat" from the perspective of an individual as a maximizing agent. We provide a definition for cheating that can be applied widely, and show that cheats can be broadly classified on the basis of four distinctions: (i) whether cooperation is an option; (ii) whether deception is involved; (iii) whether members of the same or different species are cheated; and (iv) whether the cheat is facultative or obligate. Our formal definition and classification provide a framework that allow us to resolve and clarify a number of issues, regarding the detection and evolutionary consequences of cheating, as well as illuminating common principles and similarities in the underlying selection pressures.

  15. Evolutionary ethics from Darwin to Moore.

    PubMed

    Allhoff, Fritz

    2003-01-01

    Evolutionary ethics has a long history, dating all the way back to Charles Darwin. Almost immediately after the publication of the Origin, an immense interest arose in the moral implications of Darwinism and whether the truth of Darwinism would undermine traditional ethics. Though the biological thesis was certainly exciting, nobody suspected that the impact of the Origin would be confined to the scientific arena. As one historian wrote, 'whether or not ancient populations of armadillos were transformed into the species that currently inhabit the new world was certainly a topic about which zoologists could disagree. But it was in discussing the broader implications of the theory...that tempers flared and statements were made which could transform what otherwise would have been a quiet scholarly meeting into a social scandal' (Farber 1994, 22). Some resistance to the biological thesis of Darwinism sprung from the thought that it was incompatible with traditional morality and, since one of them had to go, many thought that Darwinism should be rejected. However, some people did realize that a secular ethics was possible so, even if Darwinism did undermine traditional religious beliefs, it need not have any effects on moral thought. Before I begin my discussion of evolutionary ethics from Darwin to Moore, I would like to make some more general remarks about its development. There are three key events during this history of evolutionary ethics. First, Charles Darwin published On the Origin of the Species (Darwin 1859). Since one did not have a fully developed theory of evolution until 1859, there exists little work on evolutionary ethics until then. Shortly thereafter, Herbert Spencer (1898) penned the first systematic theory of evolutionary ethics, which was promptly attacked by T.H. Huxley (Huxley 1894). Second, at about the turn of the century, moral philosophers entered the fray and attempted to demonstrate logical errors in Spencer's work; such errors were alluded

  16. SVC: structured visualization of evolutionary sequence conservation.

    PubMed

    Roepcke, S; Fiziev, P; Seeburg, P H; Vingron, M

    2005-07-01

    We have developed a web application for the detailed analysis and visualization of evolutionary sequence conservation in complex vertebrate genes. Given a pair of orthologous genes, the protein-coding sequences are aligned. When these sequences are mapped back onto their encoding exons in the genomes, a scaffold of the conserved gene structure naturally emerges. Sequence similarity between exons and introns is analysed and embedded into the gene structure scaffold. The visualization on the SVC server provides detailed information about evolutionarily conserved features of these genes. It further allows concise representation of complex splice patterns in the context of evolutionary conservation. A particular application of our tool arises from the fact that around mRNA editing sites both exonic and intronic sequences are highly conserved. This aids in delineation of these sites. SVC is available at http://svc.molgen.mpg.de.

  17. Evolutionary Algorithm for Optimal Vaccination Scheme

    NASA Astrophysics Data System (ADS)

    Parousis-Orthodoxou, K. J.; Vlachos, D. S.

    2014-03-01

    The following work uses the dynamic capabilities of an evolutionary algorithm in order to obtain an optimal immunization strategy in a user specified network. The produced algorithm uses a basic genetic algorithm with crossover and mutation techniques, in order to locate certain nodes in the inputted network. These nodes will be immunized in an SIR epidemic spreading process, and the performance of each immunization scheme, will be evaluated by the level of containment that provides for the spreading of the disease.

  18. Evolutionary design of corrugated horn antennas

    NASA Technical Reports Server (NTRS)

    Hoorfar, F.; Manshadi, V.; Jamnejad, A.

    2002-01-01

    An evolutionary progranirnitzg (EP) algorithm is used to optimize pattern of a corrugated circularhorn subject to various constraints on return loss and antenna beamwidth and pattern circularity and low crosspolarization. The EP algorithm uses a Gaussian mutation operator. Examples on design synthesis of a 45 section corrugated horn, with a total of 90 optimization parameters, are presented. The results show excellent and efficient optimization of the desired horn parameters.

  19. High evolutionary potential of marine zooplankton

    PubMed Central

    Peijnenburg, Katja T C A; Goetze, Erica

    2013-01-01

    Abstract Open ocean zooplankton often have been viewed as slowly evolving species that have limited capacity to respond adaptively to changing ocean conditions. Hence, attention has focused on the ecological responses of zooplankton to current global change, including range shifts and changing phenology. Here, we argue that zooplankton also are well poised for evolutionary responses to global change. We present theoretical arguments that suggest plankton species may respond rapidly to selection on mildly beneficial mutations due to exceptionally large population size, and consider the circumstantial evidence that supports our inference that selection may be particularly important for these species. We also review all primary population genetic studies of open ocean zooplankton and show that genetic isolation can be achieved at the scale of gyre systems in open ocean habitats (100s to 1000s of km). Furthermore, population genetic structure often varies across planktonic taxa, and appears to be linked to the particular ecological requirements of the organism. In combination, these characteristics should facilitate adaptive evolution to distinct oceanographic habitats in the plankton. We conclude that marine zooplankton may be capable of rapid evolutionary as well as ecological responses to changing ocean conditions, and discuss the implications of this view. We further suggest two priority areas for future research to test our hypothesis of high evolutionary potential in open ocean zooplankton, which will require (1) assessing how pervasive selection is in driving population divergence and (2) rigorously quantifying the spatial and temporal scales of population differentiation in the open ocean. Recent attention has focused on the ecological responses of open ocean zooplankton to current global change, including range shifts and changing phenology. Here, we argue that marine zooplankton also are well poised for evolutionary responses to global change. PMID:24567838

  20. An evolutionary perspective on health psychology: new approaches and applications.

    PubMed

    Tybur, Joshua M; Bryan, Angela D; Hooper, Ann E Caldwell

    2012-12-20

    Although health psychologists' efforts to understand and promote health are most effective when guided by theory, health psychology has not taken full advantage of theoretical insights provided by evolutionary psychology. Here, we argue that evolutionary perspectives can fruitfully inform strategies for addressing some of the challenges facing health psychologists. Evolutionary psychology's emphasis on modular, functionally specialized psychological systems can inform approaches to understanding the myriad behaviors grouped under the umbrella of "health," as can theoretical perspectives used by evolutionary anthropologists, biologists, and psychologists (e.g., Life History Theory). We detail some early investigations into evolutionary health psychology, and we provide suggestions for directions for future research.

  1. Evolutionary Conserved Positions Define Protein Conformational Diversity.

    PubMed

    Saldaño, Tadeo E; Monzon, Alexander M; Parisi, Gustavo; Fernandez-Alberti, Sebastian

    2016-03-01

    Conformational diversity of the native state plays a central role in modulating protein function. The selection paradigm sustains that different ligands shift the conformational equilibrium through their binding to highest-affinity conformers. Intramolecular vibrational dynamics associated to each conformation should guarantee conformational transitions, which due to its importance, could possibly be associated with evolutionary conserved traits. Normal mode analysis, based on a coarse-grained model of the protein, can provide the required information to explore these features. Herein, we present a novel procedure to identify key positions sustaining the conformational diversity associated to ligand binding. The method is applied to an adequate refined dataset of 188 paired protein structures in their bound and unbound forms. Firstly, normal modes most involved in the conformational change are selected according to their corresponding overlap with structural distortions introduced by ligand binding. The subspace defined by these modes is used to analyze the effect of simulated point mutations on preserving the conformational diversity of the protein. We find a negative correlation between the effects of mutations on these normal mode subspaces associated to ligand-binding and position-specific evolutionary conservations obtained from multiple sequence-structure alignments. Positions whose mutations are found to alter the most these subspaces are defined as key positions, that is, dynamically important residues that mediate the ligand-binding conformational change. These positions are shown to be evolutionary conserved, mostly buried aliphatic residues localized in regular structural regions of the protein like β-sheets and α-helix. PMID:27008419

  2. Rerooting the evolutionary tree of malaria parasites.

    PubMed

    Outlaw, Diana C; Ricklefs, Robert E

    2011-08-01

    Malaria parasites (Plasmodium spp.) have plagued humans for millennia. Less well known are related parasites (Haemosporida), with diverse life cycles and dipteran vectors that infect other vertebrates. Understanding the evolution of parasite life histories, including switches between hosts and vectors, depends on knowledge of evolutionary relationships among parasite lineages. In particular, inferences concerning time of origin and trait evolution require correct placement of the root of the evolutionary tree. Phylogenetic reconstructions of the diversification of malaria parasites from DNA sequences have suffered from uncertainty concerning outgroup taxa, limited taxon sampling, and selection on genes used to assess relationships. As a result, inferred relationships among the Haemosporida have been unstable, and questions concerning evolutionary diversification and host switching remain unanswered. A recent phylogeny placed mammalian malaria parasites, as well as avian/reptilian Plasmodium, in a derived position relative to the avian parasite genera Leucocytozoon and Haemoproteus, implying that the ancestral forms lacked merogony in the blood and that their vectors were non-mosquito dipterans. Bayesian, outgroup-free phylogenetic reconstruction using relaxed molecular clocks with uncorrelated rates instead suggested that mammalian and avian/reptilian Plasmodium parasites, spread by mosquito vectors, are ancestral sister taxa, from which a variety of specialized parasite lineages with modified life histories have evolved.

  3. Ecology and Evolutionary Biology of Arabidopsis

    PubMed Central

    Pigliucci, Massimo

    2002-01-01

    Arabidopsis thaliana is now widely used as a model system in molecular and developmental biology, as well as in physiology and cell biology. However, ecologists and evolutionary biologists have turned their attention to the mouse ear cress only much more recently and almost reluctantly. The reason for this is the perception that A. thaliana is not particularly interesting ecologically and that it represents an oddity from an evolutionary standpoint. While there is some truth in both these attitudes, similar criticisms apply to other model systems such as the fruit fly Drosophila melanogaster, which has been extensively studied from an organismal perspective. Furthermore, the shortcomings of A. thaliana in terms of its restricted ecological niche are counterbalanced by the wealth of information on the molecular and developmental biology of this species, which makes possible to address evolutionary questions that can rarely be pursued in other species. This chapter reviews the history of the use of A. thaliana in organismal biology and discusses some of the recent work and future perspectives of research on a variety of field including life history evolution, phenotypic plasticity, natural selection and quantitative genetics. I suggest that the future of both molecular and especially organismal biology lies into expanding our knowledge from limited and idiosyncratic model systems to their phylogenetic neighborhood, which is bound to be more varied and biologically interesting. PMID:22303188

  4. An evolutionary ecology of individual differences

    PubMed Central

    Dall, Sasha R. X.; Bell, Alison M.; Bolnick, Daniel I.; Ratnieks, Francis L. W.

    2014-01-01

    Individuals often differ in what they do. This has been recognised since antiquity. Nevertheless, the ecological and evolutionary significance of such variation is attracting widespread interest, which is burgeoning to an extent that is fragmenting the literature. As a first attempt at synthesis, we focus on individual differences in behaviour within populations that exceed the day-to-day variation in individual behaviour (i.e. behavioural specialisation). Indeed, the factors promoting ecologically relevant behavioural specialisation within natural populations are likely to have far-reaching ecological and evolutionary consequences. We discuss such individual differences from three distinct perspectives: individual niche specialisations, the division of labour within insect societies and animal personality variation. In the process, while recognising that each area has its own unique motivations, we identify a number of opportunities for productive ‘crossfertilisation’ among the (largely independent) bodies of work. We conclude that a complete understanding of evolutionarily and ecologically relevant individual differences must specify how ecological interactions impact the basic biological process (e.g. Darwinian selection, development and information processing) that underpin the organismal features determining behavioural specialisations. Moreover, there is likely to be covariation amongst behavioural specialisations. Thus, we sketch the key elements of a general framework for studying the evolutionary ecology of individual differences. PMID:22897772

  5. Evolutionary Dynamics and Diversity in Microbial Populations

    NASA Astrophysics Data System (ADS)

    Thompson, Joel; Fisher, Daniel

    2013-03-01

    Diseases such as flu and cancer adapt at an astonishing rate. In large part, viruses and cancers are so difficult to prevent because they are continually evolving. Controlling such ``evolutionary diseases'' requires a better understanding of the underlying evolutionary dynamics. It is conventionally assumed that adaptive mutations are rare and therefore will occur and sweep through the population in succession. Recent experiments using modern sequencing technologies have illuminated the many ways in which real population sequence data does not conform to the predictions of conventional theory. We consider a very simple model of asexual evolution and perform simulations in a range of parameters thought to be relevant for microbes and cancer. Simulation results reveal complex evolutionary dynamics typified by competition between lineages with different sets of adaptive mutations. This dynamical process leads to a distribution of mutant gene frequencies different than expected under the conventional assumption that adaptive mutations are rare. Simulated gene frequencies share several conspicuous features with data collected from laboratory-evolved yeast and the worldwide population of influenza.

  6. Evolutionary transitions during RNA virus experimental evolution.

    PubMed

    Elena, Santiago F

    2016-08-19

    In their search to understand the evolution of biological complexity, John Maynard Smith and Eörs Szathmáry put forward the notion of major evolutionary transitions as those in which elementary units get together to generate something new, larger and more complex. The origins of chromosomes, eukaryotic cells, multicellular organisms, colonies and, more recently, language and technological societies are examples that clearly illustrate this notion. However, a transition may be considered as anecdotal or as major depending on the specific level of biological organization under study. In this contribution, I will argue that transitions may also be occurring at a much smaller scale of biological organization: the viral world. Not only that, but also that we can observe in real time how these major transitions take place during experimental evolution. I will review the outcome of recent evolution experiments with viruses that illustrate four major evolutionary transitions: (i) the origin of a new virus that infects an otherwise inaccessible host and completely changes the way it interacts with the host regulatory and metabolic networks, (ii) the incorporation and loss of genes, (iii) the origin of segmented genomes from a non-segmented one, and (iv) the evolution of cooperative behaviour and cheating between different viruses or strains during co-infection of the same host.This article is part of the themed issue 'The major synthetic evolutionary transitions'. PMID:27431519

  7. Bell-Curve Based Evolutionary Optimization Algorithm

    NASA Technical Reports Server (NTRS)

    Sobieszczanski-Sobieski, J.; Laba, K.; Kincaid, R.

    1998-01-01

    The paper presents an optimization algorithm that falls in the category of genetic, or evolutionary algorithms. While the bit exchange is the basis of most of the Genetic Algorithms (GA) in research and applications in America, some alternatives, also in the category of evolutionary algorithms, but use a direct, geometrical approach have gained popularity in Europe and Asia. The Bell-Curve Based Evolutionary Algorithm (BCB) is in this alternative category and is distinguished by the use of a combination of n-dimensional geometry and the normal distribution, the bell-curve, in the generation of the offspring. The tool for creating a child is a geometrical construct comprising a line connecting two parents and a weighted point on that line. The point that defines the child deviates from the weighted point in two directions: parallel and orthogonal to the connecting line, the deviation in each direction obeying a probabilistic distribution. Tests showed satisfactory performance of BCB. The principal advantage of BCB is its controllability via the normal distribution parameters and the geometrical construct variables.

  8. Evolutionary games on multilayer networks: a colloquium

    NASA Astrophysics Data System (ADS)

    Wang, Zhen; Wang, Lin; Szolnoki, Attila; Perc, Matjaž

    2015-05-01

    Networks form the backbone of many complex systems, ranging from the Internet to human societies. Accordingly, not only is the range of our interactions limited and thus best described and modeled by networks, it is also a fact that the networks that are an integral part of such models are often interdependent or even interconnected. Networks of networks or multilayer networks are therefore a more apt description of social systems. This colloquium is devoted to evolutionary games on multilayer networks, and in particular to the evolution of cooperation as one of the main pillars of modern human societies. We first give an overview of the most significant conceptual differences between single-layer and multilayer networks, and we provide basic definitions and a classification of the most commonly used terms. Subsequently, we review fascinating and counterintuitive evolutionary outcomes that emerge due to different types of interdependencies between otherwise independent populations. The focus is on coupling through the utilities of players, through the flow of information, as well as through the popularity of different strategies on different network layers. The colloquium highlights the importance of pattern formation and collective behavior for the promotion of cooperation under adverse conditions, as well as the synergies between network science and evolutionary game theory.

  9. Predicting polymeric crystal structures by evolutionary algorithms

    NASA Astrophysics Data System (ADS)

    Zhu, Qiang; Sharma, Vinit; Oganov, Artem R.; Ramprasad, Ramamurthy

    2014-10-01

    The recently developed evolutionary algorithm USPEX proved to be a tool that enables accurate and reliable prediction of structures. Here we extend this method to predict the crystal structure of polymers by constrained evolutionary search, where each monomeric unit is treated as a building block with fixed connectivity. This greatly reduces the search space and allows the initial structure generation with different sequences and packings of these blocks. The new constrained evolutionary algorithm is successfully tested and validated on a diverse range of experimentally known polymers, namely, polyethylene, polyacetylene, poly(glycolic acid), poly(vinyl chloride), poly(oxymethylene), poly(phenylene oxide), and poly (p-phenylene sulfide). By fixing the orientation of polymeric chains, this method can be further extended to predict the structures of complex linear polymers, such as all polymorphs of poly(vinylidene fluoride), nylon-6 and cellulose. The excellent agreement between predicted crystal structures and experimentally known structures assures a major role of this approach in the efficient design of the future polymeric materials.

  10. Virulence in malaria: an evolutionary viewpoint.

    PubMed Central

    Mackinnon, Margaret J; Read, Andrew F

    2004-01-01

    Malaria parasites cause much morbidity and mortality to their human hosts. From our evolutionary perspective, this is because virulence is positively associated with parasite transmission rate. Natural selection therefore drives virulence upwards, but only to the point where the cost to transmission caused by host death begins to outweigh the transmission benefits. In this review, we summarize data from the laboratory rodent malaria model, Plasmodium chabaudi, and field data on the human malaria parasite, P. falciparum, in relation to this virulence trade-off hypothesis. The data from both species show strong positive correlations between asexual multiplication, transmission rate, infection length, morbidity and mortality, and therefore support the underlying assumptions of the hypothesis. Moreover, the P. falciparum data show that expected total lifetime transmission of the parasite is maximized in young children in whom the fitness cost of host mortality balances the fitness benefits of higher transmission rates and slower clearance rates, thus exhibiting the hypothesized virulence trade-off. This evolutionary explanation of virulence appears to accord well with the clinical and molecular explanations of pathogenesis that involve cytoadherence, red cell invasion and immune evasion, although direct evidence of the fitness advantages of these mechanisms is scarce. One implication of this evolutionary view of virulence is that parasite populations are expected to evolve new levels of virulence in response to medical interventions such as vaccines and drugs. PMID:15306410

  11. Evolutionary morphology of the rattlesnake style

    PubMed Central

    Meik, Jesse M; Pires-daSilva, André

    2009-01-01

    Background The rattlesnake rattling system is an evolutionary novelty that includes anatomical, behavioral, and physiological modifications of the generalized pitviper tail. One such modification, the formation of a bony clublike style at the terminal region of the caudal vertebrae, has not previously been examined in a phylogenetic context. Here we used skeletal material, cleared and stained preparations, and radiographs of whole preserved specimens to examine interspecific variation in style morphology among 34 rattlesnake species. Results Evolutionary Principal Components Analysis revealed an inverse relationship between caudal segmental counts and style size, supporting the hypothesis that bone from caudal vertebral elements was reallocated to style formation during the evolution of this structure. Most of the basal rattlesnake species have small styles consisting of few compacted vertebral elements; however, early in the rattlesnake radiation there appears to have been two independent transitions to relatively large, pronged styles consisting of multiple coalesced vertebrae (once in Sistrurus catenatus, and once in Crotalus following the divergence of the Mexican long-tailed rattlesnakes). In terms of style shape, the two most divergent species, C. catalinensis and C. ericsmithi, provide insight into the possible relationship between style and rattle matrix morphology and lineage-specific evolutionary strategies for retaining rattle segments. Conclusion The considerable interspecific variation in rattle morphology appears to correspond to variation in the bony style. We hypothesize that style morphology evolves indirectly as an integrated module responding to adaptive evolution on matrix morphology. PMID:19208237

  12. Automated Hardware Design via Evolutionary Search

    NASA Technical Reports Server (NTRS)

    Lohn, Jason D.; Colombano, Silvano P.

    2000-01-01

    The goal of this research is to investigate the application of evolutionary search to the process of automated engineering design. Evolutionary search techniques involve the simulation of Darwinian mechanisms by computer algorithms. In recent years, such techniques have attracted much attention because they are able to tackle a wide variety of difficult problems and frequently produce acceptable solutions. The results obtained are usually functional, often surprising, and typically "messy" because the algorithms are told to concentrate on the overriding objective and not elegance or simplicity. advantages. First, faster design cycles translate into time and, hence, cost savings. Second, automated design techniques can be made to scale well and hence better deal with increasing amounts of design complexity. Third, design quality can increase because design properties can be specified a priori. For example, size and weight specifications of a device, smaller and lighter than the best known design, might be optimized by the automated design technique. The domain of electronic circuit design is an advantageous platform in which to study automated design techniques because it is a rich design space that is well understood, permitting human-created designs to be compared to machine- generated designs. developed for circuit design was to automatically produce high-level integrated electronic circuit designs whose properties permit physical implementation in silicon. This process entailed designing an effective evolutionary algorithm and solving a difficult multiobjective optimization problem. FY 99 saw many accomplishments in this effort.

  13. Evolutionary plant physiology: Charles Darwin's forgotten synthesis

    NASA Astrophysics Data System (ADS)

    Kutschera, Ulrich; Niklas, Karl J.

    2009-11-01

    Charles Darwin dedicated more than 20 years of his life to a variety of investigations on higher plants (angiosperms). It has been implicitly assumed that these studies in the fields of descriptive botany and experimental plant physiology were carried out to corroborate his principle of descent with modification. However, Darwin’s son Francis, who was a professional plant biologist, pointed out that the interests of his father were both of a physiological and an evolutionary nature. In this article, we describe Darwin’s work on the physiology of higher plants from a modern perspective, with reference to the following topics: circumnutations, tropisms and the endogenous oscillator model; the evolutionary patterns of auxin action; the root-brain hypothesis; phloem structure and photosynthesis research; endosymbioses and growth-promoting bacteria; photomorphogenesis and phenotypic plasticity; basal metabolic rate, the Pfeffer-Kleiber relationship and metabolic optimality theory with respect to adaptive evolution; and developmental constraints versus functional equivalence in relationship to directional natural selection. Based on a review of these various fields of inquiry, we deduce the existence of a Darwinian (evolutionary) approach to plant physiology and define this emerging scientific discipline as the experimental study and theoretical analysis of the functions of green, sessile organisms from a phylogenetic perspective.

  14. Endosymbiosis and its implications for evolutionary theory.

    PubMed

    O'Malley, Maureen A

    2015-08-18

    Historically, conceptualizations of symbiosis and endosymbiosis have been pitted against Darwinian or neo-Darwinian evolutionary theory. In more recent times, Lynn Margulis has argued vigorously along these lines. However, there are only shallow grounds for finding Darwinian concepts or population genetic theory incompatible with endosymbiosis. But is population genetics sufficiently explanatory of endosymbiosis and its role in evolution? Population genetics "follows" genes, is replication-centric, and is concerned with vertically consistent genetic lineages. It may also have explanatory limitations with regard to macroevolution. Even so, asking whether population genetics explains endosymbiosis may have the question the wrong way around. We should instead be asking how explanatory of evolution endosymbiosis is, and exactly which features of evolution it might be explaining. This paper will discuss how metabolic innovations associated with endosymbioses can drive evolution and thus provide an explanatory account of important episodes in the history of life. Metabolic explanations are both proximate and ultimate, in the same way genetic explanations are. Endosymbioses, therefore, point evolutionary biology toward an important dimension of evolutionary explanation. PMID:25883268

  15. An extended synthesis for evolutionary biology.

    PubMed

    Pigliucci, Massimo

    2009-06-01

    Evolutionary theory is undergoing an intense period of discussion and reevaluation. This, contrary to the misleading claims of creationists and other pseudoscientists, is no harbinger of a crisis but rather the opposite: the field is expanding dramatically in terms of both empirical discoveries and new ideas. In this essay I briefly trace the conceptual history of evolutionary theory from Darwinism to neo-Darwinism, and from the Modern Synthesis to what I refer to as the Extended Synthesis, a more inclusive conceptual framework containing among others evo-devo, an expanded theory of heredity, elements of complexity theory, ideas about evolvability, and a reevaluation of levels of selection. I argue that evolutionary biology has never seen a paradigm shift, in the philosophical sense of the term, except when it moved from natural theology to empirical science in the middle of the 19th century. The Extended Synthesis, accordingly, is an expansion of the Modern Synthesis of the 1930s and 1940s, and one that--like its predecessor--will probably take decades to complete.

  16. Evolutionary hotspots in the Mojave Desert

    USGS Publications Warehouse

    Vandergast, Amy G.; Inman, Richard D.; Barr, Kelly R.; Nussear, Kenneth E.; Esque, Todd C.; Hathaway, Stacie A.; Wood, Dustin A.; Medica, Philip A.; Breinholt, Jesse W.; Stephen, Catherine L.; Gottscho, Andrew D.; Marks, Sharyn B.; Jennings, W. Bryan; Fisher, Robert N.

    2013-01-01

    Genetic diversity within species provides the raw material for adaptation and evolution. Just as regions of high species diversity are conservation targets, identifying regions containing high genetic diversity and divergence within and among populations may be important to protect future evolutionary potential. When multiple co-distributed species show spatial overlap in high genetic diversity and divergence, these regions can be considered evolutionary hotspots. We mapped spatial population genetic structure for 17 animal species across the Mojave Desert, USA. We analyzed these in concurrence and located 10 regions of high genetic diversity, divergence or both among species. These were mainly concentrated along the western and southern boundaries where ecotones between mountain, grassland and desert habitat are prevalent, and along the Colorado River. We evaluated the extent to which these hotspots overlapped protected lands and utility-scale renewable energy development projects of the Bureau of Land Management. While 30–40% of the total hotspot area was categorized as protected, between 3–7% overlapped with proposed renewable energy project footprints, and up to 17% overlapped with project footprints combined with transmission corridors. Overlap of evolutionary hotspots with renewable energy development mainly occurred in 6 of the 10 identified hotspots. Resulting GIS-based maps can be incorporated into ongoing landscape planning efforts and highlight specific regions where further investigation of impacts to population persistence and genetic connectivity may be warranted.

  17. Breaking evolutionary constraint with a tradeoff ratchet

    PubMed Central

    de Vos, Marjon G. J.; Dawid, Alexandre; Sunderlikova, Vanda; Tans, Sander J.

    2015-01-01

    Epistatic interactions can frustrate and shape evolutionary change. Indeed, phenotypes may fail to evolve when essential mutations are only accessible through positive selection if they are fixed simultaneously. How environmental variability affects such constraints is poorly understood. Here, we studied genetic constraints in fixed and fluctuating environments using the Escherichia coli lac operon as a model system for genotype–environment interactions. We found that, in different fixed environments, all trajectories that were reconstructed by applying point mutations within the transcription factor–operator interface became trapped at suboptima, where no additional improvements were possible. Paradoxically, repeated switching between these same environments allows unconstrained adaptation by continuous improvements. This evolutionary mode is explained by pervasive cross-environmental tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach, we developed a mathematical framework to quantify the landscape-crossing rates and show that this ratchet-like adaptive mechanism is robust in a wide spectrum of fluctuating environments. Overall, this study shows that genetic constraints can be overcome by environmental change and that cross-environmental tradeoffs do not necessarily impede but also, can facilitate adaptive evolution. Because tradeoffs and environmental variability are ubiquitous in nature, we speculate this evolutionary mode to be of general relevance. PMID:26567153

  18. Evolutionary game theory: cells as players.

    PubMed

    Hummert, Sabine; Bohl, Katrin; Basanta, David; Deutsch, Andreas; Werner, Sarah; Theissen, Günter; Schroeter, Anja; Schuster, Stefan

    2014-12-01

    In two papers we review game theory applications in biology below the level of cognitive living beings. It can be seen that evolution and natural selection replace the rationality of the actors appropriately. Even in these micro worlds, competing situations and cooperative relationships can be found and modeled by evolutionary game theory. Also those units of the lowest levels of life show different strategies for different environmental situations or different partners. We give a wide overview of evolutionary game theory applications to microscopic units. In this first review situations on the cellular level are tackled. In particular metabolic problems are discussed, such as ATP-producing pathways, secretion of public goods and cross-feeding. Further topics are cyclic competition among more than two partners, intra- and inter-cellular signalling, the struggle between pathogens and the immune system, and the interactions of cancer cells. Moreover, we introduce the theoretical basics to encourage scientists to investigate problems in cell biology and molecular biology by evolutionary game theory.

  19. Space Politics and Policy: An Evolutionary Perspective

    NASA Astrophysics Data System (ADS)

    Sadeh, Eligar

    2002-01-01

    This paper offers an evolutionary perspective of space policy. It is argued that (1) space policy is evolutionary in that it has responded to dramatic political events, such as the launching of Sputnik and the Cold War, and has undergone dynamic and evolutionary policy changes over the course of the past fifty years of the space-age; and that (2) space policy is an integral part of and interacts with public policy processes in the United States and abroad. To this end, the paper analyzes space policy at several levels of analysis. This includes: (1) historical context, political actors and institutions, political processes, and policy outcomes; (2) the symbiotic relationships between policy and space technology; and (3) future space policy trends and developments likely to occur in the 21st century. A "Space Politics and Policy Framework" is developed in this paper to represent the evolution of space policy. Space policy involves both the process of policy formation and policy change over time (e.g., emergence of commercialization) and the courses of action taken to achieve political (and technological) determined outcomes. The evolution of space policy over time takes place through policy change. On this basis, public policy processes over the course of the space-age have involved the mobilization of governmental resources, actors, and institutions. Concomitantly, nongovernmental actors, such as private corporations and commercial enterprises, increasingly play a role in space. As a result, market factors in addition to political forces influence space policy.

  20. Space Politics and Policy. An Evolutionary Perspective

    NASA Astrophysics Data System (ADS)

    Sadeh, E.

    2003-01-01

    This book is the first comprehensive source for the Space Politics and Policies of the United States Civil, Military, Intelligence, and Commercial Space Programs. Space Politics and Policy: An Evolutionary Perspective provides a comprehensive survey of Space Policy. This book is organized around two themes. Space Policy is evolutionary in that it has responded to dramatic political events, such as the launching of Sputnik and the Cold War, and has undergone dynamic and evolutionary policy changes over the course of the space age. Space Policy is an integral part of and interacts with public policy processes in the United States and abroad. The book analyzes Space Policy at several levels including historical context, political actors and institutions, political processes and policy outcomes. It examines the symbiotic relationships between policy, technology, and science; provides a review and synthesis of the existing body of knowledge in Space Policy; and identifies Space Policy trends and developments from the beginnings of the space age through the current era of the twenty-first century. The book is intended for those interested in Space Policy, especially Space Policy decision-makers, program and project managers, as well as students and lecturers of Space Policy. Link: http://www.wkap.nl/prod/b/1-4020-0879-1 and http://www.wkap.nl/prod/b/1-4020-0902-X

  1. Evolutionary Conserved Positions Define Protein Conformational Diversity

    PubMed Central

    Saldaño, Tadeo E.; Monzon, Alexander M.; Parisi, Gustavo; Fernandez-Alberti, Sebastian

    2016-01-01

    Conformational diversity of the native state plays a central role in modulating protein function. The selection paradigm sustains that different ligands shift the conformational equilibrium through their binding to highest-affinity conformers. Intramolecular vibrational dynamics associated to each conformation should guarantee conformational transitions, which due to its importance, could possibly be associated with evolutionary conserved traits. Normal mode analysis, based on a coarse-grained model of the protein, can provide the required information to explore these features. Herein, we present a novel procedure to identify key positions sustaining the conformational diversity associated to ligand binding. The method is applied to an adequate refined dataset of 188 paired protein structures in their bound and unbound forms. Firstly, normal modes most involved in the conformational change are selected according to their corresponding overlap with structural distortions introduced by ligand binding. The subspace defined by these modes is used to analyze the effect of simulated point mutations on preserving the conformational diversity of the protein. We find a negative correlation between the effects of mutations on these normal mode subspaces associated to ligand-binding and position-specific evolutionary conservations obtained from multiple sequence-structure alignments. Positions whose mutations are found to alter the most these subspaces are defined as key positions, that is, dynamically important residues that mediate the ligand-binding conformational change. These positions are shown to be evolutionary conserved, mostly buried aliphatic residues localized in regular structural regions of the protein like β-sheets and α-helix. PMID:27008419

  2. Evolutionary problems in centrosome and centriole biology.

    PubMed

    Ross, L; Normark, B B

    2015-05-01

    Centrosomes have been an enigma to evolutionary biologists. Either they have been the subject of ill-founded speculation or they have been ignored. Here, we highlight evolutionary paradoxes and problems of centrosome and centriole evolution and seek to understand them in the light of recent advances in centrosome biology. Most evolutionary accounts of centrosome evolution have been based on the hypothesis that centrosomes are replicators, independent of the nucleus and cytoplasm. It is now clear, however, that this hypothesis is not tenable. Instead, centrosomes are formed de novo each cell division, with the presence of an old centrosome regulating, but not essential for, the assembly of a new one. Centrosomes are the microtubule-organizing centres of cells. They can potentially affect sensory and motor characters (as the basal body of cilia), as well as the movements of chromosomes during cell division. This latter role does not seem essential, however, except in male meiosis, and the reasons for this remain unclear. Although the centrosome is absent in some taxa, when it is present, its structure is extraordinarily conserved: in most taxa across eukaryotes, it does not appear to evolve at all. And yet a few insect groups display spectacular hypertrophy of the centrioles. We discuss how this might relate to the unusual reproductive system found in these insects. Finally, we discuss why the fate of centrosomes in sperm and early embryos might differ between different groups of animals.

  3. Evolutionary emergence of responsive and unresponsive personalities.

    PubMed

    Wolf, Max; van Doorn, G Sander; Weissing, Franz J

    2008-10-14

    In many animal species, individuals differ consistently in suites of correlated behaviors, comparable with human personalities. Increasing evidence suggests that one of the fundamental factors structuring personality differences is the responsiveness of individuals to environmental stimuli. Whereas some individuals tend to be highly responsive to such stimuli, others are unresponsive and show routine-like behaviors. Much research has focused on the proximate causes of these differences but little is known about their evolutionary origin. Here, we provide an evolutionary explanation. We develop a simple but general evolutionary model that is based on two key ingredients. First, the benefits of responsiveness are frequency-dependent; that is, being responsive is advantageous when rare but disadvantageous when common. This explains why responsive and unresponsive individuals can coexist within a population. Second, positive-feedback mechanisms reduce the costs of responsiveness; that is, responsiveness is less costly for individuals that have been responsive before. This explains why individuals differ consistently in their responsiveness, across contexts and over time. As a result, natural selection gives rise to stable individual differences in responsiveness. Whereas some individuals respond to environmental stimuli in all kinds of contexts, others consistently neglect such stimuli. Interestingly, such differences induce correlations among all kinds of other traits (e.g., boldness and aggressiveness), thus providing an explanation for environment-specific behavioral syndromes.

  4. Investigating intertemporal choice through experimental evolutionary robotics.

    PubMed

    Paglieri, Fabio; Parisi, Domenico; Patacchiola, Massimiliano; Petrosino, Giancarlo

    2015-06-01

    In intertemporal choices, subjects face a trade-off between value and delay: achieving the most valuable outcome requires a longer time, whereas the immediately available option is objectively poorer. Intertemporal choices are ubiquitous, and comparative studies reveal commonalities and differences across species: all species devalue future rewards as a function of delay (delay aversion), yet there is a lot of inter-specific variance in how rapidly such devaluation occurs. These differences are often interpreted in terms of ecological rationality, as depending on environmental factors (e.g., feeding ecology) and the physiological and morphological constraints of different species (e.g., metabolic rate). Evolutionary hypotheses, however, are hard to verify in vivo, since it is difficult to observe precisely enough real environments, not to mention ancestral ones. In this paper, we discuss the viability of an approach based on evolutionary robotics: in Study 1, we evolve robots without a metabolism in five different ecologies; in Study 2, we evolve metabolic robots (i.e., robots that consume energy over time) in three different ecologies. The intertemporal choices of the robots are analyzed both in their ecology and under laboratory conditions. Results confirm the generality of delay aversion and the usefulness of studying intertemporal choice through experimental evolutionary robotics.

  5. Deconstructing Darwin: Evolutionary theory in context.

    PubMed

    Hull, David L

    2005-01-01

    The topic of this paper is external versus internal explanations, first, of the genesis of evolutionary theory and, second, its reception. Victorian England was highly competitive and individualistic. So was the view of society promulgated by Malthus and the theory of evolution set out by Charles Darwin and A.R. Wallace. The fact that Darwin and Wallace independently produced a theory of evolution that was just as competitive and individualistic as the society in which they lived is taken as evidence for the impact that society has on science. The same conclusion is reached with respect to the reception of evolutionary theory. Because Darwin's contemporaries lived in such a competitive and individualistic society, they were prone to accept a theory that exhibited these same characteristics. The trouble is that Darwin and Wallace did not live in anything like the same society and did not formulate the same theory. Although the character of Victorian society may have influenced the acceptance of evolutionary theory, it was not the competitive, individualistic theory that Darwin and Wallace set out but a warmer, more comforting theory.

  6. Evolutionary plant physiology: Charles Darwin's forgotten synthesis.

    PubMed

    Kutschera, Ulrich; Niklas, Karl J

    2009-11-01

    Charles Darwin dedicated more than 20 years of his life to a variety of investigations on higher plants (angiosperms). It has been implicitly assumed that these studies in the fields of descriptive botany and experimental plant physiology were carried out to corroborate his principle of descent with modification. However, Darwin's son Francis, who was a professional plant biologist, pointed out that the interests of his father were both of a physiological and an evolutionary nature. In this article, we describe Darwin's work on the physiology of higher plants from a modern perspective, with reference to the following topics: circumnutations, tropisms and the endogenous oscillator model; the evolutionary patterns of auxin action; the root-brain hypothesis; phloem structure and photosynthesis research; endosymbioses and growth-promoting bacteria; photomorphogenesis and phenotypic plasticity; basal metabolic rate, the Pfeffer-Kleiber relationship and metabolic optimality theory with respect to adaptive evolution; and developmental constraints versus functional equivalence in relationship to directional natural selection. Based on a review of these various fields of inquiry, we deduce the existence of a Darwinian (evolutionary) approach to plant physiology and define this emerging scientific discipline as the experimental study and theoretical analysis of the functions of green, sessile organisms from a phylogenetic perspective.

  7. The evolutionary language game: an orthogonal approach.

    PubMed

    Lenaerts, Tom; Jansen, Bart; Tuyls, Karl; De Vylder, Bart

    2005-08-21

    Evolutionary game dynamics have been proposed as a mathematical framework for the cultural evolution of language and more specifically the evolution of vocabulary. This article discusses a model that is mutually exclusive in its underlying principals with some previously suggested models. The model describes how individuals in a population culturally acquire a vocabulary by actively participating in the acquisition process instead of passively observing and communicate through peer-to-peer interactions instead of vertical parent-offspring relations. Concretely, a notion of social/cultural learning called the naming game is first abstracted using learning theory. This abstraction defines the required cultural transmission mechanism for an evolutionary process. Second, the derived transmission system is expressed in terms of the well-known selection-mutation model defined in the context of evolutionary dynamics. In this way, the analogy between social learning and evolution at the level of meaning-word associations is made explicit. Although only horizontal and oblique transmission structures will be considered, extensions to vertical structures over different genetic generations can easily be incorporated. We provide a number of simplified experiments to clarify our reasoning.

  8. Evolutionary Genetics of the Cavefish Astyanax mexicanus.

    PubMed

    Casane, D; Rétaux, S

    2016-01-01

    Blind and depigmented fish belonging to the species Astyanax mexicanus are outstanding models for evolutionary genetics. During their evolution in the darkness of caves, they have undergone a number of changes at the morphological, physiological, and behavioral levels, but they can still breed with their river-dwelling conspecifics. The fertile hybrids between these two morphotypes allow forward genetic approaches, from the search of quantitative trait loci to the identification of the mutations underlying the evolution of troglomorphism. We review here the past 30years of evolutionary genetics on Astyanax: from the first crosses and the discovery of convergent evolution of different Astyanax cavefish populations to the most recent evolutionary transcriptomics and genomics studies that have provided researchers with potential candidate genes to be tested using functional genetic approaches. Although significant progress has been made and some genes have been identified, cavefish have not yet fully revealed the secret of their adaptation to the absence of light. In particular, the genetic determinism of their loss of eyes seems complex and still puzzles researchers. We also discuss future research directions, including searches for the origin of cave alleles and searches for selection genome-wide, as well as the necessary but missing information on the timing of cave colonization by surface fish. PMID:27503356

  9. Endosymbiosis and its implications for evolutionary theory

    PubMed Central

    O’Malley, Maureen A.

    2015-01-01

    Historically, conceptualizations of symbiosis and endosymbiosis have been pitted against Darwinian or neo-Darwinian evolutionary theory. In more recent times, Lynn Margulis has argued vigorously along these lines. However, there are only shallow grounds for finding Darwinian concepts or population genetic theory incompatible with endosymbiosis. But is population genetics sufficiently explanatory of endosymbiosis and its role in evolution? Population genetics “follows” genes, is replication-centric, and is concerned with vertically consistent genetic lineages. It may also have explanatory limitations with regard to macroevolution. Even so, asking whether population genetics explains endosymbiosis may have the question the wrong way around. We should instead be asking how explanatory of evolution endosymbiosis is, and exactly which features of evolution it might be explaining. This paper will discuss how metabolic innovations associated with endosymbioses can drive evolution and thus provide an explanatory account of important episodes in the history of life. Metabolic explanations are both proximate and ultimate, in the same way genetic explanations are. Endosymbioses, therefore, point evolutionary biology toward an important dimension of evolutionary explanation. PMID:25883268

  10. The evolutionary language game: an orthogonal approach.

    PubMed

    Lenaerts, Tom; Jansen, Bart; Tuyls, Karl; De Vylder, Bart

    2005-08-21

    Evolutionary game dynamics have been proposed as a mathematical framework for the cultural evolution of language and more specifically the evolution of vocabulary. This article discusses a model that is mutually exclusive in its underlying principals with some previously suggested models. The model describes how individuals in a population culturally acquire a vocabulary by actively participating in the acquisition process instead of passively observing and communicate through peer-to-peer interactions instead of vertical parent-offspring relations. Concretely, a notion of social/cultural learning called the naming game is first abstracted using learning theory. This abstraction defines the required cultural transmission mechanism for an evolutionary process. Second, the derived transmission system is expressed in terms of the well-known selection-mutation model defined in the context of evolutionary dynamics. In this way, the analogy between social learning and evolution at the level of meaning-word associations is made explicit. Although only horizontal and oblique transmission structures will be considered, extensions to vertical structures over different genetic generations can easily be incorporated. We provide a number of simplified experiments to clarify our reasoning. PMID:15935174

  11. Multiscale structure in eco-evolutionary dynamics

    NASA Astrophysics Data System (ADS)

    Stacey, Blake C.

    In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of interdependency lead to structure at multiple scales of organization. Evolution excels at producing such complex structures. In turn, the existence of these complex interrelationships within a biological system affects the evolutionary dynamics of that system. I present a mathematical formalism for multiscale structure, grounded in information theory, which makes these intuitions quantitative, and I show how dynamics defined in terms of population genetics or evolutionary game theory can lead to multiscale organization. For complex systems, "more is different," and I address this from several perspectives. Spatial host--consumer models demonstrate the importance of the structures which can arise due to dynamical pattern formation. Evolutionary game theory reveals the novel effects which can result from multiplayer games, nonlinear payoffs and ecological stochasticity. Replicator dynamics in an environment with mesoscale structure relates to generalized conditionalization rules in probability theory. The idea of natural selection "acting at multiple levels" has been mathematized in a variety of ways, not all of which are equivalent. We will face down the confusion, using the experience developed over the course of this thesis to clarify the situation.

  12. The evolutionary ecology of C4 plants.

    PubMed

    Christin, Pascal-Antoine; Osborne, Colin P

    2014-12-01

    C4 photosynthesis is a physiological syndrome resulting from multiple anatomical and biochemical components, which function together to increase the CO2 concentration around Rubisco and reduce photorespiration. It evolved independently multiple times and C4 plants now dominate many biomes, especially in the tropics and subtropics. The C4 syndrome comes in many flavours, with numerous phenotypic realizations of C4 physiology and diverse ecological strategies. In this work, we analyse the events that happened in a C3 context and enabled C4 physiology in the descendants, those that generated the C4 physiology, and those that happened in a C4 background and opened novel ecological niches. Throughout the manuscript, we evaluate the biochemical and physiological evidence in a phylogenetic context, which demonstrates the importance of contingency in evolutionary trajectories and shows how these constrained the realized phenotype. We then discuss the physiological innovations that allowed C4 plants to escape these constraints for two important dimensions of the ecological niche--growth rates and distribution along climatic gradients. This review shows that a comprehensive understanding of C4 plant ecology can be achieved by accounting for evolutionary processes spread over millions of years, including the ancestral condition, functional convergence via independent evolutionary trajectories, and physiological diversification.

  13. Ecology and evolutionary biology of Arabidopsis.

    PubMed

    Pigliucci, Massimo

    2002-01-01

    Arabidopsis thaliana is now widely used as a model system in molecular and developmental biology, as well as in physiology and cell biology. However, ecologists and evolutionary biologists have turned their attention to the mouse ear cress only much more recently and almost reluctantly. The reason for this is the perception that A. thaliana is not particularly interesting ecologically and that it represents an oddity from an evolutionary standpoint. While there is some truth in both these attitudes, similar criticisms apply to other model systems such as the fruit fly Drosophila melanogaster, which has been extensively studied from an organismal perspective. Furthermore, the shortcomings of A. thaliana in terms of its restricted ecological niche are counterbalanced by the wealth of information on the molecular and developmental biology of this species, which makes possible to address evolutionary questions that can rarely be pursued in other species. This chapter reviews the history of the use of A. thaliana in organismal biology and discusses some of the recent work and future perspectives of research on a variety of field including life history evolution, phenotypic plasticity, natural selection and quantitative genetics. I suggest that the future of both molecular and especially organismal biology lies into expanding our knowledge from limited and idiosyncratic model systems to their phylogenetic neighborhood, which is bound to be more varied and biologically interesting. PMID:22303188

  14. Cryptic Genetic Variation in Evolutionary Developmental Genetics

    PubMed Central

    Paaby, Annalise B.; Gibson, Greg

    2016-01-01

    Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes—processes that cannot be fully observed in continuously varying visible traits. PMID:27304973

  15. The evolutionary ecology of the Lygaeidae

    PubMed Central

    Burdfield-Steel, Emily R; Shuker, David M

    2014-01-01

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

  16. Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Pham, Cong-Huy; Kucukbenli, Emine; de Gironcoli, Stefano

    2015-03-01

    Ab initio crystal structure prediction of even small organic compounds is extremely challenging due to polymorphism, molecular flexibility and difficulties in addressing the dispersion interaction from first principles. We recently implemented vdW-aware density functionals and demonstrated their success in energy ordering of aminoacid crystals. In this work we combine this development with the evolutionary structure prediction method to study cholesterol polymorphs. Cholesterol crystals have paramount importance in various diseases, from cancer to atherosclerosis. The structure of some polymorphs (e.g. ChM, ChAl, ChAh) have already been resolved while some others, which display distinct NMR spectra and are involved in disease formation, are yet to be determined. Here we thoroughly assess the applicability of evolutionary structure prediction to address such real world problems. We validate the newly predicted structures with ab initio NMR chemical shift data using secondary referencing for an improved comparison with experiments.

  17. Evolutionary impact assessment: accounting for evolutionary consequences of fishing in an ecosystem approach to fisheries management

    PubMed Central

    Laugen, Ane T; Engelhard, Georg H; Whitlock, Rebecca; Arlinghaus, Robert; Dankel, Dorothy J; Dunlop, Erin S; Eikeset, Anne M; Enberg, Katja; Jørgensen, Christian; Matsumura, Shuichi; Nusslé, Sébastien; Urbach, Davnah; Baulier, Loїc; Boukal, David S; Ernande, Bruno; Johnston, Fiona D; Mollet, Fabian; Pardoe, Heidi; Therkildsen, Nina O; Uusi-Heikkilä, Silva; Vainikka, Anssi; Heino, Mikko; Rijnsdorp, Adriaan D; Dieckmann, Ulf

    2014-01-01

    Managing fisheries resources to maintain healthy ecosystems is one of the main goals of the ecosystem approach to fisheries (EAF). While a number of international treaties call for the implementation of EAF, there are still gaps in the underlying methodology. One aspect that has received substantial scientific attention recently is fisheries-induced evolution (FIE). Increasing evidence indicates that intensive fishing has the potential to exert strong directional selection on life-history traits, behaviour, physiology, and morphology of exploited fish. Of particular concern is that reversing evolutionary responses to fishing can be much more difficult than reversing demographic or phenotypically plastic responses. Furthermore, like climate change, multiple agents cause FIE, with effects accumulating over time. Consequently, FIE may alter the utility derived from fish stocks, which in turn can modify the monetary value living aquatic resources provide to society. Quantifying and predicting the evolutionary effects of fishing is therefore important for both ecological and economic reasons. An important reason this is not happening is the lack of an appropriate assessment framework. We therefore describe the evolutionary impact assessment (EvoIA) as a structured approach for assessing the evolutionary consequences of fishing and evaluating the predicted evolutionary outcomes of alternative management options. EvoIA can contribute to EAF by clarifying how evolution may alter stock properties and ecological relations, support the precautionary approach to fisheries management by addressing a previously overlooked source of uncertainty and risk, and thus contribute to sustainable fisheries. PMID:26430388

  18. The transition from evolutionary stability to branching: A catastrophic evolutionary shift

    PubMed Central

    Dercole, Fabio; Della Rossa, Fabio; Landi, Pietro

    2016-01-01

    Evolutionary branching—resident-mutant coexistence under disruptive selection—is one of the main contributions of Adaptive Dynamics (AD), the mathematical framework introduced by S.A.H. Geritz, J.A.J. Metz, and coauthors to model the long-term evolution of coevolving multi-species communities. It has been shown to be the basic mechanism for sympatric and parapatric speciation, despite the essential asexual nature of AD. After 20 years from its introduction, we unfold the transition from evolutionary stability (ESS) to branching, along with gradual change in environmental, control, or exploitation parameters. The transition is a catastrophic evolutionary shift, the branching dynamics driving the system to a nonlocal evolutionary attractor that is viable before the transition, but unreachable from the ESS. Weak evolutionary stability hence qualifies as an early-warning signal for branching and a testable measure of the community’s resilience against biodiversity. We clarify a controversial theoretical question about the smoothness of the mutant invasion fitness at incipient branching. While a supposed nonsmoothness at third order long prevented the analysis of the ESS-branching transition, we argue that smoothness is generally expected and derive a local canonical model in terms of the geometry of the invasion fitness before branching. Any generic AD model undergoing the transition qualitatively behaves like our canonical model. PMID:27215588

  19. Traits and trade-offs are insufficient for evolutionary personality psychology.

    PubMed

    Sheldon, Kennon M; Sheldon, Melanie S; Nichols, Charles P

    2007-12-01

    Comments on the article by D. Nettle, who has clearly shown that evolutionary psychologists need to focus more attention on individual differences, not just species-typical universals. Such differences are not mere "noise," and evolutionary theory will gain by understanding how they are produced and maintained. However, by focusing on personality traits and the five-factor personality model, Nettle left unaddressed many of the most important aspects of human personality. An evolutionary psychology of personality must ultimately explain not just trait differences but also differences in personal goals, values, motives, identities, and life narratives--essential elements of human individuality and functionality. K. M. Sheldon et al suggest four reasons why traits and the five-factor personality model do not provide an optimal approach for explaining the evolution of personality: (a) As constructs, traits provide little purchase for explaining the causes of behavior; (b) trait concepts do not acknowledge or explain people's variations around their own baselines, variations that are likely crucial for adaptation; (c) traits do not explain or even describe true human uniqueness, i.e. the ways in which a person is different from everybody else; and (d) traits do not explain personality from the inside, by considering what people are trying to do in their lives. In raising these issues Sheldon et al are suggesting that the important question for evolutionary personality study is not why people fall at different points on a continuum regarding traits x, y, and z, but rather why each person is inevitably unique while still sharing the same evolved psychology.

  20. Comparing Evolutionary Programs and Evolutionary Pattern Search Algorithms: A Drug Docking Application

    SciTech Connect

    Hart, W.E.

    1999-02-10

    Evolutionary programs (EPs) and evolutionary pattern search algorithms (EPSAS) are two general classes of evolutionary methods for optimizing on continuous domains. The relative performance of these methods has been evaluated on standard global optimization test functions, and these results suggest that EPSAs more robustly converge to near-optimal solutions than EPs. In this paper we evaluate the relative performance of EPSAs and EPs on a real-world application: flexible ligand binding in the Autodock docking software. We compare the performance of these methods on a suite of docking test problems. Our results confirm that EPSAs and EPs have comparable performance, and they suggest that EPSAs may be more robust on larger, more complex problems.

  1. Form of an evolutionary tradeoff affects eco-evolutionary dynamics in a predator-prey system.

    PubMed

    Kasada, Minoru; Yamamichi, Masato; Yoshida, Takehito

    2014-11-11

    Evolution on a time scale similar to ecological dynamics has been increasingly recognized for the last three decades. Selection mediated by ecological interactions can change heritable phenotypic variation (i.e., evolution), and evolution of traits, in turn, can affect ecological interactions. Hence, ecological and evolutionary dynamics can be tightly linked and important to predict future dynamics, but our understanding of eco-evolutionary dynamics is still in its infancy and there is a significant gap between theoretical predictions and empirical tests. Empirical studies have demonstrated that the presence of genetic variation can dramatically change ecological dynamics, whereas theoretical studies predict that eco-evolutionary dynamics depend on the details of the genetic variation, such as the form of a tradeoff among genotypes, which can be more important than the presence or absence of the genetic variation. Using a predator-prey (rotifer-algal) experimental system in laboratory microcosms, we studied how different forms of a tradeoff between prey defense and growth affect eco-evolutionary dynamics. Our experimental results show for the first time to our knowledge that different forms of the tradeoff produce remarkably divergent eco-evolutionary dynamics, including near fixation, near extinction, and coexistence of algal genotypes, with quantitatively different population dynamics. A mathematical model, parameterized from completely independent experiments, explains the observed dynamics. The results suggest that knowing the details of heritable trait variation and covariation within a population is essential for understanding how evolution and ecology will interact and what form of eco-evolutionary dynamics will result. PMID:25336757

  2. Evolutionary psychology and evolutionary developmental psychology: understanding the evolution of human behavior and development.

    PubMed

    Hernández Blasi, Carlos; Causey, Kayla

    2010-02-01

    This is an introduction to this special issue on evolutionary psychology (EP) and evolutionary developmental psychology (EDP). We suggest here that, contrary to some common assumptions, mainstream psychology continues to be essentially non Darwinian and that EP and EDP are new approaches that can potentially help us to change this situation. We then present the organization of the special issue (composed of six papers). We conclude that evolution is certainly not the final consideration in psychology, but emphasize its importance as the basis upon which all modern behaviors and development are built.

  3. Empirical tests of evolutionary synthesis models

    NASA Astrophysics Data System (ADS)

    Gomes, Jean Michel; Cid Fernandes, R.

    2010-04-01

    Spectral synthesis of stellar populations has proven to be one of the most powerful methods to decompose the different mixtures of stellar contributions in galaxies, and applications of this technique routinely appear in the literature nowadays. Our group, for instance, the SEAGal (Semi Empirical Analysis of Galaxies) collaboration, has derived the star formation history of all galaxies in the SDSS with the starlight code, obtaining various results of astrophysical interest. As any other fossil method, the results rely heavily on high spectral resolution evolutionary synthesis models. To test this model dependence we run starlight on samples of star-forming and passive galaxies from the SDSS using different sets of models. We explore models using “Padova 1994” and modified “Padova” evolutionary tracks with a different receipt for the asymptotic giant branch phase, as well as different stellar libraries (STELIB versus MILES+Granada). We then compare derived properties such as mean age, mean metallicity, extinction, star-formation and chemical histories. Despite a broad brush agreement, systematic differences emerge from this comparison. The different evolutionary tracks used lead to essentially the same results, at least insofar as optical spectra are concerned. Different stellar libraries, on the other hand, have a much bigger impact. The newer models produce quantifiably better fits and eliminate some pathologies (like suspicious combinations of base elements, systematical spectral residuals in some windows, and, sometimes, negative extinction) of fits derived with STELIB-based models, but there are still some caveats. These empirical tests provide useful feedback for model makers.

  4. Extrapolating Weak Selection in Evolutionary Games

    PubMed Central

    Wu, Bin; García, Julián; Hauert, Christoph; Traulsen, Arne

    2013-01-01

    In evolutionary games, reproductive success is determined by payoffs. Weak selection means that even large differences in game outcomes translate into small fitness differences. Many results have been derived using weak selection approximations, in which perturbation analysis facilitates the derivation of analytical results. Here, we ask whether results derived under weak selection are also qualitatively valid for intermediate and strong selection. By “qualitatively valid” we mean that the ranking of strategies induced by an evolutionary process does not change when the intensity of selection increases. For two-strategy games, we show that the ranking obtained under weak selection cannot be carried over to higher selection intensity if the number of players exceeds two. For games with three (or more) strategies, previous examples for multiplayer games have shown that the ranking of strategies can change with the intensity of selection. In particular, rank changes imply that the most abundant strategy at one intensity of selection can become the least abundant for another. We show that this applies already to pairwise interactions for a broad class of evolutionary processes. Even when both weak and strong selection limits lead to consistent predictions, rank changes can occur for intermediate intensities of selection. To analyze how common such games are, we show numerically that for randomly drawn two-player games with three or more strategies, rank changes frequently occur and their likelihood increases rapidly with the number of strategies . In particular, rank changes are almost certain for , which jeopardizes the predictive power of results derived for weak selection. PMID:24339769

  5. Evolutionary morphology, platyrrhine evolution, and systematics.

    PubMed

    Rosenberger, Alfred L

    2011-12-01

    This special volume of the Anatomical Record focuses on the evolutionary morphology of New World monkeys. The studies range from three-dimensional surface geometry of teeth to enamel ultrastructure; from cranioskeletal adaptations for eating leaves and seeds to the histology of taste bud proxies; from the architecture of its bones to the mechanoreceptors of the tail's skin; from the physical properties of wild foods to the feeding biomechanics of jaws and skull; from the shapes of claws and fingertips, and of elbows, to the diversity and morphology of positional behavior; from the vomeronasal organ and its biological roles to links between brains, guts, sociality, and feeding; from the gum-eating adaptations of the smallest platyrrhines to the methods used to infer how big the largest fossil platyrrhines were. They demonstrate the power of combining functional morphology, behavior, and phylogenetic thinking as an approach toward reconstructing the evolutionary history of platyrrhine primates. While contributing new findings pertaining to all the major clades and ecological guilds, these articles reinforce the view that platyrrhines are a coherent ecophylogenetic array that differentiated along niche dimensions definable principally by body size, positional behavior, and feeding strategies. In underlining the value of character analysis and derived morphological and behavioral patterns as tools for deciphering phylogenetic and adaptational history, doubts are raised about a competing small-bore morphological method, parsimony-based cladistic studies. Intentionally designed not to enlist the rich reservoir of platyrrhine evolutionary morphology, an empirical assessment of the costs incurred by this research stratagem reveals inconsistent, nonrepeatable, and often conflicting results. PMID:22042518

  6. Evolutionary Computing Methods for Spectral Retrieval

    NASA Technical Reports Server (NTRS)

    Terrile, Richard; Fink, Wolfgang; Huntsberger, Terrance; Lee, Seugwon; Tisdale, Edwin; VonAllmen, Paul; Tinetti, Geivanna

    2009-01-01

    A methodology for processing spectral images to retrieve information on underlying physical, chemical, and/or biological phenomena is based on evolutionary and related computational methods implemented in software. In a typical case, the solution (the information that one seeks to retrieve) consists of parameters of a mathematical model that represents one or more of the phenomena of interest. The methodology was developed for the initial purpose of retrieving the desired information from spectral image data acquired by remote-sensing instruments aimed at planets (including the Earth). Examples of information desired in such applications include trace gas concentrations, temperature profiles, surface types, day/night fractions, cloud/aerosol fractions, seasons, and viewing angles. The methodology is also potentially useful for retrieving information on chemical and/or biological hazards in terrestrial settings. In this methodology, one utilizes an iterative process that minimizes a fitness function indicative of the degree of dissimilarity between observed and synthetic spectral and angular data. The evolutionary computing methods that lie at the heart of this process yield a population of solutions (sets of the desired parameters) within an accuracy represented by a fitness-function value specified by the user. The evolutionary computing methods (ECM) used in this methodology are Genetic Algorithms and Simulated Annealing, both of which are well-established optimization techniques and have also been described in previous NASA Tech Briefs articles. These are embedded in a conceptual framework, represented in the architecture of the implementing software, that enables automatic retrieval of spectral and angular data and analysis of the retrieved solutions for uniqueness.

  7. Eco-evolutionary feedbacks drive species interactions

    PubMed Central

    Andrade-Domínguez, Andrés; Salazar, Emmanuel; del Carmen Vargas-Lagunas, María; Kolter, Roberto; Encarnación, Sergio

    2014-01-01

    In the biosphere, many species live in close proximity and can thus interact in many different ways. Such interactions are dynamic and fall along a continuum between antagonism and cooperation. Because interspecies interactions are the key to understanding biological communities, it is important to know how species interactions arise and evolve. Here, we show that the feedback between ecological and evolutionary processes has a fundamental role in the emergence and dynamics of species interaction. Using a two-species artificial community, we demonstrate that ecological processes and rapid evolution interact to influence the dynamics of the symbiosis between a eukaryote (Saccharomyces cerevisiae) and a bacterium (Rhizobium etli). The simplicity of our experimental design enables an explicit statement of causality. The niche-constructing activities of the fungus were the key ecological process: it allowed the establishment of a commensal relationship that switched to ammensalism and provided the selective conditions necessary for the adaptive evolution of the bacteria. In this latter state, the bacterial population radiates into more than five genotypes that vary with respect to nutrient transport, metabolic strategies and global regulation. Evolutionary diversification of the bacterial populations has strong effects on the community; the nature of interaction subsequently switches from ammensalism to antagonism where bacteria promote yeast extinction. Our results demonstrate the importance of the evolution-to-ecology pathway in the persistence of interactions and the stability of communities. Thus, eco-evolutionary dynamics have the potential to transform the structure and functioning of ecosystems. Our results suggest that these dynamics should be considered to improve our understanding of beneficial and detrimental host–microbe interactions. PMID:24304674

  8. Life Beyond Earth and the Evolutionary Synthesis

    NASA Astrophysics Data System (ADS)

    Vakoch, Douglas A.

    For many astronomers, the progressive development of life has been seen as a natural occurrence given proper environmental conditions on a planet: even though such beings would not be identical to humans, there would be significant parallels. A striking contrast is seen in writings of nonphysical scientists, who have held more widely differing views. But within this diversity, reasons for differences become more apparent when we see how views about extraterrestrials can be related to the differential emphasis placed on modern evolutionary theory by scientists of various disciplines. One clue to understanding the differences between the biologists, paleontologists, and anthropologists who speculated on extraterrestrials is suggested by noting who wrote on the subject. Given the relatively small number of commentators on the topic, it seems more than coincidental that four of the major contributors to the evolutionary synthesis in the 1930s and 1940s are among them. Upon closer examination it is evident that the exobiological arguments of Theodosius Dobzhansky and George Gaylord Simpson and, less directly, of H. J. Muller and Ernst Mayr are all related to their earlier work in formulating synthetic evolution. By examining the variety of views held by nonphysical scientists, we can see that there were significant disagreements between them about evolution into the 1960s. By the mid-1980s, many believed that "higher" life, particularly intelligent life, probably occurs quite infrequently in the universe; nevertheless, some held out the possibility that convergence of intelligence could occur across worlds. Regardless of the final conclusions these scientists reached about the likely prevalence of extraterrestrial intelligence, the use of evolutionary arguments to support their positions became increasingly common.

  9. Characterizing Phase Transitions in a Model of Neutral Evolutionary Dynamics

    NASA Astrophysics Data System (ADS)

    Scott, Adam; King, Dawn; Bahar, Sonya

    2013-03-01

    An evolutionary model was recently introduced for sympatric, phenotypic evolution over a variable fitness landscape with assortative mating (Dees & Bahar 2010). Organisms in the model are described by coordinates in a two-dimensional phenotype space, born at random coordinates with limited variation from their parents as determined by a mutation parameter, mutability. The model has been extended to include both neutral evolution and asexual reproduction in Scott et al (submitted). It has been demonstrated that a second order, non-equilibrium phase transition occurs for the temporal dynamics as the mutability is varied, for both the original model and for neutral conditions. This transition likely belongs to the directed percolation universality class. In contrast, the spatial dynamics of the model shows characteristics of an ordinary percolation phase transition. Here, we characterize the phase transitions exhibited by this model by determining critical exponents for the relaxation times, characteristic lengths, and cluster (species) mass distributions. Missouri Research Board; J.S. McDonnell Foundation

  10. Cultural Safety: An Evolutionary Concept Analysis.

    PubMed

    Parisa, Bozorgzad; Reza, Negarandeh; Afsaneh, Raiesifar; Sarieh, Poortaghi

    2016-01-01

    Healing occurs in a safe milieu, and patients feel safe when service providers view them as whole persons, recognizing the multiple underlying factors that cause illness. Cultural safety can lead to service delivery in this way, but most nurses have no clear understanding of this concept. This study aimed to clarify cultural safety on the basis of Rodgers' evolutionary concept analysis. Cultural sensitivity and cultural awareness are the antecedents of cultural safety. These concepts include a nurse's flexibility toward his or her patients with different perspectives, creating an atmosphere free from intimidation and judgment of the patients, with an overall promotion of health in multicultural communities. PMID:26633724

  11. Protein Structure Prediction with Evolutionary Algorithms

    SciTech Connect

    Hart, W.E.; Krasnogor, N.; Pelta, D.A.; Smith, J.

    1999-02-08

    Evolutionary algorithms have been successfully applied to a variety of molecular structure prediction problems. In this paper we reconsider the design of genetic algorithms that have been applied to a simple protein structure prediction problem. Our analysis considers the impact of several algorithmic factors for this problem: the confirmational representation, the energy formulation and the way in which infeasible conformations are penalized, Further we empirically evaluated the impact of these factors on a small set of polymer sequences. Our analysis leads to specific recommendations for both GAs as well as other heuristic methods for solving PSP on the HP model.

  12. Evolutionary history of CI and CM chondrites

    NASA Technical Reports Server (NTRS)

    Kerridge, J. F.; Macdougall, J. D.

    1984-01-01

    It is now clear that several different processes have acted upon various components of carbonaceous chondrites, and that at least some of those processes occurred very early in solar system history. Because these meteorites are breccias, petrographic relationships are seldom informative about the order in which those processes took place. Nonetheless, information about such an evolutionary sequence would be of potential value in defining the nature of the source region for these meteorites. Implantation of solar wind derived noble gases into CI magnetite apparently postdated the period of aqueous activity believed to be responsible for magnetite production. Carbonate crystallization roughly coincided with one or more episodes of impact driven brecciation.

  13. Using diagnostic radiology in human evolutionary studies

    PubMed Central

    SPOOR, FRED; JEFFERY, NATHAN; ZONNEVELD, FRANS

    2000-01-01

    This paper reviews the application of medical imaging and associated computer graphics techniques to the study of human evolutionary history, with an emphasis on basic concepts and on the advantages and limitations of each method. Following a short discussion of plain film radiography and pluridirectional tomography, the principles of computed tomography (CT) and magnetic resonance imaging (MRI) and their role in the investigation of extant and fossil morphology are considered in more detail. The second half of the paper deals with techniques of 3-dimensional visualisation based on CT and MRI and with quantitative analysis of digital images. PMID:10999271

  14. The evolutionary sequence: origin and emergences.

    PubMed

    Fox, S W

    1986-03-01

    The evolutionary sequence is being reexamined experimentally from a "Big Bang"origin to the protocell and from the emergence of protocell and variety of species to Darwin's mental power (mind) and society (The Descent of Man). A most fundamentally revisionary consequence of experiments is an emphasis on endogenous ordering. This principle, seen vividly in ordered copolymerization of amino acids, has had new impact on the theory of Darwinian evolution and has been found to apply to the entire sequence. Herein, I will discuss some problems of dealing with teaching controversial subjects.

  15. Evolutionary development of a lunar CELSS

    NASA Technical Reports Server (NTRS)

    Schwartzkopf, Steven H.; Brown, Mariann F.

    1991-01-01

    An evolutionary technology-integration process has been applied to a baseline, partially-closed regenerative life support system (LSS) based on Space Station Freedom-typified physicochemical (PC) technology; the result of this evolution is the Lunar-base Controlled Ecological LSS (LCELSS), which is a hybrid system incorporating both bioregenerative (BR) and PC technologies. The evolution of the LCELSS has proceeded through a sequence of additions involving (1) bioregenerative functions, (2) supplementing specific PC functions with BR ones, (3) replacement of initial PC technologies with more advanced ones, and (4) the addition of new PC technologies.

  16. Mutator Dynamics on a Smooth Evolutionary Landscape

    NASA Astrophysics Data System (ADS)

    Kessler, David A.; Levine, Herbert

    1998-03-01

    We investigate a model of evolutionary dynamics on a smooth landscape which features a ``mutator'' allele which increases the mutation rate. We show that when the fitness is far from its equilibrium value the expected proportion of mutators approaches a value governed solely by the transition rates into and out of the mutator state, resulting in a much faster fitness increase than would be the case without the mutator allele. Near the fitness equilibrium, the mutators are severely suppressed, due to the detrimental effects of a large mutation rate near the fitness maximum. We discuss the results of a recent experiment on natural selection of E. coli in the light of our model.

  17. Evolutionary models of in-group favoritism

    PubMed Central

    Fu, Feng

    2015-01-01

    In-group favoritism is the tendency for individuals to cooperate with in-group members more strongly than with out-group members. Similar concepts have been described across different domains, including in-group bias, tag-based cooperation, parochial altruism, and ethnocentrism. Both humans and other animals show this behavior. Here, we review evolutionary mechanisms for explaining this phenomenon by covering recently developed mathematical models. In fact, in-group favoritism is not easily realized on its own in theory, although it can evolve under some conditions. We also discuss the implications of these modeling results in future empirical and theoretical research. PMID:25926978

  18. The evolutionary sequence: origin and emergences

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1986-01-01

    The evolutionary sequence is being reexamined experimentally from a "Big Bang"origin to the protocell and from the emergence of protocell and variety of species to Darwin's mental power (mind) and society (The Descent of Man). A most fundamentally revisionary consequence of experiments is an emphasis on endogenous ordering. This principle, seen vividly in ordered copolymerization of amino acids, has had new impact on the theory of Darwinian evolution and has been found to apply to the entire sequence. Herein, I will discuss some problems of dealing with teaching controversial subjects.

  19. The evolutionary sequence: origin and emergences.

    PubMed

    Fox, S W

    1986-03-01

    The evolutionary sequence is being reexamined experimentally from a "Big Bang"origin to the protocell and from the emergence of protocell and variety of species to Darwin's mental power (mind) and society (The Descent of Man). A most fundamentally revisionary consequence of experiments is an emphasis on endogenous ordering. This principle, seen vividly in ordered copolymerization of amino acids, has had new impact on the theory of Darwinian evolution and has been found to apply to the entire sequence. Herein, I will discuss some problems of dealing with teaching controversial subjects. PMID:11542035

  20. Intelligence's likelihood and evolutionary time frame

    NASA Astrophysics Data System (ADS)

    Bogonovich, Marc

    2011-04-01

    This paper outlines hypotheses relevant to the evolution of intelligent life and encephalization in the Phanerozoic. If general principles are inferable from patterns of Earth life, implications could be drawn for astrobiology. Many of the outlined hypotheses, relevant data, and associated evolutionary and ecological theory are not frequently cited in astrobiological journals. Thus opportunity exists to evaluate reviewed hypotheses with an astrobiological perspective. A quantitative method is presented for testing one of the reviewed hypotheses (hypothesis i; the diffusion hypothesis). Questions are presented throughout, which illustrate that the question of intelligent life's likelihood can be expressed as multiple, broadly ranging, more tractable questions.

  1. Informations in Models of Evolutionary Dynamics

    NASA Astrophysics Data System (ADS)

    Rivoire, Olivier

    2016-03-01

    Biological organisms adapt to changes by processing informations from different sources, most notably from their ancestors and from their environment. We review an approach to quantify these informations by analyzing mathematical models of evolutionary dynamics and show how explicit results are obtained for a solvable subclass of these models. In several limits, the results coincide with those obtained in studies of information processing for communication, gambling or thermodynamics. In the most general case, however, information processing by biological populations shows unique features that motivate the analysis of specific models.

  2. On the evolutionary constraint surface of hydra

    NASA Technical Reports Server (NTRS)

    Slobodkin, L. B.; Dunn, K.

    1983-01-01

    Food consumption, body size, and budding rate were measured simultaneously in isolated individual hydra of six strains. For each individual hydra the three measurements define a point in the three dimensional space with axes: food consumption, budding rate, and body size. These points lie on a single surface, regardless of species. Floating rate and incidence of sexuality map onto this surface. It is suggested that this surface is an example of a general class of evolutionary constraint surfaces derived from the conjunction of evolutinary theory and the theory of ecological resource budgets. These constraint surfaces correspond to microevolutionary domains.

  3. Darwinism and the expansion of evolutionary theory.

    PubMed

    Gould, S J

    1982-04-23

    The essence of Darwinism lies in the claim that natural selection is a creative force, and in the reductionist assertion that selection upon individual organisms is the locus of evolutionary change. Critiques of adaptationism and gradualism call into doubt the traditional consequences of the argument for creativity, while a concept of hierarchy, with selection acting upon such higher-level "individuals" as demes and species, challenges the reductionist claim. An expanded hierarchical theory would not be Darwinism, has strictly defined, but it would capture, in abstract form, the fundamental feature of Darwin's vision--direction of evolution by selection at each level.

  4. Darwinism and the Expansion of Evolutionary Theory

    NASA Astrophysics Data System (ADS)

    Gould, Stephen Jay

    1982-04-01

    The essence of Darwinism lies in the claim that natural selection is a creative force, and in the reductionist assertion that selection upon individual organisms is the locus of evolutionary change. Critiques of adaptationism and gradualism call into doubt the traditional consequences of the argument for creativity, while a concept of hierarchy, with selection acting upon such higher-level ``individuals'' as demes and species, challenges the reductionist claim. An expanded hierarchical theory would not be Darwinism, as strictly defined, but it would capture, in abstract form, the fundamental feature of Darwin's vision--direction of evolution by selection at each level.

  5. Canonical transformations and Hamiltonian evolutionary systems

    SciTech Connect

    Al-Ashhab, Samer

    2012-06-15

    In many Lagrangian field theories, one has a Poisson bracket defined on the space of local functionals. We find necessary and sufficient conditions for a transformation on the space of local functionals to be canonical in three different cases. These three cases depend on the specific dimensions of the vector bundle of the theory and the associated Hamiltonian differential operator. We also show how a canonical transformation transforms a Hamiltonian evolutionary system and its conservation laws. Finally, we illustrate these ideas with three examples.

  6. An evolutionary biochemist's perspective on promiscuity.

    PubMed

    Copley, Shelley D

    2015-02-01

    Evolutionary biochemists define enzyme promiscuity as the ability to catalyze secondary reactions that are physiologically irrelevant, either because they are too inefficient to affect fitness or because the enzyme never encounters the substrate. Promiscuous activities are common because evolution of a perfectly specific active site is both difficult and unnecessary; natural selection ceases when the performance of a protein is 'good enough' that it no longer affects fitness. Although promiscuous functions are accidental and physiologically irrelevant, they are of great importance because they provide opportunities for the evolution of new functions in nature and in the laboratory, as well as targets for therapeutic drugs and tools for a wide range of technological applications.

  7. Evolutionary Effects on Brightest Cluster Galaxy (BCG) Detections in the CFHTLS-Deep Fields

    NASA Astrophysics Data System (ADS)

    Alis, S.

    2009-09-01

    Brightest cluster galaxies (BCGs) are the most massive and most luminous galaxies in the universe. These galaxies dominate galaxy clusters and lie at the top of the potential well of clusters. Investigating these galaxies can improve our understandings on galaxy cluster evolution. In this work, evolutionary effects on BCG detections are emphasized. For detecting BCGs, CFHTLS (Canada-France-Hawaii Telescope Legacy Survey) galaxy clusters, detected by Olsen et al. (2007) were used. To make a proper BCG detection, modeled galaxy colors should be evolved according to redshift. In this work, it is shown how unevolved galaxy colors can effect BCG detection.

  8. Evolutionary Conflict Between Maternal and Paternal Interests: Integration with Evolutionary Endocrinology.

    PubMed

    Mokkonen, Mikael; Koskela, Esa; Mappes, Tapio; Mills, Suzanne C

    2016-08-01

    Conflict between mates, as well as conflict between parents and offspring are due to divergent evolutionary interests of the interacting individuals. Hormone systems provide genetically based proximate mechanisms for mediating phenotypic adaptation and maladaptation characteristic of evolutionary conflict between individuals. Testosterone (T) is among the most commonly studied hormones in evolutionary biology, and as such, its role in shaping sexually dimorphic behaviors and physiology is relatively well understood, but its role in evolutionary conflict is not as clear. In this review, we outline the genomic conflicts arising within the family unit, and incorporate multiple lines of evidence from the bank vole (Myodes glareolus) system to outline how T impacts traits associated with reproduction and survival, resulting in a sexually antagonistic genetic trade-off in fitness. A major prediction arising from this work is that lower T is favored in females, whereas the optimal T level in males fluctuates in relation to social and ecological factors. We additionally discuss future directions to further integrate endocrinology into the study of sexual and parent-offspring conflicts. PMID:27400975

  9. Using Evolutionary Theory to Guide Mental Health Research.

    PubMed

    Durisko, Zachary; Mulsant, Benoit H; McKenzie, Kwame; Andrews, Paul W

    2016-03-01

    Evolutionary approaches to medicine can shed light on the origins and etiology of disease. Such an approach may be especially useful in psychiatry, which frequently addresses conditions with heterogeneous presentation and unknown causes. We review several previous applications of evolutionary theory that highlight the ways in which psychiatric conditions may persist despite and because of natural selection. One lesson from the evolutionary approach is that some conditions currently classified as disorders (because they cause distress and impairment) may actually be caused by functioning adaptations operating "normally" (as designed by natural selection). Such conditions suggest an alternative illness model that may generate alternative intervention strategies. Thus, the evolutionary approach suggests that psychiatry should sometimes think differently about distress and impairment. The complexity of the human brain, including normal functioning and potential for dysfunctions, has developed over evolutionary time and has been shaped by natural selection. Understanding the evolutionary origins of psychiatric conditions is therefore a crucial component to a complete understanding of etiology.

  10. Evolutionary dynamics with fluctuating population sizes and strong mutualism

    NASA Astrophysics Data System (ADS)

    Chotibut, Thiparat; Nelson, David R.

    2015-08-01

    Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

  11. The descent of words: evolutionary thinking 1780-1880.

    PubMed

    van Wyhe, John

    2005-09-01

    Histories of evolutionary thought are dominated by organic evolution. The colossus in our midst that is evolutionary biology casts its shadow over history, making it appear that what is so widespread and important today was always the primary subject of evolutionary speculation. Thus many histories assume that the core meaning of evolution is the change of organic life and that other forms of evolutionary thinking, such as linguistic, social or cultural evolution, are only analogies or offshoots of the main biological evolutionary trunk. Ironically this is an ahistorical understanding. Long before the work of Charles Darwin, scholars were independently developing evolutionary concepts such as descent with modification and divergence from a common stock in order to understand cultural change.

  12. Evolutionary dynamics with fluctuating population sizes and strong mutualism.

    PubMed

    Chotibut, Thiparat; Nelson, David R

    2015-08-01

    Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems. PMID:26382443

  13. Expansion of biological pathways based on evolutionary inference

    PubMed Central

    Li, Yang; Calvo, Sarah E.; Gutman, Roee

    2014-01-01

    Summary Availability of diverse genomes makes it possible to predict gene function based on shared evolutionary history. This approach can be challenging, however, for pathways whose components do not exhibit a shared history, but rather, consist of distinct “evolutionary modules.” We introduce a computational algorithm, CLIME (clustering by inferred models of evolution), which inputs a eukaryotic species tree, homology matrix, and pathway (gene set) of interest. CLIME partitions the gene set into disjoint evolutionary modules, simultaneously learning the number of modules and a tree-based evolutionary history that defines each module. CLIME then expands each module by scanning the genome for new components that likely arose under the inferred evolutionary model. Application of CLIME to ∼1000 annotated human pathways, organelles and proteomes of yeast, red algae, and malaria, reveals unanticipated evolutionary modularity and novel, co-evolving components. CLIME is freely available and should become increasingly powerful with the growing wealth of eukaryotic genomes. PMID:24995987

  14. Food-web formation with recursive evolutionary branching.

    PubMed

    Ito, Hiroshi C; Ikegami, Takashi

    2006-01-01

    A reaction-diffusion model describing the evolutionary dynamics of a food-web was constructed. In this model, predator-prey relationships among organisms were determined by their position in a two-dimensional phenotype space defined by two traits: as prey and as predator. The mutation process is expressed with a diffusion process of biomass in the phenotype space. Numerical simulation of this model showed co-evolutionary dynamics of isolated phenotypic clusters, including various types of evolutionary branching, which were classified into branching as prey, branching as predators, and co-evolutionary branching of both prey and predators. A complex food-web develops with recursive evolutionary branching from a single phenotypic cluster. Biodiversity peaks at the medium strength of the predator-prey interaction, where the food-web is maintained at medium biomass by a balanced frequency between evolutionary branching and extinction.

  15. Male sexual behaviour and ethanol consumption from an evolutionary perspective: A comment on "Sexual Deprivation Increases Ethanol Intake in Drosophila".

    PubMed

    Guevara-Fiore, Palestina; Endler, John A

    2014-01-01

    Shohat-Ophir et al. (1) demonstrate a connection between sexual behaviour and ethanol consumption in male Drosophila flies, and how the neuropeptide F system regulates ethanol preference. Their results are rightly discussed only in a physiological context, but this has facilitated erroneous anthropomorphic interpretations by the media. Here we discuss the link between male sexual behaviour and ethanol consumption from an evolutionary perspective, providing a broader context to interpret their results.

  16. Evolutionary lessons from California plant phylogeography.

    PubMed

    Sork, Victoria L; Gugger, Paul F; Chen, Jin-Ming; Werth, Silke

    2016-07-19

    Phylogeography documents the spatial distribution of genetic lineages that result from demographic processes, such as population expansion, population contraction, and gene movement, shaped by climate fluctuations and the physical landscape. Because most phylogeographic studies have used neutral markers, the role of selection may have been undervalued. In this paper, we contend that plants provide a useful evolutionary lesson about the impact of selection on spatial patterns of neutral genetic variation, when the environment affects which individuals can colonize new sites, and on adaptive genetic variation, when environmental heterogeneity creates divergence at specific loci underlying local adaptation. Specifically, we discuss five characteristics found in plants that intensify the impact of selection: sessile growth form, high reproductive output, leptokurtic dispersal, isolation by environment, and the potential to evolve longevity. Collectively, these traits exacerbate the impact of environment on movement between populations and local selection pressures-both of which influence phylogeographic structure. We illustrate how these unique traits shape these processes with case studies of the California endemic oak, Quercus lobata, and the western North American lichen, Ramalina menziesii Obviously, the lessons we learn from plant traits are not unique to plants, but they highlight the need for future animal, plant, and microbe studies to incorporate its impact. Modern tools that generate genome-wide sequence data are now allowing us to decipher how evolutionary processes affect the spatial distribution of different kinds of genes and also to better model future spatial distribution of species in response to climate change. PMID:27432984

  17. The evolutionary psychology of women's aggression.

    PubMed

    Campbell, Anne

    2013-01-01

    Evolutionary researchers have identified age, operational sex ratio and high variance in male resources as factors that intensify female competition. These are discussed in relation to escalated intrasexual competition for men and their resources between young women in deprived neighbourhoods. For these women, fighting is not seen as antithetical to cultural conceptions of femininity, and female weakness is disparaged. Nonetheless, even where competitive pressures are high, young women's aggression is less injurious and frequent than young men's. From an evolutionary perspective, I argue that the intensity of female aggression is constrained by the greater centrality of mothers, rather than fathers, to offspring survival. This selection pressure is realized psychologically through a lower threshold for fear among women. Neuropsychological evidence is not yet conclusive but suggests that women show heightened amygdala reactivity to threatening stimuli, may be better able to exert prefrontal cortical control over emotional behaviour and may consciously register fear more strongly via anterior cingulate activity. The impact of testosterone and oxytocin on the neural circuitry of emotion is also considered.

  18. Evolutionary inferences from the analysis of exchangeability

    PubMed Central

    Hendry, Andrew P.; Kaeuffer, Renaud; Crispo, Erika; Peichel, Catherine L.; Bolnick, Daniel I.

    2013-01-01

    Evolutionary inferences are usually based on statistical models that compare mean genotypes and phenotypes (or their frequencies) among populations. An alternative is to use the actual distribution of genotypes and phenotypes to infer the “exchangeability” of individuals among populations. We illustrate this approach by using discriminant functions on principal components to classify individuals among paired lake and stream populations of threespine stickleback in each of six independent watersheds. Classification based on neutral and non-neutral microsatellite markers was highest to the population of origin and next-highest to populations in the same watershed. These patterns are consistent with the influence of historical contingency (separate colonization of each watershed) and subsequent gene flow (within but not between watersheds). In comparison to this low genetic exchangeability, ecological (diet) and morphological (trophic and armor traits) exchangeability was relatively high – particularly among populations from similar habitats. These patterns reflect the role of natural selection in driving parallel changes adaptive changes when independent populations colonize similar habitats. Importantly, however, substantial non-parallelism was also evident. Our results show that analyses based on exchangeability can confirm inferences based on statistical analyses of means or frequencies, while also refining insights into the drivers of – and constraints on – evolutionary diversification. PMID:24299398

  19. An evolutionary link for developing mammalian lungs.

    PubMed

    Maloney, J E; Darian-Smith, C; Russell, B; Varghese, M; Cooper, J; Limpus, C J

    1989-09-01

    Lungs of the human infant and those of other mammals are filled with fluid immediately prior to birth. Studies of the ionic composition of this fluid indicate that active ionic transport processes occur in the epithelial cells of the potential airspaces. The purpose of this study was to see if these active ion pumps were present in developing species other than mammals thus providing a possible evolutionary link to mammals. A series of samples of lung liquid, amniotic fluid, and plasma were taken from embryonic marine turtles gathered from clutches incubating in the beach at Mon Repos, Queensland, Australia during the summer of 1986-87. The concentrations of sodium, potassium and chloride ions and protein measured in these liquids indicated that active pumping processes similar to that seen in the mammalian lung were present in the developing lungs of these marine reptiles and further, circumstantial evidence was gathered to suggest that this liquid was partially reabsorbed prior to hatching. The results support the notion that processes responsible for the normal development of the human lung and lungs of other mammals are also present in the hollow lungs of marine turtles. Thus there is an evolutionary counterpart controlling lung development in more ancient species. It may be possible to generalize this observation to the development of hollow lungs of other species.

  20. Evolutionary lessons from California plant phylogeography

    PubMed Central

    Sork, Victoria L.; Chen, Jin-Ming

    2016-01-01

    Phylogeography documents the spatial distribution of genetic lineages that result from demographic processes, such as population expansion, population contraction, and gene movement, shaped by climate fluctuations and the physical landscape. Because most phylogeographic studies have used neutral markers, the role of selection may have been undervalued. In this paper, we contend that plants provide a useful evolutionary lesson about the impact of selection on spatial patterns of neutral genetic variation, when the environment affects which individuals can colonize new sites, and on adaptive genetic variation, when environmental heterogeneity creates divergence at specific loci underlying local adaptation. Specifically, we discuss five characteristics found in plants that intensify the impact of selection: sessile growth form, high reproductive output, leptokurtic dispersal, isolation by environment, and the potential to evolve longevity. Collectively, these traits exacerbate the impact of environment on movement between populations and local selection pressures—both of which influence phylogeographic structure. We illustrate how these unique traits shape these processes with case studies of the California endemic oak, Quercus lobata, and the western North American lichen, Ramalina menziesii. Obviously, the lessons we learn from plant traits are not unique to plants, but they highlight the need for future animal, plant, and microbe studies to incorporate its impact. Modern tools that generate genome-wide sequence data are now allowing us to decipher how evolutionary processes affect the spatial distribution of different kinds of genes and also to better model future spatial distribution of species in response to climate change. PMID:27432984

  1. Evolutionary Dynamics of Homophily and Heterophily

    PubMed Central

    Ramazi, Pouria; Cao, Ming; Weissing, Franz J.

    2016-01-01

    Most social interactions do not take place at random. In many situations, individuals choose their interaction partners on the basis of phenotypic cues. When this happens, individuals are often homophilic, that is, they tend to interact with individuals that are similar to them. Here we investigate the joint evolution of phenotypic cues and cue-dependent interaction strategies. By a combination of individual-based simulations and analytical arguments, we show that homophily evolves less easily than earlier studies suggest. The evolutionary interplay of cues and cue-based behaviour is intricate and has many interesting facets. For example, an interaction strategy like heterophily may stably persist in the population even if it is selected against in association with any particular cue. Homophily persisted for extensive periods of time just in those simulations where homophilic interactions provide a lower (rather than a higher) payoff than heterophilic interactions. Our results indicate that even the simplest cue-based social interactions can have rich dynamics and a surprising diversity of evolutionary outcomes. PMID:26951038

  2. Evolutionary origin of rhizobium Nod factor signaling.

    PubMed

    Streng, Arend; op den Camp, Rik; Bisseling, Ton; Geurts, René

    2011-10-01

    For over two decades now, it is known that the nodule symbiosis between legume plants and nitrogen fixing rhizobium bacteria is set in motion by the bacterial signal molecule named nodulation (Nod) factor. Upon Nod factor perception a signaling cascade is activated that is also essential for endomycorrhizal symbiosis (Fig. 1). This suggests that rhizobium co-opted the evolutionary far more ancient mycorrhizal signaling pathway in order to establish an endosymbiotic interaction with legumes. As arbuscular mycorrhizal fungi of the Glomeromycota phylum can establish a symbiosis with the fast majority of land plants, it is most probable that this signaling cascade is wide spread in plant kingdom. However, Nod factor perception generally is considered to be unique to legumes. Two recent breakthroughs on the evolutionary origin of Rhizobium Nod factor signaling demonstrate that this is not the case. The purification of Nod factor-like molecules excreted by the mycorrhizal fungus Glomus intraradices and the role of the LysM-type Nod factor receptor PaNFP in the non-legume Parasponia andersonii provide novel understanding on the evolution of rhizobial Nod factor signaling.

  3. Clonality and Evolutionary History of Rhabdomyosarcoma

    PubMed Central

    Wei, Jun S.; Yohe, Marielle E.; Song, Young K.; Hurd, Laura; Liao, Hongling; Catchpoole, Daniel; Skapek, Stephen X.; Barr, Frederic G.; Hawkins, Douglas S.; Khan, Javed

    2015-01-01

    To infer the subclonality of rhabdomyosarcoma (RMS) and predict the temporal order of genetic events for the tumorigenic process, and to identify novel drivers, we applied a systematic method that takes into account germline and somatic alterations in 44 tumor-normal RMS pairs using deep whole-genome sequencing. Intriguingly, we find that loss of heterozygosity of 11p15.5 and mutations in RAS pathway genes occur early in the evolutionary history of the PAX-fusion-negative-RMS (PFN-RMS) subtype. We discover several early mutations in non-RAS mutated samples and predict them to be drivers in PFN-RMS including recurrent mutation of PKN1. In contrast, we find that PAX-fusion-positive (PFP) subtype tumors have undergone whole-genome duplication in the late stage of cancer evolutionary history and have acquired fewer mutations and subclones than PFN-RMS. Moreover we predict that the PAX3-FOXO1 fusion event occurs earlier than the whole genome duplication. Our findings provide information critical to the understanding of tumorigenesis of RMS. PMID:25768946

  4. Evolutionary inference via the Poisson Indel Process.

    PubMed

    Bouchard-Côté, Alexandre; Jordan, Michael I

    2013-01-22

    We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classic evolutionary process, the TKF91 model [Thorne JL, Kishino H, Felsenstein J (1991) J Mol Evol 33(2):114-124] is a continuous-time Markov chain model composed of insertion, deletion, and substitution events. Unfortunately, this model gives rise to an intractable computational problem: The computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The Poisson Indel Process is closely related to the TKF91 model, differing only in its treatment of insertions, but it has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared with separate inference of phylogenies and alignments.

  5. Evolutionary Games of Multiplayer Cooperation on Graphs.

    PubMed

    Peña, Jorge; Wu, Bin; Arranz, Jordi; Traulsen, Arne

    2016-08-01

    There has been much interest in studying evolutionary games in structured populations, often modeled as graphs. However, most analytical results so far have only been obtained for two-player or linear games, while the study of more complex multiplayer games has been usually tackled by computer simulations. Here we investigate evolutionary multiplayer games on graphs updated with a Moran death-Birth process. For cycles, we obtain an exact analytical condition for cooperation to be favored by natural selection, given in terms of the payoffs of the game and a set of structure coefficients. For regular graphs of degree three and larger, we estimate this condition using a combination of pair approximation and diffusion approximation. For a large class of cooperation games, our approximations suggest that graph-structured populations are stronger promoters of cooperation than populations lacking spatial structure. Computer simulations validate our analytical approximations for random regular graphs and cycles, but show systematic differences for graphs with many loops such as lattices. In particular, our simulation results show that these kinds of graphs can even lead to more stringent conditions for the evolution of cooperation than well-mixed populations. Overall, we provide evidence suggesting that the complexity arising from many-player interactions and spatial structure can be captured by pair approximation in the case of random graphs, but that it need to be handled with care for graphs with high clustering. PMID:27513946

  6. Subwavelength Lattice Optics by Evolutionary Design

    PubMed Central

    2015-01-01

    This paper describes a new class of structured optical materials—lattice opto-materials—that can manipulate the flow of visible light into a wide range of three-dimensional profiles using evolutionary design principles. Lattice opto-materials are based on the discretization of a surface into a two-dimensional (2D) subwavelength lattice whose individual lattice sites can be controlled to achieve a programmed optical response. To access a desired optical property, we designed a lattice evolutionary algorithm that includes and optimizes contributions from every element in the lattice. Lattice opto-materials can exhibit simple properties, such as on- and off-axis focusing, and can also concentrate light into multiple, discrete spots. We expanded the unit cell shapes of the lattice to achieve distinct, polarization-dependent optical responses from the same 2D patterned substrate. Finally, these lattice opto-materials can also be combined into architectures that resemble a new type of compound flat lens. PMID:25380062

  7. On the complexity of triggering evolutionary radiations.

    PubMed

    Bouchenak-Khelladi, Yanis; Onstein, Renske E; Xing, Yaowu; Schwery, Orlando; Linder, H Peter

    2015-07-01

    Recent developments in phylogenetic methods have made it possible to reconstruct evolutionary radiations from extant taxa, but identifying the triggers of radiations is still problematic. Here, we propose a conceptual framework to explore the role of variables that may impact radiations. We classify the variables into extrinsic conditions vs intrinsic traits, whether they provide background conditions, trigger the radiation, or modulate the radiation. We used three clades representing angiosperm phylogenetic and structural diversity (Ericaceae, Fagales and Poales) as test groups. We located radiation events, selected variables potentially associated with diversification, and inferred the temporal sequences of evolution. We found 13 shifts in diversification regimes in the three clades. We classified the associated variables, and determined whether they originated before the relevant radiation (backgrounds), originated simultaneously with the radiations (triggers), or evolved later (modulators). By applying this conceptual framework, we establish that radiations require both extrinsic conditions and intrinsic traits, but that the sequence of these is not important. We also show that diversification drivers can be detected by being more variable within a radiation than conserved traits that only allow occupation of a new habitat. This framework facilitates exploration of the causative factors of evolutionary radiations.

  8. Metamorphic proteins mediate evolutionary transitions of structure.

    PubMed

    Yadid, Itamar; Kirshenbaum, Noam; Sharon, Michal; Dym, Orly; Tawfik, Dan S

    2010-04-20

    The primary sequence of proteins usually dictates a single tertiary and quaternary structure. However, certain proteins undergo reversible backbone rearrangements. Such metamorphic proteins provide a means of facilitating the evolution of new folds and architectures. However, because natural folds emerged at the early stages of evolution, the potential role of metamorphic intermediates in mediating evolutionary transitions of structure remains largely unexplored. We evolved a set of new proteins based on approximately 100 amino acid fragments derived from tachylectin-2--a monomeric, 236 amino acids, five-bladed beta-propeller. Their structures reveal a unique pentameric assembly and novel beta-propeller structures. Although identical in sequence, the oligomeric subunits adopt two, or even three, different structures that together enable the pentameric assembly of two propellers connected via a small linker. Most of the subunits adopt a wild-type-like structure within individual five-bladed propellers. However, the bridging subunits exhibit domain swaps and asymmetric strand exchanges that allow them to complete the two propellers and connect them. Thus, the modular and metamorphic nature of these subunits enabled dramatic changes in tertiary and quaternary structure, while maintaining the lectin function. These oligomers therefore comprise putative intermediates via which beta-propellers can evolve from smaller elements. Our data also suggest that the ability of one sequence to equilibrate between different structures can be evolutionary optimized, thus facilitating the emergence of new structures.

  9. Stochastic evolutionary dynamics of direct reciprocity.

    PubMed

    Imhof, Lorens A; Nowak, Martin A

    2010-02-01

    Evolutionary game theory is the study of frequency-dependent selection. The success of an individual depends on the frequencies of strategies that are used in the population. We propose a new model for studying evolutionary dynamics in games with a continuous strategy space. The population size is finite. All members of the population use the same strategy. A mutant strategy is chosen from some distribution over the strategy space. The fixation probability of the mutant strategy in the resident population is calculated. The new mutant takes over the population with this probability. In this case, the mutant becomes the new resident. Otherwise, the existing resident remains. Then, another mutant is generated. These dynamics lead to a stationary distribution over the entire strategy space. Our new approach generalizes classical adaptive dynamics in three ways: (i) the population size is finite; (ii) mutants can be drawn non-locally and (iii) the dynamics are stochastic. We explore reactive strategies in the repeated Prisoner's Dilemma. We perform 'knock-out experiments' to study how various strategies affect the evolution of cooperation. We find that 'tit-for-tat' is a weak catalyst for the emergence of cooperation, while 'always cooperate' is a strong catalyst for the emergence of defection. Our analysis leads to a new understanding of the optimal level of forgiveness that is needed for the evolution of cooperation under direct reciprocity.

  10. A case study in evolutionary contingency.

    PubMed

    Blount, Zachary D

    2016-08-01

    Biological evolution is a fundamentally historical phenomenon in which intertwined stochastic and deterministic processes shape lineages with long, continuous histories that exist in a changing world that has a history of its own. The degree to which these characteristics render evolution historically contingent, and evolutionary outcomes thereby unpredictably sensitive to history has been the subject of considerable debate in recent decades. Microbial evolution experiments have proven among the most fruitful means of empirically investigating the issue of historical contingency in evolution. One such experiment is the Escherichia coli Long-Term Evolution Experiment (LTEE), in which twelve populations founded from the same clone of E. coli have evolved in parallel under identical conditions. Aerobic growth on citrate (Cit(+)), a novel trait for E. coli, evolved in one of these populations after more than 30,000 generations. Experimental replays of this population's evolution from various points in its history showed that the Cit(+) trait was historically contingent upon earlier mutations that potentiated the trait by rendering it mutationally accessible. Here I review this case of evolutionary contingency and discuss what it implies about the importance of historical contingency arising from the core processes of evolution. PMID:26787098

  11. Evolutionary Optimization of a Geometrically Refined Truss

    NASA Technical Reports Server (NTRS)

    Hull, P. V.; Tinker, M. L.; Dozier, G. V.

    2007-01-01

    Structural optimization is a field of research that has experienced noteworthy growth for many years. Researchers in this area have developed optimization tools to successfully design and model structures, typically minimizing mass while maintaining certain deflection and stress constraints. Numerous optimization studies have been performed to minimize mass, deflection, and stress on a benchmark cantilever truss problem. Predominantly traditional optimization theory is applied to this problem. The cross-sectional area of each member is optimized to minimize the aforementioned objectives. This Technical Publication (TP) presents a structural optimization technique that has been previously applied to compliant mechanism design. This technique demonstrates a method that combines topology optimization, geometric refinement, finite element analysis, and two forms of evolutionary computation: genetic algorithms and differential evolution to successfully optimize a benchmark structural optimization problem. A nontraditional solution to the benchmark problem is presented in this TP, specifically a geometrically refined topological solution. The design process begins with an alternate control mesh formulation, multilevel geometric smoothing operation, and an elastostatic structural analysis. The design process is wrapped in an evolutionary computing optimization toolset.

  12. Haplotype Fine Mapping by Evolutionary Trees

    PubMed Central

    Lam, Johnny C.; Roeder, Kathryn; Devlin, B.

    2000-01-01

    Summary To refine the location of a disease gene within the bounds provided by linkage analysis, many scientists use the pattern of linkage disequilibrium between the disease allele and alleles at nearby markers. We describe a method that seeks to refine location by analysis of “disease” and “normal” haplotypes, thereby using multivariate information about linkage disequilibrium. Under the assumption that the disease mutation occurs in a specific gap between adjacent markers, the method first combines parsimony and likelihood to build an evolutionary tree of disease haplotypes, with each node (haplotype) separated, by a single mutational or recombinational step, from its parent. If required, latent nodes (unobserved haplotypes) are incorporated to complete the tree. Once the tree is built, its likelihood is computed from probabilities of mutation and recombination. When each gap between adjacent markers is evaluated in this fashion and these results are combined with prior information, they yield a posterior probability distribution to guide the search for the disease mutation. We show, by evolutionary simulations, that an implementation of these methods, called “FineMap,” yields substantial refinement and excellent coverage for the true location of the disease mutation. Moreover, by analysis of hereditary hemochromatosis haplotypes, we show that FineMap can be robust to genetic heterogeneity. PMID:10677324

  13. Evolutionary Conditions for the Emergence of Communication

    NASA Astrophysics Data System (ADS)

    Mitri, Sara; Floreano, Dario; Keller, Laurent

    Communication plays a central role in the biology of most organisms, particularly social species. Although the neurophysiological processes of signal production and perception are well understood, the conditions conducive to the evolution of reliable systems of communication remain largely unknown. This is a particularly challenging problem because efficient communication requires tight coevolution between the signal emitted and the response elicited. We conducted experimental evolution with robots that could produce visual signals to provide information on food location. We found that communication readily evolves when colonies consist of genetically similar individuals and when selection acts at the colony level. We identified several distinct communication systems that differed in their efficiency. Once a given system of communication was well established, it constrained the evolution of more efficient communication systems. Under individual selection, the ability to produce visual signals resulted in the evolution of deceptive communication strategies in colonies of unrelated robots and a concomitant decrease in colony performance. This study generates predictions about the evolutionary conditions conducive to the emergence of communication and provides guidelines for designing artificial evolutionary systems displaying spontaneous communication.

  14. Emergence of structured communities through evolutionary dynamics.

    PubMed

    Shtilerman, Elad; Kessler, David A; Shnerb, Nadav M

    2015-10-21

    Species-rich communities, in which many competing species coexist in a single trophic level, are quite frequent in nature, but pose a formidable theoretical challenge. In particular, it is known that complex competitive systems become unstable and unfeasible when the number of species is large. Recently, many studies have attributed the stability of natural communities to the structure of the interspecific interaction network, yet the nature of such structures and the underlying mechanisms responsible for them remain open questions. Here we introduce an evolutionary model, based on the generic Lotka-Volterra competitive framework, from which a stable, structured, diverse community emerges spontaneously. The modular structure of the competition matrix reflects the phylogeny of the community, in agreement with the hierarchial taxonomic classification. Closely related species tend to have stronger niche overlap and weaker fitness differences, as opposed to pairs of species from different modules. The competitive-relatedness hypothesis and the idea of emergent neutrality are discussed in the context of this evolutionary model.

  15. Religion's evolutionary landscape: counterintuition, commitment, compassion, communion.

    PubMed

    Atran, Scott; Norenzayan, Ara

    2004-12-01

    Religion is not an evolutionary adaptation per se, but a recurring cultural by-product of the complex evolutionary landscape that sets cognitive, emotional, and material conditions for ordinary human interactions. Religion exploits only ordinary cognitive processes to passionately display costly devotion to counterintuitive worlds governed by supernatural agents. The conceptual foundations of religion are intuitively given by task-specific panhuman cognitive domains, including folkmechanics, folkbiology, and folkpsychology. Core religious beliefs minimally violate ordinary notions about how the world is, with all of its inescapable problems, thus enabling people to imagine minimally impossible supernatural worlds that solve existential problems, including death and deception. Here the focus is on folkpsychology and agency. A key feature of the supernatural agent concepts common to all religions is the triggering of an "Innate Releasing Mechanism," or "agency detector," whose proper (naturally selected) domain encompasses animate objects relevant to hominid survival--such as predators, protectors, and prey--but which actually extends to moving dots on computer screens, voices in wind, and faces on clouds. Folkpsychology also crucially involves metarepresentation, which makes deception possible and threatens any social order. However, these same metacognitive capacities provide the hope and promise of open-ended solutions through representations of counterfactual supernatural worlds that cannot be logically or empirically verified or falsified. Because religious beliefs cannot be deductively or inductively validated, validation occurs only by ritually addressing the very emotions motivating religion. Cross-cultural experimental evidence encourages these claims.

  16. Optimizing a reconfigurable material via evolutionary computation

    NASA Astrophysics Data System (ADS)

    Wilken, Sam; Miskin, Marc Z.; Jaeger, Heinrich M.

    2015-08-01

    Rapid prototyping by combining evolutionary computation with simulations is becoming a powerful tool for solving complex design problems in materials science. This method of optimization operates in a virtual design space that simulates potential material behaviors and after completion needs to be validated by experiment. However, in principle an evolutionary optimizer can also operate on an actual physical structure or laboratory experiment directly, provided the relevant material parameters can be accessed by the optimizer and information about the material's performance can be updated by direct measurements. Here we provide a proof of concept of such direct, physical optimization by showing how a reconfigurable, highly nonlinear material can be tuned to respond to impact. We report on an entirely computer controlled laboratory experiment in which a 6 ×6 grid of electromagnets creates a magnetic field pattern that tunes the local rigidity of a concentrated suspension of ferrofluid and iron filings. A genetic algorithm is implemented and tasked to find field patterns that minimize the force transmitted through the suspension. Searching within a space of roughly 1010 possible configurations, after testing only 1500 independent trials the algorithm identifies an optimized configuration of layered rigid and compliant regions.

  17. An evolutionary sequence of young radio galaxies

    NASA Astrophysics Data System (ADS)

    Collier, J. D.; Norris, R. P.; Filipović, M. D.; Tothill, N. F. H.

    2016-02-01

    We have observed the faintest sample of Gigahertz Peaked Spectrum (GPS) and Compact Steep Spectrum (CSS) sources to date, using the Australia Telescope Compact Array. We test the hypothesis that GPS and CSS sources are the youngest radio galaxies, place them into an evolutionary sequence along with a number of other young active galactic nuclei (AGN) candidates, and search for evidence of the evolving accretion mode and its relationship to star formation. GPS/CSS sources have very small radio jets that have been recently launched from the central supermassive black hole and grow in linear size as they evolve, which means that the linear size of the jets is an excellent indicator of the evolutionary stage of the AGN. We use high-resolution radio observations to determine the linear size of GPS/CSS sources, resolve their jets and observe their small-scale morphologies. We combine this with other multi-wavelength age indicators, including the spectral age, colours, optical spectra, and spectral energy distribution of the host galaxy, in an attempt to assemble all age indicators into a self-consistent model. We observe the most compact sources with Very Large Baseline Interferometry, which reveals their parsec-scale structures, giving us a range of source sizes and allowing us to test what fraction of GPS/CSS sources are young and evolving.

  18. Human growth: evolutionary and life history perspectives.

    PubMed

    Gluckman, Peter D; Beedle, Alan S; Hanson, Mark A; Low, Felicia M

    2013-01-01

    Evolutionary and life history perspectives allow a fuller understanding of both patterns of growth and development and variations in disease risk. Evolutionary processes act to ensure successful reproduction and not the preservation of health and longevity, and this entails trade-offs both between traits and across the life course. Developmental plasticity adjusts the developmental trajectory so that the phenotype in childhood and through peak reproduction will suit predicted environmental conditions - a capacity that may become maladaptive should early-life predictions be inaccurate. Bipedalism and consequent pelvic narrowing in humans have led to the evolution of secondary altricialism. Shorter inter-birth intervals enabled by appropriate social support structures have allowed increased fecundity/fitness. The age at puberty has fallen over the past two centuries, perhaps resulting from changes in maternal and infant health and nutrition. The timing of puberty is also advanced by conditions of high extrinsic mortality in hunter-gatherers and is reflected in developed countries where a poor or disadvantaged start to life may also accelerate maturation. The postpubertal individual is physically and psychosexually mature, but neural executive function only reaches full maturity in the third decade of life; this mismatch may account for increased adolescent morbidity and mortality in those with earlier pubertal onset.

  19. Evolutionary ecology of the wild cereals

    SciTech Connect

    Blumler, M.A.

    1995-12-31

    The evolutionary ecology of the Near Eastern wild cereal grasses sheds light on the environmental conditions under which the Neolithic Revolution took place. Globally, as well as in the Near East, the annual habit, large seed size, and seasonal drought are associated with each other and with agricultural origins. The connection with agricultural appears to involve ease of cultivation and necessity for seasonal storage rather than hunter-gatherer preference for large seeds. The Near Eastern wild cereal species separate ecologically according to seasonality of precipitation, primarily, though there may also be minor differences in temperature and edaphic tolerances. This reflects the evolution, over the course of the Quaternary, of species with increased seed size in response to increasingly pronounced seasonal drought. Wild emmer and wild barley, the progenitors of perhaps the very first domesticates, are evolutionary monstrosities that represent the culmination of this trend. The possibly complex changes in seasonality, aridity, and atmospheric CO2 during the millenia leading up to the Neolithic should have produced equally complex, but to some extent predictable, changes in the abundance and distribution of the different wild cereal species.

  20. Optimizing a reconfigurable material via evolutionary computation.

    PubMed

    Wilken, Sam; Miskin, Marc Z; Jaeger, Heinrich M

    2015-08-01

    Rapid prototyping by combining evolutionary computation with simulations is becoming a powerful tool for solving complex design problems in materials science. This method of optimization operates in a virtual design space that simulates potential material behaviors and after completion needs to be validated by experiment. However, in principle an evolutionary optimizer can also operate on an actual physical structure or laboratory experiment directly, provided the relevant material parameters can be accessed by the optimizer and information about the material's performance can be updated by direct measurements. Here we provide a proof of concept of such direct, physical optimization by showing how a reconfigurable, highly nonlinear material can be tuned to respond to impact. We report on an entirely computer controlled laboratory experiment in which a 6×6 grid of electromagnets creates a magnetic field pattern that tunes the local rigidity of a concentrated suspension of ferrofluid and iron filings. A genetic algorithm is implemented and tasked to find field patterns that minimize the force transmitted through the suspension. Searching within a space of roughly 10^{10} possible configurations, after testing only 1500 independent trials the algorithm identifies an optimized configuration of layered rigid and compliant regions. PMID:26382399

  1. Evolutionary Games of Multiplayer Cooperation on Graphs.

    PubMed

    Peña, Jorge; Wu, Bin; Arranz, Jordi; Traulsen, Arne

    2016-08-01

    There has been much interest in studying evolutionary games in structured populations, often modeled as graphs. However, most analytical results so far have only been obtained for two-player or linear games, while the study of more complex multiplayer games has been usually tackled by computer simulations. Here we investigate evolutionary multiplayer games on graphs updated with a Moran death-Birth process. For cycles, we obtain an exact analytical condition for cooperation to be favored by natural selection, given in terms of the payoffs of the game and a set of structure coefficients. For regular graphs of degree three and larger, we estimate this condition using a combination of pair approximation and diffusion approximation. For a large class of cooperation games, our approximations suggest that graph-structured populations are stronger promoters of cooperation than populations lacking spatial structure. Computer simulations validate our analytical approximations for random regular graphs and cycles, but show systematic differences for graphs with many loops such as lattices. In particular, our simulation results show that these kinds of graphs can even lead to more stringent conditions for the evolution of cooperation than well-mixed populations. Overall, we provide evidence suggesting that the complexity arising from many-player interactions and spatial structure can be captured by pair approximation in the case of random graphs, but that it need to be handled with care for graphs with high clustering.

  2. Collective influence in evolutionary social dilemmas

    NASA Astrophysics Data System (ADS)

    Szolnoki, Attila; Perc, Matjaž

    2016-03-01

    When evolutionary games are contested in structured populations, the degree of each player in the network plays an important role. If they exist, hubs often determine the fate of the population in remarkable ways. Recent research based on optimal percolation in random networks has shown, however, that the degree is neither the sole nor the best predictor of influence in complex networks. Low-degree nodes may also be optimal influencers if they are hierarchically linked to hubs. Taking this into account leads to the formalism of collective influence in complex networks, which as we show here, has far-reaching implications for the favorable resolution of social dilemmas. In particular, there exists an optimal hierarchical depth for the determination of collective influence that we use to describe the potency of players for passing their strategies, which depends on the strength of the social dilemma. Interestingly, the degree, which corresponds to the baseline depth zero, is optimal only when the temptation to defect is small. Our research reveals that evolutionary success stories are related to spreading processes which are rooted in favorable hierarchical structures that extend beyond local neighborhoods.

  3. Cyclic dominance in evolutionary games: a review

    PubMed Central

    Szolnoki, Attila; Mobilia, Mauro; Jiang, Luo-Luo; Szczesny, Bartosz; Rucklidge, Alastair M.; Perc, Matjaž

    2014-01-01

    Rock is wrapped by paper, paper is cut by scissors and scissors are crushed by rock. This simple game is popular among children and adults to decide on trivial disputes that have no obvious winner, but cyclic dominance is also at the heart of predator–prey interactions, the mating strategy of side-blotched lizards, the overgrowth of marine sessile organisms and competition in microbial populations. Cyclical interactions also emerge spontaneously in evolutionary games entailing volunteering, reward, punishment, and in fact are common when the competing strategies are three or more, regardless of the particularities of the game. Here, we review recent advances on the rock–paper–scissors (RPS) and related evolutionary games, focusing, in particular, on pattern formation, the impact of mobility and the spontaneous emergence of cyclic dominance. We also review mean-field and zero-dimensional RPS models and the application of the complex Ginzburg–Landau equation, and we highlight the importance and usefulness of statistical physics for the successful study of large-scale ecological systems. Directions for future research, related, for example, to dynamical effects of coevolutionary rules and invasion reversals owing to multi-point interactions, are also outlined. PMID:25232048

  4. Evolutionary strategies for solving optimization problems

    NASA Astrophysics Data System (ADS)

    Ebeling, Werner; Reimann, Axel; Molgedey, Lutz

    We will give a survey of applications of thermodynamically and biologically oriented evolutionary strategies for optimization problems. Primarily, we investigate the solution of discrete optimization problems, most of combinatorial type, using a certain class of coupled differential equations. The problem is to find the minimum on a large set of real numbers (the potential) Ui, defined on the integer set i = 1 ...s, where s is an extremely large nu mber. The stationary states of the system correspond to relative optima on the discrete set. First, several elementary evolutionary strategies are described by simple deterministic equations, leading to a high-dimensional system of coupled differential equations. The known equations for thermodynamic search processes and for simple models of biological evolution are unified by defining a two-parameter family of equations which embed both cases. The unified equations model mixed Boltzmann/Darwin- strategies including basic elements of thermodynamical and biological evolution as well. In a next step a master equation model in the occupation number space is defined. We investigate the transition probabilities and the convergence properties using tools from the theory of stochastic processes. Several examples are analyzed. In particular we study the optimization of theoretical model sequences with simple valuation rules. In order to demonstrate that the strategies developed here may also be used to investigate realistic problems we present an example application to RNA folding (search for a minimum free energy configuration).

  5. Evolutionary scenarios for double degenerate systems

    NASA Astrophysics Data System (ADS)

    Sarna, M. J.; Marks, P. B.; Connon Smith, Robert

    1996-03-01

    We propose evolutionary scenarios in which double degenerate white dwarf systems can be produced through one or two phases of stable mass transfer. We consider Algol-type evolution as well as evolution involving first a stage of common-envelope (CE) evolution followed by a phase of stable mass transfer. We also show that the final orbital period of double white dwarf systems depends on the period after the first phase of mass transfer, and that there is critical period (the bifurcation period) above which systems evolve to orbital periods of the order of days and below which systems evolve towards very short orbital periods (a few hours). This probably corresponds to the observation that double degenerate systems have periods either of hours or of days. We also find a limit on the stability of mass transfer for systems that first go through a phase of CE evolution. We suggest that our new evolutionary scheme involving two stages of stable mass transfer and our scheme involving first CE evolution followed by stable mass transfer should be included in population synthesis models.

  6. Evolutionary perspectives on human height variation.

    PubMed

    Stulp, Gert; Barrett, Louise

    2016-02-01

    Human height is a highly variable trait, both within and between populations, has a high heritability, and influences the manner in which people behave and are treated in society. Although we know much about human height, this information has rarely been brought together in a comprehensive, systematic fashion. Here, we present a synthetic review of the literature on human height from an explicit evolutionary perspective, addressing its phylogenetic history, development, and environmental and genetic influences on growth and stature. In addition to presenting evidence to suggest the past action of natural selection on human height, we also assess the evidence that natural and sexual selection continues to act on height in contemporary populations. Although there is clear evidence to suggest that selection acts on height, mainly through life-history processes but perhaps also directly, it is also apparent that methodological factors reduce the confidence with which such inferences can be drawn, and there remain surprising gaps in our knowledge. The inability to draw firm conclusions about the adaptiveness of such a highly visible and easily measured trait suggests we should show an appropriate degree of caution when dealing with other human traits in evolutionary perspective. PMID:25530478

  7. The evolutionary psychology of women's aggression

    PubMed Central

    Campbell, Anne

    2013-01-01

    Evolutionary researchers have identified age, operational sex ratio and high variance in male resources as factors that intensify female competition. These are discussed in relation to escalated intrasexual competition for men and their resources between young women in deprived neighbourhoods. For these women, fighting is not seen as antithetical to cultural conceptions of femininity, and female weakness is disparaged. Nonetheless, even where competitive pressures are high, young women's aggression is less injurious and frequent than young men's. From an evolutionary perspective, I argue that the intensity of female aggression is constrained by the greater centrality of mothers, rather than fathers, to offspring survival. This selection pressure is realized psychologically through a lower threshold for fear among women. Neuropsychological evidence is not yet conclusive but suggests that women show heightened amygdala reactivity to threatening stimuli, may be better able to exert prefrontal cortical control over emotional behaviour and may consciously register fear more strongly via anterior cingulate activity. The impact of testosterone and oxytocin on the neural circuitry of emotion is also considered. PMID:24167308

  8. The Evolutionary Potential of Phenotypic Mutations

    PubMed Central

    Yanagida, Hayato; Gispan, Ariel; Kadouri, Noam; Rozen, Shelly; Sharon, Michal; Barkai, Naama; Tawfik, Dan S.

    2015-01-01

    Errors in protein synthesis, so-called phenotypic mutations, are orders-of-magnitude more frequent than genetic mutations. Here, we provide direct evidence that alternative protein forms and phenotypic variability derived from translational errors paved the path to genetic, evolutionary adaptations via gene duplication. We explored the evolutionary origins of Saccharomyces cerevisiae IDP3 - an NADP-dependent isocitrate dehydrogenase mediating fatty acids ß-oxidation in the peroxisome. Following the yeast whole genome duplication, IDP3 diverged from a cytosolic ancestral gene by acquisition of a C-terminal peroxisomal targeting signal. We discovered that the pre-duplicated cytosolic IDPs are partially localized to the peroxisome owing to +1 translational frameshifts that bypass the stop codon and unveil cryptic peroxisomal targeting signals within the 3’-UTR. Exploring putative cryptic signals in all 3’-UTRs of yeast genomes, we found that other enzymes related to NADPH production such as pyruvate carboxylase 1 (PYC1) might be prone to peroxisomal localization via cryptic signals. Using laboratory evolution we found that these translational frameshifts are rapidly imprinted via genetic single base deletions occurring within the very same gene location. Further, as exemplified here, the sequences that promote translational frameshifts are also more prone to genetic deletions. Thus, genotypes conferring higher phenotypic variability not only meet immediate challenges by unveiling cryptic 3’-UTR sequences, but also boost the potential for future genetic adaptations. PMID:26244544

  9. The Evolutionary Potential of Phenotypic Mutations.

    PubMed

    Yanagida, Hayato; Gispan, Ariel; Kadouri, Noam; Rozen, Shelly; Sharon, Michal; Barkai, Naama; Tawfik, Dan S

    2015-08-01

    Errors in protein synthesis, so-called phenotypic mutations, are orders-of-magnitude more frequent than genetic mutations. Here, we provide direct evidence that alternative protein forms and phenotypic variability derived from translational errors paved the path to genetic, evolutionary adaptations via gene duplication. We explored the evolutionary origins of Saccharomyces cerevisiae IDP3 - an NADP-dependent isocitrate dehydrogenase mediating fatty acids ß-oxidation in the peroxisome. Following the yeast whole genome duplication, IDP3 diverged from a cytosolic ancestral gene by acquisition of a C-terminal peroxisomal targeting signal. We discovered that the pre-duplicated cytosolic IDPs are partially localized to the peroxisome owing to +1 translational frameshifts that bypass the stop codon and unveil cryptic peroxisomal targeting signals within the 3'-UTR. Exploring putative cryptic signals in all 3'-UTRs of yeast genomes, we found that other enzymes related to NADPH production such as pyruvate carboxylase 1 (PYC1) might be prone to peroxisomal localization via cryptic signals. Using laboratory evolution we found that these translational frameshifts are rapidly imprinted via genetic single base deletions occurring within the very same gene location. Further, as exemplified here, the sequences that promote translational frameshifts are also more prone to genetic deletions. Thus, genotypes conferring higher phenotypic variability not only meet immediate challenges by unveiling cryptic 3'-UTR sequences, but also boost the potential for future genetic adaptations.

  10. A case study in evolutionary contingency.

    PubMed

    Blount, Zachary D

    2016-08-01

    Biological evolution is a fundamentally historical phenomenon in which intertwined stochastic and deterministic processes shape lineages with long, continuous histories that exist in a changing world that has a history of its own. The degree to which these characteristics render evolution historically contingent, and evolutionary outcomes thereby unpredictably sensitive to history has been the subject of considerable debate in recent decades. Microbial evolution experiments have proven among the most fruitful means of empirically investigating the issue of historical contingency in evolution. One such experiment is the Escherichia coli Long-Term Evolution Experiment (LTEE), in which twelve populations founded from the same clone of E. coli have evolved in parallel under identical conditions. Aerobic growth on citrate (Cit(+)), a novel trait for E. coli, evolved in one of these populations after more than 30,000 generations. Experimental replays of this population's evolution from various points in its history showed that the Cit(+) trait was historically contingent upon earlier mutations that potentiated the trait by rendering it mutationally accessible. Here I review this case of evolutionary contingency and discuss what it implies about the importance of historical contingency arising from the core processes of evolution.

  11. Mitochondria and the evolutionary roots of cancer

    NASA Astrophysics Data System (ADS)

    Davila, Alfonso F.; Zamorano, Pedro

    2013-04-01

    Cancer disease is inherent to, and widespread among, metazoans. Yet, some of the hallmarks of cancer such as uncontrolled cell proliferation, lack of apoptosis, hypoxia, fermentative metabolism and free cell motility (metastasis) are akin to a prokaryotic lifestyle, suggesting a link between cancer disease and evolution. In this hypothesis paper, we propose that cancer cells represent a phenotypic reversion to the earliest stage of eukaryotic evolution. This reversion is triggered by the dysregulation of the mitochondria due to cumulative oxidative damage to mitochondrial and nuclear DNA. As a result, the phenotype of normal, differentiated cells gradually reverts to the phenotype of a facultative anaerobic, heterotrophic cell optimized for survival and proliferation in hypoxic environments. This phenotype matches the phenotype of the last eukaryotic common ancestor (LECA) that resulted from the endosymbiosis between an α-proteobacteria (which later became the mitochondria) and an archaebacteria. As such, the evolution of cancer within one individual can be viewed as a recapitulation of the evolution of the eukaryotic cell from fully differentiated cells to LECA. This evolutionary model of cancer is compatible with the current understanding of the disease, and explains the evolutionary basis for most of the hallmarks of cancer, as well as the link between the disease and aging. It could also open new avenues for treatment directed at reestablishing the synergy between the mitochondria and the cancerous cell.

  12. Evolutionary Stability in the Asymmetric Volunteer's Dilemma

    PubMed Central

    Li, Yao-Tang

    2014-01-01

    It is often assumed that in public goods games, contributors are either strong or weak players and each individual has an equal probability of exhibiting cooperation. It is difficult to explain why the public good is produced by strong individuals in some cooperation systems, and by weak individuals in others. Viewing the asymmetric volunteer's dilemma game as an evolutionary game, we find that whether the strong or the weak players produce the public good depends on the initial condition (i.e., phenotype or initial strategy of individuals). These different evolutionarily stable strategies (ESS) associated with different initial conditions, can be interpreted as the production modes of public goods of different cooperation systems. A further analysis revealed that the strong player adopts a pure strategy but mixed strategies for the weak players to produce the public good, and that the probability of volunteering by weak players decreases with increasing group size or decreasing cost-benefit ratio. Our model shows that the defection probability of a “strong” player is greater than the “weak” players in the model of Diekmann (1993). This contradicts Selten's (1980) model that public goods can only be produced by a strong player, is not an evolutionarily stable strategy, and will therefore disappear over evolutionary time. Our public good model with ESS has thus extended previous interpretations that the public good can only be produced by strong players in an asymmetric game. PMID:25111781

  13. Evolutionary Games of Multiplayer Cooperation on Graphs

    PubMed Central

    Arranz, Jordi; Traulsen, Arne

    2016-01-01

    There has been much interest in studying evolutionary games in structured populations, often modeled as graphs. However, most analytical results so far have only been obtained for two-player or linear games, while the study of more complex multiplayer games has been usually tackled by computer simulations. Here we investigate evolutionary multiplayer games on graphs updated with a Moran death-Birth process. For cycles, we obtain an exact analytical condition for cooperation to be favored by natural selection, given in terms of the payoffs of the game and a set of structure coefficients. For regular graphs of degree three and larger, we estimate this condition using a combination of pair approximation and diffusion approximation. For a large class of cooperation games, our approximations suggest that graph-structured populations are stronger promoters of cooperation than populations lacking spatial structure. Computer simulations validate our analytical approximations for random regular graphs and cycles, but show systematic differences for graphs with many loops such as lattices. In particular, our simulation results show that these kinds of graphs can even lead to more stringent conditions for the evolution of cooperation than well-mixed populations. Overall, we provide evidence suggesting that the complexity arising from many-player interactions and spatial structure can be captured by pair approximation in the case of random graphs, but that it need to be handled with care for graphs with high clustering. PMID:27513946

  14. Cheating and the evolutionary stability of mutualisms.

    PubMed

    Ferriere, Régis; Bronstein, Judith L; Rinaldi, Sergio; Law, Richard; Gauduchon, Mathias

    2002-04-22

    Interspecific mutualisms have been playing a central role in the functioning of all ecosystems since the early history of life. Yet the theory of coevolution of mutualists is virtually nonexistent, by contrast with well-developed coevolutionary theories of competition, predator-prey and host-parasite interactions. This has prevented resolution of a basic puzzle posed by mutualisms: their persistence in spite of apparent evolutionary instability. The selective advantage of 'cheating', that is, reaping mutualistic benefits while providing fewer commodities to the partner species, is commonly believed to erode a mutualistic interaction, leading to its dissolution or reciprocal extinction. However, recent empirical findings indicate that stable associations of mutualists and cheaters have existed over long evolutionary periods. Here, we show that asymmetrical competition within species for the commodities offered by mutualistic partners provides a simple and testable ecological mechanism that can account for the long-term persistence of mutualisms. Cheating, in effect, establishes a background against which better mutualists can display any competitive superiority. This can lead to the coexistence and divergence of mutualist and cheater phenotypes, as well as to the coexistence of ecologically similar, but unrelated mutualists and cheaters.

  15. Evolutionary Computing for Low-thrust Navigation

    NASA Technical Reports Server (NTRS)

    Lee, Seungwon; Fink, Wolfgang; vonAllmed, Paul; Petropoulos, Anastassios E.; Russell, Ryan P.; Terrile, Richard J.

    2005-01-01

    The development of new mission concepts requires efficient methodologies to analyze, design and simulate the concepts before implementation. New mission concepts are increasingly considering the use of ion thrusters for fuel-efficient navigation in deep space. This paper presents parallel, evolutionary computing methods to design trajectories of spacecraft propelled by ion thrusters and to assess the trade-off between delivered payload mass and required flight time. The developed methods utilize a distributed computing environment in order to speed up computation, and use evolutionary algorithms to find globally Pareto-optimal solutions. The methods are coupled with two main traditional trajectory design approaches, which are called direct and indirect. In the direct approach, thrust control is discretized in either arc time or arc length, and the resulting discrete thrust vectors are optimized. In the indirect approach, a thrust control problem is transformed into a costate control problem, and the initial values of the costate vector are optimized. The developed methods are applied to two problems: 1) an orbit transfer around the Earth and 2) a transfer between two distance retrograde orbits around Europa, the closest to Jupiter of the icy Galilean moons. The optimal solutions found with the present methods are comparable to other state-of-the-art trajectory optimizers and to analytical approximations for optimal transfers, while the required computational time is several orders of magnitude shorter than other optimizers thanks to an intelligent design of control vector discretization, advanced algorithmic parameterization, and parallel computing.

  16. Emergence of structured communities through evolutionary dynamics.

    PubMed

    Shtilerman, Elad; Kessler, David A; Shnerb, Nadav M

    2015-10-21

    Species-rich communities, in which many competing species coexist in a single trophic level, are quite frequent in nature, but pose a formidable theoretical challenge. In particular, it is known that complex competitive systems become unstable and unfeasible when the number of species is large. Recently, many studies have attributed the stability of natural communities to the structure of the interspecific interaction network, yet the nature of such structures and the underlying mechanisms responsible for them remain open questions. Here we introduce an evolutionary model, based on the generic Lotka-Volterra competitive framework, from which a stable, structured, diverse community emerges spontaneously. The modular structure of the competition matrix reflects the phylogeny of the community, in agreement with the hierarchial taxonomic classification. Closely related species tend to have stronger niche overlap and weaker fitness differences, as opposed to pairs of species from different modules. The competitive-relatedness hypothesis and the idea of emergent neutrality are discussed in the context of this evolutionary model. PMID:26231415

  17. Mitochondria and the evolutionary roots of cancer.

    PubMed

    Davila, Alfonso F; Zamorano, Pedro

    2013-04-01

    Cancer disease is inherent to, and widespread among, metazoans. Yet, some of the hallmarks of cancer such as uncontrolled cell proliferation, lack of apoptosis, hypoxia, fermentative metabolism and free cell motility (metastasis) are akin to a prokaryotic lifestyle, suggesting a link between cancer disease and evolution. In this hypothesis paper, we propose that cancer cells represent a phenotypic reversion to the earliest stage of eukaryotic evolution. This reversion is triggered by the dysregulation of the mitochondria due to cumulative oxidative damage to mitochondrial and nuclear DNA. As a result, the phenotype of normal, differentiated cells gradually reverts to the phenotype of a facultative anaerobic, heterotrophic cell optimized for survival and proliferation in hypoxic environments. This phenotype matches the phenotype of the last eukaryotic common ancestor (LECA) that resulted from the endosymbiosis between an α-proteobacteria (which later became the mitochondria) and an archaebacteria. As such, the evolution of cancer within one individual can be viewed as a recapitulation of the evolution of the eukaryotic cell from fully differentiated cells to LECA. This evolutionary model of cancer is compatible with the current understanding of the disease, and explains the evolutionary basis for most of the hallmarks of cancer, as well as the link between the disease and aging. It could also open new avenues for treatment directed at reestablishing the synergy between the mitochondria and the cancerous cell. PMID:23519071

  18. Wolbachia: Evolutionary novelty in a rickettsial bacteria

    PubMed Central

    Anderson, Cort L; Karr, Timothy L

    2001-01-01

    Background Although closely related, the alpha-proteobacteria Wolbachia and the Rickettsiacae (Rickettsia and Ehrlichia), employ different evolutionary life history strategies. Wolbachia are obligate endocellular symbionts that infect an extraordinary host range and, in contrast to the infectious and pathogenic Rickettsia and Ehrlichia, profoundly influence host reproductive biology. Results Phylogenies of the Rickettsia, Ehrlichia, and Wolbachia were independently inferred from 16S rDNA sequences and GroEL amino acid sequences. Topologies inferred from both sets of sequence data were consistent with one another, and both indicate the genus Wolbachia shared a common ancestor most recently with Ehrlichia. These two genera are a sister group to the genus Rickettsia. Mapping biological properties onto this phylogeny reveals that manipulation of host reproduction, characteristic of Wolbachia strains, is a derived characteristic. This evolutionary novelty is accompanied by the loss of the ability to infect vertebrate hosts. Conclusions Because of the contrasting transmission strategies employed by each, Wolbachia is expected to maximize efficiency of vertical transmission, while Ehrlichia and Rickettsia will optimize horizontal transfer of infection. Wolbachia manipulation of host reproduction could thus be viewed as strategy employed by this bacterium to foster its own propagation via vertical transmission. PMID:11734058

  19. Evolutionary origins of metabolic compartmentalization in eukaryotes

    PubMed Central

    Martin, William

    2010-01-01

    Many genes in eukaryotes are acquisitions from the free-living antecedents of chloroplasts and mitochondria. But there is no evolutionary ‘homing device’ that automatically directs the protein product of a transferred gene back to the organelle of its provenance. Instead, the products of genes acquired from endosymbionts can explore all targeting possibilities within the cell. They often replace pre-existing host genes, or even whole pathways. But the transfer of an enzymatic pathway from one compartment to another poses severe problems: over evolutionary time, the enzymes of the pathway acquire their targeting signals for the new compartment individually, not in unison. Until the whole pathway is established in the new compartment, newly routed individual enzymes are useless, and their genes will be lost through mutation. Here it is suggested that pathways attain novel compartmentation variants via a ‘minor mistargeting’ mechanism. If protein targeting in eukaryotic cells possesses enough imperfection such that small amounts of entire pathways continuously enter novel compartments, selectable units of biochemical function would exist in new compartments, and the genes could become selected. Dual-targeting of proteins is indeed very common within eukaryotic cells, suggesting that targeting variation required for this minor mistargeting mechanism to operate exists in nature. PMID:20124349

  20. The evolutionary neuroscience of tool making.

    PubMed

    Stout, Dietrich; Chaminade, Thierry

    2007-03-14

    The appearance of the first intentionally modified stone tools over 2.5 million years ago marked a watershed in human evolutionary history, expanding the human adaptive niche and initiating a trend of technological elaboration that continues to the present day. However, the cognitive foundations of this behavioral revolution remain controversial, as do its implications for the nature and evolution of modern human technological abilities. Here we shed new light on the neural and evolutionary foundations of human tool making skill by presenting functional brain imaging data from six inexperienced subjects learning to make stone tools of the kind found in the earliest archaeological record. Functional imaging of this complex, naturalistic task was accomplished through positron emission tomography with the slowly decaying radiological tracer (18)flouro-2-deoxyglucose. Results show that simple stone tool making is supported by a mosaic of primitive and derived parietofrontal perceptual-motor systems, including recently identified human specializations for representation of the central visual field and perception of three-dimensional form from motion. In the naïve tool makers reported here, no activation was observed in prefrontal executive cortices associated with strategic action planning or in inferior parietal cortex thought to play a role in the representation of everyday tool use skills. We conclude that uniquely human capacities for sensorimotor adaptation and affordance perception, rather than abstract conceptualization and planning, were central factors in the initial stages of human technological evolution.