Metabolic engineering to guide evolution - Creating a novel mode for L-valine production with Corynebacterium glutamicum.

PubMed

Schwentner, Andreas; Feith, André; Münch, Eugenia; Busche, Tobias; Rückert, Christian; Kalinowski, Jörn; Takors, Ralf; Blombach, Bastian

2018-03-06

Evolutionary approaches are often undirected and mutagen-based yielding numerous mutations, which need elaborate screenings to identify relevant targets. We here apply Metabolic engineering to Guide Evolution (MGE), an evolutionary approach evolving and identifying new targets to improve microbial producer strains. MGE is based on the idea to impair the cell's metabolism by metabolic engineering, thereby generating guided evolutionary pressure. It consists of three distinct phases: (i) metabolic engineering to create the evolutionary pressure on the applied strain followed by (ii) a cultivation phase with growth as straightforward screening indicator for the evolutionary event, and (iii) comparative whole genome sequencing (WGS), to identify mutations in the evolved strains, which are eventually re-engineered for verification. Applying MGE, we evolved the PEP and pyruvate carboxylase-deficient strain C. glutamicum Δppc Δpyc to grow on glucose as substrate with rates up to 0.31 ± 0.02 h -1 which corresponds to 80% of the growth rate of the wildtype strain. The intersection of the mutations identified by WGS revealed isocitrate dehydrogenase (ICD) as consistent target in three independently evolved mutants. Upon re-engineering in C. glutamicum Δppc Δpyc, the identified mutations led to diminished ICD activities and activated the glyoxylate shunt replenishing oxaloacetate required for growth. Intracellular relative quantitative metabolome analysis showed that the pools of citrate, isocitrate, cis-aconitate, and L-valine were significantly higher compared to the WT control. As an alternative to existing L-valine producer strains based on inactivated or attenuated pyruvate dehydrogenase complex, we finally engineered the PEP and pyruvate carboxylase-deficient C. glutamicum strains with identified ICD mutations for L-valine production by overexpression of the L-valine biosynthesis genes. Among them, C. glutamicum Δppc Δpyc ICD G407S (pJC4ilvBNCE) produced up to 8.9 ± 0.4 g L-valine L -1 , with a product yield of 0.22 ± 0.01 g L-valine per g glucose. Copyright © 2018 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Hybridization affects life-history traits and host specificity in Diorhabda spp

USDA-ARS?s Scientific Manuscript database

Hybridization is an influential evolutionary process that has been viewed alternatively as an evolutionary dead-end or as an important creative evolutionary force. In colonizing species, such as introduced biological control agents, hybridization can negate the effects of bottlenecks and genetic dri...

Depletion of CpG Dinucleotides in Papillomaviruses and Polyomaviruses: A Role for Divergent Evolutionary Pressures.

PubMed

Upadhyay, Mohita; Vivekanandan, Perumal

2015-01-01

Papillomaviruses and polyomaviruses are small ds-DNA viruses infecting a wide-range of vertebrate hosts. Evidence supporting co-evolution of the virus with the host does not fully explain the evolutionary path of papillomaviruses and polyomaviruses. Studies analyzing CpG dinucleotide frequencies in virus genomes have provided interesting insights on virus evolution. CpG dinucleotide depletion has not been extensively studied among papillomaviruses and polyomaviruses. We sought to analyze the relative abundance of dinucleotides and the relative roles of evolutionary pressures in papillomaviruses and polyomaviruses. We studied 127 full-length sequences from papillomaviruses and 56 full-length sequences from polyomaviruses. We analyzed the relative abundance of dinucleotides, effective codon number (ENC), differences in synonymous codon usage. We examined the association, if any, between the extent of CpG dinucleotide depletion and the evolutionary lineage of the infected host. We also investigated the contribution of mutational pressure and translational selection to the evolution of papillomaviruses and polyomaviruses. All papillomaviruses and polyomaviruses are CpG depleted. Interestingly, the evolutionary lineage of the infected host determines the extent of CpG depletion among papillomaviruses and polyomaviruses. CpG dinucleotide depletion was more pronounced among papillomaviruses and polyomaviruses infecting human and other mammals as compared to those infecting birds. Our findings demonstrate that CpG depletion among papillomaviruses is linked to mutational pressure; while CpG depletion among polyomaviruses is linked to translational selection. We also present evidence that suggests methylation of CpG dinucleotides may explain, at least in part, the depletion of CpG dinucleotides among papillomaviruses but not polyomaviruses. The extent of CpG depletion among papillomaviruses and polyomaviruses is linked to the evolutionary lineage of the infected host. Our results highlight the existence of divergent evolutionary pressures leading to CpG dinucleotide depletion among small ds-DNA viruses infecting vertebrate hosts.

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution.

PubMed

Kendall, Michelle; Colijn, Caroline

2016-10-01

Evolutionary relationships are frequently described by phylogenetic trees, but a central barrier in many fields is the difficulty of interpreting data containing conflicting phylogenetic signals. We present a metric-based method for comparing trees which extracts distinct alternative evolutionary relationships embedded in data. We demonstrate detection and resolution of phylogenetic uncertainty in a recent study of anole lizards, leading to alternate hypotheses about their evolutionary relationships. We use our approach to compare trees derived from different genes of Ebolavirus and find that the VP30 gene has a distinct phylogenetic signature composed of three alternatives that differ in the deep branching structure. phylogenetics, evolution, tree metrics, genetics, sequencing. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Advanced Chemical Propulsion

NASA Technical Reports Server (NTRS)

Alexander, Leslie, Jr.

2006-01-01

Advanced Chemical Propulsion (ACP) provides near-term incremental improvements in propulsion system performance and/or cost. It is an evolutionary approach to technology development that produces useful products along the way to meet increasingly more demanding mission requirements while focusing on improving payload mass fraction to yield greater science capability. Current activities are focused on two areas: chemical propulsion component, subsystem, and manufacturing technologies that offer measurable system level benefits; and the evaluation of high-energy storable propellants with enhanced performance for in-space application. To prioritize candidate propulsion technology alternatives, a variety of propulsion/mission analyses and trades have been conducted for SMD missions to yield sufficient data for investment planning. They include: the Advanced Chemical Propulsion Assessment; an Advanced Chemical Propulsion System Model; a LOx-LH2 small pumps conceptual design; a space storables propellant study; a spacecraft cryogenic propulsion study; an advanced pressurization and mixture ratio control study; and a pump-fed vs. pressure-fed study.

Insights into an evolutionary strategy leading to antibiotic resistance

NASA Astrophysics Data System (ADS)

Hou, Chun-Feng D.; Liu, Jian-Wei; Collyer, Charles; Mitić, Nataša; Pedroso, Marcelo Monteiro; Schenk, Gerhard; Ollis, David L.

2017-01-01

Metallo-β-lactamases (MBLs) with activity towards a broad-spectrum of β-lactam antibiotics have become a major threat to public health, not least due to their ability to rapidly adapt their substrate preference. In this study, the capability of the MBL AIM-1 to evade antibiotic pressure by introducing specific mutations was probed by two alternative methods, i.e. site-saturation mutagenesis (SSM) of active site residues and in vitro evolution. Both approaches demonstrated that a single mutation in AIM-1 can greatly enhance a pathogen’s resistance towards broad spectrum antibiotics without significantly compromising the catalytic efficiency of the enzyme. Importantly, the evolution experiments demonstrated that relevant amino acids are not necessarily in close proximity to the catalytic centre of the enzyme. This observation is a powerful demonstration that MBLs have a diverse array of possibilities to adapt to new selection pressures, avenues that cannot easily be predicted from a crystal structure alone.

Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton.

PubMed

von Dassow, Peter; John, Uwe; Ogata, Hiroyuki; Probert, Ian; Bendif, El Mahdi; Kegel, Jessica U; Audic, Stéphane; Wincker, Patrick; Da Silva, Corinne; Claverie, Jean-Michel; Doney, Scott; Glover, David M; Flores, Daniella Mella; Herrera, Yeritza; Lescot, Magali; Garet-Delmas, Marie-José; de Vargas, Colomban

2015-06-01

Emiliania huxleyi is the most abundant calcifying plankton in modern oceans with substantial intraspecific genome variability and a biphasic life cycle involving sexual alternation between calcified 2N and flagellated 1N cells. We show that high genome content variability in Emiliania relates to erosion of 1N-specific genes and loss of the ability to form flagellated cells. Analysis of 185 E. huxleyi strains isolated from world oceans suggests that loss of flagella occurred independently in lineages inhabiting oligotrophic open oceans over short evolutionary timescales. This environmentally linked physiogenomic change suggests life cycling is not advantageous in very large/diluted populations experiencing low biotic pressure and low ecological variability. Gene loss did not appear to reflect pressure for genome streamlining in oligotrophic oceans as previously observed in picoplankton. Life-cycle modifications might be common in plankton and cause major functional variability to be hidden from traditional taxonomic or molecular markers.

Evolution of the α2-adrenoreceptors in vertebrates: ADRA2D is absent in mammals and crocodiles.

PubMed

Céspedes, Héctor A; Zavala, Kattina; Vandewege, Michael W; Opazo, Juan C

2017-09-01

Evolutionary studies of genes that have been functionally characterized and whose variation has been associated with pathological conditions represent an opportunity to understand the genetic basis of pathologies. α 2 -Adrenoreceptors (ADRA2) are a class of G protein-coupled receptors that regulate several physiological processes including blood pressure, platelet aggregation, insulin secretion, lipolysis, and neurotransmitter release. This gene family has been extensively studied from a molecular/physiological perspective, yet much less is known about its evolutionary history. Accordingly, the goal of this study was to investigate the evolutionary history of α 2 -adrenoreceptors (ADRA2) in vertebrates. Our results show that in addition to the three well-recognized α 2 -adrenoreceptor genes (ADRA2A, ADRA2B and ADRA2C), we recovered a clade that corresponds to the fourth member of the α 2 -adrenoreceptor gene family (ADRA2D). We also recovered a clade that possesses two ADRA2 sequences found in two lamprey species. Furthermore, our results show that mammals and crocodiles are characterized by possessing three α 2 -adrenoreceptor genes, whereas all other vertebrate groups possess the full repertoire of α 2 -adrenoreceptor genes. Among vertebrates ADRA2D seems to be a dispensable gene, as it was lost two independent times during the evolutionary history of the group. Additionally, we found that most examined species possess the most common alleles described for humans; however, there are cases in which non-human mammals possess the alternative variant. Finally, transcript abundance profiles revealed that during the early evolutionary history of gnathostomes, the expression of ADRA2D in different taxonomic groups became specialized to different tissues, but in the ancestor of sarcopterygians this specialization would have been lost. Copyright © 2017 Elsevier Inc. All rights reserved.

What to expect from an evolutionary hypothesis for a human disease: The case of type 2 diabetes.

PubMed

Watve, Milind; Diwekar-Joshi, Manawa

2016-10-01

Evolutionary medicine has a promise to bring in a conceptual revolution in medicine. However, as yet the field does not have the same theoretical rigour as that of many other fields in evolutionary studies. We discuss here with reference to type 2 diabetes mellitus (T2DM) what role an evolutionary hypothesis should play in the development of thinking in medicine. Starting with the thrifty gene hypothesis, evolutionary thinking in T2DM has undergone several transitions, modifications and refinements of the thrift family of hypotheses. In addition alternative hypotheses independent of thrift are also suggested. However, most hypotheses look at partial pictures; make selective use of supportive data ignoring inconvenient truths. Most hypotheses look at a superficial picture and avoid getting into the intricacies of underlying molecular, neuronal and physiological processes. Very few hypotheses have suggested clinical implications and none of them have been tested with randomized clinical trials. In the meanwhile the concepts in the pathophysiology of T2DM are undergoing radical changes and evolutionary hypotheses need to take them into account. We suggest an approach and a set of criteria to evaluate the relative merits of the alternative hypotheses. A number of hypotheses are likely to fail when critically evaluated against these criteria. It is possible that more than one selective process are at work in the evolution of propensity to T2DM, but the intercompatibility of the alternative selective forces and their relative contribution needs to be examined. The approach we describe could potentially lead to a sound evolutionary theory that is clinically useful and testable by randomized controlled clinical trials. Copyright © 2016 Elsevier GmbH. All rights reserved.

Macaca specific exon creation event generates a novel ZKSCAN5 transcript.

PubMed

Kim, Young-Hyun; Choe, Se-Hee; Song, Bong-Seok; Park, Sang-Je; Kim, Myung-Jin; Park, Young-Ho; Yoon, Seung-Bin; Lee, Youngjeon; Jin, Yeung Bae; Sim, Bo-Woong; Kim, Ji-Su; Jeong, Kang-Jin; Kim, Sun-Uk; Lee, Sang-Rae; Park, Young-Il; Huh, Jae-Won; Chang, Kyu-Tae

2016-02-15

ZKSCAN5 (also known as ZFP95) is a zinc-finger protein belonging to the Krűppel family. ZKSCAN5 contains a SCAN box and a KRAB A domain and is proposed to play a distinct role during spermatogenesis. In humans, alternatively spliced ZKSCAN5 transcripts with different 5'-untranslated regions (UTRs) have been identified. However, investigation of our Macaca UniGene Database revealed novel alternative ZKSCAN5 transcripts that arose due to an exon creation event. Therefore, in this study, we identified the full-length sequences of ZKSCAN5 and its alternative transcripts in Macaca spp. Additionally, we investigated different nonhuman primate sequences to elucidate the molecular mechanism underlying the exon creation event. We analyzed the evolutionary features of the ZKSCAN5 transcripts by reverse transcription polymerase chain reaction (RT-PCR) and genomic PCR, and by sequencing various nonhuman primate DNA and RNA samples. The exon-created transcript was only detected in the Macaca lineage (crab-eating monkey and rhesus monkey). Full-length sequence analysis by rapid amplification of cDNA ends (RACE) identified ten full-length transcripts and four functional isoforms of ZKSCAN5. Protein sequence analyses revealed the presence of two groups of isoforms that arose because of differences in start-codon usage. Together, our results demonstrate that there has been specific selection for a discrete set of ZKSCAN5 variants in the Macaca lineage. Furthermore, study of this locus (and perhaps others) in Macaca spp. might facilitate our understanding of the evolutionary pressures that have shaped the mechanism of exon creation in primates. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Evolutionary stasis in Euphorbiaceae pollen: selection and constraints.

PubMed

Matamoro-Vidal, A; Furness, C A; Gouyon, P-H; Wurdack, K J; Albert, B

2012-06-01

Although much attention has been paid to the role of stabilizing selection, empirical analyses testing the role of developmental constraints in evolutionary stasis remain rare, particularly for plants. This topic is studied here with a focus on the evolution of a pollen ontogenetic feature, the last points of callose deposition (LPCD) pattern, involved in the determination of an adaptive morphological pollen character (aperture pattern). The LPCD pattern exhibits a low level of evolution in eudicots, as compared to the evolution observed in monocots. Stasis in this pattern might be explained by developmental constraints expressed during male meiosis (microsporogenesis) or by selective pressures expressed through the adaptive role of the aperture pattern. Here, we demonstrate that the LPCD pattern is conserved in Euphorbiaceae s.s. and that this conservatism is primarily due to selective pressures. A phylogenetic association was found between the putative removal of selective pressures on pollen morphology after the origin of inaperturate pollen, and the appearance of variation in microsporogenesis and in the resulting LPCD pattern, suggesting that stasis was due to these selective pressures. However, even in a neutral context, variation in microsporogenesis was biased. This should therefore favour the appearance of some developmental and morphological phenotypes rather than others. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

The major synthetic evolutionary transitions.

PubMed

Solé, Ricard

2016-08-19

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

The major synthetic evolutionary transitions

PubMed Central

Solé, Ricard

2016-01-01

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

Predator confusion is sufficient to evolve swarming behaviour

PubMed Central

Olson, Randal S.; Hintze, Arend; Dyer, Fred C.; Knoester, David B.; Adami, Christoph

2013-01-01

Swarming behaviours in animals have been extensively studied owing to their implications for the evolution of cooperation, social cognition and predator–prey dynamics. An important goal of these studies is discerning which evolutionary pressures favour the formation of swarms. One hypothesis is that swarms arise because the presence of multiple moving prey in swarms causes confusion for attacking predators, but it remains unclear how important this selective force is. Using an evolutionary model of a predator–prey system, we show that predator confusion provides a sufficient selection pressure to evolve swarming behaviour in prey. Furthermore, we demonstrate that the evolutionary effect of predator confusion on prey could in turn exert pressure on the structure of the predator's visual field, favouring the frontally oriented, high-resolution visual systems commonly observed in predators that feed on swarming animals. Finally, we provide evidence that when prey evolve swarming in response to predator confusion, there is a change in the shape of the functional response curve describing the predator's consumption rate as prey density increases. Thus, we show that a relatively simple perceptual constraint—predator confusion—could have pervasive evolutionary effects on prey behaviour, predator sensory mechanisms and the ecological interactions between predators and prey. PMID:23740485

Predator confusion is sufficient to evolve swarming behaviour.

PubMed

Olson, Randal S; Hintze, Arend; Dyer, Fred C; Knoester, David B; Adami, Christoph

2013-08-06

Swarming behaviours in animals have been extensively studied owing to their implications for the evolution of cooperation, social cognition and predator-prey dynamics. An important goal of these studies is discerning which evolutionary pressures favour the formation of swarms. One hypothesis is that swarms arise because the presence of multiple moving prey in swarms causes confusion for attacking predators, but it remains unclear how important this selective force is. Using an evolutionary model of a predator-prey system, we show that predator confusion provides a sufficient selection pressure to evolve swarming behaviour in prey. Furthermore, we demonstrate that the evolutionary effect of predator confusion on prey could in turn exert pressure on the structure of the predator's visual field, favouring the frontally oriented, high-resolution visual systems commonly observed in predators that feed on swarming animals. Finally, we provide evidence that when prey evolve swarming in response to predator confusion, there is a change in the shape of the functional response curve describing the predator's consumption rate as prey density increases. Thus, we show that a relatively simple perceptual constraint--predator confusion--could have pervasive evolutionary effects on prey behaviour, predator sensory mechanisms and the ecological interactions between predators and prey.

Reservoir and vector evolutionary pressures shaped the adaptation of Borrelia.

PubMed

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

2018-04-12

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

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.

Evolutionary contributions to the study of human fertility.

PubMed

Sear, Rebecca

2015-01-01

Demography, lacking an overarching theoretical framework of its own, has drawn on theories in many other social sciences to inform its analyses. The aim of this paper is to bring to the demographic community's attention research in the evolutionary sciences on fertility, and to demonstrate that evolutionary theory can be another useful tool in the demographer's toolkit. I first dispel some myths which impede the incorporation of evolutionary theory into demography: I make it clear that evolutionary explanations do not assume that all human behaviour is hardwired and functions to maximize genetic fitness; that they are able to explain variation in human behaviour; and that they are not necessarily alternatives to social science explanations. I then describe the diversity of work on fertility by evolutionary researchers, particularly human evolutionary ecologists and cultural evolutionists, and illustrate the usefulness of the evolutionary approach with examples of its application to age at first birth and the fertility transition.

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

PubMed Central

Novikova, Irina V.; Hennelly, Scott P.; Sanbonmatsu, Karissa Y.

2012-01-01

While functional roles of several long non-coding RNAs (lncRNAs) have been determined, the molecular mechanisms are not well understood. Here, we report the first experimentally derived secondary structure of a human lncRNA, the steroid receptor RNA activator (SRA), 0.87 kB in size. The SRA RNA is a non-coding RNA that coactivates several human sex hormone receptors and is strongly associated with breast cancer. Coding isoforms of SRA are also expressed to produce proteins, making the SRA gene a unique bifunctional system. Our experimental findings (SHAPE, in-line, DMS and RNase V1 probing) reveal that this lncRNA has a complex structural organization, consisting of four domains, with a variety of secondary structure elements. We examine the coevolution of the SRA gene at the RNA structure and protein structure levels using comparative sequence analysis across vertebrates. Rapid evolutionary stabilization of RNA structure, combined with frame-disrupting mutations in conserved regions, suggests that evolutionary pressure preserves the RNA structural core rather than its translational product. We perform similar experiments on alternatively spliced SRA isoforms to assess their structural features. PMID:22362738

Adaptation, allometry, and hypertension.

PubMed

Weder, A B; Schork, N J

1994-08-01

Essential hypertension is a "disease of civilization" but has a clear genetic component. From an evolutionary perspective, persistence in the human genome of elements capable of raising blood pressure presupposes their adaptive significance. Recently, two hypotheses that explicitly appeal to selectionist arguments, the "slavery" and "thrifty gene" theories, have been forwarded. We find neither completely successful, and we advance an alternative explanation of the adaptive importance of genes responsible for hypertension. We propose that blood pressure rises during childhood and adolescence to subserve homeostatic needs of the organism. Specifically, we contend that blood pressure is a flexible element in the repertoire of renal homeostatic mechanisms serving to match renal function to growth. The effect of modern diet and lifestyle on human growth stimulates earlier and more vigorous development, straining biologically necessary relationships between renal and general somatic growth and requiring compensation via homeostatic mechanisms preserved during evolution. Prime among such mechanisms is blood pressure, which rises as a compensation to maintain renal function in the face of greater growth. Since virtually all members of acculturated societies share in the modern lifestyle, the demands imposed by accelerated growth and development result in a populational shift to higher blood pressures, with a consequent increase in the prevalence of hypertension. We propose that hypertension is the product of maladaptation of highly genetically conserved mechanisms subserving important biological homeostatic needs. Elucidation of the mechanisms underlying hypertension will require approaches that examine the developmental processes linking growth to blood pressure.

Contrasting effects of intralocus sexual conflict on sexually antagonistic coevolution

PubMed Central

Pennell, Tanya M.; de Haas, Freek J. H.; Morrow, Edward H.; van Doorn, G. Sander

2016-01-01

Evolutionary conflict between the sexes can induce arms races in which males evolve traits that are detrimental to the fitness of their female partners, and vice versa. This interlocus sexual conflict (IRSC) has been proposed as a cause of perpetual intersexual antagonistic coevolution with wide-ranging evolutionary consequences. However, theory suggests that the scope for perpetual coevolution is limited, if traits involved in IRSC are subject to pleiotropic constraints. Here, we consider a biologically plausible form of pleiotropy that has hitherto been ignored in treatments of IRSC and arrive at drastically different conclusions. Our analysis is based on a quantitative genetic model of sexual conflict, in which genes controlling IRSC traits have side effects in the other sex, due to incompletely sex-limited gene expression. As a result, the genes are exposed to intralocus sexual conflict (IASC), a tug-of-war between opposing male- and female-specific selection pressures. We find that the interaction between the two forms of sexual conflict has contrasting effects on antagonistic coevolution: Pleiotropic constraints stabilize the dynamics of arms races if the mating traits are close to evolutionary equilibrium but can prevent populations from ever reaching such a state. Instead, the sexes are drawn into a continuous cycle of arms races, causing the buildup of IASC, alternated by phases of IASC resolution that trigger the next arms race. These results encourage an integrative perspective on the biology of sexual conflict and generally caution against relying exclusively on equilibrium stability analysis. PMID:26755609

Pressure relieving support surfaces (PRESSURE) trial: cost effectiveness analysis.

PubMed

Iglesias, Cynthia; Nixon, Jane; Cranny, Gillian; Nelson, E Andrea; Hawkins, Kim; Phillips, Angela; Torgerson, David; Mason, Su; Cullum, Nicky

2006-06-17

To assess the cost effectiveness of alternating pressure mattresses compared with alternating pressure overlays for the prevention of pressure ulcers in patients admitted to hospital. Cost effectiveness analysis carried out alongside the pressure relieving support surfaces (PRESSURE) trial; a multicentre UK based pragmatic randomised controlled trial. 11 hospitals in six UK NHS trusts. Intention to treat population comprising 1971 participants. Kaplan Meier estimates of restricted mean time to development of pressure ulcers and total costs for treatment in hospital. Alternating pressure mattresses were associated with lower overall costs (283.6 pounds sterling per patient on average, 95% confidence interval--377.59 pounds sterling to 976.79 pounds sterling) mainly due to reduced length of stay in hospital, and greater benefits (a delay in time to ulceration of 10.64 days on average,--24.40 to 3.09). The differences in health benefits and total costs for hospital stay between alternating pressure mattresses and alternating pressure overlays were not statistically significant; however, a cost effectiveness acceptability curve indicated that on average alternating pressure mattresses compared with alternating pressure overlays were associated with an 80% probability of being cost saving. Alternating pressure mattresses for the prevention of pressure ulcers are more likely to be cost effective and are more acceptable to patients than alternating pressure overlays.

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…

CRITTERS! A Realistic Simulation for Teaching Evolutionary Biology

ERIC Educational Resources Information Center

Latham, Luke G., II; Scully, Erik P.

2008-01-01

Evolutionary processes can be studied in nature and in the laboratory, but time and financial constraints result in few opportunities for undergraduate and high school students to explore the agents of genetic change in populations. One alternative to time consuming and expensive teaching laboratories is the use of computer simulations. We…

Shifts in Selective Pressures on Snake Phototransduction Genes Associated with Photoreceptor Transmutation and Dim-Light Ancestry.

PubMed

Schott, Ryan K; Van Nynatten, Alexander; Card, Daren C; Castoe, Todd A; S W Chang, Belinda

2018-06-01

The visual systems of snakes are heavily modified relative to other squamates, a condition often thought to reflect their fossorial origins. Further modifications are seen in caenophidian snakes, where evolutionary transitions between rod and cone photoreceptors, termed photoreceptor transmutations, have occurred in many lineages. Little previous work, however, has focused on the molecular evolutionary underpinnings of these morphological changes. To address this, we sequenced seven snake eye transcriptomes and utilized new whole-genome and targeted capture sequencing data. We used these data to analyze gene loss and shifts in selection pressures in phototransduction genes that may be associated with snake evolutionary origins and photoreceptor transmutation. We identified the surprising loss of rhodopsin kinase (GRK1), despite a low degree of gene loss overall and a lack of relaxed selection early during snake evolution. These results provide some of the first evolutionary genomic corroboration for a dim-light ancestor that lacks strong fossorial adaptations. Our results also indicate that snakes with photoreceptor transmutation experienced significantly different selection pressures from other reptiles. Significant positive selection was found primarily in cone-specific genes, but not rod-specific genes, contrary to our expectations. These results reveal potential molecular adaptations associated with photoreceptor transmutation and also highlight unappreciated functional differences between rod- and cone-specific phototransduction proteins. This intriguing example of snake visual system evolution illustrates how the underlying molecular components of a complex system can be reshaped in response to changing selection pressures.

Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes.

PubMed

Lin, Chieh-Hua; Lian, Chun-Yi; Hsiung, Chao Agnes; Chen, Feng-Chi

2011-10-05

Changes in transcriptional orientation ("CTOs") occur frequently in prokaryotic genomes. Such changes usually result from genomic inversions, which may cause a conflict between the directions of replication and transcription and an increase in mutation rate. However, CTOs do not always lead to the replication-transcription confrontation. Furthermore, CTOs may cause deleterious disruptions of operon structure and/or gene regulations. The currently existing CTOs may indicate relaxation of selection pressure. Therefore, it is of interest to investigate whether CTOs have an independent effect on the evolutionary rates of the affected genes, and whether these genes are subject to any type of selection pressure in prokaryotes. Three closely related enterbacteria, Escherichia coli, Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium, were selected for comparisons of synonymous (dS) and nonsynonymous (dN) substitution rate between the genes that have experienced changes in transcriptional orientation (changed-orientation genes, "COGs") and those that do not (same-orientation genes, "SOGs"). The dN/dS ratio was also derived to evaluate the selection pressure on the analyzed genes. Confounding factors in the estimation of evolutionary rates, such as gene essentiality, gene expression level, replication-transcription confrontation, and decreased dS at gene terminals were controlled in the COG-SOG comparisons. We demonstrate that COGs have significantly higher dN and dS than SOGs when a series of confounding factors are controlled. However, the dN/dS ratios are similar between the two gene groups, suggesting that the increase in dS can sufficiently explain the increase in dN in COGs. Therefore, the increases in evolutionary rates in COGs may be mainly mutation-driven. Here we show that CTOs can increase the evolutionary rates of the affected genes. This effect is independent of the replication-transcription confrontation, which is suggested to be the major cause of inversion-associated evolutionary rate increases. The real cause of such evolutionary rate increases remains unclear but is worth further explorations.

An obligate brood parasite trapped in the intraspecific arms race of its hosts.

PubMed

Lyon, Bruce E; Eadie, John McA

2004-11-18

Reciprocal selection pressures often lead to close and adaptive matching of traits in coevolved species. A failure of one species to match the evolutionary trajectories of another is often attributed to evolutionary lags or to differing selection pressures across a geographic mosaic. Here we show that mismatches in adaptation of interacting species--an obligate brood parasitic duck and each of its two main hosts--are best explained by the evolutionary dynamics within the host species. Rejection of the brood parasite's eggs was common by both hosts, despite a lack of detectable cost of parasitism to the hosts. Egg rejection markedly reduced parasite fitness, but egg mimicry experiments revealed no phenotypic natural selection for more mimetic parasitic eggs. These paradoxical results were resolved by the discovery of intraspecific brood parasitism and conspecific egg rejection within the hosts themselves. The apparent arms race between species seems instead to be an incidental by-product of within-species conflict, with little recourse for evolutionary response by the parasite.

Thinking Evolutionarily About Obesity

PubMed Central

Genné-Bacon, Elizabeth A.

2014-01-01

Obesity, diabetes, and metabolic syndrome are growing worldwide health concerns, yet their causes are not fully understood. Research into the etiology of the obesity epidemic is highly influenced by our understanding of the evolutionary roots of metabolic control. For half a century, the thrifty gene hypothesis, which argues that obesity is an evolutionary adaptation for surviving periods of famine, has dominated the thinking on this topic. Obesity researchers are often not aware that there is, in fact, limited evidence to support the thrifty gene hypothesis and that alternative hypotheses have been suggested. This review presents evidence for and against the thrifty gene hypothesis and introduces readers to additional hypotheses for the evolutionary origins of the obesity epidemic. Because these alternate hypotheses imply significantly different strategies for research and clinical management of obesity, their consideration is critical to halting the spread of this epidemic. PMID:24910556

Communications system evolutionary scenarios for Martian SEI support

NASA Technical Reports Server (NTRS)

Kwong, Paulman W.; Bruno, Ronald C.

1992-01-01

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

Evolutionary rescue in vertebrates: evidence, applications and uncertainty

PubMed Central

Vander Wal, E.; Garant, D.; Festa-Bianchet, M.; Pelletier, F.

2013-01-01

The current rapid rate of human-driven environmental change presents wild populations with novel conditions and stresses. Theory and experimental evidence for evolutionary rescue present a promising case for species facing environmental change persisting via adaptation. Here, we assess the potential for evolutionary rescue in wild vertebrates. Available information on evolutionary rescue was rare and restricted to abundant and highly fecund species that faced severe intentional anthropogenic selective pressures. However, examples from adaptive tracking in common species and genetic rescues in species of conservation concern provide convincing evidence in favour of the mechanisms of evolutionary rescue. We conclude that low population size, long generation times and limited genetic variability will result in evolutionary rescue occurring rarely for endangered species without intervention. Owing to the risks presented by current environmental change and the possibility of evolutionary rescue in nature, we suggest means to study evolutionary rescue by mapping genotype → phenotype → demography → fitness relationships, and priorities for applying evolutionary rescue to wild populations. PMID:23209171

Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes

PubMed Central

Alekseyenko, Alexander V.; Kim, Namshin; Lee, Christopher J.

2007-01-01

Association of alternative splicing (AS) with accelerated rates of exon evolution in some organisms has recently aroused widespread interest in its role in evolution of eukaryotic gene structure. Previous studies were limited to analysis of exon creation or lost events in mouse and/or human only. Our multigenome approach provides a way for (1) distinguishing creation and loss events on the large scale; (2) uncovering details of the evolutionary mechanisms involved; (3) estimating the corresponding rates over a wide range of evolutionary times and organisms; and (4) assessing the impact of AS on those evolutionary rates. We use previously unpublished independent analyses of alternative splicing in five species (human, mouse, dog, cow, and zebrafish) from the ASAP database combined with genomewide multiple alignment of 17 genomes to analyze exon creation and loss of both constitutively and alternatively spliced exons in mammals, fish, and birds. Our analysis provides a comprehensive database of exon creation and loss events over 360 million years of vertebrate evolution, including tens of thousands of alternative and constitutive exons. We find that exon inclusion level is inversely related to the rate of exon creation. In addition, we provide a detailed in-depth analysis of mechanisms of exon creation and loss, which suggests that a large fraction of nonrepetitive created exons are results of ab initio creation from purely intronic sequences. Our data indicate an important role for alternative splicing in creation of new exons and provide a useful novel database resource for future genome evolution research. PMID:17369312

Learning the Language of Evolution: Lexical Ambiguity and Word Meaning in Student Explanations

ERIC Educational Resources Information Center

Rector, Meghan A.; Nehm, Ross H.; Pearl, Dennis

2013-01-01

Our study investigates the challenges introduced by students' use of lexically ambiguous language in evolutionary explanations. Specifically, we examined students' meaning of five key terms incorporated into their written evolutionary explanations: "pressure", "select", "adapt", "need", and "must". We utilized a new technological tool known as the…

Adaptive Memory: Young Children Show Enhanced Retention of Fitness-Related Information

ERIC Educational Resources Information Center

Aslan, Alp; Bauml, Karl-Heinz T.

2012-01-01

Evolutionary psychologists propose that human cognition evolved through natural selection to solve adaptive problems related to survival and reproduction, with its ultimate function being the enhancement of reproductive fitness. Following this proposal and the evolutionary-developmental view that ancestral selection pressures operated not only on…

Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins

PubMed Central

Kalyna, Maria; Lopato, Sergiy; Voronin, Viktor; Barta, Andrea

2006-01-01

Alternative splicing is an important mechanism for fine tuning of gene expression at the post-transcriptional level. SR proteins govern splice site selection and spliceosome assembly. The Arabidopsis genome encodes 19 SR proteins, several of which have no orthologues in metazoan. Three of the plant specific subfamilies are characterized by the presence of a relatively long alternatively spliced intron located in their first RNA recognition motif, which potentially results in an extremely truncated protein. In atRSZ33, a member of the RS2Z subfamily, this alternative splicing event was shown to be autoregulated. Here we show that atRSp31, a member of the RS subfamily, does not autoregulate alternative splicing of its similarily positioned intron. Interestingly, this alternative splicing event is regulated by atRSZ33. We demonstrate that the positions of these long introns and their capability for alternative splicing are conserved from green algae to flowering plants. Moreover, in particular alternative splicing events the splicing signals are embedded into highly conserved sequences. In different taxa, these conserved sequences occur in at least one gene within a subfamily. The evolutionary preservation of alternative splice forms together with highly conserved intron features argues for additional functions hidden in the genes of these plant-specific SR proteins. PMID:16936312

Iron silicides at pressures of the Earth's inner core

NASA Astrophysics Data System (ADS)

Zhang, Feiwu; Oganov, Artem R.

2010-01-01

The Earth's core is expected to contain around 10 wt % light elements (S, Si, O, possibly C, H, etc.) alloyed with Fe and Ni. Very little is known about these alloys at pressures and temperatures of the core. Here, using the evolutionary crystal structure prediction methodology, we investigate Fe-Si compounds at pressures of up to 400 GPa, i.e. covering the pressure range of the Earth's core. Evolutionary simulations correctly find that at atmospheric pressure the known non-trivial structure with P213 symmetry is stable, while at pressures above 20 GPa the CsCl-type structure is stable. We show that among the possible Fe silicides (Fe3Si, Fe2Si, Fe5Si3, FeSi, FeSi2 and FeSi3) only FeSi with CsCl-type structure is thermodynamically stable at core pressures, while the other silicides are unstable to decomposition into Fe + FeSi or FeSi + Si. This is consistent with previous works and suggests that Si impurities contribute to stabilization of the body-centered cubic phase of Fe in the inner core.

Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans.

PubMed

Awan, Ali R; Manfredo, Amanda; Pleiss, Jeffrey A

2013-07-30

Alternative splicing is a potent regulator of gene expression that vastly increases proteomic diversity in multicellular eukaryotes and is associated with organismal complexity. Although alternative splicing is widespread in vertebrates, little is known about the evolutionary origins of this process, in part because of the absence of phylogenetically conserved events that cross major eukaryotic clades. Here we describe a lariat-sequencing approach, which offers high sensitivity for detecting splicing events, and its application to the unicellular fungus, Schizosaccharomyces pombe, an organism that shares many of the hallmarks of alternative splicing in mammalian systems but for which no previous examples of exon-skipping had been demonstrated. Over 200 previously unannotated splicing events were identified, including examples of regulated alternative splicing. Remarkably, an evolutionary analysis of four of the exons identified here as subject to skipping in S. pombe reveals high sequence conservation and perfect length conservation with their homologs in scores of plants, animals, and fungi. Moreover, alternative splicing of two of these exons have been documented in multiple vertebrate organisms, making these the first demonstrations of identical alternative-splicing patterns in species that are separated by over 1 billion y of evolution.

Exploration of stable compounds, crystal structures, and superconductivity in the Be-H system

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

Yu, Shuyin, E-mail: yushuyin2014@gmail.com; Zeng, Qingfeng; Zhang, Litong

2014-10-15

Using first-principles variable-composition evolutionary methodology, we explored the high-pressure structures of beryllium hydrides between 0 and 400 GPa. We found that BeH{sub 2} remains the only stable compound in this pressure range. The pressure-induced transformations are predicted as Ibam→P3{sup -}m1→R3{sup -}m→Cmcm→P4/nmm, which occur at 24, 139, 204 and 349 GPa, respectively. P3{sup -}m1 and R3{sup -}m structures are layered polytypes based on close packings of H atoms with Be atoms filling all octahedral voids in alternating layers. Cmcm and P4/nmm contain two-dimensional triangular networks with each layer forming a kinked slab in the ab-plane. P3{sup -}m1 and R3{sup -}m aremore » semiconductors while Cmcm and P4/nmm are metallic. We have explored superconductivity of both metal phases, and found large electron-phonon coupling parameters of λ = 0.63 for Cmcm with a T{sub c} of 32.1-44.1 K at 250 GPa and λ = 0.65 for P4/nmm with a T{sub c} of 46.1-62.4 K at 400 GPa. The dependence of T{sub c} on pressure indicates that T{sub c} initially increases to a maximum of 45.1 K for Cmcm at 275 GPa and 97.0 K for P4/nmm at 365 GPa, and then decreases with increasing pressure for both phases.« less

Economic irrationality is optimal during noisy decision making

PubMed Central

Moreland, James; Chater, Nick; Usher, Marius; Summerfield, Christopher

2016-01-01

According to normative theories, reward-maximizing agents should have consistent preferences. Thus, when faced with alternatives A, B, and C, an individual preferring A to B and B to C should prefer A to C. However, it has been widely argued that humans can incur losses by violating this axiom of transitivity, despite strong evolutionary pressure for reward-maximizing choices. Here, adopting a biologically plausible computational framework, we show that intransitive (and thus economically irrational) choices paradoxically improve accuracy (and subsequent economic rewards) when decision formation is corrupted by internal neural noise. Over three experiments, we show that humans accumulate evidence over time using a “selective integration” policy that discards information about alternatives with momentarily lower value. This policy predicts violations of the axiom of transitivity when three equally valued alternatives differ circularly in their number of winning samples. We confirm this prediction in a fourth experiment reporting significant violations of weak stochastic transitivity in human observers. Crucially, we show that relying on selective integration protects choices against “late” noise that otherwise corrupts decision formation beyond the sensory stage. Indeed, we report that individuals with higher late noise relied more strongly on selective integration. These findings suggest that violations of rational choice theory reflect adaptive computations that have evolved in response to irreducible noise during neural information processing. PMID:26929353

Economic irrationality is optimal during noisy decision making.

PubMed

Tsetsos, Konstantinos; Moran, Rani; Moreland, James; Chater, Nick; Usher, Marius; Summerfield, Christopher

2016-03-15

According to normative theories, reward-maximizing agents should have consistent preferences. Thus, when faced with alternatives A, B, and C, an individual preferring A to B and B to C should prefer A to C. However, it has been widely argued that humans can incur losses by violating this axiom of transitivity, despite strong evolutionary pressure for reward-maximizing choices. Here, adopting a biologically plausible computational framework, we show that intransitive (and thus economically irrational) choices paradoxically improve accuracy (and subsequent economic rewards) when decision formation is corrupted by internal neural noise. Over three experiments, we show that humans accumulate evidence over time using a "selective integration" policy that discards information about alternatives with momentarily lower value. This policy predicts violations of the axiom of transitivity when three equally valued alternatives differ circularly in their number of winning samples. We confirm this prediction in a fourth experiment reporting significant violations of weak stochastic transitivity in human observers. Crucially, we show that relying on selective integration protects choices against "late" noise that otherwise corrupts decision formation beyond the sensory stage. Indeed, we report that individuals with higher late noise relied more strongly on selective integration. These findings suggest that violations of rational choice theory reflect adaptive computations that have evolved in response to irreducible noise during neural information processing.

Can evolutionary principles explain patterns of family violence?

PubMed

Archer, John

2013-03-01

The article's aim is to evaluate the application of the evolutionary principles of kin selection, reproductive value, and resource holding power to the understanding of family violence. The principles are described in relation to specific predictions and the mechanisms underlying these. Predictions are evaluated for physical violence perpetrated by (a) parents to unrelated children, (b) parents to genetic offspring, and (c) offspring to parents and between (d) siblings and (e) sexual partners. Precise figures for risks have been calculated where possible. The major conclusions are that most of the evidence is consistent with evolutionary predictions derived from kin selection and reproductive value: There were (a) higher rates of violence to stepchildren, (b) a decline in violence with the age of offspring, and (c) an increase in violence with parental age, while (d) violence between siblings was generally at a low level and concerned resource disputes. The issue of distinguishing evolutionary from alternative explanations is addressed throughout and is problematic for predictions derived from reproductive value. The main evolutionary explanation for male partner violence, mate guarding as a result of paternity uncertainty, cannot explain Western studies where sex differences in control and violence between partners were absent, although other aspects of male partner violence are consistent with it, and it may explain sex differences in traditional cultures. Recurrent problems in evaluating the evidence were to control for possible confounds and thus to distinguish evolutionary from alternative explanations. Suggestions are outlined to address this and other issues arising from the review. © 2013 American Psychological Association

An alternating pressure sequence proposal for an air-cell cushion for preventing pressure ulcers.

PubMed

Arias, Sandra; Cardiel, Eladio; Rogeli, Pablo; Mori, Taketoshi; Nakagami, Gojiro; Noguchi, Hiroshi; Sanada, Hiromi

2014-01-01

The distribution and release of pressure on ischial regions are two important parameters for evaluating the effectiveness of a cushion; especially the release of pressure over time on ischial tuberosities, which is significant for preventing pressure ulcers. The aim of this work is to evaluate the effect on interface pressure through the application of a proposed alternating pressure sequence for an air-cell cushion. Six healthy volunteers were asked to sit on the air cell cushion, in static and alternating modes, as well as on a typical foam cushion for 12 minutes. Interface pressure was monitored with a matrix sensor system. Interface pressure values on ischial tuberosities, user contact area and pressure distribution were analyzed. Results showed that IP on IT tends to increase in both foam and static cushions, while in alternating cushion IP on IT tends to decrease. User contact area was significantly larger in alternating cushion than in static or foam cushions. Moreover, there is a better pressure re-distribution with alternating cushion than with the other cushions. The goal of the alternating sequence is to redistribute pressure and stimulate the ischial regions in order to promote blood flow and prevent pressure occurring in wheelchair users.

Hidden long evolutionary memory in a model biochemical network

NASA Astrophysics Data System (ADS)

Ali, Md. Zulfikar; Wingreen, Ned S.; Mukhopadhyay, Ranjan

2018-04-01

We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. Starting with a functional core module, random evolutionary drift increases network complexity even in the absence of specific selective pressures. Surprisingly, we uncover a hidden order in sequence space that gives rise to long-term evolutionary memory, implying strong constraints on network evolution due to the topology of accessible sequence space.

Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention.

PubMed

Johnston, Iain G; Williams, Ben P

2016-02-24

Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species. Copyright © 2016 Elsevier Inc. All rights reserved.

Stone tools, language and the brain in human evolution.

PubMed

Stout, Dietrich; Chaminade, Thierry

2012-01-12

Long-standing speculations and more recent hypotheses propose a variety of possible evolutionary connections between language, gesture and tool use. These arguments have received important new support from neuroscientific research on praxis, observational action understanding and vocal language demonstrating substantial functional/anatomical overlap between these behaviours. However, valid reasons for scepticism remain as well as substantial differences in detail between alternative evolutionary hypotheses. Here, we review the current status of alternative 'gestural' and 'technological' hypotheses of language origins, drawing on current evidence of the neural bases of speech and tool use generally, and on recent studies of the neural correlates of Palaeolithic technology specifically.

Stone tools, language and the brain in human evolution

PubMed Central

Stout, Dietrich; Chaminade, Thierry

2012-01-01

Long-standing speculations and more recent hypotheses propose a variety of possible evolutionary connections between language, gesture and tool use. These arguments have received important new support from neuroscientific research on praxis, observational action understanding and vocal language demonstrating substantial functional/anatomical overlap between these behaviours. However, valid reasons for scepticism remain as well as substantial differences in detail between alternative evolutionary hypotheses. Here, we review the current status of alternative ‘gestural’ and ‘technological’ hypotheses of language origins, drawing on current evidence of the neural bases of speech and tool use generally, and on recent studies of the neural correlates of Palaeolithic technology specifically. PMID:22106428

An Evolutionary Comparison of the Handicap Principle and Hybrid Equilibrium Theories of Signaling.

PubMed

Kane, Patrick; Zollman, Kevin J S

2015-01-01

The handicap principle has come under significant challenge both from empirical studies and from theoretical work. As a result, a number of alternative explanations for honest signaling have been proposed. This paper compares the evolutionary plausibility of one such alternative, the "hybrid equilibrium," to the handicap principle. We utilize computer simulations to compare these two theories as they are instantiated in Maynard Smith's Sir Philip Sidney game. We conclude that, when both types of communication are possible, evolution is unlikely to lead to handicap signaling and is far more likely to result in the partially honest signaling predicted by hybrid equilibrium theory.

Loss of genetic diversity as a consequence of selection in response to high pCO2.

PubMed

Lloyd, Melanie M; Makukhov, April D; Pespeni, Melissa H

2016-10-01

Standing genetic variation may allow for rapid evolutionary response to the geologically unprecedented changes in global conditions. However, there is little known about the consequences of such rapid evolutionary change. Here, we measure genetic responses to experimental low and high p CO 2 levels in purple sea urchin larvae, Strongylocentrotus purpuratus . We found greater loss of nucleotide diversity in high p CO 2 levels (18.61%; 900 μatm) compared to low p CO 2 levels (10.12%; 400 μatm). In the wild, this loss could limit the evolutionary capacity of future generations. In contrast, we found minimal evidence that purple sea urchin larvae physiologically respond to high p CO 2 through alternative splicing of transcripts (11 genes), despite a strong signal of alternative splicing between different developmental stages (1193 genes). However, in response to high p CO 2 , four of the 11 alternatively spliced transcripts encoded ribosomal proteins, suggesting the regulation of translation as a potential response mechanism. The results of this study indicate that while the purple urchin presently may have enough standing genetic variation in response to rapid environmental change, this reservoir of resilience is a finite resource and could quickly diminish.

The predictability of evolution: glimpses into a post-Darwinian world.

PubMed

Conway Morris, Simon

2009-11-01

The very success of the Darwinian explanation, in not only demonstrating evolution from multiple lines of evidence but also in providing some plausible explanations, paradoxically seems to have served to have stifled explorations into other areas of investigation. The fact of evolution is now almost universally yoked to the assumption that its outcomes are random, trends are little more than drunkard's walks, and most evolutionary products are masterpieces of improvisation and far from perfect. But is this correct? Let us consider some alternatives. Is there evidence that evolution could in anyway be predictable? Can we identify alternative forms of biological organizations and if so how viable are they? Why are some molecules so extraordinarily versatile, while others can be spoken of as "molecules of choice"? How fortuitous are the major transitions in the history of life? What implications might this have for the Tree of Life? To what extent is evolutionary diversification constrained or facilitated by prior states? Are evolutionary outcomes merely sufficient or alternatively are they highly efficient, even superb? Here I argue that in sharp contradistinction to an orthodox Darwinian view, not only is evolution much more predictable than generally assumed but also investigation of its organizational substrates, including those of sensory systems, which indicates that it is possible to identify a predictability to the process and outcomes of evolution. If correct, the implications may be of some significance, not least in separating the unexceptional Darwinian mechanisms from underlying organizational principles, which may indicate evolutionary inevitabilities.

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.

Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population.

PubMed

Bonnet, Timothée; Wandeler, Peter; Camenisch, Glauco; Postma, Erik

2017-01-01

In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called "stasis paradox" highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is superior to purely phenotypic estimates of selection and evolutionary change.

Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population

PubMed Central

Wandeler, Peter; Camenisch, Glauco

2017-01-01

In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called “stasis paradox” highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is superior to purely phenotypic estimates of selection and evolutionary change. PMID:28125583

Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes

PubMed Central

2011-01-01

Background Changes in transcriptional orientation (“CTOs”) occur frequently in prokaryotic genomes. Such changes usually result from genomic inversions, which may cause a conflict between the directions of replication and transcription and an increase in mutation rate. However, CTOs do not always lead to the replication-transcription confrontation. Furthermore, CTOs may cause deleterious disruptions of operon structure and/or gene regulations. The currently existing CTOs may indicate relaxation of selection pressure. Therefore, it is of interest to investigate whether CTOs have an independent effect on the evolutionary rates of the affected genes, and whether these genes are subject to any type of selection pressure in prokaryotes. Methods Three closely related enterbacteria, Escherichia coli, Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium, were selected for comparisons of synonymous (dS) and nonsynonymous (dN) substitution rate between the genes that have experienced changes in transcriptional orientation (changed-orientation genes, “COGs”) and those that do not (same-orientation genes, “SOGs”). The dN/dS ratio was also derived to evaluate the selection pressure on the analyzed genes. Confounding factors in the estimation of evolutionary rates, such as gene essentiality, gene expression level, replication-transcription confrontation, and decreased dS at gene terminals were controlled in the COG-SOG comparisons. Results We demonstrate that COGs have significantly higher dN and dS than SOGs when a series of confounding factors are controlled. However, the dN/dS ratios are similar between the two gene groups, suggesting that the increase in dS can sufficiently explain the increase in dN in COGs. Therefore, the increases in evolutionary rates in COGs may be mainly mutation-driven. Conclusions Here we show that CTOs can increase the evolutionary rates of the affected genes. This effect is independent of the replication-transcription confrontation, which is suggested to be the major cause of inversion-associated evolutionary rate increases. The real cause of such evolutionary rate increases remains unclear but is worth further explorations. PMID:22152004

A Genetic Representation for Evolutionary Fault Recovery in Virtex FPGAs

NASA Technical Reports Server (NTRS)

Lohn, Jason; Larchev, Greg; DeMara, Ronald; Korsmeyer, David (Technical Monitor)

2003-01-01

Most evolutionary approaches to fault recovery in FPGAs focus on evolving alternative logic configurations as opposed to evolving the intra-cell routing. Since the majority of transistors in a typical FPGA are dedicated to interconnect, nearly 80% according to one estimate, evolutionary fault-recovery systems should benefit hy accommodating routing. In this paper, we propose an evolutionary fault-recovery system employing a genetic representation that takes into account both logic and routing configurations. Experiments were run using a software model of the Xilinx Virtex FPGA. We report that using four Virtex combinational logic blocks, we were able to evolve a 100% accurate quadrature decoder finite state machine in the presence of a stuck-at-zero fault.

Magnetostrictive Alternator

NASA Technical Reports Server (NTRS)

Bruder, Geoffrey A. (Inventor); Dyson, Jr., Rodger W. (Inventor)

2018-01-01

A magnetostrictive alternator configured to convert pressure waves into electrical energy is provided. It should be appreciated that the magnetostrictive alternator may be combined in some embodiments with a Stirling engine to produce electrical power. The Stirling engine creates the oscillating pressure wave and the magnetostrictive alternator converts the pressure wave into electricity. In some embodiments, the magnetostrictive alternator may include aerogel material and magnetostrictive material. The aerogel material may be configured to convert a higher amplitude pressure wave into a lower amplitude pressure wave. The magnetostrictive material may be configured to generate an oscillating magnetic field when the magnetostrictive material is compressed by the lower amplitude pressure wave.

Development links psychological causes to evolutionary explanations.

PubMed

Fedyk, Mark; Kushnir, Tamar

2014-04-01

Our conscious abilities are learned in environments that have evolved to support them. This insight provides an alternative way of framing Huang & Bargh's (H&B's) provocative hypothesis. To understand the conflict between unconscious goals and consciousness, we can study the emergence of conscious thought and control in childhood. These developmental processes are also central to the best available current evolutionary theories.

Comparative phylogenetic analysis of male alternative reproductive tactics in ray-finned fishes.

PubMed

Mank, Judith E; Avise, John C

2006-06-01

Using comparative phylogenetic analysis, we analyzed the evolution of male alternative reproductive tactics (MARTs) in ray-finned fishes (Actinopterygii). Numerous independent origins for each type of MART (involving sneaker males, female mimics, pirates, and satellite males) indicate that these behaviors have been highly labile across actinopterygiian evolution, consistent with a previous notion that convergent selection in fishes can readily mold the underlying suites of reproductive hormones into similar behaviors. The evolutionary appearance of MARTs was significantly correlated with the presence of sexually selected traits in bourgeois males (P = 0.001) but not with the presence of male parental care. This suggests that MARTs often arise from selection on some males to circumvent bourgeois male investment in mate monopolization, rather than to avoid male brood care per se. We found parsimony evidence for an evolutionary progression of MARTs wherein sneaking is usually the evolutionary precursor to the presumably more complex MARTs of female mimicry and cooperative satellite behavior. Nest piracy appears not to be part of this evolutionary progression, possibly because its late onset in the life cycle of most ray-finned fishes reduces the effects of selection on this reproductive tactic.

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

PubMed

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

2013-04-01

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

Evolutionary dynamics of the leaf phenological cycle in an oak metapopulation along an elevation gradient.

PubMed

Firmat, C; Delzon, S; Louvet, J-M; Parmentier, J; Kremer, A

2017-12-01

It has been predicted that environmental changes will radically alter the selective pressures on phenological traits. Long-lived species, such as trees, will be particularly affected, as they may need to undergo major adaptive change over only one or a few generations. The traits describing the annual life cycle of trees are generally highly evolvable, but nothing is known about the strength of their genetic correlations. Tight correlations can impose strong evolutionary constraints, potentially hampering the adaptation of multivariate phenological phenotypes. In this study, we investigated the evolutionary, genetic and environmental components of the timing of leaf unfolding and senescence within an oak metapopulation along an elevation gradient. Population divergence, estimated from in situ and common-garden data, was compared to expectations under neutral evolution, based on microsatellite markers. This approach made it possible (1) to evaluate the influence of genetic correlation on multivariate local adaptation to elevation and (2) to identify traits probably exposed to past selective pressures due to the colder climate at high elevation. The genetic correlation was positive but very weak, indicating that genetic constraints did not shape the local adaptation pattern for leaf phenology. Both spring and fall (leaf unfolding and senescence, respectively) phenology timings were involved in local adaptation, but leaf unfolding was probably the trait most exposed to climate change-induced selection. Our data indicated that genetic variation makes a much smaller contribution to adaptation than the considerable plastic variation displayed by a tree during its lifetime. The evolutionary potential of leaf phenology is, therefore, probably not the most critical aspect for short-term population survival in a changing climate. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

The role of selection on evolutionary rescue

NASA Astrophysics Data System (ADS)

Amirjanov, Adil

The paper investigates the role of selection on evolutionary rescue of population. The statistical mechanics technique is used to model dynamics of a population experiencing a natural selection and an abrupt change in the environment. The paper assesses the selective pressure produced by two different mechanisms: by strength of resistance and by strength of selection (by intraspecific competition). It is shown that both mechanisms are capable of providing an evolutionary rescue of population in particular conditions. However, for a small level of an extinction rate, the population cannot be rescued without intraspecific competition.

An Evolutionary Comparison of the Handicap Principle and Hybrid Equilibrium Theories of Signaling

PubMed Central

Kane, Patrick; Zollman, Kevin J. S.

2015-01-01

The handicap principle has come under significant challenge both from empirical studies and from theoretical work. As a result, a number of alternative explanations for honest signaling have been proposed. This paper compares the evolutionary plausibility of one such alternative, the “hybrid equilibrium,” to the handicap principle. We utilize computer simulations to compare these two theories as they are instantiated in Maynard Smith’s Sir Philip Sidney game. We conclude that, when both types of communication are possible, evolution is unlikely to lead to handicap signaling and is far more likely to result in the partially honest signaling predicted by hybrid equilibrium theory. PMID:26348617

Design Mining Interacting Wind Turbines.

PubMed

Preen, Richard J; Bull, Larry

2016-01-01

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

Evolutionary Models of Irregular Warfare

DTIC Science & Technology

2013-03-01

repro- duction. These adaptations include both physiological and behavioral strategies ranging from armour and immunity to complex nervous sys- tems...evolutionary principles to the level of grand strategy and international politics. This has given rise to some unexpected results: for example, work...forces, while only needing a small number of parameters to do so. Furthermore, they allow one to explore the effect of alternative strategies —whether

Commentary: An Exciting Evolutionary Framework for New Bridges between Social-Emotional and Cognitive Development--A Reflection on Suor et al. (2017)

ERIC Educational Resources Information Center

Kochanska, Grazyna; Goffin, Kathryn C.

2017-01-01

Suor et al. (2017) present a compelling new evolutionary framework that offers an alternative interpretation of the well-established findings of cognitive deficits in children raised in harsh early environments. They argue that such findings do not convey a complete picture of those children's cognitive development, because children's cognition…

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

ERIC Educational Resources Information Center

Cherif, Abour H.; Jedlicka, Dianne M.

2012-01-01

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

Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons

PubMed Central

Gelfman, Sahar; Burstein, David; Penn, Osnat; Savchenko, Anna; Amit, Maayan; Schwartz, Schraga; Pupko, Tal; Ast, Gil

2012-01-01

Exon–intron architecture is one of the major features directing the splicing machinery to the short exons that are located within long flanking introns. However, the evolutionary dynamics of exon–intron architecture and its impact on splicing is largely unknown. Using a comparative genomic approach, we analyzed 17 vertebrate genomes and reconstructed the ancestral motifs of both 3′ and 5′ splice sites, as also the ancestral length of exons and introns. Our analyses suggest that vertebrate introns increased in length from the shortest ancestral introns to the longest primate introns. An evolutionary analysis of splice sites revealed that weak splice sites act as a restrictive force keeping introns short. In contrast, strong splice sites allow recognition of exons flanked by long introns. Reconstruction of the ancestral state suggests these phenomena were not prevalent in the vertebrate ancestor, but appeared during vertebrate evolution. By calculating evolutionary rate shifts in exons, we identified cis-acting regulatory sequences that became fixed during the transition from early vertebrates to mammals. Experimental validations performed on a selection of these hexamers confirmed their regulatory function. We additionally revealed many features of exons that can discriminate alternative from constitutive exons. These features were integrated into a machine-learning approach to predict whether an exon is alternative. Our algorithm obtains very high predictive power (AUC of 0.91), and using these predictions we have identified and successfully validated novel alternatively spliced exons. Overall, we provide novel insights regarding the evolutionary constraints acting upon exons and their recognition by the splicing machinery. PMID:21974994

Evolution of Swarming Behavior Is Shaped by How Predators Attack.

PubMed

Olson, Randal S; Knoester, David B; Adami, Christoph

2016-01-01

Animal grouping behaviors have been widely studied due to their implications for understanding social intelligence, collective cognition, and potential applications in engineering, artificial intelligence, and robotics. An important biological aspect of these studies is discerning which selection pressures favor the evolution of grouping behavior. In the past decade, researchers have begun using evolutionary computation to study the evolutionary effects of these selection pressures in predator-prey models. The selfish herd hypothesis states that concentrated groups arise because prey selfishly attempt to place their conspecifics between themselves and the predator, thus causing an endless cycle of movement toward the center of the group. Using an evolutionary model of a predator-prey system, we show that how predators attack is critical to the evolution of the selfish herd. Following this discovery, we show that density-dependent predation provides an abstraction of Hamilton's original formulation of domains of danger. Finally, we verify that density-dependent predation provides a sufficient selective advantage for prey to evolve the selfish herd in response to predation by coevolving predators. Thus, our work corroborates Hamilton's selfish herd hypothesis in a digital evolutionary model, refines the assumptions of the selfish herd hypothesis, and generalizes the domain of danger concept to density-dependent predation.

A Case-by-Case Evolutionary Analysis of Four Imprinted Retrogenes

PubMed Central

McCole, Ruth B; Loughran, Noeleen B; Chahal, Mandeep; Fernandes, Luis P; Roberts, Roland G; Fraternali, Franca; O'Connell, Mary J; Oakey, Rebecca J

2011-01-01

Retroposition is a widespread phenomenon resulting in the generation of new genes that are initially related to a parent gene via very high coding sequence similarity. We examine the evolutionary fate of four retrogenes generated by such an event; mouse Inpp5f_v2, Mcts2, Nap1l5, and U2af1-rs1. These genes are all subject to the epigenetic phenomenon of parental imprinting. We first provide new data on the age of these retrogene insertions. Using codon-based models of sequence evolution, we show these retrogenes have diverse evolutionary trajectories, including divergence from the parent coding sequence under positive selection pressure, purifying selection pressure maintaining parent-retrogene similarity, and neutral evolution. Examination of the expression pattern of retrogenes shows an atypical, broad pattern across multiple tissues. Protein 3D structure modeling reveals that a positively selected residue in U2af1-rs1, not shared by its parent, may influence protein conformation. Our case-by-case analysis of the evolution of four imprinted retrogenes reveals that this interesting class of imprinted genes, while similar in regulation and sequence characteristics, follow very varied evolutionary paths. PMID:21166792

Selecting the Best: Evolutionary Engineering of Chemical Production in Microbes.

PubMed

Shepelin, Denis; Hansen, Anne Sofie Lærke; Lennen, Rebecca; Luo, Hao; Herrgård, Markus J

2018-05-11

Microbial cell factories have proven to be an economical means of production for many bulk, specialty, and fine chemical products. However, we still lack both a holistic understanding of organism physiology and the ability to predictively tune enzyme activities in vivo, thus slowing down rational engineering of industrially relevant strains. An alternative concept to rational engineering is to use evolution as the driving force to select for desired changes, an approach often described as evolutionary engineering. In evolutionary engineering, in vivo selections for a desired phenotype are combined with either generation of spontaneous mutations or some form of targeted or random mutagenesis. Evolutionary engineering has been used to successfully engineer easily selectable phenotypes, such as utilization of a suboptimal nutrient source or tolerance to inhibitory substrates or products. In this review, we focus primarily on a more challenging problem-the use of evolutionary engineering for improving the production of chemicals in microbes directly. We describe recent developments in evolutionary engineering strategies, in general, and discuss, in detail, case studies where production of a chemical has been successfully achieved through evolutionary engineering by coupling production to cellular growth.

Associations of stream geomorphic conditions and prevalence of alternative reproductive tactics among sockeye salmon populations.

PubMed

DeFilippo, L B; Schindler, D E; Carter, J L; Walsworth, T E; Cline, T J; Larson, W A; Buehrens, T

2018-02-01

In many species, males may exhibit alternative life histories to circumvent the costs of intrasexual competition and female courtship. While the evolution and underlying genetic and physiological mechanisms behind alternative reproductive tactics are well studied, there has been less consideration of the ecological factors that regulate their prevalence. Here, we examine six decades of age composition records from thirty-six populations of sockeye salmon (Oncorhynchus nerka) to quantify associations between spawning habitat characteristics and the prevalence of precocious sneakers known as 'jacks'. Jack prevalence was independent of neutral genetic structure among stream populations, but varied among habitat types and as a function of continuous geomorphic characteristics. Jacks were more common in streams relative to beaches and rivers, and their prevalence was negatively associated with stream width, depth, elevation, slope and area, but positively related to bank cover. Behavioural observations showed that jacks made greater use of banks, wood and shallows than guard males, indicating that their reproductive success depends on the availability of such refuges. Our results emphasize the role of the physical habitat in shaping reproductive tactic frequencies among populations, likely through local adaptation in response to variable fitness expectations under different geomorphic conditions. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

The role of protein dynamics in the evolution of new enzyme function.

PubMed

Campbell, Eleanor; Kaltenbach, Miriam; Correy, Galen J; Carr, Paul D; Porebski, Benjamin T; Livingstone, Emma K; Afriat-Jurnou, Livnat; Buckle, Ashley M; Weik, Martin; Hollfelder, Florian; Tokuriki, Nobuhiko; Jackson, Colin J

2016-11-01

Enzymes must be ordered to allow the stabilization of transition states by their active sites, yet dynamic enough to adopt alternative conformations suited to other steps in their catalytic cycles. The biophysical principles that determine how specific protein dynamics evolve and how remote mutations affect catalytic activity are poorly understood. Here we examine a 'molecular fossil record' that was recently obtained during the laboratory evolution of a phosphotriesterase from Pseudomonas diminuta to an arylesterase. Analysis of the structures and dynamics of nine protein variants along this trajectory, and three rationally designed variants, reveals cycles of structural destabilization and repair, evolutionary pressure to 'freeze out' unproductive motions and sampling of distinct conformations with specific catalytic properties in bi-functional intermediates. This work establishes that changes to the conformational landscapes of proteins are an essential aspect of molecular evolution and that change in function can be achieved through enrichment of preexisting conformational sub-states.

Meta-structure correlation in protein space unveils different selection rules for folded and intrinsically disordered proteins.

PubMed

Naranjo, Yandi; Pons, Miquel; Konrat, Robert

2012-01-01

The number of existing protein sequences spans a very small fraction of sequence space. Natural proteins have overcome a strong negative selective pressure to avoid the formation of insoluble aggregates. Stably folded globular proteins and intrinsically disordered proteins (IDPs) use alternative solutions to the aggregation problem. While in globular proteins folding minimizes the access to aggregation prone regions, IDPs on average display large exposed contact areas. Here, we introduce the concept of average meta-structure correlation maps to analyze sequence space. Using this novel conceptual view we show that representative ensembles of folded and ID proteins show distinct characteristics and respond differently to sequence randomization. By studying the way evolutionary constraints act on IDPs to disable a negative function (aggregation) we might gain insight into the mechanisms by which function-enabling information is encoded in IDPs.

Development and evaluation of a self-regulating alternating pressure air cushion.

PubMed

Nakagami, Gojiro; Sanada, Hiromi; Sugama, Junko

2015-03-01

To investigate the effect of alternating air cells of a newly developed dynamic cushion on interface pressure and tissue oxygenation levels. This cross-over experimental study included 19 healthy volunteers. The dynamic cushion used has an automatic self-regulating alternating pressure air-cell system with 35 small and four large air cells for maintaining posture while seated. This cushion also has 17 bottoming-out detectors that automatically inflate the air cells to release a high interface pressure. To assess the effect of this alternating system, participants sat on the new cushion with an alternating system or static system for 30 min and then performed push-ups. The interface pressure was monitored by pressure-sensitive and conductive ink film sensors and tissue oxygenation levels were monitored by near-infrared spectroscopy. A reactive hyperaemia indicator was calculated using tissue oxygenation levels as an outcome measure. The peak interface pressure was not significantly different between the groups. The reactive hyperaemia indicator was significantly higher in the static group than in the alternating group. An alternating system has beneficial effects on blood oxygenation levels without increasing interface pressure. Therefore, our new cushion is promising for preventing pressure ulcers with patients with limited ability to perform push-ups. Implications for Rehabilitation A dynamic cushion was developed, which consists of a uniquely-designed air-cell layout, detectors for bottoming out, and an alternating system with multiple air-cell lines. The alternating system did not increase interface pressure and it significantly reduced reactive hyperaemia after 30 min of sitting in healthy volunteers. This cushion is a new option for individuals who require stable posture but have limitations in performing scheduled push-ups for prevention of pressure ulcers.

21 CFR 880.5550 - Alternating pressure air flotation mattress.

Code of Federal Regulations, 2013 CFR

2013-04-01

... body pressure. The device is used to prevent and treat decubitus ulcers (bed sores). (b) Classification... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Alternating pressure air flotation mattress. 880... Personal Use Therapeutic Devices § 880.5550 Alternating pressure air flotation mattress. (a) Identification...

21 CFR 880.5550 - Alternating pressure air flotation mattress.

Code of Federal Regulations, 2010 CFR

2010-04-01

... body pressure. The device is used to prevent and treat decubitus ulcers (bed sores). (b) Classification... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Alternating pressure air flotation mattress. 880... Personal Use Therapeutic Devices § 880.5550 Alternating pressure air flotation mattress. (a) Identification...

21 CFR 880.5550 - Alternating pressure air flotation mattress.

Code of Federal Regulations, 2014 CFR

2014-04-01

... body pressure. The device is used to prevent and treat decubitus ulcers (bed sores). (b) Classification... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Alternating pressure air flotation mattress. 880... Personal Use Therapeutic Devices § 880.5550 Alternating pressure air flotation mattress. (a) Identification...

21 CFR 880.5550 - Alternating pressure air flotation mattress.

Code of Federal Regulations, 2011 CFR

2011-04-01

... body pressure. The device is used to prevent and treat decubitus ulcers (bed sores). (b) Classification... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Alternating pressure air flotation mattress. 880... Personal Use Therapeutic Devices § 880.5550 Alternating pressure air flotation mattress. (a) Identification...

21 CFR 880.5550 - Alternating pressure air flotation mattress.

Code of Federal Regulations, 2012 CFR

2012-04-01

... body pressure. The device is used to prevent and treat decubitus ulcers (bed sores). (b) Classification... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Alternating pressure air flotation mattress. 880... Personal Use Therapeutic Devices § 880.5550 Alternating pressure air flotation mattress. (a) Identification...

Mutation Supply and Relative Fitness Shape the Genotypes of Ciprofloxacin-Resistant Escherichia coli.

PubMed

Huseby, Douglas L; Pietsch, Franziska; Brandis, Gerrit; Garoff, Linnéa; Tegehall, Angelica; Hughes, Diarmaid

2017-05-01

Ciprofloxacin is an important antibacterial drug targeting Type II topoisomerases, highly active against Gram-negatives including Escherichia coli. The evolution of resistance to ciprofloxacin in E. coli always requires multiple genetic changes, usually including mutations affecting two different drug target genes, gyrA and parC. Resistant mutants selected in vitro or in vivo can have many different mutations in target genes and efflux regulator genes that contribute to resistance. Among resistant clinical isolates the genotype, gyrA S83L D87N, parC S80I is significantly overrepresented suggesting that it has a selective advantage. However, the evolutionary or functional significance of this high frequency resistance genotype is not fully understood. By combining experimental data and mathematical modeling, we addressed the reasons for the predominance of this specific genotype. The experimental data were used to model trajectories of mutational resistance evolution under different conditions of drug exposure and population bottlenecks. We identified the order in which specific mutations are selected in the clinical genotype, showed that the high frequency genotype could be selected over a range of drug selective pressures, and was strongly influenced by the relative fitness of alternative mutations and factors affecting mutation supply. Our data map for the first time the fitness landscape that constrains the evolutionary trajectories taken during the development of clinical resistance to ciprofloxacin and explain the predominance of the most frequently selected genotype. This study provides strong support for the use of in vitro competition assays as a tool to trace evolutionary trajectories, not only in the antibiotic resistance field. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A phylogenetic test for adaptive convergence in rock-dwelling lizards.

PubMed

Revell, Liam J; Johnson, Michele A; Schulte, James A; Kolbe, Jason J; Losos, Jonathan B

2007-12-01

Phenotypic similarity of species occupying similar habitats has long been taken as strong evidence of adaptation, but this approach implicitly assumes that similarity is evolutionarily derived. However, even derived similarities may not represent convergent adaptation if the similarities did not evolve as a result of the same selection pressures; an alternative possibility is that the similar features evolved for different reasons, but subsequently allowed the species to occupy the same habitat, in which case the convergent evolution of the same feature by species occupying similar habitats would be the result of exaptation. Many lizard lineages have evolved to occupy vertical rock surfaces, a habitat that places strong functional and ecological demands on lizards. We examined four clades in which species that use vertical rock surfaces exhibit long hindlimbs and flattened bodies. Morphological change on the phylogenetic branches leading to the rock-dwelling species in the four clades differed from change on other branches of the phylogeny; evolutionary transitions to rock-dwelling generally were associated with increases in limb length and decreases in head depth. Examination of particular characters revealed several different patterns of evolutionary change. Rock-dwelling lizards exhibited similarities in head depth as a result of both adaptation and exaptation. Moreover, even though rock-dwelling species generally had longer limbs than their close relatives, clade-level differences in limb length led to an overall lack of difference between rock- and non-rock-dwelling lizards. These results indicate that evolutionary change in the same direction in independent lineages does not necessarily produce convergence, and that the existence of similar advantageous structures among species independently occupying the same environment may not indicate adaptation.

Commentary on "The Evolutionary Origin of Female Orgasm" by M. Pavlicev and G. Wagner, 2016, J. Exp. Zool. (Mol. Dev. Evol.) 326(6):326-337.

PubMed

Komisaruk, Barry R

2016-12-01

Evidence is presented as an alternative to the authors' claims that in the course of evolution, a link between orgasm and ovulation has been lost in women, that evolutionary changes in clitoral anatomy underlie this loss, and that women's orgasm plays no significant role in reproduction. © 2016 Wiley Periodicals, Inc.

Inferring explicit weighted consensus networks to represent alternative evolutionary histories

PubMed Central

2013-01-01

Background The advent of molecular biology techniques and constant increase in availability of genetic material have triggered the development of many phylogenetic tree inference methods. However, several reticulate evolution processes, such as horizontal gene transfer and hybridization, have been shown to blur the species evolutionary history by causing discordance among phylogenies inferred from different genes. Methods To tackle this problem, we hereby describe a new method for inferring and representing alternative (reticulate) evolutionary histories of species as an explicit weighted consensus network which can be constructed from a collection of gene trees with or without prior knowledge of the species phylogeny. Results We provide a way of building a weighted phylogenetic network for each of the following reticulation mechanisms: diploid hybridization, intragenic recombination and complete or partial horizontal gene transfer. We successfully tested our method on some synthetic and real datasets to infer the above-mentioned evolutionary events which may have influenced the evolution of many species. Conclusions Our weighted consensus network inference method allows one to infer, visualize and validate statistically major conflicting signals induced by the mechanisms of reticulate evolution. The results provided by the new method can be used to represent the inferred conflicting signals by means of explicit and easy-to-interpret phylogenetic networks. PMID:24359207

Achieving sustainable plant disease management through evolutionary principles.

PubMed

Zhan, Jiasui; Thrall, Peter H; Burdon, Jeremy J

2014-09-01

Plants and their pathogens are engaged in continuous evolutionary battles and sustainable disease management requires novel systems to create environments conducive for short-term and long-term disease control. In this opinion article, we argue that knowledge of the fundamental factors that drive host-pathogen coevolution in wild systems can provide new insights into disease development in agriculture. Such evolutionary principles can be used to guide the formulation of sustainable disease management strategies which can minimize disease epidemics while simultaneously reducing pressure on pathogens to evolve increased infectivity and aggressiveness. To ensure agricultural sustainability, disease management programs that reflect the dynamism of pathogen population structure are essential and evolutionary biologists should play an increasing role in their design. Copyright © 2014 Elsevier Ltd. All rights reserved.

Clownfishes evolution below and above the species level

PubMed Central

Litsios, Glenn; Faye, Laurélène; Salamin, Nicolas

2018-01-01

The difference between rapid morphological evolutionary changes observed in populations and the long periods of stasis detected in the fossil record has raised a decade-long debate about the exact role played by intraspecific mechanisms at the interspecific level. Although they represent different scales of the same evolutionary process, micro- and macroevolution are rarely studied together and few empirical studies have compared the rates of evolution and the selective pressures between both scales. Here, we analyse morphological, genetic and ecological traits in clownfishes at different evolutionary scales and demonstrate that the tempo of molecular and morphological evolution at the species level can be, to some extent, predicted from parameters estimated below the species level, such as the effective population size or the rate of evolution within populations. We also show that similar codons in the gene of the rhodopsin RH1, a light-sensitive receptor protein, are under positive selection at the intra and interspecific scales, suggesting that similar selective pressures are acting at both levels. PMID:29467260

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.

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

Assessing fluctuating evolutionary pressure in yeast and mammal evolutionary rate covariation using bioinformatics of meiotic protein genetic sequences

NASA Astrophysics Data System (ADS)

Dehipawala, Sunil; Nguyen, A.; Tremberger, G.; Cheung, E.; Holden, T.; Lieberman, D.; Cheung, T.

2013-09-01

The evolutionary rate co-variation in meiotic proteins has been reported for yeast and mammal using phylogenic branch lengths which assess retention, duplication and mutation. The bioinformatics of the corresponding DNA sequences could be classified as a diagram of fractal dimension and Shannon entropy. Results from biomedical gene research provide examples on the diagram methodology. The identification of adaptive selection using entropy marker and functional-structural diversity using fractal dimension would support a regression analysis where the coefficient of determination would serve as evolutionary pathway marker for DNA sequences and be an important component in the astrobiology community. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, clinical trial targeted cancer gene CD47, SIRT6 in spermatogenesis, and HLA-C in mosquito bite immunology demonstrate the diagram classification methodology. Comparisons to the SEPT4-XIAP pair in stem cell apoptosis, testesexpressed taste genes TAS1R3-GNAT3 pair, and amyloid beta APLP1-APLP2 pair with the yeast-mammal DNA sequences for meiotic proteins RAD50-MRE11 pair and NCAPD2-ICK pair have accounted for the observed fluctuating evolutionary pressure systematically. Regression with high R-sq values or a triangular-like cluster pattern for concordant pairs in co-variation among the studied species could serve as evidences for the possible location of common ancestors in the entropy-fractal dimension diagram, consistent with an example of the human-chimp common ancestor study using the FOXP2 regulated genes reported in human fetal brain study. The Deinococcus radiodurans R1 Rad-A could be viewed as an outlier in the RAD50 diagram and also in the free energy versus fractal dimension regression Cook's distance, consistent with a non-Earth source for this radiation resistant bacterium. Convergent and divergent fluctuating evolutionary pressure could be studied with extension to genetic sequences in organisms in possible astrobiology conditions, with the assumption that the continuation of a book of life would require meiotic proteins everywhere in the universe.

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

Viruses and mobile elements as drivers of evolutionary transitions

PubMed Central

2016-01-01

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

Viruses and mobile elements as drivers of evolutionary transitions.

PubMed

Koonin, Eugene V

2016-08-19

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

Sperm competition, but not major histocompatibility divergence, drives differential fertilization success between alternative reproductive tactics in Chinook salmon.

PubMed

Lehnert, S J; Helou, L; Pitcher, T E; Heath, J W; Heath, D D

2018-01-01

Post-copulatory sexual selection processes, including sperm competition and cryptic female choice (CFC), can operate based on major histocompatibility (MH) genes. We investigated sperm competition between male alternative reproductive tactics [jack (sneaker) and hooknose (guard)] of Chinook salmon (Oncorhynchus tshawytscha). Using a full factorial design, we examined in vitro competitive fertilization success of paired jack and hooknose males at three time points after sperm activation (0, 15 and 60 s) to test for male competition, CFC and time effects on male fertilization success. We also examined egg-mediated CFC at two MH genes by examining both the relationship between competitive fertilization success and MH divergence as well as inheritance patterns of MH alleles in resulting offspring. We found that jacks sired more offspring than hooknose males at 0 s post-activation; however, jack fertilization success declined over time post-activation, suggesting a trade-off between sperm speed and longevity. Enhanced fertilization success of jacks (presumably via higher sperm quality) may serve to increase sneaker tactic competitiveness relative to dominant hooknose males. We also found evidence of egg-mediated CFC (i.e. female × male interaction) influencing competitive fertilization success; however, CFC was not acting on the MH genes as we found no relationship between fertilization success and MH II β 1 or MH I α 1 divergence and we found no deviations from Mendelian inheritance of MH alleles in the offspring. Our study provides insight into evolutionary mechanisms influencing variation in male mating success within alternative reproductive tactics, thus underscoring different strategies that males can adopt to attain success. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

The Evolution of Different Forms of Sociality: Behavioral Mechanisms and Eco-Evolutionary Feedback

PubMed Central

van der Post, Daniel J.; Verbrugge, Rineke; Hemelrijk, Charlotte K.

2015-01-01

Different forms of sociality have evolved via unique evolutionary trajectories. However, it remains unknown to what extent trajectories of social evolution depend on the specific characteristics of different species. Our approach to studying such trajectories is to use evolutionary case-studies, so that we can investigate how grouping co-evolves with a multitude of individual characteristics. Here we focus on anti-predator vigilance and foraging. We use an individual-based model, where behavioral mechanisms are specified, and costs and benefits are not predefined. We show that evolutionary changes in grouping alter selection pressures on vigilance, and vice versa. This eco-evolutionary feedback generates an evolutionary progression from “leader-follower” societies to “fission-fusion” societies, where cooperative vigilance in groups is maintained via a balance between within- and between-group selection. Group-level selection is generated from an assortment that arises spontaneously when vigilant and non-vigilant foragers have different grouping tendencies. The evolutionary maintenance of small groups, and cooperative vigilance in those groups, is therefore achieved simultaneously. The evolutionary phases, and the transitions between them, depend strongly on behavioral mechanisms. Thus, integrating behavioral mechanisms and eco-evolutionary feedback is critical for understanding what kinds of intermediate stages are involved during the evolution of particular forms of sociality. PMID:25629313

The evolution of different forms of sociality: behavioral mechanisms and eco-evolutionary feedback.

PubMed

van der Post, Daniel J; Verbrugge, Rineke; Hemelrijk, Charlotte K

2015-01-01

Different forms of sociality have evolved via unique evolutionary trajectories. However, it remains unknown to what extent trajectories of social evolution depend on the specific characteristics of different species. Our approach to studying such trajectories is to use evolutionary case-studies, so that we can investigate how grouping co-evolves with a multitude of individual characteristics. Here we focus on anti-predator vigilance and foraging. We use an individual-based model, where behavioral mechanisms are specified, and costs and benefits are not predefined. We show that evolutionary changes in grouping alter selection pressures on vigilance, and vice versa. This eco-evolutionary feedback generates an evolutionary progression from "leader-follower" societies to "fission-fusion" societies, where cooperative vigilance in groups is maintained via a balance between within- and between-group selection. Group-level selection is generated from an assortment that arises spontaneously when vigilant and non-vigilant foragers have different grouping tendencies. The evolutionary maintenance of small groups, and cooperative vigilance in those groups, is therefore achieved simultaneously. The evolutionary phases, and the transitions between them, depend strongly on behavioral mechanisms. Thus, integrating behavioral mechanisms and eco-evolutionary feedback is critical for understanding what kinds of intermediate stages are involved during the evolution of particular forms of sociality.

Periodic table of virus capsids: implications for natural selection and design.

PubMed

Mannige, Ranjan V; Brooks, Charles L

2010-03-04

For survival, most natural viruses depend upon the existence of spherical capsids: protective shells of various sizes composed of protein subunits. So far, general evolutionary pressures shaping capsid design have remained elusive, even though an understanding of such properties may help in rationally impeding the virus life cycle and designing efficient nano-assemblies. This report uncovers an unprecedented and species-independent evolutionary pressure on virus capsids, based on the the notion that the simplest capsid designs (or those capsids with the lowest "hexamer complexity", C(h)) are the fittest, which was shown to be true for all available virus capsids. The theories result in a physically meaningful periodic table of virus capsids that uncovers strong and overarching evolutionary pressures, while also offering geometric explanations to other capsid properties (rigidity, pleomorphy, auxiliary requirements, etc.) that were previously considered to be unrelatable properties of the individual virus. Apart from describing a universal rule for virus capsid evolution, our work (especially the periodic table) provides a language with which highly diverse virus capsids, unified only by geometry, may be described and related to each other. Finally, the available virus structure databases and other published data reiterate the predicted geometry-derived rules, reinforcing the role of geometry in the natural selection and design of virus capsids.

An evolutionary psychological investigation of parental distress and reproductive coercion during the "coming out" of gay sons.

PubMed

Wisniewski, Timothy J; Robinson, Thomas N; Deluty, Robert H

2010-01-01

The lack of success of the "coming out" studies over the last three decades to explain and predict parental responses has motivated an evolutionary psychological reconceptualization. According to this reconceptualization, it was predicted that (a) biological mothers would experience more distress and apply more pressure on gay sons to change than would biological fathers and; (b) obligate investment for fathers on dependent sons would cause fathers to experience more distress and apply more pressure on gay sons to change than it would fathers without this obligate investment. In contrast, a cultural-norm hypothesis predicted that fathers would experience more distress and apply more pressure on gay sons to change than mothers. The majority of predictions were tested using 787 participants from two-biological parent families, who were drawn from a total sample of 891 participants from various family backgrounds. As predicted by the evolutionary hypothesis, biological mothers were reported to have been more distressed and coercive than biological fathers, in spite of a strong, societal expectation to the contrary. Furthermore, the results supported the obligate investment argument for paternal reactions. The model not only correctly explained and predicted parental behavior during coming out, but also was shown to unify within its theoretical framework discrepant results from the literature previously considered inconsistent.

49 CFR 195.303 - Risk-based alternative to pressure testing older hazardous liquid and carbon dioxide pipelines.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Pressure Testing § 195.303 Risk-based alternative to pressure testing older hazardous liquid and carbon... 49 Transportation 3 2014-10-01 2014-10-01 false Risk-based alternative to pressure testing older hazardous liquid and carbon dioxide pipelines. 195.303 Section 195.303 Transportation Other Regulations...

49 CFR 195.303 - Risk-based alternative to pressure testing older hazardous liquid and carbon dioxide pipelines.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Pressure Testing § 195.303 Risk-based alternative to pressure testing older hazardous liquid and carbon... 49 Transportation 3 2013-10-01 2013-10-01 false Risk-based alternative to pressure testing older hazardous liquid and carbon dioxide pipelines. 195.303 Section 195.303 Transportation Other Regulations...

49 CFR 195.303 - Risk-based alternative to pressure testing older hazardous liquid and carbon dioxide pipelines.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Pressure Testing § 195.303 Risk-based alternative to pressure testing older hazardous liquid and carbon... 49 Transportation 3 2012-10-01 2012-10-01 false Risk-based alternative to pressure testing older hazardous liquid and carbon dioxide pipelines. 195.303 Section 195.303 Transportation Other Regulations...

Disturbances, organisms and ecosystems: a global change perspective

PubMed Central

Ponge, Jean-François

2013-01-01

The present text exposes a theory of the role of disturbances in the assemblage and evolution of species within ecosystems, based principally, but not exclusively, on terrestrial ecosystems. Two groups of organisms, doted of contrasted strategies when faced with environmental disturbances, are presented, based on the classical r-K dichotomy, but enriched with more modern concepts from community and evolutionary ecology. Both groups participate in the assembly of known animal, plant, and microbial communities, but with different requirements about environmental fluctuations. The so-called “civilized” organisms are doted with efficient anticipatory mechanisms, allowing them to optimize from an energetic point of view their performances in a predictable environment (stable or fluctuating cyclically at the scale of life expectancy), and they developed advanced specializations in the course of evolutionary time. On the opposite side, the so-called “barbarians” are weakly efficient in a stable environment because they waste energy for foraging, growth, and reproduction, but they are well adapted to unpredictably changing conditions, in particular during major ecological crises. Both groups of organisms succeed or alternate each other in the course of spontaneous or geared successional processes, as well as in the course of evolution. The balance of “barbarians” against “civilized” strategies within communities is predicted to shift in favor of the first type under present-day anthropic pressure, exemplified among others by climate warming, land use change, pollution, and biological invasions. PMID:23610648

Disturbances, organisms and ecosystems: a global change perspective.

PubMed

Ponge, Jean-François

2013-04-01

The present text exposes a theory of the role of disturbances in the assemblage and evolution of species within ecosystems, based principally, but not exclusively, on terrestrial ecosystems. Two groups of organisms, doted of contrasted strategies when faced with environmental disturbances, are presented, based on the classical r-K dichotomy, but enriched with more modern concepts from community and evolutionary ecology. Both groups participate in the assembly of known animal, plant, and microbial communities, but with different requirements about environmental fluctuations. The so-called "civilized" organisms are doted with efficient anticipatory mechanisms, allowing them to optimize from an energetic point of view their performances in a predictable environment (stable or fluctuating cyclically at the scale of life expectancy), and they developed advanced specializations in the course of evolutionary time. On the opposite side, the so-called "barbarians" are weakly efficient in a stable environment because they waste energy for foraging, growth, and reproduction, but they are well adapted to unpredictably changing conditions, in particular during major ecological crises. Both groups of organisms succeed or alternate each other in the course of spontaneous or geared successional processes, as well as in the course of evolution. The balance of "barbarians" against "civilized" strategies within communities is predicted to shift in favor of the first type under present-day anthropic pressure, exemplified among others by climate warming, land use change, pollution, and biological invasions.

Refuge alternatives relief valve testing and design with updated test stand.

PubMed

Lutz, T J; Bissert, P T; Homce, G T; Yonkey, J A

2018-03-01

Underground refuge alternatives require an air source to supply breathable air to the occupants. This requires pressure relief valves to prevent unsafe pressures from building up within the refuge alternative. The U.S. Mine Safety and Health Administration (MSHA) mandates that pressure relief valves prevent pressure from exceeding 1.25 kPa (0.18 psi), or as specified by the manufacturer, above mine atmospheric pressure when a fan or compressor is used for the air supply. The U.S. National Institute for Occupational Safety and Health (NIOSH) tested a variety of pressure relief valves using an instrumented test fixture consisting of data acquisition equipment, a centrifugal blower, ductwork and various sensors to determine if the subject pressure relief valves meet the MSHA requirement. Relief pressures and flow characteristics, including opening pressure and flow rate, were measured for five different pressure relief valves under a variety of conditions. The subject pressure relief valves included two off-the-shelf modified check valves, two check valves used in MSHA-approved built-in-place refuge alternatives, and a commercially available valve that was designed for a steel refuge alternative and is currently being used in some built-in-place refuge alternatives. The test results showed relief pressures ranging from 0.20 to 1.53 kPa (0.03 to 0.22 psi) and flow rates up to 19.3 m 3 /min (683 scfm). As tested, some of the pressure relief valves did not meet the 1.25 kPa (0.18 psi) relief specification.

Stored Carbon Dynamics are Controlled by a Combination of Evolutionary, Physiological, and Ecological Pressures

NASA Astrophysics Data System (ADS)

Aubrey, D. P.; Mims, J. T.; Oswald, S. W.; Teskey, R. O.; Mitchell, R. J.

2016-12-01

Allocation of assimilated carbon to storage provides a critical carbohydrate buffer when metabolic demands exceed current photosynthetic supply; however, our process-level understanding of controls on carbon storage pools and fluxes remains relatively poor. Recent studies have shifted the paradigm from the concept that stored carbon pools are a sink of low priority that accumulate passively when photosynthetic inputs exceed demand toward the concept that these pools are active sinks of high priority. It follows that allocation toward storage—at the expense of growth—is a trait that would be under selective pressure since species that allocate toward storage should be more resilient to disturbance. Using fire-dependent longleaf pine in a series of manipulative and observational studies, we explore how stored carbon dynamics are controlled by a combination of evolutionary, physiological, and ecological pressures. Our manipulative studies revealed large stored carbon pools in roots that maintained belowground metabolism for a year after current photosynthetic supply was restricted. Likewise, the concentration of stored carbon in the smallest, most metabolically active roots was not influenced until nearly one year later. Our observational studies indicated that stored carbon pools differ among closely related species with overlapping natural distributions, but evolutionary histories of different disturbance frequencies and thus, different selective pressures on carbon storage. Our comparisons of stored carbon pools between longleaf trees growing under xeric or mesic soil moisture regimes indicated that allocation toward storage exhibits plasticity through space and time in response to both short- and long-term variations in resource availability. We expect a continuum of responses to disturbances related to ecological niche and evolutionary adaptation that influence the availability of carbohydrates for metabolic demands. We also expect a continuum in stored carbon pools and metabolic buffering capacity among species as well as spatially, temporally, and developmentally within individual species.

The current status of REH theory. [Random Evolutionary Hits in biological molecular evolution

NASA Technical Reports Server (NTRS)

Holmquist, R.; Jukes, T. H.

1981-01-01

A response is made to the evaluation of Fitch (1980) of REH (random evolutionary hits) theory for the evolutionary divergence of proteins and nucleic acids. Correct calculations for the beta hemoglobin mRNAs of the human, mouse and rabbit in the absence and presence of selective constraints are summarized, and it is shown that the alternative evolutionary analysis of Fitch underestimates the total fixed mutations. It is further shown that the model used by Fitch to test for the completeness of the count of total base substitutions is in fact a variant of REH theory. Considerations of the variance inherent in evolutionary estimations are also presented which show the REH model to produce no more variance than other evolutionary models. In the reply, it is argued that, despite the objections raised, REH theory applied to proteins gives inaccurate estimates of total gene substitutions. It is further contended that REH theory developed for nucleic sequences suffers from problems relating to the frequency of nucleotide substitutions, the identity of the codons accepting silent and amino acid-changing substitutions, and estimate uncertainties.

A Study of Driver's Route Choice Behavior Based on Evolutionary Game Theory

PubMed Central

Jiang, Xiaowei; Ji, Yanjie; Deng, Wei

2014-01-01

This paper proposes a route choice analytic method that embeds cumulative prospect theory in evolutionary game theory to analyze how the drivers adjust their route choice behaviors under the influence of the traffic information. A simulated network with two alternative routes and one variable message sign is built to illustrate the analytic method. We assume that the drivers in the transportation system are bounded rational, and the traffic information they receive is incomplete. An evolutionary game model is constructed to describe the evolutionary process of the drivers' route choice decision-making behaviors. Here we conclude that the traffic information plays an important role in the route choice behavior. The driver's route decision-making process develops towards different evolutionary stable states in accordance with different transportation situations. The analysis results also demonstrate that employing cumulative prospect theory and evolutionary game theory to study the driver's route choice behavior is effective. This analytic method provides an academic support and suggestion for the traffic guidance system, and may optimize the travel efficiency to a certain extent. PMID:25610455

A study of driver's route choice behavior based on evolutionary game theory.

PubMed

Jiang, Xiaowei; Ji, Yanjie; Du, Muqing; Deng, Wei

2014-01-01

This paper proposes a route choice analytic method that embeds cumulative prospect theory in evolutionary game theory to analyze how the drivers adjust their route choice behaviors under the influence of the traffic information. A simulated network with two alternative routes and one variable message sign is built to illustrate the analytic method. We assume that the drivers in the transportation system are bounded rational, and the traffic information they receive is incomplete. An evolutionary game model is constructed to describe the evolutionary process of the drivers' route choice decision-making behaviors. Here we conclude that the traffic information plays an important role in the route choice behavior. The driver's route decision-making process develops towards different evolutionary stable states in accordance with different transportation situations. The analysis results also demonstrate that employing cumulative prospect theory and evolutionary game theory to study the driver's route choice behavior is effective. This analytic method provides an academic support and suggestion for the traffic guidance system, and may optimize the travel efficiency to a certain extent.

Evolutionary game based control for biological systems with applications in drug delivery.

PubMed

Li, Xiaobo; Lenaghan, Scott C; Zhang, Mingjun

2013-06-07

Control engineering and analysis of biological systems have become increasingly important for systems and synthetic biology. Unfortunately, no widely accepted control framework is currently available for these systems, especially at the cell and molecular levels. This is partially due to the lack of appropriate mathematical models to describe the unique dynamics of biological systems, and the lack of implementation techniques, such as ultra-fast and ultra-small devices and corresponding control algorithms. This paper proposes a control framework for biological systems subject to dynamics that exhibit adaptive behavior under evolutionary pressures. The control framework was formulated based on evolutionary game based modeling, which integrates both the internal dynamics and the population dynamics. In the proposed control framework, the adaptive behavior was characterized as an internal dynamic, and the external environment was regarded as an external control input. The proposed open-interface control framework can be integrated with additional control algorithms for control of biological systems. To demonstrate the effectiveness of the proposed framework, an optimal control strategy was developed and validated for drug delivery using the pathogen Giardia lamblia as a test case. In principle, the proposed control framework can be applied to any biological system exhibiting adaptive behavior under evolutionary pressures. Copyright © 2013 Elsevier Ltd. All rights reserved.

Evolution of sparsity and modularity in a model of protein allostery

NASA Astrophysics Data System (ADS)

Hemery, Mathieu; Rivoire, Olivier

2015-04-01

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

The semaphorontic view of homology.

PubMed

Havstad, Joyce C; Assis, Leandro C S; Rieppel, Olivier

2015-11-01

The relation of homology is generally characterized as an identity relation, or alternatively as a correspondence relation, both of which are transitive. We use the example of the ontogenetic development and evolutionary origin of the gnathostome jaw to discuss identity and transitivity of the homology relation under the transformationist and emergentist paradigms respectively. Token identity and consequent transitivity of homology relations are shown to be requirements that are too strong to allow the origin of genuine evolutionary novelties. We consequently introduce the concept of compositional identity that is grounded in relations prevailing between parts (organs and organ systems) of a whole (organism). We recognize an ontogenetic identity of parts within a whole throughout the sequence of successive developmental stages of those parts: this is an intra-organismal character identity maintained throughout developmental trajectory. Correspondingly, we recognize a phylogenetic identity of homologous parts within two or more organisms of different species: this is an inter-species character identity maintained throughout evolutionary trajectory. These different dimensions of character identity--ontogenetic (through development) and phylogenetic (via shared evolutionary history)--break the transitivity of homology relations. Under the transformationist paradigm, the relation of homology reigns over the entire character (-state) transformation series, and thus encompasses the plesiomorphic as well as the apomorphic condition of form. In contrast, genuine evolutionary novelties originate not through transformation of ancestral characters (-states), but instead through deviating developmental trajectories that result in alternate characters. Under the emergentist paradigm, homology is thus synonymous with synapomorphy. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution Published by Wiley Periodicals, Inc.

Multi-stage versus single-stage inflation and deflation cycle for alternating low pressure air mattresses to prevent pressure ulcers in hospitalised patients: a randomised-controlled clinical trial.

PubMed

Demarré, L; Beeckman, D; Vanderwee, K; Defloor, T; Grypdonck, M; Verhaeghe, S

2012-04-01

The duration and the amount of pressure and shear must be reduced in order to minimize the risk of pressure ulcer development. Alternating low pressure air mattresses with multi-stage inflation and deflation cycle of the air cells have been developed to relieve pressure by sequentially inflating and deflating the air cells. Evidence about the effectiveness of this type of mattress in clinical practice is lacking. This study aimed to compare the effectiveness of an alternating low pressure air mattress that has a standard single-stage inflation and deflation cycle of the air cells with an alternating low pressure air mattress with multi-stage inflation and deflation cycle of the air cells. A randomised controlled trial was performed in a convenience sample of 25 wards in five hospitals in Belgium. In total, 610 patients were included and randomly assigned to the experimental group (n=298) or the control group (n=312). In the experimental group, patients were allocated to an alternating low pressure air mattress with multi-stage inflation and deflation cycle of the air cells. In the control group, patients were allocated to an alternating low pressure air mattress with a standard single-stage inflation and deflation cycle of the air cells. The outcome was defined as cumulative pressure ulcer incidence (Grade II-IV). An intention-to-treat analysis was performed. There was no significant difference in cumulative pressure ulcer incidence (Grade II-IV) between both groups (Exp.=5.7%, Contr.=5.8%, p=0.97). When patients developed a pressure ulcer, the median time was 5.0 days in the experimental group (IQR=3.0-8.5) and 8.0 days in the control group (IQR=3.0-8.5) (Mann-Whitney U-test=113, p=0.182). The probability to remain pressure ulcer free during the observation period in this trial did not differ significantly between the experimental group and the control group (log-rank χ(2)=0.013, df=1, p=0.911). An alternating low pressure air mattress with multi-stage inflation and deflation of the air cells does not result in a significantly lower pressure ulcer incidence compared to an alternating low pressure air mattress with a standard single-stage inflation and deflation cycle of the air cells. Both alternating mattress types are equally effective to prevent pressure ulcer development. © 2011 Elsevier Ltd. All rights reserved.

Asynchronous spatial evolutionary games.

PubMed

Newth, David; Cornforth, David

2009-02-01

Over the past 50 years, much attention has been given to the Prisoner's Dilemma as a metaphor for problems surrounding the evolution and maintenance of cooperative and altruistic behavior. The bulk of this work has dealt with the successfulness and robustness of various strategies. Nowak and May (1992) considered an alternative approach to studying evolutionary games. They assumed that players were distributed across a two-dimensional (2D) lattice, interactions between players occurred locally, rather than at long range as in the well mixed situation. The resulting spatial evolutionary games display dynamics not seen in their well-mixed counterparts. An assumption underlying much of the work on spatial evolutionary games is that the state of all players is updated in unison or in synchrony. Using the framework outlined in Nowak and May (1992), we examine the effect of various asynchronous updating schemes on the dynamics of spatial evolutionary games. There are potential implications for the dynamics of a wide variety of spatially extended systems in biology, physics and chemistry.

Phylogenetic inertia and Darwin's higher law.

PubMed

Shanahan, Timothy

2011-03-01

The concept of 'phylogenetic inertia' is routinely deployed in evolutionary biology as an alternative to natural selection for explaining the persistence of characteristics that appear sub-optimal from an adaptationist perspective. However, in many of these contexts the precise meaning of 'phylogenetic inertia' and its relationship to selection are far from clear. After tracing the history of the concept of 'inertia' in evolutionary biology, I argue that treating phylogenetic inertia and natural selection as alternative explanations is mistaken because phylogenetic inertia is, from a Darwinian point of view, simply an expected effect of selection. Although Darwin did not discuss 'phylogenetic inertia,' he did assert the explanatory priority of selection over descent. An analysis of 'phylogenetic inertia' provides a perspective from which to assess Darwin's view. Copyright © 2010 Elsevier Ltd. All rights reserved.

Exploration of Venus' Deep Atmosphere and Surface Environment

NASA Technical Reports Server (NTRS)

Glaze, L. S.; Amato, M.; Garvin, J. B.; Johnson, N. M.

2017-01-01

Venus formed in the same part of our solar system as Earth, apparently from similar materials. Although both planets are about the same size, their differences are profound. Venus and Earth experienced vastly different evolutionary pathways resulting in unexplained differences in atmospheric composition and dynamics, as well as in geophysical processes of the planetary surfaces and interiors. Understanding when and why the evolutionary pathways of Venus and Earth diverged is key to understanding how terrestrial planets form and how their atmospheres and surfaces evolve. Measurements made in situ, within the near-surface or surface environment, are critical to addressing unanswered questions. We have made substantial progress modernizing and maturing pressure vessel technologies to enable science operations in the high temperature and pressure near-surface/surfaceenvironment of Venus.

Refuge alternatives relief valve testing and design with updated test stand

PubMed Central

Lutz, T.J.; Bissert, P.T.; Homce, G.T.; Yonkey, J.A.

2018-01-01

Underground refuge alternatives require an air source to supply breathable air to the occupants. This requires pressure relief valves to prevent unsafe pressures from building up within the refuge alternative. The U.S. Mine Safety and Health Administration (MSHA) mandates that pressure relief valves prevent pressure from exceeding 1.25 kPa (0.18 psi), or as specified by the manufacturer, above mine atmospheric pressure when a fan or compressor is used for the air supply. The U.S. National Institute for Occupational Safety and Health (NIOSH) tested a variety of pressure relief valves using an instrumented test fixture consisting of data acquisition equipment, a centrifugal blower, ductwork and various sensors to determine if the subject pressure relief valves meet the MSHA requirement. Relief pressures and flow characteristics, including opening pressure and flow rate, were measured for five different pressure relief valves under a variety of conditions. The subject pressure relief valves included two off-the-shelf modified check valves, two check valves used in MSHA-approved built-in-place refuge alternatives, and a commercially available valve that was designed for a steel refuge alternative and is currently being used in some built-in-place refuge alternatives. The test results showed relief pressures ranging from 0.20 to 1.53 kPa (0.03 to 0.22 psi) and flow rates up to 19.3 m3/min (683 scfm). As tested, some of the pressure relief valves did not meet the 1.25 kPa (0.18 psi) relief specification. PMID:29563650

33 CFR 154.2180 - Alternative testing program-Generally.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Control Systems Alternative Analyzer and Pressure Sensor Reliability Testing § 154.2180 Alternative... and pressure sensor safety testing requirements provided by 33 CFR 154.2150(c) and 33 CFR 154.2250(c... 33 CFR 154.2181. (d) All pressure sensors/switches used in a VCS must be tested for safety system...

The Roles of Standing Genetic Variation and Evolutionary History in Determining the Evolvability of Anti-Predator Strategies

PubMed Central

Dworkin, Ian; Wagner, Aaron P.

2014-01-01

Standing genetic variation and the historical environment in which that variation arises (evolutionary history) are both potentially significant determinants of a population's capacity for evolutionary response to a changing environment. Using the open-ended digital evolution software Avida, we evaluated the relative importance of these two factors in influencing evolutionary trajectories in the face of sudden environmental change. We examined how historical exposure to predation pressures, different levels of genetic variation, and combinations of the two, affected the evolvability of anti-predator strategies and competitive abilities in the presence or absence of threats from new, invasive predator populations. We show that while standing genetic variation plays some role in determining evolutionary responses, evolutionary history has the greater influence on a population's capacity to evolve anti-predator traits, i.e. traits effective against novel predators. This adaptability likely reflects the relative ease of repurposing existing, relevant genes and traits, and the broader potential value of the generation and maintenance of adaptively flexible traits in evolving populations. PMID:24955847

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

PubMed

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

2010-09-28

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

Understanding the mind from an evolutionary perspective: an overview of evolutionary psychology.

PubMed

Shackelford, Todd K; Liddle, James R

2014-05-01

The theory of evolution by natural selection provides the only scientific explanation for the existence of complex adaptations. The design features of the brain, like any organ, are the result of selection pressures operating over deep time. Evolutionary psychology posits that the human brain comprises a multitude of evolved psychological mechanisms, adaptations to specific and recurrent problems of survival and reproduction faced over human evolutionary history. Although some mistakenly view evolutionary psychology as promoting genetic determinism, evolutionary psychologists appreciate and emphasize the interactions between genes and environments. This approach to psychology has led to a richer understanding of a variety of psychological phenomena, and has provided a powerful foundation for generating novel hypotheses. Critics argue that evolutionary psychologists resort to storytelling, but as with any branch of science, empirical testing is a vital component of the field, with hypotheses standing or falling with the weight of the evidence. Evolutionary psychology is uniquely suited to provide a unifying theoretical framework for the disparate subdisciplines of psychology. An evolutionary perspective has provided insights into several subdisciplines of psychology, while simultaneously demonstrating the arbitrary nature of dividing psychological science into such subdisciplines. Evolutionary psychologists have amassed a substantial empirical and theoretical literature, but as a relatively new approach to psychology, many questions remain, with several promising directions for future research. For further resources related to this article, please visit the WIREs website. The authors have declared no conflicts of interest for this article. © 2014 John Wiley & Sons, Ltd.

Support surfaces for pressure ulcer prevention.

PubMed

McInnes, Elizabeth; Jammali-Blasi, Asmara; Bell-Syer, Sally E M; Dumville, Jo C; Middleton, Victoria; Cullum, Nicky

2015-09-03

Pressure ulcers (i.e. bedsores, pressure sores, pressure injuries, decubitus ulcers) are areas of localised damage to the skin and underlying tissue. They are common in the elderly and immobile, and costly in financial and human terms. Pressure-relieving support surfaces (i.e. beds, mattresses, seat cushions etc) are used to help prevent ulcer development. This systematic review seeks to establish:(1) the extent to which pressure-relieving support surfaces reduce the incidence of pressure ulcers compared with standard support surfaces, and,(2) their comparative effectiveness in ulcer prevention. In April 2015, for this fourth update we searched The Cochrane Wounds Group Specialised Register (searched 15 April 2015) which includes the results of regular searches of MEDLINE, EMBASE and CINAHL and The Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library 2015, Issue 3). Randomised controlled trials (RCTs) and quasi-randomised trials, published or unpublished, that assessed the effects of any support surface for prevention of pressure ulcers, in any patient group or setting which measured pressure ulcer incidence. Trials reporting only proxy outcomes (e.g. interface pressure) were excluded. Two review authors independently selected trials. Data were extracted by one review author and checked by another. Where appropriate, estimates from similar trials were pooled for meta-analysis. For this fourth update six new trials were included, bringing the total of included trials to 59.Foam alternatives to standard hospital foam mattresses reduce the incidence of pressure ulcers in people at risk (RR 0.40 95% CI 0.21 to 0.74). The relative merits of alternating- and constant low-pressure devices are unclear. One high-quality trial suggested that alternating-pressure mattresses may be more cost effective than alternating-pressure overlays in a UK context.Pressure-relieving overlays on the operating table reduce postoperative pressure ulcer incidence, although two trials indicated that foam overlays caused adverse skin changes. Meta-analysis of three trials suggest that Australian standard medical sheepskins prevent pressure ulcers (RR 0.56 95% CI 0.32 to 0.97).  People at high risk of developing pressure ulcers should use higher-specification foam mattresses rather than standard hospital foam mattresses. The relative merits of higher-specification constant low-pressure and alternating-pressure support surfaces for preventing pressure ulcers are unclear, but alternating-pressure mattresses may be more cost effective than alternating-pressure overlays in a UK context. Medical grade sheepskins are associated with a decrease in pressure ulcer development. Organisations might consider the use of some forms of pressure relief for high risk patients in the operating theatre.

Evolution of dispersal and life history interact to drive accelerating spread of an invasive species.

PubMed

Perkins, T Alex; Phillips, Benjamin L; Baskett, Marissa L; Hastings, Alan

2013-08-01

Populations on the edge of an expanding range are subject to unique evolutionary pressures acting on their life-history and dispersal traits. Empirical evidence and theory suggest that traits there can evolve rapidly enough to interact with ecological dynamics, potentially giving rise to accelerating spread. Nevertheless, which of several evolutionary mechanisms drive this interaction between evolution and spread remains an open question. We propose an integrated theoretical framework for partitioning the contributions of different evolutionary mechanisms to accelerating spread, and we apply this model to invasive cane toads in northern Australia. In doing so, we identify a previously unrecognised evolutionary process that involves an interaction between life-history and dispersal evolution during range shift. In roughly equal parts, life-history evolution, dispersal evolution and their interaction led to a doubling of distance spread by cane toads in our model, highlighting the potential importance of multiple evolutionary processes in the dynamics of range expansion. © 2013 John Wiley & Sons Ltd/CNRS.

Treatment resistance in urothelial carcinoma: an evolutionary perspective.

PubMed

Vlachostergios, Panagiotis J; Faltas, Bishoy M

2018-05-02

The emergence of treatment-resistant clones is a critical barrier to cure in patients with urothelial carcinoma. Setting the stage for the evolution of resistance, urothelial carcinoma is characterized by extensive mutational heterogeneity, which is detectable even in patients with early stage disease. Chemotherapy and immunotherapy both act as selective pressures that shape the evolutionary trajectory of urothelial carcinoma throughout the course of the disease. A detailed understanding of the dynamics of evolutionary drivers is required for the rational development of curative therapies. Herein, we describe the molecular basis of the clonal evolution of urothelial carcinomas and the use of genomic approaches to predict treatment responses. We discuss various mechanisms of resistance to chemotherapy with a focus on the mutagenic effects of the DNA dC->dU-editing enzymes APOBEC3 family of proteins. We also review the evolutionary mechanisms underlying resistance to immunotherapy, such as the loss of clonal tumour neoantigens. By dissecting treatment resistance through an evolutionary lens, the field will advance towards true precision medicine for urothelial carcinoma.

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.

PubMed

Vierstra, Jeff; Rynes, Eric; Sandstrom, Richard; Zhang, Miaohua; Canfield, Theresa; Hansen, R Scott; Stehling-Sun, Sandra; Sabo, Peter J; Byron, Rachel; Humbert, Richard; Thurman, Robert E; Johnson, Audra K; Vong, Shinny; Lee, Kristen; Bates, Daniel; Neri, Fidencio; Diegel, Morgan; Giste, Erika; Haugen, Eric; Dunn, Douglas; Wilken, Matthew S; Josefowicz, Steven; Samstein, Robert; Chang, Kai-Hsin; Eichler, Evan E; De Bruijn, Marella; Reh, Thomas A; Skoultchi, Arthur; Rudensky, Alexander; Orkin, Stuart H; Papayannopoulou, Thalia; Treuting, Piper M; Selleri, Licia; Kaul, Rajinder; Groudine, Mark; Bender, M A; Stamatoyannopoulos, John A

2014-11-21

To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I-hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS maps from orthologous compartments. We found that the mouse and human genomes have undergone extensive cis-regulatory rewiring that combines branch-specific evolutionary innovation and loss with widespread repurposing of conserved DHSs to alternative cell fates, and that this process is mediated by turnover of transcription factor (TF) recognition elements. Despite pervasive evolutionary remodeling of the location and content of individual cis-regulatory regions, within orthologous mouse and human cell types the global fraction of regulatory DNA bases encoding recognition sites for each TF has been strictly conserved. Our findings provide new insights into the evolutionary forces shaping mammalian regulatory DNA landscapes. Copyright © 2014, American Association for the Advancement of Science.

The semaphorontic view of homology

PubMed Central

Assis, Leandro C.S.; Rieppel, Olivier

2015-01-01

ABSTRACT The relation of homology is generally characterized as an identity relation, or alternatively as a correspondence relation, both of which are transitive. We use the example of the ontogenetic development and evolutionary origin of the gnathostome jaw to discuss identity and transitivity of the homology relation under the transformationist and emergentist paradigms respectively. Token identity and consequent transitivity of homology relations are shown to be requirements that are too strong to allow the origin of genuine evolutionary novelties. We consequently introduce the concept of compositional identity that is grounded in relations prevailing between parts (organs and organ systems) of a whole (organism). We recognize an ontogenetic identity of parts within a whole throughout the sequence of successive developmental stages of those parts: this is an intra‐organismal character identity maintained throughout developmental trajectory. Correspondingly, we recognize a phylogenetic identity of homologous parts within two or more organisms of different species: this is an inter‐species character identity maintained throughout evolutionary trajectory. These different dimensions of character identity—ontogenetic (through development) and phylogenetic (via shared evolutionary history)—break the transitivity of homology relations. Under the transformationist paradigm, the relation of homology reigns over the entire character (‐state) transformation series, and thus encompasses the plesiomorphic as well as the apomorphic condition of form. In contrast, genuine evolutionary novelties originate not through transformation of ancestral characters (‐states), but instead through deviating developmental trajectories that result in alternate characters. Under the emergentist paradigm, homology is thus synonymous with synapomorphy. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 578–587, 2015. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution published by Wiley Periodicals, Inc. PMID:26175214

Natural selection. IV. The Price equation.

PubMed

Frank, S A

2012-06-01

The Price equation partitions total evolutionary change into two components. The first component provides an abstract expression of natural selection. The second component subsumes all other evolutionary processes, including changes during transmission. The natural selection component is often used in applications. Those applications attract widespread interest for their simplicity of expression and ease of interpretation. Those same applications attract widespread criticism by dropping the second component of evolutionary change and by leaving unspecified the detailed assumptions needed for a complete study of dynamics. Controversies over approximation and dynamics have nothing to do with the Price equation itself, which is simply a mathematical equivalence relation for total evolutionary change expressed in an alternative form. Disagreements about approach have to do with the tension between the relative valuation of abstract versus concrete analyses. The Price equation's greatest value has been on the abstract side, particularly the invariance relations that illuminate the understanding of natural selection. Those abstract insights lay the foundation for applications in terms of kin selection, information theory interpretations of natural selection and partitions of causes by path analysis. I discuss recent critiques of the Price equation by Nowak and van Veelen. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

An Evolutionary Framework for Understanding the Origin of Eukaryotes.

PubMed

Blackstone, Neil W

2016-04-27

Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real-the endosymbiosis that led to the mitochondrion is often described as "non-Darwinian" because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious-all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

The physiology of dinosaurs: circulatory and respiratory function in the largest animals ever to walk the earth.

PubMed

Pierson, David J

2009-07-01

The cardiopulmonary physiology of dinosaurs-and especially of the long-necked sauropods, which grew much larger than any land animals before or since-should be inherently fascinating to anyone involved in respiratory care. What would the blood pressure be in an animal 12 m (40 ft) tall? How could airway resistance and dead space be overcome while breathing through a trachea 9 m (30 ft) long? The last decade has seen a dramatic increase in evidence bearing on these questions. Insight has come not only from new fossil discoveries but also from comparative studies of living species, clarification of evolutionary relationships, new evaluation techniques, computer modeling, and discoveries about the earth's ancient atmosphere. Pumping a vertical column of blood 8 m (26 ft) above the heart would probably require an arterial blood pressure > 600 mm Hg, and the implications of this for cardiac size and function have led to the proposal of several alternative cardiopulmonary designs. Diverse lines of evidence suggest that the giant sauropods were probably warm-blooded and metabolically active when young, but slowed their metabolism as they approached adult size, which diminished the load on the circulatory system. Circulatory considerations leave little doubt that the dinosaurs had 4-chambered hearts. Birds evolved from dinosaurs, and the avian-type air-sac respiratory system, which is more efficient than its mammalian counterpart, may hold the answer to the breathing problems posed by the sauropods' very long necks. Geochemical and other data indicate that, at the time the dinosaurs first appeared, the atmospheric oxygen concentration was only about half of what it is today, and development of the avian-type respiratory system may have been key in the dinosaurs' evolutionary success, enabling them to out-compete the mammals and dominate the land for 150 million years.

Analysis of codon usage bias of envelope glycoprotein genes in nuclear polyhedrosis virus (NPV) and its relation to evolution.

PubMed

Zhao, Yongchao; Zheng, Hao; Xu, Anying; Yan, Donghua; Jiang, Zijian; Qi, Qi; Sun, Jingchen

2016-08-24

Analysis of codon usage bias is an extremely versatile method using in furthering understanding of the genetic and evolutionary paths of species. Codon usage bias of envelope glycoprotein genes in nuclear polyhedrosis virus (NPV) has remained largely unexplored at present. Hence, the codon usage bias of NPV envelope glycoprotein was analyzed here to reveal the genetic and evolutionary relationships between different viral species in baculovirus genus. A total of 9236 codons from 18 different species of NPV of the baculovirus genera were used to perform this analysis. Glycoprotein of NPV exhibits weaker codon usage bias. Neutrality plot analysis and correlation analysis of effective number of codons (ENC) values indicate that natural selection is the main factor influencing codon usage bias, and that the impact of mutation pressure is relatively smaller. Another cluster analysis shows that the kinship or evolutionary relationships of these viral species can be divided into two broad categories despite all of these 18 species are from the same baculovirus genus. There are many elements that can affect codon bias, such as the composition of amino acids, mutation pressure, natural selection, gene expression level, and etc. In the meantime, cluster analysis also illustrates that codon usage bias of virus envelope glycoprotein can serve as an effective means of evolutionary classification in baculovirus genus.

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A

PubMed Central

Ndhlovu, Andrew; Durand, Pierre M.; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. Database URL: http://www.bioinf.wits.ac.za/software/fire/evodb PMID:26140928

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A.

PubMed

Ndhlovu, Andrew; Durand, Pierre M; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. © The Author(s) 2015. Published by Oxford University Press.

Historical contingency and its biophysical basis in glucocorticoid receptor evolution.

PubMed

Harms, Michael J; Thornton, Joseph W

2014-08-14

Understanding how chance historical events shape evolutionary processes is a central goal of evolutionary biology. Direct insights into the extent and causes of evolutionary contingency have been limited to experimental systems, because it is difficult to know what happened in the deep past and to characterize other paths that evolution could have followed. Here we combine ancestral protein reconstruction, directed evolution and biophysical analysis to explore alternative 'might-have-been' trajectories during the ancient evolution of a novel protein function. We previously found that the evolution of cortisol specificity in the ancestral glucocorticoid receptor (GR) was contingent on permissive substitutions, which had no apparent effect on receptor function but were necessary for GR to tolerate the large-effect mutations that caused the shift in specificity. Here we show that alternative mutations that could have permitted the historical function-switching substitutions are extremely rare in the ensemble of genotypes accessible to the ancestral GR. In a library of thousands of variants of the ancestral protein, we recovered historical permissive substitutions but no alternative permissive genotypes. Using biophysical analysis, we found that permissive mutations must satisfy at least three physical requirements--they must stabilize specific local elements of the protein structure, maintain the correct energetic balance between functional conformations, and be compatible with the ancestral and derived structures--thus revealing why permissive mutations are rare. These findings demonstrate that GR evolution depended strongly on improbable, non-deterministic events, and this contingency arose from intrinsic biophysical properties of the protein.

Extraordinary intelligence and the care of infants

PubMed Central

Piantadosi, Steven T.; Kidd, Celeste

2016-01-01

We present evidence that pressures for early childcare may have been one of the driving factors of human evolution. We show through an evolutionary model that runaway selection for high intelligence may occur when (i) altricial neonates require intelligent parents, (ii) intelligent parents must have large brains, and (iii) large brains necessitate having even more altricial offspring. We test a prediction of this account by showing across primate genera that the helplessness of infants is a particularly strong predictor of the adults’ intelligence. We discuss related implications, including this account’s ability to explain why human-level intelligence evolved specifically in mammals. This theory complements prior hypotheses that link human intelligence to social reasoning and reproductive pressures and explains how human intelligence may have become so distinctive compared with our closest evolutionary relatives. PMID:27217560

Evolutionary selective pressure on three mitochondrial SNPs is consistent with their influence on metabolic efficiency in Pima Indians.

PubMed

Chamala, Srikar; Beckstead, Wesley A; Rowe, Mark J; McClellan, David A

2007-01-01

We investigated whether the effect of evolutionary selection on three recent Single Nucleotide Polymorphisms (SNPs) in the mitochondrial sub-haplogroups of Pima Indians is consistent with their effects on metabolic efficiency. The mitochondrial SNPs impact metabolic rate and respiratory quotient, and may be adaptations to caloric restriction in a desert habitat. Using TreeSAAP software, we examined evolutionary selection in 107 mammalian species at these SNPs, characterising the biochemical shifts produced by the amino acid substitutions. Our results suggest that two SNPs were affected by selection during mammalian evolution in a manner consistent with their effects on metabolic efficiency in Pima Indians.

Pancreatic cancer biology and genetics from an evolutionary perspective

PubMed Central

Makohon-Moore, Alvin; Iacobuzio-Donahue, Christine A.

2017-01-01

Cancer is an evolutionary disease, containing the hallmarks of an asexually reproducing unicellular organism subject to evolutionary paradigms. Pancreatic ductal adenocarcinoma (hereafter referred to as pancreatic cancer) is a particularly robust example of this phenomenon. Genomic features indicate that pancreatic cancer cells are selected for fitness advantages when encountering the geographic and resource-depleted constraints of the microenvironment. Phenotypic adaptations to these pressures help disseminated cells to survive in secondary sites, a major clinical problem for patients with this disease. In this Review we gather the wide-ranging aspects of pancreatic cancer research into a single concept rooted in Darwinian evolution, with the goal of identifying novel insights and opportunities for study. PMID:27444064

New Possible Structure of Silicide Mg2Si under Pressure

NASA Astrophysics Data System (ADS)

Luniakov, Yu. V.

2018-05-01

As a result of an evolutionary search based on the density functional theory, a new low-symmetry structure of silicide Mg2Si under pressure was discovered. This structure can exist along with the known structures of the symmetry Pnma and P63/mmc and is stable at a pressure of about 20 GPa. The lattice parameters of the discovered structure are in better agreement with the experimental values than the lattice parameters of the known structures.

Developmental decoupling of alternative phenotypes: insights from the transcriptomes of horn-polyphenic beetles

PubMed Central

Snell-Rood, Emilie C.; Cash, Amy; Han, Mira V.; Kijimoto, Teiya; Andrews, Justen; Moczek, Armin P.

2010-01-01

Developmental mechanisms play an important role in determining the costs, limits, and evolutionary consequences of phenotypic plasticity. One issue central to these claims is the hypothesis of developmental decoupling, where alternate morphs result from evolutionarily independent developmental pathways. We address this assumption through a microarray study that tests whether differences in gene expression between alternate morphs are as divergent as those between sexes, a classic example of developmental decoupling. We then examine whether genes with morph-biased expression are less conserved than genes with shared expression between morphs, as predicted if developmental decoupling relaxes pleiotropic constraints on divergence. We focus on the developing horns and brains of two species of horned beetles with spectacular sexual- and morph-dimorphism in the expression of horns and fighting behavior. We find that patterns of gene expression were as divergent between morphs as they were between sexes. However, overall patterns of gene expression were also highly correlated across morphs and sexes. Morph-biased genes were more evolutionarily divergent, suggesting a role of relaxed pleiotropic constraints or relaxed selection. Together these results suggest that alternate morphs are to some extent developmentally decoupled, and that this decoupling has significant evolutionary consequences. However, alternative morphs may not be as developmentally decoupled as sometimes assumed and such hypotheses of development should be revisited and refined. PMID:20731717

The effect of conflicting pressures on the evolution of division of labor.

PubMed

Goldsby, Heather J; Knoester, David B; Kerr, Benjamin; Ofria, Charles

2014-01-01

Within nature, many groups exhibit division of labor. Individuals in these groups are under seemingly antagonistic pressures to perform the task most directly beneficial to themselves and to potentially perform a less desirable task to ensure the success of the group. Performing experiments to study how these pressures interact in an evolutionary context is challenging with organic systems because of long generation times and difficulties related to group propagation and fine-grained control of within-group and between-group pressures. Here, we use groups of digital organisms (i.e., self-replicating computer programs) to explore how populations respond to antagonistic multilevel selection pressures. Specifically, we impose a within-group pressure to perform a highly-rewarded role and a between-group pressure to perform a diverse suite of roles. Thus, individuals specializing on highly-rewarded roles will have a within-group advantage, but groups of such specialists have a between-group disadvantage. We find that digital groups could evolve to be either single-lineage or multi-lineage, depending on experimental parameters. These group compositions are reminiscent of different kinds of major evolutionary transitions that occur within nature, where either relatives divide labor (fraternal transitions) or multiple different organisms coordinate activities to form a higher-level individual (egalitarian transitions). Regardless of group composition, organisms embraced phenotypic plasticity as a means for genetically similar individuals to perform different roles. Additionally, in multi-lineage groups, organisms from lineages performing highly-rewarded roles also employed reproductive restraint to ensure successful coexistence with organisms from other lineages.

Effect of Geometric Parameters on the Performance of Second Throat Annular Steam Ejectors

DTIC Science & Technology

1991-07-01

Cell Pressure versus Rake Average Exit Pitot Pressure . . . . . . . . . . . 42 15. Baseline Wall Pressure Profiles...diffuser exit plane pitot pressure rake . 2.5.2 Alternate Configurations Six alternate ejector diffuser configurations were tested. A summary of...along the walls of the diffusers to help characterize the flow. The ejector diffuser exit pitot pressure was measured with a 6-probe pitot pressure rake

Evolutionary Interactions Between Visual and Chemical Signals: Chemosignals Compensate for the Loss of a Visual Signal in Male Sceloporus Lizards.

PubMed

Pruett, Jake A; Zúñiga-Vega, J Jaime; Campos, Stephanie M; Soini, Helena A; Novotny, Milos V; Vital-García, Cuauhcihuatl; Martins, Emília P; Hews, Diana K

2016-11-01

Animals rely on multimodal signals to obtain information from conspecifics through alternative sensory systems, and the evolutionary loss of a signal in one modality may lead to compensation through increased use of signals in an alternative modality. We investigated associations between chemical signaling and evolutionary loss of abdominal color patches in males of four species (two plain-bellied and two colorful-bellied) of Sceloporus lizards. We conducted field trials to compare behavioral responses of male lizards to swabs with femoral gland (FG) secretions from conspecific males and control swabs (clean paper). We also analyzed the volatile organic compound (VOC) composition of male FG secretions by stir bar extraction and gas chromatography-mass spectrometry (GC-MS) to test the hypothesis that loss of the visual signal is associated with elaboration of the chemical signal. Males of plain-bellied, but not colorful-bellied species exhibited different rates of visual displays when exposed to swabs of conspecific FG secretions relative to control swabs. The VOC composition of male Sceloporus FG secretions was similar across all four species, and no clear association between relative abundances of VOCs and evolutionary loss of abdominal color patches was observed. The emerging pattern is that behavioral responses to conspecific chemical signals are species- and context-specific in male Sceloporus, and compensatory changes in receivers, but not signalers may be involved in mediating increased responsiveness to chemical signals in males of plain-bellied species.

Role of Water in the Selection of Stable Proteins at Ambient and Extreme Thermodynamic Conditions

NASA Astrophysics Data System (ADS)

Bianco, Valentino; Franzese, Giancarlo; Dellago, Christoph; Coluzza, Ivan

2017-04-01

Proteins that are functional at ambient conditions do not necessarily work at extreme conditions of temperature T and pressure P . Furthermore, there are limits of T and P above which no protein has a stable functional state. Here, we show that these limits and the selection mechanisms for working proteins depend on how the properties of the surrounding water change with T and P . We find that proteins selected at high T are superstable and are characterized by a nonextreme segregation of a hydrophilic surface and a hydrophobic core. Surprisingly, a larger segregation reduces the stability range in T and P . Our computer simulations, based on a new protein design protocol, explain the hydropathy profile of proteins as a consequence of a selection process influenced by water. Our results, potentially useful for engineering proteins and drugs working far from ambient conditions, offer an alternative rationale to the evolutionary action exerted by the environment in extreme conditions.

Under pressure: evolutionary engineering of yeast strains for improved performance in fuels and chemicals production.

PubMed

Mans, Robert; Daran, Jean-Marc G; Pronk, Jack T

2018-04-01

Evolutionary engineering, which uses laboratory evolution to select for industrially relevant traits, is a popular strategy in the development of high-performing yeast strains for industrial production of fuels and chemicals. By integrating whole-genome sequencing, bioinformatics, classical genetics and genome-editing techniques, evolutionary engineering has also become a powerful approach for identification and reverse engineering of molecular mechanisms that underlie industrially relevant traits. New techniques enable acceleration of in vivo mutation rates, both across yeast genomes and at specific loci. Recent studies indicate that phenotypic trade-offs, which are often observed after evolution under constant conditions, can be mitigated by using dynamic cultivation regimes. Advances in research on synthetic regulatory circuits offer exciting possibilities to extend the applicability of evolutionary engineering to products of yeasts whose synthesis requires a net input of cellular energy. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Navy ManTech 2010 Project Book

DTIC Science & Technology

2010-01-01

31 S2253 Ultrasonic Testing as an Alternative to Radiography for the Inspection of Naval Piping, Pressure Vessel and Machinery Welds...for Inspection S2253 — Ultrasonic Testing as an Alternative to Radiography for the Inspection of Naval Piping, Pressure Vessel and Machinery Welds...Ultrasonic Testing as an Alternative to Radiography for the Inspection of Naval Piping, Pressure Vessel and Machinery Welds

75 FR 13 - Alternate Fracture Toughness Requirements for Protection Against Pressurized Thermal Shock Events

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-04

...The Nuclear Regulatory Commission (NRC) is amending its regulations to provide alternate fracture toughness requirements for protection against pressurized thermal shock (PTS) events for pressurized water reactor (PWR) pressure vessels. This final rule provides alternate PTS requirements based on updated analysis methods. This action is desirable because the existing requirements are based on unnecessarily conservative probabilistic fracture mechanics analyses. This action reduces regulatory burden for those PWR licensees who expect to exceed the existing requirements before the expiration of their licenses, while maintaining adequate safety, and may choose to comply with the final rule as an alternative to complying with the existing requirements.

Sex determination strategies in 2012: towards a common regulatory model?

PubMed Central

2012-01-01

Sex determination is a complicated process involving large-scale modifications in gene expression affecting virtually every tissue in the body. Although the evolutionary origin of sex remains controversial, there is little doubt that it has developed as a process of optimizing metabolic control, as well as developmental and reproductive functions within a given setting of limited resources and environmental pressure. Evidence from various model organisms supports the view that sex determination may occur as a result of direct environmental induction or genetic regulation. The first process has been well documented in reptiles and fish, while the second is the classic case for avian species and mammals. Both of the latter have developed a variety of sex-specific/sex-related genes, which ultimately form a complete chromosome pair (sex chromosomes/gonosomes). Interestingly, combinations of environmental and genetic mechanisms have been described among different classes of animals, thus rendering the possibility of a unidirectional continuous evolutionary process from the one type of mechanism to the other unlikely. On the other hand, common elements appear throughout the animal kingdom, with regard to a) conserved key genes and b) a central role of sex steroid control as a prerequisite for ultimately normal sex differentiation. Studies in invertebrates also indicate a role of epigenetic chromatin modification, particularly with regard to alternative splicing options. This review summarizes current evidence from research in this hot field and signifies the need for further study of both normal hormonal regulators of sexual phenotype and patterns of environmental disruption. PMID:22357269

Urotensin-II System in Genetic Control of Blood Pressure and Renal Function

PubMed Central

Debiec, Radoslaw; Christofidou, Paraskevi; Denniff, Matthew; Bloomer, Lisa D.; Bogdanski, Pawel; Wojnar, Lukasz; Musialik, Katarzyna; Charchar, Fadi J.; Thompson, John R.; Waterworth, Dawn; Song, Kijoung; Vollenweider, Peter; Waeber, Gerard; Zukowska-Szczechowska, Ewa; Samani, Nilesh J.; Lambert, David; Tomaszewski, Maciej

2013-01-01

Urotensin-II controls ion/water homeostasis in fish and vascular tone in rodents. We hypothesised that common genetic variants in urotensin-II pathway genes are associated with human blood pressure or renal function. We performed family-based analysis of association between blood pressure, glomerular filtration and genes of the urotensin-II pathway (urotensin-II, urotensin-II related peptide, urotensin-II receptor) saturated with 28 tagging single nucleotide polymorphisms in 2024 individuals from 520 families; followed by an independent replication in 420 families and 7545 unrelated subjects. The expression studies of the urotensin-II pathway were carried out in 97 human kidneys. Phylogenetic evolutionary analysis was conducted in 17 vertebrate species. One single nucleotide polymorphism (rs531485 in urotensin-II gene) was associated with adjusted estimated glomerular filtration rate in the discovery cohort (p = 0.0005). It showed no association with estimated glomerular filtration rate in the combined replication resource of 8724 subjects from 6 populations. Expression of urotensin-II and its receptor showed strong linear correlation (r = 0.86, p<0.0001). There was no difference in renal expression of urotensin-II system between hypertensive and normotensive subjects. Evolutionary analysis revealed accumulation of mutations in urotensin-II since the divergence of primates and weaker conservation of urotensin-II receptor in primates than in lower vertebrates. Our data suggest that urotensin-II system genes are unlikely to play a major role in genetic control of human blood pressure or renal function. The signatures of evolutionary forces acting on urotensin-II system indicate that it may have evolved towards loss of function since the divergence of primates. PMID:24391740

Autoimmunity as a Driving Force of Cognitive Evolution

PubMed Central

Nataf, Serge

2017-01-01

In the last decades, increasingly robust experimental approaches have formally demonstrated that autoimmunity is a physiological process involved in a large range of functions including cognition. On this basis, the recently enunciated “brain superautoantigens” theory proposes that autoimmunity has been a driving force of cognitive evolution. It is notably suggested that the immune and nervous systems have somehow co-evolved and exerted a mutual selection pressure benefiting to both systems. In this two-way process, the evolutionary-determined emergence of neurons expressing specific immunogenic antigens (brain superautoantigens) has exerted a selection pressure on immune genes shaping the T-cell repertoire. Such a selection pressure on immune genes has translated into the emergence of a finely tuned autoimmune T-cell repertoire that promotes cognition. In another hand, the evolutionary-determined emergence of brain-autoreactive T-cells has exerted a selection pressure on neural genes coding for brain superautoantigens. Such a selection pressure has translated into the emergence of a neural repertoire (defined here as the whole of neurons, synapses and non-neuronal cells involved in cognitive functions) expressing brain superautoantigens. Overall, the brain superautoantigens theory suggests that cognitive evolution might have been primarily driven by internal cues rather than external environmental conditions. Importantly, while providing a unique molecular connection between neural and T-cell repertoires under physiological conditions, brain superautoantigens may also constitute an Achilles heel responsible for the particular susceptibility of Homo sapiens to “neuroimmune co-pathologies” i.e., disorders affecting both neural and T-cell repertoires. These may notably include paraneoplastic syndromes, multiple sclerosis as well as autism, schizophrenia and neurodegenerative diseases. In the context of this theoretical frame, a specific emphasis is given here to the potential evolutionary role exerted by two families of genes, namely the MHC class II genes, involved in antigen presentation to T-cells, and the Foxp genes, which play crucial roles in language (Foxp2) and the regulation of autoimmunity (Foxp3). PMID:29123465

Towards an alternative evolution model.

PubMed

van Waesberghe, H

1982-01-01

Lamarck and Darwin agreed on the inconstancy of species and on the exclusive gradualism of evolution (nature does not jump). Darwinism, revived as neo-Darwinism, was almost generally accepted from about 1930 till 1960. In the sixties the evolutionary importance of selection has been called in question by the neutralists. The traditional conception of the gene is disarranged by recent molecular-biological findings. Owing to the increasing confusion about the concept of genotype, this concept is reconsidered. The idea of the genotype as a cluster of genes is replaced by a cybernetical interpretation of the genotype. As nature does jump, exclusive gradualism is dismissed. Saltatory evolution is a natural phenomenon, provided by a sudden collapse of the thresholds which resist against evolution. The fossil record and the taxonomic system call for a macromutational interpretation. As Lamarck and Darwin overlooked the resistance of evolutionary thresholds, an alternative evolution model is needed, the first to be constructed on a palaeontological and taxonomic basis.

EVOLUTIONARY TRAJECTORIES OF ULTRACOMPACT 'BLACK WIDOW' PULSARS WITH VERY LOW MASS COMPANIONS

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

Benvenuto, O. G.; De Vito, M. A.; Horvath, J. E., E-mail: obenvenu@fcaglp.unlp.edu.ar, E-mail: adevito@fcaglp.unlp.edu.ar, E-mail: foton@astro.iag.usp.br

The existence of millisecond pulsars with planet-mass companions in close orbits is challenging from the stellar evolution point of view. We calculate in detail the evolution of binary systems self-consistently, including mass transfer, evaporation, and irradiation of the donor by X-ray feedback, demonstrating the existence of a new evolutionary path leading to short periods and compact donors as required by the observations of PSR J1719-1438. We also point out the alternative of an exotic nature of the companion planet-mass star.

Size selection from fishways and potential evolutionary responses in a threatened Atlantic salmon population

USGS Publications Warehouse

Maynard, George A.; Kinnison, M.T.; Zydlewski, Joseph D.

2017-01-01

The evolutionary effects of harvest on wild fish populations have been documented around the world; however, sublethal selective pressures can also cause evolutionary changes in phenotypes. For migratory fishes, passage facilities may represent instances of nonlethal selective pressure. Our analysis of 6 years of passage data suggests that certain fish passage facilities on the Penobscot River have been exerting selective pressure against large-bodied, anadromous Atlantic salmon (Salmo salar). At the second and third dams in the river, a 91-cm salmon was 21%–27% and 12%–16% less likely to pass than a 45-cm salmon, respectively. Fish size positively influences egg survival and number and is a heritable trait. Therefore, in a wild-reproducing population, exclusion of large fish from spawning areas may have population-level impacts. In the Penobscot River, most returning adults derive from a hatchery program that collects its broodstock after passing the first dam in the river. Analysis of fork lengths of salmon returning to the Penobscot River from 1978 to 2012 provided mixed support for evolution of size at maturity in different age classes in a pattern that may be expected from interactions with conservation hatchery operations. Additionally, slow-maturing and iteroparous individuals that represent the largest salmon size classes were essentially lost from the population during that time, and Penobscot River fish have shorter fork lengths at maturity than Atlantic salmon in undammed systems.

The evolutionary legacy of size-selective harvesting extends from genes to populations

PubMed Central

Uusi-Heikkilä, Silva; Whiteley, Andrew R; Kuparinen, Anna; Matsumura, Shuichi; Venturelli, Paul A; Wolter, Christian; Slate, Jon; Primmer, Craig R; Meinelt, Thomas; Killen, Shaun S; Bierbach, David; Polverino, Giovanni; Ludwig, Arne; Arlinghaus, Robert

2015-01-01

Size-selective harvesting is assumed to alter life histories of exploited fish populations, thereby negatively affecting population productivity, recovery, and yield. However, demonstrating that fisheries-induced phenotypic changes in the wild are at least partly genetically determined has proved notoriously difficult. Moreover, the population-level consequences of fisheries-induced evolution are still being controversially discussed. Using an experimental approach, we found that five generations of size-selective harvesting altered the life histories and behavior, but not the metabolic rate, of wild-origin zebrafish (Danio rerio). Fish adapted to high positively size selective fishing pressure invested more in reproduction, reached a smaller adult body size, and were less explorative and bold. Phenotypic changes seemed subtle but were accompanied by genetic changes in functional loci. Thus, our results provided unambiguous evidence for rapid, harvest-induced phenotypic and evolutionary change when harvesting is intensive and size selective. According to a life-history model, the observed life-history changes elevated population growth rate in harvested conditions, but slowed population recovery under a simulated moratorium. Hence, the evolutionary legacy of size-selective harvesting includes populations that are productive under exploited conditions, but selectively disadvantaged to cope with natural selection pressures that often favor large body size. PMID:26136825

The evolution of photosynthesis...again?

PubMed

Rothschild, Lynn J

2008-08-27

'Replaying the tape' is an intriguing 'would it happen again?' exercise. With respect to broad evolutionary innovations, such as photosynthesis, the answers are central to our search for life elsewhere. Photosynthesis permits a large planetary biomass on Earth. Specifically, oxygenic photosynthesis has allowed an oxygenated atmosphere and the evolution of large metabolically demanding creatures, including ourselves. There are at least six prerequisites for the evolution of biological carbon fixation: a carbon-based life form; the presence of inorganic carbon; the availability of reductants; the presence of light; a light-harvesting mechanism to convert the light energy into chemical energy; and carboxylating enzymes. All were present on the early Earth. To provide the evolutionary pressure, organic carbon must be a scarce resource in contrast to inorganic carbon. The probability of evolving a carboxylase is approached by creating an inventory of carbon-fixation enzymes and comparing them, leading to the conclusion that carbon fixation in general is basic to life and has arisen multiple times. Certainly, the evolutionary pressure to evolve new pathways for carbon fixation would have been present early in evolution. From knowledge about planetary systems and extraterrestrial chemistry, if organic carbon-based life occurs elsewhere, photosynthesis -- although perhaps not oxygenic photosynthesis -- would also have evolved.

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

PubMed Central

Bai, Shu-Nong

2017-01-01

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

An Evolutionary Framework for Understanding the Origin of Eukaryotes

PubMed Central

Blackstone, Neil W.

2016-01-01

Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes. PMID:27128953

Seasonal variation in male alternative reproductive tactics.

PubMed

Monroe, M J; Amundsen, T; Utne-Palm, A C; Mobley, K B

2016-12-01

Genetic parentage analyses reveal considerable diversity in alternative reproductive behaviours (e.g. sneaking) in many taxa. However, little is known about whether these behaviours vary seasonally and between populations. Here, we investigate seasonal variation in male reproductive behaviours in a population of two-spotted gobies (Gobiusculus flavescens) in Norway. Male two-spotted gobies guard nests, attract females and care for fertilized eggs. We collected clutches and nest-guarding males early and late in the breeding season in artificial nests and used microsatellite markers to reconstruct parentage from a subset of offspring from each nest. We hypothesized that mating, reproductive success and sneaking should be more prevalent early in the breeding season when competition for mates among males is predicted to be higher. However, parentage analyses revealed similar values of mating, reproductive success and high frequencies of successful sneaking early (30% of nests) and late (27% of nests) in the season. We also found that multiple females with eggs in the same nest were fertilized by one or more sneaker males, indicating that some males in this population engage in a satellite strategy. We contrast our results to previous work that demonstrates low levels of cuckoldry in a population in Sweden. Our results demonstrate marked stability in both the genetic mating system and male alternative reproductive tactics over the breeding season. However, sneaking rates may vary geographically within a species, likely due to local selection influencing ecological factors encountered at different locations. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Modeling and simulation of clutch pressure plate casting using alternate materials

NASA Astrophysics Data System (ADS)

Madhuraj, H. N.; Bharath, M. R.

2018-04-01

Clutch Pressure Plate is a stress bearing component in the clutch assembly. Cast iron alloys like FG300, G2500 are commonly used for clutch pressure plate castings. These materials have high compressive strength, low tensile strength & no ductility but these cost high for the manufacturers. There is a need for alternate material so as to reduce cost, defects in castings without losing the life and effectiveness of the clutch plate. The work carried out here is modeling the clutch pressure plate using CAD tool. And then the casting process is simulated by casting simulation for fluid flow and solidification analysis by trying alternate material. Here the castability of the alternate material En-Gjs-400-15 and the commonly used material FG300 for the clutch pressure plate component is analyzed by designing and optimizing a proper gating system.

An evolutionary perspective on gradual formation of superego in the primal horde

PubMed Central

Pulcu, Erdem

2014-01-01

Freud proposed that the processes which occurred in the primal horde are essential for understanding superego formation and therefore, the successful dissolution of the Oedipus complex. However, Freud theorized superego formation in the primal horde as if it is an instant, all-or-none achievement. The present paper proposes an alternative model aiming to explain gradual development of superego in the primitive man. The proposed model is built on knowledge from evolutionary and neural sciences as well as anthropology, and it particularly focuses on the evolutionary significance of the acquisition of fire by hominids in the Pleistocene period in the light of up-to-date archaeological findings. Acquisition of fire is discussed as a form of sublimation which might have helped Prehistoric man to maximize the utility of limited evolutionary biological resources, potentially contributing to the rate and extent of bodily evolution. The limitations of both Freud's original conceptualization and the present model are discussed accordingly in an interdisciplinary framework. PMID:24478740

Evolving cell models for systems and synthetic biology.

PubMed

Cao, Hongqing; Romero-Campero, Francisco J; Heeb, Stephan; Cámara, Miguel; Krasnogor, Natalio

2010-03-01

This paper proposes a new methodology for the automated design of cell models for systems and synthetic biology. Our modelling framework is based on P systems, a discrete, stochastic and modular formal modelling language. The automated design of biological models comprising the optimization of the model structure and its stochastic kinetic constants is performed using an evolutionary algorithm. The evolutionary algorithm evolves model structures by combining different modules taken from a predefined module library and then it fine-tunes the associated stochastic kinetic constants. We investigate four alternative objective functions for the fitness calculation within the evolutionary algorithm: (1) equally weighted sum method, (2) normalization method, (3) randomly weighted sum method, and (4) equally weighted product method. The effectiveness of the methodology is tested on four case studies of increasing complexity including negative and positive autoregulation as well as two gene networks implementing a pulse generator and a bandwidth detector. We provide a systematic analysis of the evolutionary algorithm's results as well as of the resulting evolved cell models.

Test of Von Baer's law of the conservation of early development.

PubMed

Poe, Steven

2006-11-01

One of the oldest and most pervasive ideas in comparative embryology is the perceived evolutionary conservation of early ontogeny relative to late ontogeny. Karl Von Baer first noted the similarity of early ontogeny across taxa, and Ernst Haeckel and Charles Darwin gave evolutionary interpretation to this phenomenon. In spite of a resurgence of interest in comparative embryology and the development of mechanistic explanations for Von Baer's law, the pattern itself has been largely untested. Here, I use statistical phylogenetic approaches to show that Von Baer's law is an unnecessarily complex explanation of the patterns of ontogenetic timing in several clades of vertebrates. Von Baer's law suggests a positive correlation between ontogenetic time and amount of evolutionary change. I compare ranked position in ontogeny to frequency of evolutionary change in rank for developmental events and find that these measures are not correlated, thus failing to support Von Baer's model. An alternative model that postulates that small changes in ontogenetic rank are evolutionarily easier than large changes is tentatively supported.

Characterization and evolutionary analysis of tributyltin-binding protein and pufferfish saxitoxin and tetrodotoxin-binding protein genes in toxic and nontoxic pufferfishes.

PubMed

Hashiguchi, Y; Lee, J M; Shiraishi, M; Komatsu, S; Miki, S; Shimasaki, Y; Mochioka, N; Kusakabe, T; Oshima, Y

2015-05-01

Understanding the evolutionary mechanisms of toxin accumulation in pufferfishes has been long-standing problem in toxicology and evolutionary biology. Pufferfish saxitoxin and tetrodotoxin-binding protein (PSTBP) is involved in the transport and accumulation of tetrodotoxin and is one of the most intriguing proteins related to the toxicity of pufferfishes. PSTBPs are fusion proteins consisting of two tandem repeated tributyltin-binding protein type 2 (TBT-bp2) domains. In this study, we examined the evolutionary dynamics of TBT-bp2 and PSTBP genes to understand the evolution of toxin accumulation in pufferfishes. Database searches and/or PCR-based cDNA cloning in nine pufferfish species (6 toxic and 3 nontoxic) revealed that all species possessed one or more TBT-bp2 genes, but PSTBP genes were found only in 5 toxic species belonging to genus Takifugu. These toxic Takifugu species possessed two or three copies of PSTBP genes. Phylogenetic analysis of TBT-bp2 and PSTBP genes suggested that PSTBPs evolved in the common ancestor of Takifugu species by repeated duplications and fusions of TBT-bp2 genes. In addition, a detailed comparison of Takifugu TBT-bp2 and PSTBP gene sequences detected a signature of positive selection under the pressure of gene conversion. The complicated evolutionary dynamics of TBT-bp2 and PSTBP genes may reflect the diversity of toxicity in pufferfishes. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

On the need for widespread horizontal gene transfers under genome size constraint.

PubMed

Isambert, Hervé; Stein, Richard R

2009-08-25

While eukaryotes primarily evolve by duplication-divergence expansion (and reduction) of their own gene repertoire with only rare horizontal gene transfers, prokaryotes appear to evolve under both gene duplications and widespread horizontal gene transfers over long evolutionary time scales. But, the evolutionary origin of this striking difference in the importance of horizontal gene transfers remains by and large a mystery. We propose that the abundance of horizontal gene transfers in free-living prokaryotes is a simple but necessary consequence of two opposite effects: i) their apparent genome size constraint compared to typical eukaryote genomes and ii) their underlying genome expansion dynamics through gene duplication-divergence evolution, as demonstrated by the presence of many tandem and block repeated genes. In principle, this combination of genome size constraint and underlying duplication expansion should lead to a coalescent-like process with extensive turnover of functional genes. This would, however, imply the unlikely, systematic reinvention of functions from discarded genes within independent phylogenetic lineages. Instead, we propose that the long-term evolutionary adaptation of free-living prokaryotes must have resulted in the emergence of efficient non-phylogenetic pathways to circumvent gene loss. This need for widespread horizontal gene transfers due to genome size constraint implies, in particular, that prokaryotes must remain under strong selection pressure in order to maintain the long-term evolutionary adaptation of their "mutualized" gene pool, beyond the inevitable turnover of individual prokaryote species. By contrast, the absence of genome size constraint for typical eukaryotes has presumably relaxed their need for widespread horizontal gene transfers and strong selection pressure. Yet, the resulting loss of genetic functions, due to weak selection pressure and inefficient gene recovery mechanisms, must have ultimately favored the emergence of more complex life styles and ecological integration of many eukaryotes. This article was reviewed by Pierre Pontarotti, Eugene V Koonin and Sergei Maslov.

Physiologically tolerable decompression profiles for supersonic transport type certification.

DOT National Transportation Integrated Search

1970-07-01

The Supersonic Transport represents a quantum step in civil aeronautics. It will cruise at altitudes having low ambient gaseous pressures far exceeding human capacities for compensatory respiration. In consideration of this evolutionary step, tentati...

Altruism, egoism, or neither: A cognitive-efficiency-based evolutionary biological perspective on helping behavior.

PubMed

Schulz, Armin W

2016-04-01

I argue for differences in the cognitive efficiency of different psychologies underlying helping behavior, and present an account of the adaptive pressures that result from these differences. Specifically, I argue that organisms often face pressure to move away from only being egoistically motivated to help: non-egoistic organisms are often able to determine how to help other organisms more quickly and with less recourse to costly cognitive resources like concentration and attention. Furthermore, I also argue that, while these pressures away from pure egoism can lead to the evolution of altruists, they can also lead to the evolution of reciprocation-focused behaviorist helpers or even of reflex-driven helpers (who are neither altruists nor egoists). In this way, I seek to broaden the set of considerations typically taken into account when assessing the evolution of the psychology of helping behavior-which tend to be restricted to matters of reliability-and also try to make clearer the role of evolutionary biological considerations in the discussion of this apparently straightforwardly psychological phenomenon. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Effect of Conflicting Pressures on the Evolution of Division of Labor

PubMed Central

Goldsby, Heather J.; Knoester, David B.; Kerr, Benjamin; Ofria, Charles

2014-01-01

Within nature, many groups exhibit division of labor. Individuals in these groups are under seemingly antagonistic pressures to perform the task most directly beneficial to themselves and to potentially perform a less desirable task to ensure the success of the group. Performing experiments to study how these pressures interact in an evolutionary context is challenging with organic systems because of long generation times and difficulties related to group propagation and fine-grained control of within-group and between-group pressures. Here, we use groups of digital organisms (i.e., self-replicating computer programs) to explore how populations respond to antagonistic multilevel selection pressures. Specifically, we impose a within-group pressure to perform a highly-rewarded role and a between-group pressure to perform a diverse suite of roles. Thus, individuals specializing on highly-rewarded roles will have a within-group advantage, but groups of such specialists have a between-group disadvantage. We find that digital groups could evolve to be either single-lineage or multi-lineage, depending on experimental parameters. These group compositions are reminiscent of different kinds of major evolutionary transitions that occur within nature, where either relatives divide labor (fraternal transitions) or multiple different organisms coordinate activities to form a higher-level individual (egalitarian transitions). Regardless of group composition, organisms embraced phenotypic plasticity as a means for genetically similar individuals to perform different roles. Additionally, in multi-lineage groups, organisms from lineages performing highly-rewarded roles also employed reproductive restraint to ensure successful coexistence with organisms from other lineages. PMID:25093399

A Way Forward Beyond Karl Popper's and Donald T. Campbell's Dead-End Evolutionary Epistemologies.

PubMed

Wettersten, John

2016-01-01

Theories of natural thought processes have traditionally served as foundations for philosophies of science. The source of all knowledge is passively received observations; these are combined to produce certain knowledge. After David Hume showed that this was not possible, deductivist alternatives, that is, theories that find a source of knowledge in ideas not derived from observations, from Immanuel Kant to William Whewell in the mid-1 9th century, were introduced. In response, traditional associationist and inductivist views were refurbished; a deductivist alternative was developed by the W6rzburg School. Much later Karl Popper in philosophy and Donald T. Campbell in psychology integrated this view with evolutionary theory. Campbell wanted thereby to find a justificationist view, which would reduce philosophy of science to cognitive psychology; Popper rejected both justificationism and the reduction of philosophy of science to psychology. Campbell thought all rational processes were innate psychological processes; Popper thought psychological processes were used to develop various rational processes. Campbell could not show that all rational thought was reducible to innate psychological processes, nor how some justification of scientific theories was possible. Popper could not show how evolutionary theory contributed to our knowledge of psychological thought processes. Both failed to observe that cognitive processes are social; people have learned how to think by learning how to interact in social groups seeking understanding. When innate thought processes are studied as social characteristics, evolutionary theory can contribute to both cognitive psychology and the theory of rationality, as both Popper and Campbell wanted it to do.

Physics and evolution of thermophilic adaptation.

PubMed

Berezovsky, Igor N; Shakhnovich, Eugene I

2005-09-06

Analysis of structures and sequences of several hyperthermostable proteins from various sources reveals two major physical mechanisms of their thermostabilization. The first mechanism is "structure-based," whereby some hyperthermostable proteins are significantly more compact than their mesophilic homologues, while no particular interaction type appears to cause stabilization; rather, a sheer number of interactions is responsible for thermostability. Other hyperthermostable proteins employ an alternative, "sequence-based" mechanism of their thermal stabilization. They do not show pronounced structural differences from mesophilic homologues. Rather, a small number of apparently strong interactions is responsible for high thermal stability of these proteins. High-throughput comparative analysis of structures and complete genomes of several hyperthermophilic archaea and bacteria revealed that organisms develop diverse strategies of thermophilic adaptation by using, to a varying degree, two fundamental physical mechanisms of thermostability. The choice of a particular strategy depends on the evolutionary history of an organism. Proteins from organisms that originated in an extreme environment, such as hyperthermophilic archaea (Pyrococcus furiosus), are significantly more compact and more hydrophobic than their mesophilic counterparts. Alternatively, organisms that evolved as mesophiles but later recolonized a hot environment (Thermotoga maritima) relied in their evolutionary strategy of thermophilic adaptation on "sequence-based" mechanism of thermostability. We propose an evolutionary explanation of these differences based on physical concepts of protein designability.

Periodically Relieving Ischial Sitting Load to Decrease the Risk of Pressure Ulcers

PubMed Central

Makhsous, Mohsen; Rowles, Diane M.; Rymer, William Z.; Bankard, James; Nam, Ellis K.; Chen, David; Lin, Fang

2010-01-01

Objective To investigate the relieving effect on interface pressure of an alternate sitting protocol involving a sitting posture that reduces ischial support. Design Repeated measures in 2 protocols on 3 groups of subjects. Setting Laboratory. Participants Twenty able-bodied persons, 20 persons with paraplegia, and 20 persons with tetraplegia. Interventions Two 1-hour protocols were used: alternate and normal plus pushup. In the alternate protocol, sitting posture was alternated every 10 minutes between normal (sitting upright with ischial support) and with partially removed ischial support (WO-BPS) postures; in the normal plus pushup protocol, sitting was in normal posture with pushups (lifting the subject off the seat) performed every 20 minutes. Main Outcome Measure Interface pressure on seat and backrest. Results In WO-BPS posture, the concentrated interface pressure observed around the ischia in normal posture was significantly repositioned to the thighs. By cyclically repositioning the interface pressure, the alternate protocol was superior to the normal plus pushup protocol in terms of a significantly lower average interface pressure over the buttocks. Conclusions A sitting protocol periodically reducing the ischial support helps lower the sitting load on the buttocks, especially the area close to ischial tuberosities. PMID:17601466

Why don't zebras have machine guns? Adaptation, selection, and constraints in evolutionary theory.

PubMed

Shanahan, Timothy

2008-03-01

In an influential paper, Stephen Jay Gould and Richard Lewontin (1979) contrasted selection-driven adaptation with phylogenetic, architectural, and developmental constraints as distinct causes of phenotypic evolution. In subsequent publications Gould (e.g., 1997a,b, 2002) has elaborated this distinction into one between a narrow "Darwinian Fundamentalist" emphasis on "external functionalist" processes, and a more inclusive "pluralist" emphasis on "internal structuralist" principles. Although theoretical integration of functionalist and structuralist explanations is the ultimate aim, natural selection and internal constraints are treated as distinct causes of evolutionary change. This distinction is now routinely taken for granted in the literature in evolutionary biology. I argue that this distinction is problematic because the effects attributed to non-selective constraints are more parsimoniously explained as the ordinary effects of selection itself. Although it may still be a useful shorthand to speak of phylogenetic, architectural, and developmental constraints on phenotypic evolution, it is important to understand that such "constraints" do not constitute an alternative set of causes of evolutionary change. The result of this analysis is a clearer understanding of the relationship between adaptation, selection and constraints as explanatory concepts in evolutionary theory.

An alternative to reduction of surface pressure to sea level

NASA Technical Reports Server (NTRS)

Deardorff, J. W.

1982-01-01

The pitfalls of the present method of reducing surface pressure to sea level are reviewed, and an alternative, adjusted pressure, P, is proposed. P is obtained from solution of a Poisson equation over a continental region, using the simplest boundary condition along the perimeter or coastline where P equals the sea level pressure. The use of P would avoid the empiricisms and disadvantages of pressure reduction to sea level, and would produce surface pressure charts which depict the true geostrophic wind at the surface.

Modeling Tumor Clonal Evolution for Drug Combinations Design.

PubMed

Zhao, Boyang; Hemann, Michael T; Lauffenburger, Douglas A

2016-03-01

Cancer is a clonal evolutionary process. This presents challenges for effective therapeutic intervention, given the constant selective pressure towards drug resistance. Mathematical modeling from population genetics, evolutionary dynamics, and engineering perspectives are being increasingly employed to study tumor progression, intratumoral heterogeneity, drug resistance, and rational drug scheduling and combinations design. In this review, we discuss promising opportunities these inter-disciplinary approaches hold for advances in cancer biology and treatment. We propose that quantitative modeling perspectives can complement emerging experimental technologies to facilitate enhanced understanding of disease progression and improved capabilities for therapeutic drug regimen designs.

Selective modes determine evolutionary rates, gene compactness and expression patterns in Brassica.

PubMed

Guo, Yue; Liu, Jing; Zhang, Jiefu; Liu, Shengyi; Du, Jianchang

2017-07-01

It has been well documented that most nuclear protein-coding genes in organisms can be classified into two categories: positively selected genes (PSGs) and negatively selected genes (NSGs). The characteristics and evolutionary fates of different types of genes, however, have been poorly understood. In this study, the rates of nonsynonymous substitution (K a ) and the rates of synonymous substitution (K s ) were investigated by comparing the orthologs between the two sequenced Brassica species, Brassica rapa and Brassica oleracea, and the evolutionary rates, gene structures, expression patterns, and codon bias were compared between PSGs and NSGs. The resulting data show that PSGs have higher protein evolutionary rates, lower synonymous substitution rates, shorter gene length, fewer exons, higher functional specificity, lower expression level, higher tissue-specific expression and stronger codon bias than NSGs. Although the quantities and values are different, the relative features of PSGs and NSGs have been largely verified in the model species Arabidopsis. These data suggest that PSGs and NSGs differ not only under selective pressure (K a /K s ), but also in their evolutionary, structural and functional properties, indicating that selective modes may serve as a determinant factor for measuring evolutionary rates, gene compactness and expression patterns in Brassica. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Constraints and spandrels of interareal connectomes

PubMed Central

Rubinov, Mikail

2016-01-01

Interareal connectomes are whole-brain wiring diagrams of white-matter pathways. Recent studies have identified modules, hubs, module hierarchies and rich clubs as structural hallmarks of these wiring diagrams. An influential current theory postulates that connectome modules are adequately explained by evolutionary pressures for wiring economy, but that the other hallmarks are not explained by such pressures and are therefore less trivial. Here, we use constraint network models to test these postulates in current gold-standard vertebrate and invertebrate interareal-connectome reconstructions. We show that empirical wiring-cost constraints inadequately explain connectome module organization, and that simultaneous module and hub constraints induce the structural byproducts of hierarchies and rich clubs. These byproducts, known as spandrels in evolutionary biology, include the structural substrate of the default-mode network. Our results imply that currently standard connectome characterizations are based on circular analyses or double dipping, and we emphasize an integrative approach to future connectome analyses for avoiding such pitfalls. PMID:27924867

Constraints and spandrels of interareal connectomes.

PubMed

Rubinov, Mikail

2016-12-07

Interareal connectomes are whole-brain wiring diagrams of white-matter pathways. Recent studies have identified modules, hubs, module hierarchies and rich clubs as structural hallmarks of these wiring diagrams. An influential current theory postulates that connectome modules are adequately explained by evolutionary pressures for wiring economy, but that the other hallmarks are not explained by such pressures and are therefore less trivial. Here, we use constraint network models to test these postulates in current gold-standard vertebrate and invertebrate interareal-connectome reconstructions. We show that empirical wiring-cost constraints inadequately explain connectome module organization, and that simultaneous module and hub constraints induce the structural byproducts of hierarchies and rich clubs. These byproducts, known as spandrels in evolutionary biology, include the structural substrate of the default-mode network. Our results imply that currently standard connectome characterizations are based on circular analyses or double dipping, and we emphasize an integrative approach to future connectome analyses for avoiding such pitfalls.

The Evolutionary Ecology of Plant Disease: A Phylogenetic Perspective.

PubMed

Gilbert, Gregory S; Parker, Ingrid M

2016-08-04

An explicit phylogenetic perspective provides useful tools for phytopathology and plant disease ecology because the traits of both plants and microbes are shaped by their evolutionary histories. We present brief primers on phylogenetic signal and the analytical tools of phylogenetic ecology. We review the literature and find abundant evidence of phylogenetic signal in pathogens and plants for most traits involved in disease interactions. Plant nonhost resistance mechanisms and pathogen housekeeping functions are conserved at deeper phylogenetic levels, whereas molecular traits associated with rapid coevolutionary dynamics are more labile at branch tips. Horizontal gene transfer disrupts the phylogenetic signal for some microbial traits. Emergent traits, such as host range and disease severity, show clear phylogenetic signals. Therefore pathogen spread and disease impact are influenced by the phylogenetic structure of host assemblages. Phylogenetically rare species escape disease pressure. Phylogenetic tools could be used to develop predictive tools for phytosanitary risk analysis and reduce disease pressure in multispecies cropping systems.

Is sociality required for the evolution of communicative complexity? Evidence weighed against alternative hypotheses in diverse taxonomic groups

PubMed Central

Ord, Terry J.; Garcia-Porta, Joan

2012-01-01

Complex social communication is expected to evolve whenever animals engage in many and varied social interactions; that is, sociality should promote communicative complexity. Yet, informal comparisons among phylogenetically independent taxonomic groups seem to cast doubt on the putative role of social factors in the evolution of complex communication. Here, we provide a formal test of the sociality hypothesis alongside alternative explanations for the evolution of communicative complexity. We compiled data documenting variations in signal complexity among closely related species for several case study groups—ants, frogs, lizards and birds—and used new phylogenetic methods to investigate the factors underlying communication evolution. Social factors were only implicated in the evolution of complex visual signals in lizards. Ecology, and to some degree allometry, were most likely explanations for complexity in the vocal signals of frogs (ecology) and birds (ecology and allometry). There was some evidence for adaptive evolution in the pheromone complexity of ants, although no compelling selection pressure was identified. For most taxa, phylogenetic null models were consistently ranked above adaptive models and, for some taxa, signal complexity seems to have accumulated in species via incremental or random changes over long periods of evolutionary time. Becoming social presumably leads to the origin of social communication in animals, but its subsequent influence on the trajectory of signal evolution has been neither clear-cut nor general among taxonomic groups. PMID:22641820

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

PubMed

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

2014-03-01

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.

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

Courses of action for effects based operations using evolutionary algorithms

NASA Astrophysics Data System (ADS)

Haider, Sajjad; Levis, Alexander H.

2006-05-01

This paper presents an Evolutionary Algorithms (EAs) based approach to identify effective courses of action (COAs) in Effects Based Operations. The approach uses Timed Influence Nets (TINs) as the underlying mathematical model to capture a dynamic uncertain situation. TINs provide a concise graph-theoretic probabilistic approach to specify the cause and effect relationships that exist among the variables of interest (actions, desired effects, and other uncertain events) in a problem domain. The purpose of building these TIN models is to identify and analyze several alternative courses of action. The current practice is to use trial and error based techniques which are not only labor intensive but also produce sub-optimal results and are not capable of modeling constraints among actionable events. The EA based approach presented in this paper is aimed to overcome these limitations. The approach generates multiple COAs that are close enough in terms of achieving the desired effect. The purpose of generating multiple COAs is to give several alternatives to a decision maker. Moreover, the alternate COAs could be generalized based on the relationships that exist among the actions and their execution timings. The approach also allows a system analyst to capture certain types of constraints among actionable events.

EVOLUTION OF INTERMEDIATE-MASS X-RAY BINARIES DRIVEN BY THE MAGNETIC BRAKING OF AP/BP STARS. I. ULTRACOMPACT X-RAY BINARIES

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

Chen, Wen-Cong; Podsiadlowski, Philipp, E-mail: chenwc@pku.edu.cn

2016-10-20

It is generally believed that ultracompact X-ray binaries (UCXBs) evolved from binaries consisting of a neutron star accreting from a low-mass white dwarf (WD) or helium star where mass transfer is driven by gravitational radiation. However, the standard WD evolutionary channel cannot produce the relatively long-period (40–60 minutes) UCXBs with a high time-averaged mass-transfer rate. In this work, we explore an alternative evolutionary route toward UCXBs, where the companions evolve from intermediate-mass Ap/Bp stars with an anomalously strong magnetic field (100–10,000 G). Including the magnetic braking caused by the coupling between the magnetic field and an irradiation-driven wind induced bymore » the X-ray flux from the accreting component, we show that intermediate-mass X-ray binaries (IMXBs) can evolve into UCXBs. Using the MESA code, we have calculated evolutionary sequences for a large number of IMXBs. The simulated results indicate that, for a small wind-driving efficiency f = 10{sup −5}, the anomalous magnetic braking can drive IMXBs to an ultra-short period of 11 minutes. Comparing our simulated results with the observed parameters of 15 identified UCXBs, the anomalous magnetic braking evolutionary channel can account for the formation of seven and eight sources with f = 10{sup −3}, and 10{sup −5}, respectively. In particular, a relatively large value of f can fit three of the long-period, persistent sources with a high mass-transfer rate. Though the proportion of Ap/Bp stars in intermediate-mass stars is only 5%, the lifetime of the UCXB phase is ≳2 Gyr, producing a relatively high number of observable systems, making this an alternative evolutionary channel for the formation of UCXBs.« less

Environment determines evolutionary trajectory in a constrained phenotypic space

PubMed Central

Fraebel, David T; Mickalide, Harry; Schnitkey, Diane; Merritt, Jason; Kuhlman, Thomas E; Kuehn, Seppe

2017-01-01

Constraints on phenotypic variation limit the capacity of organisms to adapt to the multiple selection pressures encountered in natural environments. To better understand evolutionary dynamics in this context, we select Escherichia coli for faster migration through a porous environment, a process which depends on both motility and growth. We find that a trade-off between swimming speed and growth rate constrains the evolution of faster migration. Evolving faster migration in rich medium results in slow growth and fast swimming, while evolution in minimal medium results in fast growth and slow swimming. In each condition parallel genomic evolution drives adaptation through different mutations. We show that the trade-off is mediated by antagonistic pleiotropy through mutations that affect negative regulation. A model of the evolutionary process shows that the genetic capacity of an organism to vary traits can qualitatively depend on its environment, which in turn alters its evolutionary trajectory. DOI: http://dx.doi.org/10.7554/eLife.24669.001 PMID:28346136

Evolutionary mysteries in meiosis.

PubMed

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

2016-10-19

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

Evolutionary mysteries in meiosis

PubMed Central

2016-01-01

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

A review of estimation of distribution algorithms in bioinformatics

PubMed Central

Armañanzas, Rubén; Inza, Iñaki; Santana, Roberto; Saeys, Yvan; Flores, Jose Luis; Lozano, Jose Antonio; Peer, Yves Van de; Blanco, Rosa; Robles, Víctor; Bielza, Concha; Larrañaga, Pedro

2008-01-01

Evolutionary search algorithms have become an essential asset in the algorithmic toolbox for solving high-dimensional optimization problems in across a broad range of bioinformatics problems. Genetic algorithms, the most well-known and representative evolutionary search technique, have been the subject of the major part of such applications. Estimation of distribution algorithms (EDAs) offer a novel evolutionary paradigm that constitutes a natural and attractive alternative to genetic algorithms. They make use of a probabilistic model, learnt from the promising solutions, to guide the search process. In this paper, we set out a basic taxonomy of EDA techniques, underlining the nature and complexity of the probabilistic model of each EDA variant. We review a set of innovative works that make use of EDA techniques to solve challenging bioinformatics problems, emphasizing the EDA paradigm's potential for further research in this domain. PMID:18822112

Manual praxis in stone tool manufacture: implications for language evolution.

PubMed

Ruck, Lana

2014-12-01

Alternative functions of the left-hemisphere dominant Broca's region have induced hypotheses regarding the evolutionary parallels between manual praxis and language in humans. Many recent studies on Broca's area reveal several assumptions about the cognitive mechanisms that underlie both functions, including: (1) an accurate, finely controlled body schema, (2) increasing syntactical abilities, particularly for goal-oriented actions, and (3) bilaterality and fronto-parietal connectivity. Although these characteristics are supported by experimental paradigms, many researchers have failed to acknowledge a major line of evidence for the evolutionary development of these traits: stone tools. The neuroscience of stone tool manufacture is a viable proxy for understanding evolutionary aspects of manual praxis and language, and may provide key information for evaluating competing hypotheses on the co-evolution of these cognitive domains in our species. Copyright © 2014 Elsevier Inc. All rights reserved.

An experimental description of the flow in a centrifugal compressor from alternate stall to surge

NASA Astrophysics Data System (ADS)

Moënne-Loccoz, V.; Trébinjac, I.; Benichou, E.; Goguey, S.; Paoletti, B.; Laucher, P.

2017-08-01

The present paper gives the experimental results obtained in a centrifugal compressor stage designed and built by SAFRAN Helicopter Engines. The compressor is composed of inlet guide vanes, a backswept splittered unshrouded impeller, a splittered vaned radial diffuser and axial outlet guide vanes. Previous numerical simulations revealed a particular S-shape pressure rise characteristic at partial rotation speed and predicted an alternate flow pattern in the vaned radial diffuser at low mass flow rate. This alternate flow pattern involves two adjacent vane passages. One passage exhibits very low momentum and a low pressure recovery, whereas the adjacent passage has very high momentum in the passage inlet and diffuses efficiently. Experimental measurements confirm the S-shape of the pressure rise characteristic even if the stability limit experimentally occurs at higher mass flow than numerically predicted. At low mass flow the alternate stall pattern is confirmed thanks to the data obtained by high-frequency pressure sensors. As the compressor is throttled the path to instability has been registered and a first scenario of the surge inception is given. The compressor first experiences a steady alternate stall in the diffuser. As the mass flow decreases, the alternate stall amplifies and triggers the mild surge in the vaned diffuser. An unsteady behavior results from the interaction of the alternate stall and the mild surge. Finally, when the pressure gradient becomes too strong, the alternate stall blows away and the compressor enters into deep surge.

Polymorphism at a mimicry supergene maintained by opposing frequency-dependent selection pressures.

PubMed

Chouteau, Mathieu; Llaurens, Violaine; Piron-Prunier, Florence; Joron, Mathieu

2017-08-01

Explaining the maintenance of adaptive diversity within populations is a long-standing goal in evolutionary biology, with important implications for conservation, medicine, and agriculture. Adaptation often leads to the fixation of beneficial alleles, and therefore it erodes local diversity so that understanding the coexistence of multiple adaptive phenotypes requires deciphering the ecological mechanisms that determine their respective benefits. Here, we show how antagonistic frequency-dependent selection (FDS), generated by natural and sexual selection acting on the same trait, maintains mimicry polymorphism in the toxic butterfly Heliconius numata Positive FDS imposed by predators on mimetic signals favors the fixation of the most abundant and best-protected wing-pattern morph, thereby limiting polymorphism. However, by using mate-choice experiments, we reveal disassortative mate preferences of the different wing-pattern morphs. The resulting negative FDS on wing-pattern alleles is consistent with the excess of heterozygote genotypes at the supergene locus controlling wing-pattern variation in natural populations of H. numata The combined effect of positive and negative FDS on visual signals is sufficient to maintain a diversity of morphs displaying accurate mimicry with other local prey, although some of the forms only provide moderate protection against predators. Our findings help understand how alternative adaptive phenotypes can be maintained within populations and emphasize the need to investigate interactions between selective pressures in other cases of puzzling adaptive polymorphism.

Polymorphism at a mimicry supergene maintained by opposing frequency-dependent selection pressures

PubMed Central

Chouteau, Mathieu; Llaurens, Violaine; Piron-Prunier, Florence; Joron, Mathieu

2017-01-01

Explaining the maintenance of adaptive diversity within populations is a long-standing goal in evolutionary biology, with important implications for conservation, medicine, and agriculture. Adaptation often leads to the fixation of beneficial alleles, and therefore it erodes local diversity so that understanding the coexistence of multiple adaptive phenotypes requires deciphering the ecological mechanisms that determine their respective benefits. Here, we show how antagonistic frequency-dependent selection (FDS), generated by natural and sexual selection acting on the same trait, maintains mimicry polymorphism in the toxic butterfly Heliconius numata. Positive FDS imposed by predators on mimetic signals favors the fixation of the most abundant and best-protected wing-pattern morph, thereby limiting polymorphism. However, by using mate-choice experiments, we reveal disassortative mate preferences of the different wing-pattern morphs. The resulting negative FDS on wing-pattern alleles is consistent with the excess of heterozygote genotypes at the supergene locus controlling wing-pattern variation in natural populations of H. numata. The combined effect of positive and negative FDS on visual signals is sufficient to maintain a diversity of morphs displaying accurate mimicry with other local prey, although some of the forms only provide moderate protection against predators. Our findings help understand how alternative adaptive phenotypes can be maintained within populations and emphasize the need to investigate interactions between selective pressures in other cases of puzzling adaptive polymorphism. PMID:28673971

Photosynthesis: what color was its origin?

PubMed Central

Xiong, Jin

2006-01-01

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

Common Mechanism Underlies Repeated Evolution of Extreme Pollution Tolerance

EPA Science Inventory

Human alterations to the environment can exert strong evolutionary pressures, yet contemporary adaptation to human-mediated stressors is rarely documented in wild populations. A common-garden experimental design was coupled with comparative transcriptomics to discover evolved me...

Sex determination strategies in 2012: towards a common regulatory model?

PubMed

Angelopoulou, Roxani; Lavranos, Giagkos; Manolakou, Panagiota

2012-02-22

Sex determination is a complicated process involving large-scale modifications in gene expression affecting virtually every tissue in the body. Although the evolutionary origin of sex remains controversial, there is little doubt that it has developed as a process of optimizing metabolic control, as well as developmental and reproductive functions within a given setting of limited resources and environmental pressure. Evidence from various model organisms supports the view that sex determination may occur as a result of direct environmental induction or genetic regulation. The first process has been well documented in reptiles and fish, while the second is the classic case for avian species and mammals. Both of the latter have developed a variety of sex-specific/sex-related genes, which ultimately form a complete chromosome pair (sex chromosomes/gonosomes). Interestingly, combinations of environmental and genetic mechanisms have been described among different classes of animals, thus rendering the possibility of a unidirectional continuous evolutionary process from the one type of mechanism to the other unlikely. On the other hand, common elements appear throughout the animal kingdom, with regard to a) conserved key genes and b) a central role of sex steroid control as a prerequisite for ultimately normal sex differentiation. Studies in invertebrates also indicate a role of epigenetic chromatin modification, particularly with regard to alternative splicing options. This review summarizes current evidence from research in this hot field and signifies the need for further study of both normal hormonal regulators of sexual phenotype and patterns of environmental disruption. © 2012 Angelopoulou et al; licensee BioMed Central Ltd.

Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts

PubMed Central

Sikosek, Tobias; Bornberg-Bauer, Erich; Chan, Hue Sun

2012-01-01

Experimental studies have shown that some proteins exist in two alternative native-state conformations. It has been proposed that such bi-stable proteins can potentially function as evolutionary bridges at the interface between two neutral networks of protein sequences that fold uniquely into the two different native conformations. Under adaptive conflict scenarios, bi-stable proteins may be of particular advantage if they simultaneously provide two beneficial biological functions. However, computational models that simulate protein structure evolution do not yet recognize the importance of bi-stability. Here we use a biophysical model to analyze sequence space to identify bi-stable or multi-stable proteins with two or more equally stable native-state structures. The inclusion of such proteins enhances phenotype connectivity between neutral networks in sequence space. Consideration of the sequence space neighborhood of bridge proteins revealed that bi-stability decreases gradually with each mutation that takes the sequence further away from an exactly bi-stable protein. With relaxed selection pressures, we found that bi-stable proteins in our model are highly successful under simulated adaptive conflict. Inspired by these model predictions, we developed a method to identify real proteins in the PDB with bridge-like properties, and have verified a clear bi-stability gradient for a series of mutants studied by Alexander et al. (Proc Nat Acad Sci USA 2009, 106:21149–21154) that connect two sequences that fold uniquely into two different native structures via a bridge-like intermediate mutant sequence. Based on these findings, new testable predictions for future studies on protein bi-stability and evolution are discussed. PMID:23028272

The extended evolutionary synthesis: its structure, assumptions and predictions

PubMed Central

Laland, Kevin N.; Uller, Tobias; Feldman, Marcus W.; Sterelny, Kim; Müller, Gerd B.; Moczek, Armin; Jablonka, Eva; Odling-Smee, John

2015-01-01

Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the ‘extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology. PMID:26246559

Contemporary and historical evolutionary processes interact to shape patterns of within-lake phenotypic divergences in polyphenic pumpkinseed sunfish, Lepomis gibbosus.

PubMed

Weese, Dylan J; Ferguson, Moira M; Robinson, Beren W

2012-03-01

Historical and contemporary evolutionary processes can both contribute to patterns of phenotypic variation among populations of a species. Recent studies are revealing how interactions between historical and contemporary processes better explain observed patterns of phenotypic divergence than either process alone. Here, we investigate the roles of evolutionary history and adaptation to current environmental conditions in structuring phenotypic variation among polyphenic populations of sunfish inhabiting 12 postglacial lakes in eastern North America. The pumpkinseed sunfish polyphenism includes sympatric ecomorphs specialized for littoral or pelagic lake habitats. First, we use population genetic methods to test the evolutionary independence of within-lake phenotypic divergences of ecomorphs and to describe patterns of genetic structure among lake populations that clustered into three geographical groupings. We then used multivariate analysis of covariance (MANCOVA) to partition body shape variation (quantified with geometric morphometrics) among the effects of evolutionary history (reflecting phenotypic variation among genetic clusters), the shared phenotypic response of all populations to alternate habitats within lakes (reflecting adaptation to contemporary conditions), and unique phenotypic responses to habitats within lakes nested within genetic clusters. All effects had a significant influence on body form, but the effects of history and the interaction between history and contemporary habitat were larger than contemporary processes in structuring phenotypic variation. This highlights how divergence can be better understood against a known backdrop of evolutionary history.

Network Analysis of Protein Adaptation: Modeling the Functional Impact of Multiple Mutations

PubMed Central

Beleva Guthrie, Violeta; Masica, David L; Fraser, Andrew; Federico, Joseph; Fan, Yunfan; Camps, Manel; Karchin, Rachel

2018-01-01

Abstract The evolution of new biochemical activities frequently involves complex dependencies between mutations and rapid evolutionary radiation. Mutation co-occurrence and covariation have previously been used to identify compensating mutations that are the result of physical contacts and preserve protein function and fold. Here, we model pairwise functional dependencies and higher order interactions that enable evolution of new protein functions. We use a network model to find complex dependencies between mutations resulting from evolutionary trade-offs and pleiotropic effects. We present a method to construct these networks and to identify functionally interacting mutations in both extant and reconstructed ancestral sequences (Network Analysis of Protein Adaptation). The time ordering of mutations can be incorporated into the networks through phylogenetic reconstruction. We apply NAPA to three distantly homologous β-lactamase protein clusters (TEM, CTX-M-3, and OXA-51), each of which has experienced recent evolutionary radiation under substantially different selective pressures. By analyzing the network properties of each protein cluster, we identify key adaptive mutations, positive pairwise interactions, different adaptive solutions to the same selective pressure, and complex evolutionary trajectories likely to increase protein fitness. We also present evidence that incorporating information from phylogenetic reconstruction and ancestral sequence inference can reduce the number of spurious links in the network, whereas preserving overall network community structure. The analysis does not require structural or biochemical data. In contrast to function-preserving mutation dependencies, which are frequently from structural contacts, gain-of-function mutation dependencies are most commonly between residues distal in protein structure. PMID:29522102

[Theories of evolution shaping Victorian anthropology. The science-politics of the X-Club, 1860-1872].

PubMed

Gondermann, Thomas

2008-01-01

This paper discusses the role that a group of evolutionists, the X-Club, played in the epistemic and institutional transformation of Victorian anthropology in the 1860s. It analyses how anthropology has been brought into line with the theory of evolution, which gained currency at the same time. The X-Club was a highly influential pressure group in the Victorian scientific community. It campaigned for the theory of evolution in several fields of the natural sciences and had a considerable influence on the modernization of the sciences. Yet, this club also intervened in the anthropological discourse of these years. The X-Club's meddling with anthropology led to the latter's evolutionary turn. The introduction of an evolutionary agenda into Victorian anthropology depended not only on the X-Club's theoretical contributions but also on the structural reformation of the discipline. Its campaigns also aimed at marginalizing the proponents of pre-evolutionary anthropology in its institutions and led to the foundation of a new organization in anthropology: The Anthropological Institute of Great Britain and Ireland. Thus, evolutionary anthropology emerged in the 1860s also as the result of science-politicking rather than just from the transmission of evolutionary concepts through discourse.

The Paradox of Isochrony in the Evolution of Human Rhythm

PubMed Central

Ravignani, Andrea; Madison, Guy

2017-01-01

Isochrony is crucial to the rhythm of human music. Some neural, behavioral and anatomical traits underlying rhythm perception and production are shared with a broad range of species. These may either have a common evolutionary origin, or have evolved into similar traits under different evolutionary pressures. Other traits underlying rhythm are rare across species, only found in humans and few other animals. Isochrony, or stable periodicity, is common to most human music, but isochronous behaviors are also found in many species. It appears paradoxical that humans are particularly good at producing and perceiving isochronous patterns, although this ability does not conceivably confer any evolutionary advantage to modern humans. This article will attempt to solve this conundrum. To this end, we define the concept of isochrony from the present functional perspective of physiology, cognitive neuroscience, signal processing, and interactive behavior, and review available evidence on isochrony in the signals of humans and other animals. We then attempt to resolve the paradox of isochrony by expanding an evolutionary hypothesis about the function that isochronous behavior may have had in early hominids. Finally, we propose avenues for empirical research to examine this hypothesis and to understand the evolutionary origin of isochrony in general. PMID:29163252

Evolution caused by extreme events.

PubMed

Grant, Peter R; Grant, B Rosemary; Huey, Raymond B; Johnson, Marc T J; Knoll, Andrew H; Schmitt, Johanna

2017-06-19

Extreme events can be a major driver of evolutionary change over geological and contemporary timescales. Outstanding examples are evolutionary diversification following mass extinctions caused by extreme volcanism or asteroid impact. The evolution of organisms in contemporary time is typically viewed as a gradual and incremental process that results from genetic change, environmental perturbation or both. However, contemporary environments occasionally experience strong perturbations such as heat waves, floods, hurricanes, droughts and pest outbreaks. These extreme events set up strong selection pressures on organisms, and are small-scale analogues of the dramatic changes documented in the fossil record. Because extreme events are rare, almost by definition, they are difficult to study. So far most attention has been given to their ecological rather than to their evolutionary consequences. We review several case studies of contemporary evolution in response to two types of extreme environmental perturbations, episodic (pulse) or prolonged (press). Evolution is most likely to occur when extreme events alter community composition. We encourage investigators to be prepared for evolutionary change in response to rare events during long-term field studies.This article is part of the themed issue 'Behavioural, ecological and evolutionary responses to extreme climatic events'. © 2017 The Author(s).

The evolutionary origins of Syngnathidae: pipefishes and seahorses.

PubMed

Wilson, A B; Orr, J W

2011-06-01

Despite their importance as evolutionary and ecological model systems, the phylogenetic relationships among gasterosteiforms remain poorly understood, complicating efforts to understand the evolutionary origins of the exceptional morphological and behavioural diversity of this group. The present review summarizes current knowledge on the origin and evolution of syngnathids, a gasterosteiform family with a highly developed form of male parental care, combining inferences based on morphological and molecular data with paleontological evidence documenting the evolutionary history of the group. Molecular methods have provided new tools for the study of syngnathid relationships and have played an important role in recent conservation efforts. Despite recent insights into syngnathid evolution, however, a survey of the literature reveals a strong taxonomic bias towards studies on the species-rich genera Hippocampus and Syngnathus, with a lack of data for many morphologically unique members of the family. The study of the evolutionary pressures responsible for generating the high diversity of syngnathids would benefit from a wider perspective, providing a comparative framework in which to investigate the evolution of the genetic, morphological and behavioural traits of the group as a whole. © 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.

Foraging environment determines the genetic architecture and evolutionary potential of trophic morphology in cichlid fishes.

PubMed

Parsons, Kevin J; Concannon, Moira; Navon, Dina; Wang, Jason; Ea, Ilene; Groveas, Kiran; Campbell, Calum; Albertson, R Craig

2016-12-01

Phenotypic plasticity allows organisms to change their phenotype in response to shifts in the environment. While a central topic in current discussions of evolutionary potential, a comprehensive understanding of the genetic underpinnings of plasticity is lacking in systems undergoing adaptive diversification. Here, we investigate the genetic basis of phenotypic plasticity in a textbook adaptive radiation, Lake Malawi cichlid fishes. Specifically, we crossed two divergent species to generate an F 3 hybrid mapping population. At early juvenile stages, hybrid families were split and reared in alternate foraging environments that mimicked benthic/scraping or limnetic/sucking modes of feeding. These alternate treatments produced a variation in morphology that was broadly similar to the major axis of divergence among Malawi cichlids, providing support for the flexible stem theory of adaptive radiation. Next, we found that the genetic architecture of several morphological traits was highly sensitive to the environment. In particular, of 22 significant quantitative trait loci (QTL), only one was shared between the environments. In addition, we identified QTL acting across environments with alternate alleles being differentially sensitive to the environment. Thus, our data suggest that while plasticity is largely determined by loci specific to a given environment, it may also be influenced by loci operating across environments. Finally, our mapping data provide evidence for the evolution of plasticity via genetic assimilation at an important regulatory locus, ptch1. In all, our data address long-standing discussions about the genetic basis and evolution of plasticity. They also underscore the importance of the environment in affecting developmental outcomes, genetic architectures, morphological diversity and evolutionary potential. © 2016 John Wiley & Sons Ltd.

A Hydraulic Motor-Alternator System for Ocean-Submersible Vehicles

NASA Technical Reports Server (NTRS)

Aintablian, Harry O.; Valdez, Thomas I.; Jones, Jack A.

2012-01-01

An ocean-submersible vehicle has been developed at JPL that moves back and forth between sea level and a depth of a few hundred meters. A liquid volumetric change at a pressure of 70 bars is created by means of thermal phase change. During vehicle ascent, the phase-change material (PCM) is melted by the circulation of warm water and thus pressure is increased. During vehicle descent, the PCM is cooled resulting in reduced pressure. This pressure change is used to generate electric power by means of a hydraulic pump that drives a permanent magnet (PM) alternator. The output energy of the alternator is stored in a rechargeable battery that powers an on-board computer, instrumentation and other peripherals.The focus of this paper is the performance evaluation of a specific hydraulic motor-alternator system. Experimental and theoretical efficiency data of the hydraulic motor and the alternator are presented. The results are used to evaluate the optimization of the hydraulic motor-alternator system. The integrated submersible vehicle was successfully operated in the Pacific Ocean near Hawaii. A brief overview of the actual test results is presented.

Transgenerational Adaptation to Pollution Changes Energy Allocation in Populations of Nematodes.

PubMed

Goussen, Benoit; Péry, Alexandre R R; Bonzom, Jean-Marc; Beaudouin, Rémy

2015-10-20

Assessing the evolutionary responses of long-term exposed populations requires multigeneration ecotoxicity tests. However, the analysis of the data from these tests is not straightforward. Mechanistic models allow the in-depth analysis of the variation of physiological traits over many generations, by quantifying the trend of the physiological and toxicological parameters of the model. In the present study, a bioenergetic mechanistic model has been used to assess the evolution of two populations of the nematode Caenorhabditis elegans in control conditions or exposed to uranium. This evolutionary pressure resulted in a brood size reduction of 60%. We showed an adaptation of individuals of both populations to experimental conditions (increase of maximal length, decrease of growth rate, decrease of brood size, and decrease of the elimination rate). In addition, differential evolution was also highlighted between the two populations once the maternal effects had been diminished after several generations. Thus, individuals that were greater in maximal length, but with apparently a greater sensitivity to uranium were selected in the uranium population. In this study, we showed that this bioenergetics mechanistic modeling approach provided a precise, certain, and powerful analysis of the life strategy of C. elegans populations exposed to heavy metals resulting in an evolutionary pressure across successive generations.

Differential influences of allometry, phylogeny and environment on the rostral shape diversity of extinct South American notoungulates

NASA Astrophysics Data System (ADS)

Gomes Rodrigues, Helder; Cornette, Raphaël; Clavel, Julien; Cassini, Guillermo; Bhullar, Bhart-Anjan S.; Fernández-Monescillo, Marcos; Moreno, Karen; Herrel, Anthony; Billet, Guillaume

2018-01-01

Understanding the mechanisms responsible for phenotypic diversification, and the associated underlying constraints and ecological factors represents a central issue in evolutionary biology. Mammals present a wide variety of sizes and shapes, and are characterized by a high number of morphological convergences that are hypothesized to reflect similar environmental pressures. Extinct South American notoungulates evolved in isolation from northern mammalian faunas in highly disparate environments. They present a wide array of skeletal phenotypes and convergences, such as ever-growing dentition. Here, we focused on the origins of the rostral diversity of notoungulates by quantifying the shape of 26 genera using three-dimensional geometric morphometric analysis. We tested the influence of allometry and phylogeny on rostral shape and evaluated rates of evolutionary change in the different clades. We found strong allometric and phylogenetic signals concerning the rostral shape of notoungulates. Despite convergent forms, we observed a diffuse diversification of rostral shape, with no significant evidence of influence by large-scaled environmental variation. This contrasts with the increase in dental crown height that occurred in four late-diverging families in response to similar environmental pressures. These results illustrate the importance of considering both biological components and evolutionary rates to better understand some aspects of phenotypic diversity.

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

PubMed Central

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

2013-01-01

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

Long-term evolution of the Luteoviridae: time scale and mode of virus speciation.

PubMed

Pagán, Israel; Holmes, Edward C

2010-06-01

Despite their importance as agents of emerging disease, the time scale and evolutionary processes that shape the appearance of new viral species are largely unknown. To address these issues, we analyzed intra- and interspecific evolutionary processes in the Luteoviridae family of plant RNA viruses. Using the coat protein gene of 12 members of the family, we determined their phylogenetic relationships, rates of nucleotide substitution, times to common ancestry, and patterns of speciation. An associated multigene analysis enabled us to infer the nature of selection pressures and the genomic distribution of recombination events. Although rates of evolutionary change and selection pressures varied among genes and species and were lower in some overlapping gene regions, all fell within the range of those seen in animal RNA viruses. Recombination breakpoints were commonly observed at gene boundaries but less so within genes. Our molecular clock analysis suggested that the origin of the currently circulating Luteoviridae species occurred within the last 4 millennia, with intraspecific genetic diversity arising within the last few hundred years. Speciation within the Luteoviridae may therefore be associated with the expansion of agricultural systems. Finally, our phylogenetic analysis suggested that viral speciation events tended to occur within the same plant host species and country of origin, as expected if speciation is largely sympatric, rather than allopatric, in nature.

Crystal Structure Prediction and its Application in Earth and Materials Sciences

NASA Astrophysics Data System (ADS)

Zhu, Qiang

First of all, we describe how to predict crystal structure by evolutionary approach, and extend this method to study the packing of organic molecules, by our specially designed constrained evolutionary algorithm. The main feature of this new approach is that each unit or molecule is treated as a whole body, which drastically reduces the search space and improves the efficiency. The improved method is possibly to be applied in the fields of (1) high pressure phase of simple molecules (H2O, NH3, CH4, etc); (2) pharmaceutical molecules (glycine, aspirin, etc); (3) complex inorganic crystals containing cluster or molecular unit, (Mg(BH4)2, Ca(BH4)2, etc). One application of the constrained evolutionary algorithm is given by the study of (Mg(BH4)2, which is a promising materials for hydrogen storage. Our prediction does not only reproduce the previous work on Mg(BH4)2 at ambient condition, but also yields two new tetragonal structures at high pressure, with space groups P4 and I41/acd are predicted to be lower in enthalpy, by 15.4 kJ/mol and 21.2 kJ/mol, respectively, than the earlier proposed P42nm phase. We have simulated X-ray diffraction spectra, lattice dynamics, and equations of state of these phases. The density, volume contraction, bulk modulus, and the simulated XRD patterns of P4 and I41/acd structures are in excellent agreement with the experimental results. Two kinds of oxides (Xe-O and Mg-O) have been studied under megabar pressures. For XeO, we predict the existence of thermodynamically stable Xe-O compounds at high pressures (XeO, XeO2 and XeO3 become stable at pressures of 83, 102 and 114 GPa, respectively). For Mg-O, our calculations find that two extraordinary compounds MgO2 and Mg3O 2 become thermodynamically stable at 116 GPa and 500 GPa, respectively. Our calculations indicate large charge transfer in these oxides for both systems, suggesting that large electronegativity difference and pressure are the key factors favouring their formations. We also discuss if these oxides might exist at earth and planetary conditions. If the target properties are set as the global fitness functions while structure relaxations are energy/enthalpy minimization, such hybrid optimization technique could effectively explore the landscape of properties for the given systems. Here we illustrate this function by the case of searching for superdense carbon allotropes. We find three structures (hP3, tI12, and tP12) that have significantly greater density. Furthermore, we find a collection of other superdense structures based on different ways of packing carbon tetrahedral. Superdense carbon allotropes are predicted to have remarkably high refractive indices and strong dispersion of light. Apart from evolutionary approach, there also exist some other methods for structural prediction. One can also combine the features from different methods. We develop a novel method for crystal structure prediction, based on metadynamics and evolutionary algorithms. This technique can be used to produce efficiently both the ground state and metastable states easily reachable from a reasonable initial structure. We use the cell shape as collective variable and evolutionary variation operators developed in the context of the USPEX method to equilibrate the system as a function of the collective variables. We illustrate how this approach helps one to find stable and metastable states for Al2SiO5, SiO2, MgSiO3. Apart from predicting crystal structures, the new method can also provide insight into mechanisms of phase transitions. This method is especially powerful in sampling the metastable structures from a given configuration. Experiments on cold compression indicated the existence of a new superhard carbon allotrope. Numerous metastable candidate structures featuring different topologies have been proposed for this allotrope. We use evolutionary metadynamics to systematically search for possible candidates which could be accessible from graphite. (Abstract shortened by UMI.)

Evolutionary computation in zoology and ecology.

PubMed

Boone, Randall B

2017-12-01

Evolutionary computational methods have adopted attributes of natural selection and evolution to solve problems in computer science, engineering, and other fields. The method is growing in use in zoology and ecology. Evolutionary principles may be merged with an agent-based modeling perspective to have individual animals or other agents compete. Four main categories are discussed: genetic algorithms, evolutionary programming, genetic programming, and evolutionary strategies. In evolutionary computation, a population is represented in a way that allows for an objective function to be assessed that is relevant to the problem of interest. The poorest performing members are removed from the population, and remaining members reproduce and may be mutated. The fitness of the members is again assessed, and the cycle continues until a stopping condition is met. Case studies include optimizing: egg shape given different clutch sizes, mate selection, migration of wildebeest, birds, and elk, vulture foraging behavior, algal bloom prediction, and species richness given energy constraints. Other case studies simulate the evolution of species and a means to project shifts in species ranges in response to a changing climate that includes competition and phenotypic plasticity. This introduction concludes by citing other uses of evolutionary computation and a review of the flexibility of the methods. For example, representing species' niche spaces subject to selective pressure allows studies on cladistics, the taxon cycle, neutral versus niche paradigms, fundamental versus realized niches, community structure and order of colonization, invasiveness, and responses to a changing climate.

Evolutionary computation in zoology and ecology

PubMed Central

2017-01-01

Abstract Evolutionary computational methods have adopted attributes of natural selection and evolution to solve problems in computer science, engineering, and other fields. The method is growing in use in zoology and ecology. Evolutionary principles may be merged with an agent-based modeling perspective to have individual animals or other agents compete. Four main categories are discussed: genetic algorithms, evolutionary programming, genetic programming, and evolutionary strategies. In evolutionary computation, a population is represented in a way that allows for an objective function to be assessed that is relevant to the problem of interest. The poorest performing members are removed from the population, and remaining members reproduce and may be mutated. The fitness of the members is again assessed, and the cycle continues until a stopping condition is met. Case studies include optimizing: egg shape given different clutch sizes, mate selection, migration of wildebeest, birds, and elk, vulture foraging behavior, algal bloom prediction, and species richness given energy constraints. Other case studies simulate the evolution of species and a means to project shifts in species ranges in response to a changing climate that includes competition and phenotypic plasticity. This introduction concludes by citing other uses of evolutionary computation and a review of the flexibility of the methods. For example, representing species’ niche spaces subject to selective pressure allows studies on cladistics, the taxon cycle, neutral versus niche paradigms, fundamental versus realized niches, community structure and order of colonization, invasiveness, and responses to a changing climate. PMID:29492029

Impacts of invasive fish removal through angling on population characteristics and juvenile growth rate.

PubMed

Evangelista, Charlotte; Britton, Robert J; Cucherousset, Julien

2015-06-01

Exploitation can modify the characteristics of fish populations through the selective harvesting of individuals, with this potentially leading to rapid ecological and evolutionary changes. Despite the well-known effects of invasive fishes on aquatic ecosystems generally, the potential effects of their selective removal through angling, a strategy commonly used to manage invasive fish, are poorly understood. The aim of this field-based study was to use the North American pumpkinseed Lepomis gibbosus as the model species to investigate the consequences of selective removal on their population characteristics and juvenile growth rates across 10 populations in artificial lakes in southern France. We found that the maximal individual mass in populations decreased as removal pressure through angling increased, whereas we did not observed any changes in the maximal individual length in populations as removal pressure increased. Total population abundance did not decrease as removal pressure increased; instead, here was a U-shaped relationship between removal pressure and the abundance of medium-bodied individuals. In addition, population biomass had a U-shaped curve response to removal pressure, implying that invasive fish populations can modulate their characteristics to compensate for the negative effects of selective removals. In addition, individual lengths at age 2 and juvenile growth rates decreased as removal pressure through angling increased, suggesting a shift toward an earlier size at maturity and an overall slower growing phenotype. Therefore, these outputs challenge the efficiency of selective management methods, suggesting the use of more proactive strategies to control invasive populations, and the need to investigate the potential ecological and evolutionary repercussions of nonrandom removal.

Impacts of invasive fish removal through angling on population characteristics and juvenile growth rate

PubMed Central

Evangelista, Charlotte; Britton, Robert J; Cucherousset, Julien

2015-01-01

Exploitation can modify the characteristics of fish populations through the selective harvesting of individuals, with this potentially leading to rapid ecological and evolutionary changes. Despite the well-known effects of invasive fishes on aquatic ecosystems generally, the potential effects of their selective removal through angling, a strategy commonly used to manage invasive fish, are poorly understood. The aim of this field-based study was to use the North American pumpkinseed Lepomis gibbosus as the model species to investigate the consequences of selective removal on their population characteristics and juvenile growth rates across 10 populations in artificial lakes in southern France. We found that the maximal individual mass in populations decreased as removal pressure through angling increased, whereas we did not observed any changes in the maximal individual length in populations as removal pressure increased. Total population abundance did not decrease as removal pressure increased; instead, here was a U-shaped relationship between removal pressure and the abundance of medium-bodied individuals. In addition, population biomass had a U-shaped curve response to removal pressure, implying that invasive fish populations can modulate their characteristics to compensate for the negative effects of selective removals. In addition, individual lengths at age 2 and juvenile growth rates decreased as removal pressure through angling increased, suggesting a shift toward an earlier size at maturity and an overall slower growing phenotype. Therefore, these outputs challenge the efficiency of selective management methods, suggesting the use of more proactive strategies to control invasive populations, and the need to investigate the potential ecological and evolutionary repercussions of nonrandom removal. PMID:26078856

Comparative Analysis of Evolutionary Mechanisms of the Hemagglutinin and Three Internal Protein Genes of Influenza B Virus: Multiple Cocirculating Lineages and Frequent Reassortment of the NP, M, and NS Genes

PubMed Central

Lindstrom, Stephen E.; Hiromoto, Yasuaki; Nishimura, Hidekazu; Saito, Takehiko; Nerome, Reiko; Nerome, Kuniaki

1999-01-01

Phylogenetic profiles of the genes coding for the hemagglutinin (HA) protein, nucleoprotein (NP), matrix (M) protein, and nonstructural (NS) proteins of influenza B viruses isolated from 1940 to 1998 were analyzed in a parallel manner in order to understand the evolutionary mechanisms of these viruses. Unlike human influenza A (H3N2) viruses, the evolutionary pathways of all four genes of recent influenza B viruses revealed similar patterns of genetic divergence into two major lineages. Although evolutionary rates of the HA, NP, M, and NS genes of influenza B viruses were estimated to be generally lower than those of human influenza A viruses, genes of influenza B viruses demonstrated complex phylogenetic patterns, indicating alternative mechanisms for generation of virus variability. Topologies of the evolutionary trees of each gene were determined to be quite distinct from one another, showing that these genes were evolving in an independent manner. Furthermore, variable topologies were apparently the result of frequent genetic exchange among cocirculating epidemic viruses. Evolutionary analysis done in the present study provided further evidence for cocirculation of multiple lineages as well as sequestering and reemergence of phylogenetic lineages of the internal genes. In addition, comparison of deduced amino acid sequences revealed a novel amino acid deletion in the HA1 domain of the HA protein of recent isolates from 1998 belonging to the B/Yamagata/16/88-like lineage. It thus became apparent that, despite lower evolutionary rates, influenza B viruses were able to generate genetic diversity among circulating viruses through a combination of evolutionary mechanisms involving cocirculating lineages and genetic reassortment by which new variants with distinct gene constellations emerged. PMID:10196339

Evolutionary genomics of peach and almond domestication

USDA-ARS?s Scientific Manuscript database

The domesticated almond [Prunus dulcis (L.) Batsch] and peach [P. persica (Mill.) D. A. Webb] originate on opposite sides of Asia and were independently domesticated approximately 5000 years ago. While interfertile, they possess alternate mating systems and di er in a number of morphological and ph...

Molecular evolution of the enzymes involved in the sphingolipid metabolism of Leishmania: selection pressure in relation to functional divergence and conservation.

PubMed

Mandlik, Vineetha; Shinde, Sonali; Singh, Shailza

2014-06-21

Selection pressure governs the relative mutability and the conservedness of a protein across the protein family. Biomolecules (DNA, RNA and proteins) continuously evolve under the effect of evolutionary pressure that arises as a consequence of the host parasite interaction. IPCS (Inositol phosphorylceramide synthase), SPL (Sphingosine-1-P lyase) and SPT (Serine palmitoyl transferase) represent three important enzymes involved in the sphingolipid metabolism of Leishmania. These enzymes are responsible for maintaining the viability and infectivity of the parasite and have been classified as druggable targets in the parasite metabolome. The present work relates to the role of selection pressure deciding functional conservedness and divergence of the drug targets. IPCS and SPL protein families appear to diverge from the SPT family. The three protein families were largely under the influence of purifying selection and were moderately conserved baring two residues in the IPCS protein which were under the influence of positive selection. To further explore the selection pressure at the codon level, codon usage bias indices were calculated to analyze genes for their synonymous codon usage pattern. IPCS gene exhibited slightly lower codon bias as compared to SPL and SPT protein families. Evolutionary tracing of the proposed drug targets has been done with a viewpoint that the amino-acids lining the drug binding pocket should have a lower evolvability. Sites under positive selection (HIS20 and CYS30 of IPCS) should be avoided during devising strategies for inhibitor design.

The rock-paper-scissors game and the evolution of alternative male strategies

NASA Astrophysics Data System (ADS)

Sinervo, B.; Lively, C. M.

1996-03-01

MANY species exhibit colour polymorphisms associated with alternative male reproductive strategies, including territorial males and 'sneaker males' that behave and look like females1-3. The prevalence of multiple morphs is a challenge to evolutionary theory because a single strategy should prevail unless morphs have exactly equal fitness4,5 or a fitness advantage when rare6,7. We report here the application of an evolutionary stable strategy model to a three-morph mating system in the side-blotched lizard. Using parameter estimates from field data, the model predicted oscillations in morph frequency, and the frequencies of the three male morphs were found to oscillate over a six-year period in the field. The fitnesses of each morph relative to other morphs were non-transitive in that each morph could invade another morph when rare, but was itself invadable by another morph when common. Concordance between frequency-dependent selection and the among-year changes in morph fitnesses suggest that male interactions drive a dynamic 'rock-paper-scissors' game7.

The evolutionary origin and diversification of feathers.

PubMed

Prum, Richard O; Brush, Alan H

2002-09-01

Progress on the evolutionary origin and diversification of feathers has been hampered by conceptual problems and by the lack of plesiomorphic feather fossils. Recently, both of these limitations have been overcome by the proposal of the developmental theory of the origin of feathers, and the discovery of primitive feather fossils on nonavian theropod dinosaurs. The conceptual problems of previous theories of the origin of feathers are reviewed, and the alternative developmental theory is presented and discussed. The developmental theory proposes that feathers evolved through a series of evolutionary novelties in developmental mechanisms of the follicle and feather germ. The discovery of primitive and derived fossil feathers on a diversity of coelurosaurian theropod dinosaurs documents that feathers evolved and diversified in nonavian theropods before the origin of birds and before the origin of flight. The morphologies of these primitive feathers are congruent with the predictions of the developmental theory. Alternatives to the theropod origin of feathers are critique and rejected. Hypotheses for the initial function of feathers are reviewed. The aerodynamic theory of feather origins is falsified, but many other functions remain developmentally and phylogenetically plausible. Whatever their function, feathers evolved by selection for a follicle that would grow an emergent tubular appendage. Feathers are inherently tubular structures. The homology of feathers and scales is weakly supported. Feathers are composed of a suite of evolutionary novelties that evolved by the duplication, hierarchical organization, interaction, dissociation, and differentiation of morphological modules. The unique capacity for modular subdivision of the tubular feather follicle and germ has fostered the evolution of numerous innovations that characterize feathers. The evolution of feather keratin and the molecular basis of feather development are also discussed.

Rates of morphological evolution, asymmetry and morphological integration of shell shape in scallops.

PubMed

Sherratt, Emma; Serb, Jeanne M; Adams, Dean C

2017-12-08

Rates of morphological evolution vary across different taxonomic groups, and this has been proposed as one of the main drivers for the great diversity of organisms on Earth. Of the extrinsic factors pertaining to this variation, ecological hypotheses feature prominently in observed differences in phenotypic evolutionary rates across lineages. But complex organisms are inherently modular, comprising distinct body parts that can be differentially affected by external selective pressures. Thus, the evolution of trait covariation and integration in modular systems may also play a prominent role in shaping patterns of phenotypic diversity. Here we investigate the role ecological diversity plays in morphological integration, and the tempo of shell shape evolution and of directional asymmetry in bivalved scallops. Overall, the shape of both valves and the magnitude of asymmetry of the whole shell (difference in shape between valves) are traits that are evolving fast in ecomorphs under strong selective pressures (gliders, recessers and nestling), compared to low rates observed in other ecomorphs (byssal-attaching, free-living and cementing). Given that different parts of an organism can be under different selective pressures from the environment, we also examined the degree of evolutionary integration between the valves as it relates to ecological shifts. We find that evolutionary morphological integration is consistent and surprisingly high across species, indicating that while the left and right valves of a scallop shell are diversifying in accordance with ecomorphology, they are doing so in a concerted fashion. Our study on scallops adds another strong piece of evidence that ecological shifts play an important role in the tempo and mode of morphological evolution. Strong selective pressures from the environment, inferred from the repeated evolution of distinct ecomorphs, have influenced the rate of morphological evolution in valve shape and the magnitude of asymmetry between valves. Our observation that morphological integration of the valves making up the shell is consistently strong suggests tight developmental pathways are responsible for the concerted evolution of these structures while environmental pressures are driving whole shell shape. Finally, our study shows that directional asymmetry in shell shape among species is an important aspect of scallop macroevolution.

Evidence of Atlantic salmon Salmo salar fry movement between fresh water and a brackish environment.

PubMed

Taal, I; Rohtla, M; Saks, L; Svirgsden, R; Kesler, M; Matetski, L; Vetemaa, M

2017-08-01

This study reports descent of Atlantic salmon Salmo salar fry from their natal streams to brackish waters of the Baltic Sea and their use of this environment as an alternative rearing habitat before ascending back to freshwater streams. To the authors' knowledge, residency in a brackish environment has not previously been demonstrated in S. salar fry. Recruitment success and evolutionary significance of this alternative life-history strategy are presently not known. © 2017 The Fisheries Society of the British Isles.

On the preservation of cooperation in two-strategy games with nonlocal interactions.

PubMed

Aydogmus, Ozgur; Zhou, Wen; Kang, Yun

2017-03-01

Nonlocal interactions such as spatial interaction are ubiquitous in nature and may alter the equilibrium in evolutionary dynamics. Models including nonlocal spatial interactions can provide a further understanding on the preservation and emergence of cooperation in evolutionary dynamics. In this paper, we consider a variety of two-strategy evolutionary spatial games with nonlocal interactions based on an integro-differential replicator equation. By defining the invasion speed and minimal traveling wave speed for the derived model, we study the effects of the payoffs, the selection pressure and the spatial parameter on the preservation of cooperation. One of our most interesting findings is that, for the Prisoners Dilemma games in which the defection is the only evolutionary stable strategy for unstructured populations, analyses on its asymptotic speed of propagation suggest that, in contrast with spatially homogeneous games, the cooperators can invade the habitat under proper conditions. Other two-strategy evolutionary spatial games are also explored. Both our theoretical and numerical studies show that the nonlocal spatial interaction favors diversity in strategies in a population and is able to preserve cooperation in a competing environment. A real data application in a virus mutation study echoes our theoretical observations. In addition, we compare the results of our model to the partial differential equation approach to demonstrate the importance of including non-local interaction component in evolutionary game models. Copyright © 2016 Elsevier Inc. All rights reserved.

Evolutionary distinctiveness of fatty acid and polyketide synthesis in eukaryotes

PubMed Central

Kohli, Gurjeet S; John, Uwe; Van Dolah, Frances M; Murray, Shauna A

2016-01-01

Fatty acids, which are essential cell membrane constituents and fuel storage molecules, are thought to share a common evolutionary origin with polyketide toxins in eukaryotes. While fatty acids are primary metabolic products, polyketide toxins are secondary metabolites that are involved in ecologically relevant processes, such as chemical defence, and produce the adverse effects of harmful algal blooms. Selection pressures on such compounds may be different, resulting in differing evolutionary histories. Surprisingly, some studies of dinoflagellates have suggested that the same enzymes may catalyse these processes. Here we show the presence and evolutionary distinctiveness of genes encoding six key enzymes essential for fatty acid production in 13 eukaryotic lineages for which no previous sequence data were available (alveolates: dinoflagellates, Vitrella, Chromera; stramenopiles: bolidophytes, chrysophytes, pelagophytes, raphidophytes, dictyochophytes, pinguiophytes, xanthophytes; Rhizaria: chlorarachniophytes, haplosporida; euglenids) and 8 other lineages (apicomplexans, bacillariophytes, synurophytes, cryptophytes, haptophytes, chlorophyceans, prasinophytes, trebouxiophytes). The phylogeny of fatty acid synthase genes reflects the evolutionary history of the organism, indicating selection to maintain conserved functionality. In contrast, polyketide synthase gene families are highly expanded in dinoflagellates and haptophytes, suggesting relaxed constraints in their evolutionary history, while completely absent from some protist lineages. This demonstrates a vast potential for the production of bioactive polyketide compounds in some lineages of microbial eukaryotes, indicating that the evolution of these compounds may have played an important role in their ecological success. PMID:26784357

Replicated evolutionary divergence in the cuticular hydrocarbon profile of male crickets associated with the loss of song in the Hawaiian archipelago.

PubMed

Simmons, L W; Thomas, M L; Gray, B; Zuk, M

2014-10-01

Female choice based on male secondary sexual traits is well documented, although the extent to which this selection can drive an evolutionary divergence in male traits among populations is less clear. Male field crickets Teleogryllus oceanicus attract females using a calling song and once contacted switch to courtship song to persuade them to mate. These crickets also secrete onto their cuticle a cocktail of long-chained fatty acids or cuticular hydrocarbons (CHCs). Females choose among potential mates based on the structure of male acoustic signals and on the composition of male CHC profiles. Here, we utilize two naturally occurring mutations that have arisen independently on two Hawaiian islands and render the male silent to ask whether the evolutionary loss of acoustic signalling can drive an evolutionary divergence in the alternative signalling modality, male CHC profiles. QST -FST comparisons revealed strong patterns of CHC divergence among three populations of crickets on the islands of Hawaii, Oahu and Kauai. Contrasts between wild-type and flatwing males on the islands of Oahu and Kauai indicated that variation in male CHC profiles within populations is associated with the loss of acoustic signalling; flatwing males had a relatively low abundance of long-chained CHCs relative to the short-chained CHCs that females find attractive. Given their dual functions in desiccation resistance and sexual signalling, insect CHCs may be particularly important traits for reproductive isolation and ultimately speciation. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

The economics of new age arthroplasty: can we afford it?

PubMed

Sculco, Thomas P

2010-09-07

New technology in joint replacement design and materials adds cost that must be documented by improved outcomes. This is not always the case as the recent metal/metal data has shown. The current economics of arthroplasty have put increasing financial pressure on hospitals and will progress under new health care legislation. New technology must be cost-effective and this will be increasingly difficult in an era of outstanding long-term results with current designs. Cost may necessitate less expensive alternatives, eg, generic implants, in arthroplasty patients. Joint replacement surgery has evolved over the past 4 decades into a highly successful surgical procedure. Earlier designs and materials that demonstrated inferior functional and long-term results have disappeared in a Darwinian fashion. Through this evolutionary process many of the current designs have proven efficacy and durability. Current outcome data indicates that hip and knee designs demonstrate 90% to 95% success rates at 15-year follow-up. Technologic advances are necessary to improve implant design and materials, however, only in an environment of reduced reimbursement to hospitals can the increase cost be justified. Copyright 2010, SLACK Incorporated.

An additional step in the transmission of Yersinia pestis?

PubMed Central

Easterday, W Ryan; Kausrud, Kyrre L; Star, Bastiaan; Heier, Lise; Haley, Bradd J; Ageyev, Vladimir; Colwell, Rita R; Stenseth, Nils Chr

2012-01-01

Plague, caused by the bacterium Yersinia pestis, is a mammalian vector-borne disease, transmitted by fleas that serve as the vector between rodent hosts. For many pathogens, including Y. pestis, there are strong evolutionary pressures that lead to a reduction in ‘useless genes', with only those retained that reflect function in the specific environment inhabited by the pathogen. Genetic traits critical for survival and transmission between two environments, the rodent and the flea, are conserved in epizootic/epidemic plague strains. However, there are genes that remain conserved for which no function in the flea–rodent cycle has yet been observed, indicating an additional environment may exist in the transmission cycle of plague. Here, we present evidence for highly conserved genes that suggests a role in the persistence of Y. pestis after death of its host. Furthermore, maintenance of these genes points to Y. pestis traversing a post-mortem path between, and possibly within, epizootic periods and offering insight into mechanisms that may allow Y. pestis an alternative route of transmission in the natural environment. PMID:21833036

Modeling Tumor Clonal Evolution for Drug Combinations Design

PubMed Central

Zhao, Boyang; Hemann, Michael T.; Lauffenburger, Douglas A.

2016-01-01

Cancer is a clonal evolutionary process. This presents challenges for effective therapeutic intervention, given the constant selective pressure towards drug resistance. Mathematical modeling from population genetics, evolutionary dynamics, and engineering perspectives are being increasingly employed to study tumor progression, intratumoral heterogeneity, drug resistance, and rational drug scheduling and combinations design. In this review, we discuss promising opportunities these inter-disciplinary approaches hold for advances in cancer biology and treatment. We propose that quantitative modeling perspectives can complement emerging experimental technologies to facilitate enhanced understanding of disease progression and improved capabilities for therapeutic drug regimen designs. PMID:28435907

Genetic Architecture of Parallel Pelvic Reduction in Ninespine Sticklebacks

PubMed Central

Shikano, Takahito; Laine, Veronika N.; Herczeg, Gábor; Vilkki, Johanna; Merilä, Juha

2013-01-01

Teleost fish genomes are known to be evolving faster than those of other vertebrate taxa. Thus, fish are suited to address the extent to which the same vs. different genes are responsible for similar phenotypic changes in rapidly evolving genomes of evolutionary independent lineages. To gain insights into the genetic basis and evolutionary processes behind parallel phenotypic changes within and between species, we identified the genomic regions involved in pelvic reduction in Northern European ninespine sticklebacks (Pungitius pungitius) and compared them to those of North American ninespine and threespine sticklebacks (Gasterosteus aculeatus). To this end, we conducted quantitative trait locus (QTL) mapping using 283 F2 progeny from an interpopulation cross. Phenotypic analyses indicated that pelvic reduction is a recessive trait and is inherited in a simple Mendelian fashion. Significant QTL for pelvic spine and girdle lengths were identified in the region of the Pituitary homeobox transcription factor 1 (Pitx1) gene, also responsible for pelvic reduction in threespine sticklebacks. The fact that no QTL was observed in the region identified in the mapping study of North American ninespine sticklebacks suggests that an alternative QTL for pelvic reduction has emerged in this species within the past 1.6 million years after the split between Northern European and North American populations. In general, our study provides empirical support for the view that alternative genetic mechanisms that lead to similar phenotypes can evolve over short evolutionary time scales. PMID:23979937

Aggressive mimicry coexists with mutualism in an aphid.

PubMed

Salazar, Adrián; Fürstenau, Benjamin; Quero, Carmen; Pérez-Hidalgo, Nicolás; Carazo, Pau; Font, Enrique; Martínez-Torres, David

2015-01-27

Understanding the evolutionary transition from interspecific exploitation to cooperation is a major challenge in evolutionary biology. Ant-aphid relationships represent an ideal system to this end because they encompass a coevolutionary continuum of interactions ranging from mutualism to antagonism. In this study, we report an unprecedented interaction along this continuum: aggressive mimicry in aphids. We show that two morphs clonally produced by the aphid Paracletus cimiciformis during its root-dwelling phase establish relationships with ants at opposite sides of the mutualism-antagonism continuum. Although one of these morphs exhibits the conventional trophobiotic (mutualistic) relationship with ants of the genus Tetramorium, aphids of the alternative morph are transported by the ants to their brood chamber and cared for as if they were true ant larvae. Gas chromatography-mass spectrometry analyses reveal that the innate cuticular hydrocarbon profile of the mimic morph resembles the profile of ant larvae more than that of the alternative, genetically identical nonmimic morph. Furthermore, we show that, once in the brood chamber, mimic aphids suck on ant larva hemolymph. These results not only add aphids to the limited list of arthropods known to biosynthesize the cuticular chemicals of their deceived hosts to exploit their resources but describe a remarkable case of plastic aggressive mimicry. The present work adds a previously unidentified dimension to the classical textbook paradigm of aphid-ant relationships by showcasing a complex system at the evolutionary interface between cooperation and exploitation.

Aggressive mimicry coexists with mutualism in an aphid

PubMed Central

Salazar, Adrián; Fürstenau, Benjamin; Quero, Carmen; Pérez-Hidalgo, Nicolás; Carazo, Pau; Font, Enrique; Martínez-Torres, David

2015-01-01

Understanding the evolutionary transition from interspecific exploitation to cooperation is a major challenge in evolutionary biology. Ant–aphid relationships represent an ideal system to this end because they encompass a coevolutionary continuum of interactions ranging from mutualism to antagonism. In this study, we report an unprecedented interaction along this continuum: aggressive mimicry in aphids. We show that two morphs clonally produced by the aphid Paracletus cimiciformis during its root-dwelling phase establish relationships with ants at opposite sides of the mutualism–antagonism continuum. Although one of these morphs exhibits the conventional trophobiotic (mutualistic) relationship with ants of the genus Tetramorium, aphids of the alternative morph are transported by the ants to their brood chamber and cared for as if they were true ant larvae. Gas chromatography-mass spectrometry analyses reveal that the innate cuticular hydrocarbon profile of the mimic morph resembles the profile of ant larvae more than that of the alternative, genetically identical nonmimic morph. Furthermore, we show that, once in the brood chamber, mimic aphids suck on ant larva hemolymph. These results not only add aphids to the limited list of arthropods known to biosynthesize the cuticular chemicals of their deceived hosts to exploit their resources but describe a remarkable case of plastic aggressive mimicry. The present work adds a previously unidentified dimension to the classical textbook paradigm of aphid–ant relationships by showcasing a complex system at the evolutionary interface between cooperation and exploitation. PMID:25583474

The relationship between familial resemblance and sexual attraction: an update on Westermarck, Freud, and the incest taboo.

PubMed

Lieberman, Debra; Fessler, Daniel M T; Smith, Adam

2011-09-01

Foundational principles of evolutionary theory predict that inbreeding avoidance mechanisms should exist in all species--including humans--in which close genetic relatives interact during periods of sexual maturity. Voluminous empirical evidence, derived from diverse taxa, supports this prediction. Despite such results, Fraley and Marks claim to provide evidence that humans are sexually attracted to close genetic relatives and that such attraction is held in check by cultural taboos. Here, the authors show that Fraley and Marks, in their search for an alternate explanation of inbreeding avoidance, misapply theoretical constructs from evolutionary biology and social psychology, leading to an incorrect interpretation of their results. The authors propose that Fraley and Marks's central findings can be explained in ways consistent with existing evolutionary models of inbreeding avoidance. The authors conclude that appropriate application of relevant theory and stringent experimental design can generate fruitful investigations into sexual attraction, inbreeding avoidance, and incest taboos.

The Meaningful Roles Intervention: An Evolutionary Approach to Reducing Bullying and Increasing Prosocial Behavior.

PubMed

Ellis, Bruce J; Volk, Anthony A; Gonzalez, Jose-Michael; Embry, Dennis D

2016-12-01

Bullying is a problem that affects adolescents worldwide. Efforts to prevent bullying have been moderately successful at best, or iatrogenic at worst. We offer an explanation for this limited success by employing an evolutionary-psychological perspective to analyze antibullying interventions. We argue that bullying is a goal-directed behavior that is sensitive to benefits as well as costs, and that interventions must address these benefits. This perspective led us to develop a novel antibullying intervention, Meaningful Roles, which offers bullies prosocial alternatives-meaningful roles and responsibilities implemented through a school jobs program and reinforced through peer-to-peer praise notes-that effectively meet the same status goals as bullying behavior. We describe this new intervention and how its theoretical evolutionary roots may be applicable to other intervention programs. © 2015 The Authors. Journal of Research on Adolescence © 2015 Society for Research on Adolescence.

Does evolution matter?: a case study in Brazil of the effects of an evolutionary-thinking academic atmosphere in postgraduate students' belief in God/religious belief.

PubMed

Dias, Ivan A; Willemart, Rodrigo H; Marques, Antonio C

2012-06-01

Although the theory of evolution is more than 150 years old, a substantial proportion of the world population does not mention it when explaining the origin of human beings. The usual alternative conception is offered by creationism, one of the main obstacles to full acceptance of evolution in many countries. National polls have demonstrated that schooling and religiosity are negatively correlated, with scientists being one of the least religious professionals. Herein we analyzed both (1) the profile of 1st semester undergraduate students and (2), thesis and dissertations, concerning religious and evolutionary thoughts from Biology and Veterinary Schools at the largest university of South America. We have shown that students of Biology are biased towards evolution before they enter university and also that the presence of an evolutionary-thinking academic atmosphere influences the deism/religiosity beliefs of postgraduate students.

Efficient fractal-based mutation in evolutionary algorithms from iterated function systems

NASA Astrophysics Data System (ADS)

Salcedo-Sanz, S.; Aybar-Ruíz, A.; Camacho-Gómez, C.; Pereira, E.

2018-03-01

In this paper we present a new mutation procedure for Evolutionary Programming (EP) approaches, based on Iterated Function Systems (IFSs). The new mutation procedure proposed consists of considering a set of IFS which are able to generate fractal structures in a two-dimensional phase space, and use them to modify a current individual of the EP algorithm, instead of using random numbers from different probability density functions. We test this new proposal in a set of benchmark functions for continuous optimization problems. In this case, we compare the proposed mutation against classical Evolutionary Programming approaches, with mutations based on Gaussian, Cauchy and chaotic maps. We also include a discussion on the IFS-based mutation in a real application of Tuned Mass Dumper (TMD) location and optimization for vibration cancellation in buildings. In both practical cases, the proposed EP with the IFS-based mutation obtained extremely competitive results compared to alternative classical mutation operators.

Turbopump Performance Improved by Evolutionary Algorithms

NASA Technical Reports Server (NTRS)

Oyama, Akira; Liou, Meng-Sing

2002-01-01

The development of design optimization technology for turbomachinery has been initiated using the multiobjective evolutionary algorithm under NASA's Intelligent Synthesis Environment and Revolutionary Aeropropulsion Concepts programs. As an alternative to the traditional gradient-based methods, evolutionary algorithms (EA's) are emergent design-optimization algorithms modeled after the mechanisms found in natural evolution. EA's search from multiple points, instead of moving from a single point. In addition, they require no derivatives or gradients of the objective function, leading to robustness and simplicity in coupling any evaluation codes. Parallel efficiency also becomes very high by using a simple master-slave concept for function evaluations, since such evaluations often consume the most CPU time, such as computational fluid dynamics. Application of EA's to multiobjective design problems is also straightforward because EA's maintain a population of design candidates in parallel. Because of these advantages, EA's are a unique and attractive approach to real-world design optimization problems.

Darwin without borders? Looking at 'generalised Darwinism' through the prism of the 'hourglass model'.

PubMed

Levit, Georgy S; Hossfeld, Uwe

2011-12-01

This article critically analyzes the arguments of the 'generalized Darwinism' recently proposed for the analysis of social-economical systems. We argue that 'generalized Darwinism' is both restrictive and empty. It is restrictive because it excludes alternative (non-selectionist) evolutionary mechanisms such as orthogenesis, saltationism and mutationism without any examination of their suitability for modeling socio-economic processes and ignoring their important roles in the development of contemporary evolutionary theory. It is empty, because it reduces Darwinism to an abstract triple-principle scheme (variation, selection and inheritance) thus ignoring the actual structure of Darwinism as a complex and dynamic theoretical structure inseparable from a very detailed system of theoretical constraints. Arguing against 'generalised Darwinism' we present our vision of the history of evolutionary biology with the help of the 'hourglass model' reflecting the internal dynamic of competing theories of evolution.

The Price Equation, Gradient Dynamics, and Continuous Trait Game Theory.

PubMed

Lehtonen, Jussi

2018-01-01

A recent article convincingly nominated the Price equation as the fundamental theorem of evolution and used it as a foundation to derive several other theorems. A major section of evolutionary theory that was not addressed is that of game theory and gradient dynamics of continuous traits with frequency-dependent fitness. Deriving fundamental results in these fields under the unifying framework of the Price equation illuminates similarities and differences between approaches and allows a simple, unified view of game-theoretical and dynamic concepts. Using Taylor polynomials and the Price equation, I derive a dynamic measure of evolutionary change, a condition for singular points, the convergence stability criterion, and an alternative interpretation of evolutionary stability. Furthermore, by applying the Price equation to a multivariable Taylor polynomial, the direct fitness approach to kin selection emerges. Finally, I compare these results to the mean gradient equation of quantitative genetics and the canonical equation of adaptive dynamics.

Construction of multiple trade-offs to obtain arbitrary singularities of adaptive dynamics.

PubMed

Kisdi, Éva

2015-04-01

Evolutionary singularities are central to the adaptive dynamics of evolving traits. The evolutionary singularities are strongly affected by the shape of any trade-off functions a model assumes, yet the trade-off functions are often chosen in an ad hoc manner, which may unjustifiably constrain the evolutionary dynamics exhibited by the model. To avoid this problem, critical function analysis has been used to find a trade-off function that yields a certain evolutionary singularity such as an evolutionary branching point. Here I extend this method to multiple trade-offs parameterized with a scalar strategy. I show that the trade-off functions can be chosen such that an arbitrary point in the viability domain of the trait space is a singularity of an arbitrary type, provided (next to certain non-degeneracy conditions) that the model has at least two environmental feedback variables and at least as many trade-offs as feedback variables. The proof is constructive, i.e., it provides an algorithm to find trade-off functions that yield the desired singularity. I illustrate the construction of trade-offs with an example where the virulence of a pathogen evolves in a small ecosystem of a host, its pathogen, a predator that attacks the host and an alternative prey of the predator.

Bipartite graphs as models of population structures in evolutionary multiplayer games.

PubMed

Peña, Jorge; Rochat, Yannick

2012-01-01

By combining evolutionary game theory and graph theory, "games on graphs" study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner's dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner's dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures.

Evolution of ribonuclease in relation to polypeptide folding mechanisms.

NASA Technical Reports Server (NTRS)

Barnard, E. A.; Cohen, M. S.; Gold, M. H.; Kim, J.-K.

1972-01-01

Comparisons of the N-terminal region of pancreatic RNAase in seven species are presented, taking into account cow, bison, deer, rat, pig, kangaroo, and turtle. The available limited evidence on hypervariable regions indicates that there is still an evolutionary constraint on them. It is proposed that there is a selection pressure acting on all regions of a protein sequence in evolution. Mutations that tend to obstruct the folding process can lead to various intensities of selection pressure.

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

PubMed

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

2016-06-01

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

Rapid evolution leads to differential population dynamics and top-down control in resurrected Daphnia populations.

PubMed

Goitom, Eyerusalem; Kilsdonk, Laurens J; Brans, Kristien; Jansen, Mieke; Lemmens, Pieter; De Meester, Luc

2018-01-01

There is growing evidence of rapid genetic adaptation of natural populations to environmental change, opening the perspective that evolutionary trait change may subsequently impact ecological processes such as population dynamics, community composition, and ecosystem functioning. To study such eco-evolutionary feedbacks in natural populations, however, requires samples across time. Here, we capitalize on a resurrection ecology study that documented rapid and adaptive evolution in a natural population of the water flea Daphnia magna in response to strong changes in predation pressure by fish, and carry out a follow-up mesocosm experiment to test whether the observed genetic changes influence population dynamics and top-down control of phytoplankton. We inoculated populations of the water flea D. magna derived from three time periods of the same natural population known to have genetically adapted to changes in predation pressure in replicate mesocosms and monitored both Daphnia population densities and phytoplankton biomass in the presence and absence of fish. Our results revealed differences in population dynamics and top-down control of algae between mesocosms harboring populations from the time period before, during, and after a peak in fish predation pressure caused by human fish stocking. The differences, however, deviated from our a priori expectations. An S-map approach on time series revealed that the interactions between adults and juveniles strongly impacted the dynamics of populations and their top-down control on algae in the mesocosms, and that the strength of these interactions was modulated by rapid evolution as it occurred in nature. Our study provides an example of an evolutionary response that fundamentally alters the processes structuring population dynamics and impacts ecosystem features.

Early constraints in sexual dimorphism: survival benefits of feminized phenotypes.

PubMed

López-Rull, I; Vergara, P; Martínez-Padilla, J; Fargallo, J A

2016-02-01

Sexual dimorphism (SD) has evolved in response to selection pressures that differ between sexes. Since such pressures change across an individual's life, SD may vary within age classes. Yet, little is known about how selection on early phenotypes may drive the final SD observed in adults. In many dimorphic species, juveniles resemble adult females rather than adult males, meaning that out of the selective pressures established by sexual selection feminized phenotypes may be adaptive. If true, fitness benefits of early female-like phenotypes may constrain the expression of male phenotypes in adulthood. Using the common kestrel Falco tinnunculus as a study model, we evaluated the fitness advantages of expressing more feminized phenotypes at youth. Although more similar to adult females than to adult males, common kestrel fledglings are still sexually dimorphic in size and coloration. Integrating morphological and chromatic variables, we analysed the phenotypic divergence between sexes as a measure of how much each individual looks like the sex to which it belongs (phenotypic sexual resemblance, PSR). We then tested the fitness benefits associated with PSR by means of the probability of recruitment in the population. We found a significant interaction between PSR and sex, showing that in both sexes more feminized phenotypes recruited more into the population than less feminized phenotypes. Moreover, males showed lower PSR than females and a higher proportion of incorrect sex classifications. These findings suggest that the mechanisms in males devoted to resembling female phenotypes in youth, due to a trend to increase fitness through more feminized phenotypes, may provide a mechanism to constrain the SD in adulthood. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Effect of an alternate winglet on the pressure and spanwise load distributions of a first generation jet transport wing

NASA Technical Reports Server (NTRS)

Montoya, L. C.; Flechner, S. G.; Jacobs, P. F.

1978-01-01

Pressure and spanwise load distributions on a first-generation jet transport semispan model at subsonic speeds are presented. The wind tunnel data were measured for the wing with and without an alternate winglet. The results show that the winglet affected outboard wing pressure distributions and increased the spanwise loads near the tip.

Assessment of student learning associated with tree thinking in an undergraduate introductory organismal biology course.

PubMed

Smith, James J; Cheruvelil, Kendra Spence; Auvenshine, Stacie

2013-01-01

Phylogenetic trees provide visual representations of ancestor-descendant relationships, a core concept of evolutionary theory. We introduced "tree thinking" into our introductory organismal biology course (freshman/sophomore majors) to help teach organismal diversity within an evolutionary framework. Our instructional strategy consisted of designing and implementing a set of experiences to help students learn to read, interpret, and manipulate phylogenetic trees, with a particular emphasis on using data to evaluate alternative phylogenetic hypotheses (trees). To assess the outcomes of these learning experiences, we designed and implemented a Phylogeny Assessment Tool (PhAT), an open-ended response instrument that asked students to: 1) map characters on phylogenetic trees; 2) apply an objective criterion to decide which of two trees (alternative hypotheses) is "better"; and 3) demonstrate understanding of phylogenetic trees as depictions of ancestor-descendant relationships. A pre-post test design was used with the PhAT to collect data from students in two consecutive Fall semesters. Students in both semesters made significant gains in their abilities to map characters onto phylogenetic trees and to choose between two alternative hypotheses of relationship (trees) by applying the principle of parsimony (Occam's razor). However, learning gains were much lower in the area of student interpretation of phylogenetic trees as representations of ancestor-descendant relationships.

Assessment of Student Learning Associated with Tree Thinking in an Undergraduate Introductory Organismal Biology Course

PubMed Central

Smith, James J.; Cheruvelil, Kendra Spence; Auvenshine, Stacie

2013-01-01

Phylogenetic trees provide visual representations of ancestor–descendant relationships, a core concept of evolutionary theory. We introduced “tree thinking” into our introductory organismal biology course (freshman/sophomore majors) to help teach organismal diversity within an evolutionary framework. Our instructional strategy consisted of designing and implementing a set of experiences to help students learn to read, interpret, and manipulate phylogenetic trees, with a particular emphasis on using data to evaluate alternative phylogenetic hypotheses (trees). To assess the outcomes of these learning experiences, we designed and implemented a Phylogeny Assessment Tool (PhAT), an open-ended response instrument that asked students to: 1) map characters on phylogenetic trees; 2) apply an objective criterion to decide which of two trees (alternative hypotheses) is “better”; and 3) demonstrate understanding of phylogenetic trees as depictions of ancestor–descendant relationships. A pre–post test design was used with the PhAT to collect data from students in two consecutive Fall semesters. Students in both semesters made significant gains in their abilities to map characters onto phylogenetic trees and to choose between two alternative hypotheses of relationship (trees) by applying the principle of parsimony (Occam's razor). However, learning gains were much lower in the area of student interpretation of phylogenetic trees as representations of ancestor–descendant relationships. PMID:24006401

Evolutionary game theory using agent-based methods.

PubMed

Adami, Christoph; Schossau, Jory; Hintze, Arend

2016-12-01

Evolutionary game theory is a successful mathematical framework geared towards understanding the selective pressures that affect the evolution of the strategies of agents engaged in interactions with potential conflicts. While a mathematical treatment of the costs and benefits of decisions can predict the optimal strategy in simple settings, more realistic settings such as finite populations, non-vanishing mutations rates, stochastic decisions, communication between agents, and spatial interactions, require agent-based methods where each agent is modeled as an individual, carries its own genes that determine its decisions, and where the evolutionary outcome can only be ascertained by evolving the population of agents forward in time. While highlighting standard mathematical results, we compare those to agent-based methods that can go beyond the limitations of equations and simulate the complexity of heterogeneous populations and an ever-changing set of interactors. We conclude that agent-based methods can predict evolutionary outcomes where purely mathematical treatments cannot tread (for example in the weak selection-strong mutation limit), but that mathematics is crucial to validate the computational simulations. Copyright © 2016 Elsevier B.V. All rights reserved.

Genome-Wide Analysis of PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) Genes in Plants Reveals the Eudicot-Wide PDAT Gene Expansion and Altered Selective Pressures Acting on the Core Eudicot PDAT Paralogs1[OPEN

PubMed Central

Pan, Xue; Peng, Fred Y.; Weselake, Randall J.

2015-01-01

PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) is an enzyme that catalyzes the transfer of a fatty acyl moiety from the sn-2 position of a phospholipid to the sn-3-position of sn-1,2-diacylglyerol, thus forming triacylglycerol and a lysophospholipid. Although the importance of PDAT in triacylglycerol biosynthesis has been illustrated in some previous studies, the evolutionary relationship of plant PDATs has not been studied in detail. In this study, we investigated the evolutionary relationship of the PDAT gene family across the green plants using a comparative phylogenetic framework. We found that the PDAT candidate genes are present in all examined green plants, including algae, lowland plants (a moss and a lycophyte), monocots, and eudicots. Phylogenetic analysis revealed the evolutionary division of the PDAT gene family into seven major clades. The separation is supported by the conservation and variation in the gene structure, protein properties, motif patterns, and/or selection constraints. We further demonstrated that there is a eudicot-wide PDAT gene expansion, which appears to have been mainly caused by the eudicot-shared ancient gene duplication and subsequent species-specific segmental duplications. In addition, selection pressure analyses showed that different selection constraints have acted on three core eudicot clades, which might enable paleoduplicated PDAT paralogs to either become nonfunctionalized or develop divergent expression patterns during evolution. Overall, our study provides important insights into the evolution of the plant PDAT gene family and explores the evolutionary mechanism underlying the functional diversification among the core eudicot PDAT paralogs. PMID:25585619

Solar Energy Education Packet for Elementary & Secondary Students.

ERIC Educational Resources Information Center

Center for Renewable Resources, Washington, DC.

The arrangement of this packet is essentially evolutionary, with a conscious effort to alternate reading assignments, activities and experiments. It begins with solar energy facts and terminology as background to introduce the reader to basic concepts. It progresses into a discussion of passive solar systems. This is followed by several projects…

Educational Tool for Optimal Controller Tuning Using Evolutionary Strategies

ERIC Educational Resources Information Center

Carmona Morales, D.; Jimenez-Hornero, J. E.; Vazquez, F.; Morilla, F.

2012-01-01

In this paper, an optimal tuning tool is presented for control structures based on multivariable proportional-integral-derivative (PID) control, using genetic algorithms as an alternative to traditional optimization algorithms. From an educational point of view, this tool provides students with the necessary means to consolidate their knowledge on…

Linking environmental flows to sediment dynamics

Treesearch

Diego García de Jalón; Martina Bussettini; Massimo Rinaldi; Gordon Grant; Nikolai Friberg; Ian G. Cowx; Fernando Magdaleno; Tom Buijse

2016-01-01

This is a policy discussion paper aimed at addressing possible alternative approaches for environmental flows (e-Flows) assessment and identification within the context of best strategies for fluvial restoration. We focus on dammed rivers in Mediterranean regions. Fluvial species and their ecological integrity are the result of their evolutionary adaptation to river...

Current developments in marine microbiology: high-pressure biotechnology and the genetic engineering of piezophiles.

PubMed

Zhang, Yu; Li, Xuegong; Bartlett, Douglas H; Xiao, Xiang

2015-06-01

A key aspect of marine environments is elevated pressure; for example, ∼70% of the ocean is at a pressure of at least 38MPa. Many types of Bacteria and Archaea reside under these high pressures, which drive oceanic biogeochemical cycles and catalyze reactions among rocks, sediments and fluids. Most marine prokaryotes are classified as piezotolerant or as (obligate)-piezophiles with few cultivated relatives. The biochemistry and physiology of these organisms are largely unknown. Recently, high-pressure cultivation technology has been combined with omics and DNA recombination methodologies to examine the physiology of piezophilic marine microorganisms. We are now beginning to understand the adaptive mechanisms of these organisms, along with their ecological functions and evolutionary processes. This knowledge is leading to the further development of high-pressure-based biotechnology. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evolution of high-level resistance during low-level antibiotic exposure.

PubMed

Wistrand-Yuen, Erik; Knopp, Michael; Hjort, Karin; Koskiniemi, Sanna; Berg, Otto G; Andersson, Dan I

2018-04-23

It has become increasingly clear that low levels of antibiotics present in many environments can select for resistant bacteria, yet the evolutionary pathways for resistance development during exposure to low amounts of antibiotics remain poorly defined. Here we show that Salmonella enterica exposed to sub-MIC levels of streptomycin evolved high-level resistance via novel mechanisms that are different from those observed during lethal selections. During lethal selection only rpsL mutations are found, whereas at sub-MIC selection resistance is generated by several small-effect resistance mutations that combined confer high-level resistance via three different mechanisms: (i) alteration of the ribosomal RNA target (gidB mutations), (ii) reduction in aminoglycoside uptake (cyoB, nuoG, and trkH mutations), and (iii) induction of the aminoglycoside-modifying enzyme AadA (znuA mutations). These results demonstrate how the strength of the selective pressure influences evolutionary trajectories and that even weak selective pressures can cause evolution of high-level resistance.

Leveraging ecological theory to guide natural product discovery.

PubMed

Smanski, Michael J; Schlatter, Daniel C; Kinkel, Linda L

2016-03-01

Technological improvements have accelerated natural product (NP) discovery and engineering to the point that systematic genome mining for new molecules is on the horizon. NP biosynthetic potential is not equally distributed across organisms, environments, or microbial life histories, but instead is enriched in a number of prolific clades. Also, NPs are not equally abundant in nature; some are quite common and others markedly rare. Armed with this knowledge, random 'fishing expeditions' for new NPs are increasingly harder to justify. Understanding the ecological and evolutionary pressures that drive the non-uniform distribution of NP biosynthesis provides a rational framework for the targeted isolation of strains enriched in new NP potential. Additionally, ecological theory leads to testable hypotheses regarding the roles of NPs in shaping ecosystems. Here we review several recent strain prioritization practices and discuss the ecological and evolutionary underpinnings for each. Finally, we offer perspectives on leveraging microbial ecology and evolutionary biology for future NP discovery.

Newly rare or newly common: evolutionary feedbacks through changes in population density and relative species abundance, and their management implications

PubMed Central

Lankau, Richard A; Strauss, Sharon Y

2011-01-01

Environmental management typically seeks to increase or maintain the population sizes of desirable species and to decrease population sizes of undesirable pests, pathogens, or invaders. With changes in population size come long-recognized changes in ecological processes that act in a density-dependent fashion. While the ecological effects of density dependence have been well studied, the evolutionary effects of changes in population size, via changes in ecological interactions with community members, are underappreciated. Here, we provide examples of changing selective pressures on, or evolution in, species as a result of changes in either density of conspecifics or changes in the frequency of heterospecific versus conspecific interactions. We also discuss the management implications of such evolutionary responses in species that have experienced rapid increases or decreases in density caused by human actions. PMID:25567977

Genomic signature of natural and anthropogenic stress in wild populations of the waterflea Daphnia magna: validation in space, time and experimental evolution.

PubMed

Orsini, Luisa; Spanier, Katina I; DE Meester, Luc

2012-05-01

Natural populations are confronted with multiple selection pressures resulting in a mosaic of environmental stressors at the landscape level. Identifying the genetic underpinning of adaptation to these complex selection environments and assigning causes of natural selection within multidimensional selection regimes in the wild is challenging. The water flea Daphnia is a renowned ecological model system with its well-documented ecology, the possibility to analyse subfossil dormant egg banks and the short generation time allowing an experimental evolution approach. Capitalizing on the strengths of this model system, we here link candidate genome regions to three selection pressures, known to induce micro-evolutionary responses in Daphnia magna: fish predation, parasitism and land use. Using a genome scan approach in space, time and experimental evolution trials, we provide solid evidence of selection at the genome level under well-characterized environmental gradients in the wild and identify candidate genes linked to the three environmental stressors. Our study reveals differential selection at the genome level in Daphnia populations and provides evidence for repeatable patterns of local adaptation in a geographic mosaic of environmental stressors fuelled by standing genetic variation. Our results imply high evolutionary potential of local populations, which is relevant to understand the dynamics of trait changes in natural populations and their impact on community and ecosystem responses through eco-evolutionary feedbacks. © 2012 Blackwell Publishing Ltd.

It's a bear market: evolutionary and ecological effects of predation on two wild sockeye salmon populations

PubMed Central

Lin, J E; Hard, J J; Naish, K A; Peterson, D; Hilborn, R; Hauser, L

2016-01-01

Predation can affect both phenotypic variation and population productivity in the wild, but quantifying evolutionary and demographic effects of predation in natural environments is challenging. The aim of this study was to estimate selection differentials and coefficients associated with brown bear (Ursus arctos) predation in wild sockeye salmon (Oncorhynchus nerka) populations spawning in pristine habitat that is often subject to intense predation pressure. Using reconstructed genetic pedigrees, individual reproductive success (RS) was estimated in two sockeye salmon populations for two consecutive brood years with very different predation intensities across brood years. Phenotypic data on individual adult body length, body depth, stream entry timing and reproductive lifespan were used to calculate selection coefficients based on RS, and genetic variance components were estimated using animal models. Bears consistently killed larger and more recently arrived adults, although selection differentials were small. In both populations, mean RS was higher in the brood year experiencing lower predation intensity. Selection coefficients were similar across brood years with different levels of predation, often indicating stabilizing selection on reproductive lifespan as well as directional selection for longer reproductive lifespan. Despite these selection pressures, genetic covariation of morphology, phenology and lifespan appears to have maintained variation in spawner body size and stream entry timing in both populations. Our results therefore suggest considerable demographic but limited evolutionary effects of bear predation in the two study populations. PMID:26860201

It's a bear market: evolutionary and ecological effects of predation on two wild sockeye salmon populations.

PubMed

Lin, J E; Hard, J J; Naish, K A; Peterson, D; Hilborn, R; Hauser, L

2016-05-01

Predation can affect both phenotypic variation and population productivity in the wild, but quantifying evolutionary and demographic effects of predation in natural environments is challenging. The aim of this study was to estimate selection differentials and coefficients associated with brown bear (Ursus arctos) predation in wild sockeye salmon (Oncorhynchus nerka) populations spawning in pristine habitat that is often subject to intense predation pressure. Using reconstructed genetic pedigrees, individual reproductive success (RS) was estimated in two sockeye salmon populations for two consecutive brood years with very different predation intensities across brood years. Phenotypic data on individual adult body length, body depth, stream entry timing and reproductive lifespan were used to calculate selection coefficients based on RS, and genetic variance components were estimated using animal models. Bears consistently killed larger and more recently arrived adults, although selection differentials were small. In both populations, mean RS was higher in the brood year experiencing lower predation intensity. Selection coefficients were similar across brood years with different levels of predation, often indicating stabilizing selection on reproductive lifespan as well as directional selection for longer reproductive lifespan. Despite these selection pressures, genetic covariation of morphology, phenology and lifespan appears to have maintained variation in spawner body size and stream entry timing in both populations. Our results therefore suggest considerable demographic but limited evolutionary effects of bear predation in the two study populations.

Long-Term Evolution of the Luteoviridae: Time Scale and Mode of Virus Speciation▿ †

PubMed Central

Pagán, Israel; Holmes, Edward C.

2010-01-01

Despite their importance as agents of emerging disease, the time scale and evolutionary processes that shape the appearance of new viral species are largely unknown. To address these issues, we analyzed intra- and interspecific evolutionary processes in the Luteoviridae family of plant RNA viruses. Using the coat protein gene of 12 members of the family, we determined their phylogenetic relationships, rates of nucleotide substitution, times to common ancestry, and patterns of speciation. An associated multigene analysis enabled us to infer the nature of selection pressures and the genomic distribution of recombination events. Although rates of evolutionary change and selection pressures varied among genes and species and were lower in some overlapping gene regions, all fell within the range of those seen in animal RNA viruses. Recombination breakpoints were commonly observed at gene boundaries but less so within genes. Our molecular clock analysis suggested that the origin of the currently circulating Luteoviridae species occurred within the last 4 millennia, with intraspecific genetic diversity arising within the last few hundred years. Speciation within the Luteoviridae may therefore be associated with the expansion of agricultural systems. Finally, our phylogenetic analysis suggested that viral speciation events tended to occur within the same plant host species and country of origin, as expected if speciation is largely sympatric, rather than allopatric, in nature. PMID:20375155

How evolutionary crystal structure prediction works--and why.

PubMed

Oganov, Artem R; Lyakhov, Andriy O; Valle, Mario

2011-03-15

Once the crystal structure of a chemical substance is known, many properties can be predicted reliably and routinely. Therefore if researchers could predict the crystal structure of a material before it is synthesized, they could significantly accelerate the discovery of new materials. In addition, the ability to predict crystal structures at arbitrary conditions of pressure and temperature is invaluable for the study of matter at extreme conditions, where experiments are difficult. Crystal structure prediction (CSP), the problem of finding the most stable arrangement of atoms given only the chemical composition, has long remained a major unsolved scientific problem. Two problems are entangled here: search, the efficient exploration of the multidimensional energy landscape, and ranking, the correct calculation of relative energies. For organic crystals, which contain a few molecules in the unit cell, search can be quite simple as long as a researcher does not need to include many possible isomers or conformations of the molecules; therefore ranking becomes the main challenge. For inorganic crystals, quantum mechanical methods often provide correct relative energies, making search the most critical problem. Recent developments provide useful practical methods for solving the search problem to a considerable extent. One can use simulated annealing, metadynamics, random sampling, basin hopping, minima hopping, and data mining. Genetic algorithms have been applied to crystals since 1995, but with limited success, which necessitated the development of a very different evolutionary algorithm. This Account reviews CSP using one of the major techniques, the hybrid evolutionary algorithm USPEX (Universal Structure Predictor: Evolutionary Xtallography). Using recent developments in the theory of energy landscapes, we unravel the reasons evolutionary techniques work for CSP and point out their limitations. We demonstrate that the energy landscapes of chemical systems have an overall shape and explore their intrinsic dimensionalities. Because of the inverse relationships between order and energy and between the dimensionality and diversity of an ensemble of crystal structures, the chances that a random search will find the ground state decrease exponentially with increasing system size. A well-designed evolutionary algorithm allows for much greater computational efficiency. We illustrate the power of evolutionary CSP through applications that examine matter at high pressure, where new, unexpected phenomena take place. Evolutionary CSP has allowed researchers to make unexpected discoveries such as a transparent phase of sodium, a partially ionic form of boron, complex superconducting forms of calcium, a novel superhard allotrope of carbon, polymeric modifications of nitrogen, and a new class of compounds, perhydrides. These methods have also led to the discovery of novel hydride superconductors including the "impossible" LiH(n) (n=2, 6, 8) compounds, and CaLi(2). We discuss extensions of the method to molecular crystals, systems of variable composition, and the targeted optimization of specific physical properties. © 2011 American Chemical Society

Regulation of alternative splicing at the single-cell level.

PubMed

Faigenbloom, Lior; Rubinstein, Nimrod D; Kloog, Yoel; Mayrose, Itay; Pupko, Tal; Stein, Reuven

2015-12-28

Alternative splicing is a key cellular mechanism for generating distinct isoforms, whose relative abundances regulate critical cellular processes. It is therefore essential that inclusion levels of alternative exons be tightly regulated. However, how the precision of inclusion levels among individual cells is governed is poorly understood. Using single-cell gene expression, we show that the precision of inclusion levels of alternative exons is determined by the degree of evolutionary conservation at their flanking intronic regions. Moreover, the inclusion levels of alternative exons, as well as the expression levels of the transcripts harboring them, also contribute to this precision. We further show that alternative exons whose inclusion levels are considerably changed during stem cell differentiation are also subject to this regulation. Our results imply that alternative splicing is coordinately regulated to achieve accuracy in relative isoform abundances and that such accuracy may be important in determining cell fate. © 2015 The Authors. Published under the terms of the CC BY 4.0 license.

Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts

PubMed Central

Troupin, Cécile; Dacheux, Laurent; Tanguy, Marion; Sabeta, Claude; Blanc, Hervé; Bouchier, Christiane; Vignuzzi, Marco; Holmes, Edward C.; Bourhy, Hervé

2016-01-01

The natural evolution of rabies virus (RABV) provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics. PMID:27977811

Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts.

PubMed

Troupin, Cécile; Dacheux, Laurent; Tanguy, Marion; Sabeta, Claude; Blanc, Hervé; Bouchier, Christiane; Vignuzzi, Marco; Duchene, Sebastián; Holmes, Edward C; Bourhy, Hervé

2016-12-01

The natural evolution of rabies virus (RABV) provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics.

Neurohypophyseal hormones as evolutionary tracers: identification of oxytocin, lysine vasopressin, and arginine vasopressin in two South American opossums (Didelphis marsupialis and Philander opossum).

PubMed

Chauvet, J; Hurpet, D; Colne, T; Michel, G; Chauvet, M T; Acher, R

1985-02-01

The neurohypophyseal hormones of two South American opossums (Didelphis marsupialis and Philander opossum) were isolated by molecular sieving and preparative high-pressure liquid chromatography (HPLC). One oxytocin-like and two vasopressin-like peptides were found in each species. These peptides have been identified by their amino acid composition and by their retention time in HPLC. Oxytocin, lysine vasopressin, and arginine vasopressin have been characterized in both species. Lysine vasopressin is roughly as abundant as arginine vasopressin. Comparison is made with Australian marsupials Macropodidae and Phalangeridae, and possible evolutionary mechanisms are discussed.

The Potential Feasibility of Chlorinic Photosynthesis on Exoplanets

NASA Astrophysics Data System (ADS)

Haas, Johnson R.

2010-11-01

The modern search for life-bearing exoplanets emphasizes the potential detection of O2 and O3 absorption spectra in exoplanetary atmospheres as ideal signatures of biology. However, oxygenic photosynthesis may not arise ubiquitously in exoplanetary biospheres. Alternative evolutionary paths may yield planetary atmospheres tinted with the waste products of other dominant metabolisms, including potentially exotic biochemistries. This paper defines chlorinic photosynthesis (CPS) as biologically mediated photolytic oxidation of aqueous Cl- to form halocarbon or dihalogen products, coupled with CO2 assimilation. This hypothetical metabolism appears to be feasible energetically, physically, and geochemically, and could potentially develop under conditions that approximate the terrestrial Archean. It is hypothesized that an exoplanetary biosphere in which chlorinic photosynthesis dominates primary production would tend to evolve a strongly oxidizing, halogen-enriched atmosphere over geologic time. It is recommended that astronomical observations of exoplanetary outgoing thermal emission spectra consider signs of halogenated chemical species as likely indicators of the presence of a chlorinic biosphere. Planets that favor the evolution of CPS would probably receive equivalent or greater surface UV flux than is produced by the Sun, which would promote stronger abiotic UV photolysis of aqueous halides than occurred during Earth's Archean era and impose stronger evolutionary selection pressures on endemic life to accommodate and utilize halogenated compounds. Ocean-bearing planets of stars with metallicities equivalent to, or greater than, the Sun should especially favor the evolution of chlorinic biospheres because of the higher relative seawater abundances of Cl, Br, and I such planets would tend to host. Directed searches for chlorinic biospheres should probably focus on G0-G2, F, and A spectral class stars that have bulk metallicities of +0.0 Dex or greater.

The potential feasibility of chlorinic photosynthesis on exoplanets.

PubMed

Haas, Johnson R

2010-11-01

The modern search for life-bearing exoplanets emphasizes the potential detection of O(2) and O(3) absorption spectra in exoplanetary atmospheres as ideal signatures of biology. However, oxygenic photosynthesis may not arise ubiquitously in exoplanetary biospheres. Alternative evolutionary paths may yield planetary atmospheres tinted with the waste products of other dominant metabolisms, including potentially exotic biochemistries. This paper defines chlorinic photosynthesis (CPS) as biologically mediated photolytic oxidation of aqueous Cl(-) to form halocarbon or dihalogen products, coupled with CO(2) assimilation. This hypothetical metabolism appears to be feasible energetically, physically, and geochemically, and could potentially develop under conditions that approximate the terrestrial Archean. It is hypothesized that an exoplanetary biosphere in which chlorinic photosynthesis dominates primary production would tend to evolve a strongly oxidizing, halogen-enriched atmosphere over geologic time. It is recommended that astronomical observations of exoplanetary outgoing thermal emission spectra consider signs of halogenated chemical species as likely indicators of the presence of a chlorinic biosphere. Planets that favor the evolution of CPS would probably receive equivalent or greater surface UV flux than is produced by the Sun, which would promote stronger abiotic UV photolysis of aqueous halides than occurred during Earth's Archean era and impose stronger evolutionary selection pressures on endemic life to accommodate and utilize halogenated compounds. Ocean-bearing planets of stars with metallicities equivalent to, or greater than, the Sun should especially favor the evolution of chlorinic biospheres because of the higher relative seawater abundances of Cl, Br, and I such planets would tend to host. Directed searches for chlorinic biospheres should probably focus on G0-G2, F, and A spectral class stars that have bulk metallicities of +0.0 Dex or greater.

Accelerated evolution of CES7, a gene encoding a novel major urinary protein in the cat family.

PubMed

Li, Gang; Janecka, Jan E; Murphy, William J

2011-02-01

Cauxin is a novel urinary protein recently identified in the domestic cat that regulates the excretion of felinine, a pheromone precursor involved in sociochemical communication and territorial marking of domestic and wild felids. Understanding the evolutionary history of cauxin may therefore illuminate molecular adaptations involved in the evolution of pheromone-based communication, recognition, and mate selection in wild animals. We sequenced the gene encoding cauxin, CES7, in 22 species representing all major felid lineages, and multiple outgroups and showed that it has undergone rapid evolutionary change preceding and during the diversification of the cat family. A comparison between feline cauxin and orthologous carboxylesterases from other mammalian lineages revealed evidence of strong positive Darwinian selection within and between several cat lineages, enriched at functionally important sites of the protein. The higher rate of radical amino acid replacements in small felids, coupled with the lack of felinine and extremely low levels of cauxin in the urine of the great cats (Panthera), correlates with functional divergence of this gene in Panthera, and its putative loss in the snow leopard. Expression studies found evidence for several alternatively spliced transcripts in testis and brain, suggesting additional roles in male reproductive fitness and behavior. Our work presents the first report of strong positive natural selection acting on a major urinary protein of nonrodent mammals, providing evidence for parallel selection pressure on the regulation of pheromones in different mammalian lineages, despite the use of different metabolic pathways. Our results imply that natural selection may drive rapid changes in the regulation of pheromones in urine among the different cat species, which in turn may influence social behavior, such as territorial marking and conspecific recognition, therefore serving as an important mechanism for the radiation of this group of mammals.

Integrating Evolutionary and Functional Tests of Adaptive Hypotheses: A Case Study of Altitudinal Differentiation in Hemoglobin Function in an Andean Sparrow, Zonotrichia capensis

PubMed Central

Cheviron, Zachary A.; Natarajan, Chandrasekhar; Projecto-Garcia, Joana; Eddy, Douglas K.; Jones, Jennifer; Carling, Matthew D.; Witt, Christopher C.; Moriyama, Hideaki; Weber, Roy E.; Fago, Angela; Storz, Jay F.

2014-01-01

In air-breathing vertebrates, the physiologically optimal blood-O2 affinity is jointly determined by the prevailing partial pressure of atmospheric O2, the efficacy of pulmonary O2 transfer, and internal metabolic demands. Consequently, genetic variation in the oxygenation properties of hemoglobin (Hb) may be subject to spatially varying selection in species with broad elevational distributions. Here we report the results of a combined functional and evolutionary analysis of Hb polymorphism in the rufous-collared sparrow (Zonotrichia capensis), a species that is continuously distributed across a steep elevational gradient on the Pacific slope of the Peruvian Andes. We integrated a population genomic analysis that included all postnatally expressed Hb genes with functional studies of naturally occurring Hb variants, as well as recombinant Hb (rHb) mutants that were engineered through site-directed mutagenesis. We identified three clinally varying amino acid polymorphisms: Two in the αA-globin gene, which encodes the α-chain subunits of the major HbA isoform, and one in the αD-globin gene, which encodes the α-chain subunits of the minor HbD isoform. We then constructed and experimentally tested single- and double-mutant rHbs representing each of the alternative αA-globin genotypes that predominate at different elevations. Although the locus-specific patterns of altitudinal differentiation suggested a history of spatially varying selection acting on Hb polymorphism, the experimental tests demonstrated that the observed amino acid mutations have no discernible effect on respiratory properties of the HbA or HbD isoforms. These results highlight the importance of experimentally validating the hypothesized effects of genetic changes in protein function to avoid the pitfalls of adaptive storytelling. PMID:25135942

Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation

PubMed Central

Harrison, Abby; Lemey, Philippe; Hurles, Matthew; Moyes, Chris; Horn, Susanne; Pryor, Jan; Malani, Joji; Supuri, Mathias; Masta, Andrew; Teriboriki, Burentau; Toatu, Tebuka; Penny, David; Rambaut, Andrew; Shapiro, Beth

2011-01-01

Hepatitis B virus (HBV) genomes are small, semi-double-stranded DNA circular genomes that contain alternating overlapping reading frames and replicate through an RNA intermediary phase. This complex biology has presented a challenge to estimating an evolutionary rate for HBV, leading to difficulties resolving the evolutionary and epidemiological history of the virus. Here, we re-examine rates of HBV evolution using a novel data set of 112 within-host, transmission history (pedigree) and among-host genomes isolated over 20 years from the indigenous peoples of the South Pacific, combined with 313 previously published HBV genomes. We employ Bayesian phylogenetic approaches to examine several potential causes and consequences of evolutionary rate variation in HBV. Our results reveal rate variation both between genotypes and across the genome, as well as strikingly slower rates when genomes are sampled in the Hepatitis B e antigen positive state, compared to the e antigen negative state. This Hepatitis B e antigen rate variation was found to be largely attributable to changes during the course of infection in the preCore and Core genes and their regulatory elements. PMID:21765983

Natural selection. IV. The Price equation*

PubMed Central

Frank, Steven A.

2012-01-01

The Price equation partitions total evolutionary change into two components. The first component provides an abstract expression of natural selection. The second component subsumes all other evolutionary processes, including changes during transmission. The natural selection component is often used in applications. Those applications attract widespread interest for their simplicity of expression and ease of interpretation. Those same applications attract widespread criticism by dropping the second component of evolutionary change and by leaving unspecified the detailed assumptions needed for a complete study of dynamics. Controversies over approximation and dynamics have nothing to do with the Price equation itself, which is simply a mathematical equivalence relation for total evolutionary change expressed in an alternative form. Disagreements about approach have to do with the tension between the relative valuation of abstract versus concrete analyses. The Price equation’s greatest value has been on the abstract side, particularly the invariance relations that illuminate the understanding of natural selection. Those abstract insights lay the foundation for applications in terms of kin selection, information theory interpretations of natural selection, and partitions of causes by path analysis. I discuss recent critiques of the Price equation by Nowak and van Veelen. PMID:22487312

Genome-Wide Motif Statistics are Shaped by DNA Binding Proteins over Evolutionary Time Scales

NASA Astrophysics Data System (ADS)

Qian, Long; Kussell, Edo

The composition of genomes with respect to short DNA motifs impacts the ability of DNA binding proteins to locate and bind their target sites. Since nonfunctional DNA binding can be detrimental to cellular functions and ultimately to organismal fitness, organisms could benefit from reducing the number of nonfunctional binding sites genome wide. Using in vitro measurements of binding affinities for a large collection of DNA binding proteins, in multiple species, we detect a significant global avoidance of weak binding sites in genomes. The underlying evolutionary process leaves a distinct genomic hallmark in that similar words have correlated frequencies, which we detect in all species across domains of life. We hypothesize that natural selection against weak binding sites contributes to this process, and using an evolutionary model we show that the strength of selection needed to maintain global word compositions is on the order of point mutation rates. Alternative contributions may come from interference of protein-DNA binding with replication and mutational repair processes, which operates with similar rates. We conclude that genome-wide word compositions have been molded by DNA binding proteins through tiny evolutionary steps over timescales spanning millions of generations.

A model of ecological and evolutionary consequences of color polymorphism.

PubMed

Forsman, Anders; Ahnesjö, Jonas; Caesar, Sofia; Karlsson, Magnus

2008-01-01

We summarize direct and indirect effects on fitness components of animal color pattern and present a synthesis of theories concerning the ecological and evolutionary dynamics of chromatic multiple niche polymorphisms. Previous endeavors have aimed primarily at identifying conditions that promote the evolution and maintenance of polymorphisms. We consider in a conceptual model also the reciprocal influence of color polymorphism on population processes and propose that polymorphism entails selective advantages that may promote the ecological success of polymorphic species. The model begins with an evolutionary branching event from mono- to polymorphic condition that, under the influence of correlational selection, is predicted to promote the evolution of physical integration of coloration and other traits (cf. multi-trait coevolution and complex phenotypes). We propose that the coexistence within a population of alternative ecomorphs with coadapted gene complexes promotes utilization of diverse environmental resources, population stability and persistence, colonization success, and range expansions, and enhances the evolutionary potential and speciation. Conversely, we predict polymorphic populations to be less vulnerable to environmental change and at lower risk of range contractions and extinctions compared with monomorphic populations. We offer brief suggestions as to how these falsifiable predictions may be tested.

Turbo-alternator-compressor design for supercritical high density working fluids

DOEpatents

Wright, Steven A.; Fuller, Robert L.

2013-03-19

Techniques for generating power are provided. Such techniques involve a thermodynamic system including a housing, a turbine positioned in a turbine cavity of the housing, a compressor positioned in a compressor cavity of the housing, and an alternator positioned in a rotor cavity between the turbine and compressor cavities. The compressor has a high-pressure face facing an inlet of the compressor cavity and a low-pressure face on an opposite side thereof. The alternator has a rotor shaft operatively connected to the turbine and compressor, and is supported in the housing by bearings. Ridges extending from the low-pressure face of the compressor may be provided for balancing thrust across the compressor. Seals may be positioned about the alternator for selectively leaking fluid into the rotor cavity to reduce the temperature therein.

Pattern and Process in the Comparative Study of Convergent Evolution.

PubMed

Mahler, D Luke; Weber, Marjorie G; Wagner, Catherine E; Ingram, Travis

2017-08-01

Understanding processes that have shaped broad-scale biodiversity patterns is a fundamental goal in evolutionary biology. The development of phylogenetic comparative methods has yielded a tool kit for analyzing contemporary patterns by explicitly modeling processes of change in the past, providing neontologists tools for asking questions previously accessible only for select taxa via the fossil record or laboratory experimentation. The comparative approach, however, differs operationally from alternative approaches to studying convergence in that, for studies of only extant species, convergence must be inferred using evolutionary process models rather than being directly measured. As a result, investigation of evolutionary pattern and process cannot be decoupled in comparative studies of convergence, even though such a decoupling could in theory guard against adaptationist bias. Assumptions about evolutionary process underlying comparative tools can shape the inference of convergent pattern in sometimes profound ways and can color interpretation of such patterns. We discuss these issues and other limitations common to most phylogenetic comparative approaches and suggest ways that they can be avoided in practice. We conclude by promoting a multipronged approach to studying convergence that integrates comparative methods with complementary tests of evolutionary mechanisms and includes ecological and biogeographical perspectives. Carefully employed, the comparative method remains a powerful tool for enriching our understanding of convergence in macroevolution, especially for investigation of why convergence occurs in some settings but not others.

Evolutionary perspectives on ageing.

PubMed

Reichard, Martin

2017-10-01

From an evolutionary perspective, ageing is a decrease in fitness with chronological age - expressed by an increase in mortality risk and/or decline in reproductive success and mediated by deterioration of functional performance. While this makes ageing intuitively paradoxical - detrimental to individual fitness - evolutionary theory offers answers as to why ageing has evolved. In this review, I first briefly examine the classic evolutionary theories of ageing and their empirical tests, and highlight recent findings that have advanced our understanding of the evolution of ageing (condition-dependent survival, positive pleiotropy). I then provide an overview of recent theoretical extensions and modifications that accommodate those new discoveries. I discuss the role of indeterminate (asymptotic) growth for lifetime increases in fecundity and ageing trajectories. I outline alternative views that challenge a universal existence of senescence - namely the lack of a germ-soma distinction and the ability of tissue replacement and retrogression to younger developmental stages in modular organisms. I argue that rejuvenation at the organismal level is plausible, but includes a return to a simple developmental stage. This may exempt a particular genotype from somatic defects but, correspondingly, removes any information acquired during development. A resolution of the question of whether a rejuvenated individual is the same entity is central to the recognition of whether current evolutionary theories of ageing, with their extensions and modifications, can explain the patterns of ageing across the Tree of Life. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games

PubMed Central

Peña, Jorge; Rochat, Yannick

2012-01-01

By combining evolutionary game theory and graph theory, “games on graphs” study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner’s dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner’s dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures. PMID:22970237

TARGETED CAPTURE IN EVOLUTIONARY AND ECOLOGICAL GENOMICS

PubMed Central

Jones, Matthew R.; Good, Jeffrey M.

2016-01-01

The rapid expansion of next-generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various genome partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole genome sequencing in ecological and evolutionary genomic studies. High throughput targeted capture is one such strategy that involves the parallel enrichment of pre-selected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across labs focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to 1) increase the accessibility of targeted capture to researchers working in non-model taxa by discussing capture methods that circumvent the need of a reference genome, 2) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy, and 3) discuss the future of targeted capture and other genome partitioning approaches in light of the increasing accessibility of whole genome sequencing. Given the practical advantages and increasing feasibility of high-throughput targeted capture, we anticipate an ongoing expansion of capture-based approaches in evolutionary and ecological research, synergistic with an expansion of whole genome sequencing. PMID:26137993

Evolutionary space platform concept study. Volume 2, part B: Manned space platform concepts

NASA Technical Reports Server (NTRS)

1982-01-01

Logical, cost-effective steps in the evolution of manned space platforms are investigated and assessed. Tasks included the analysis of requirements for a manned space platform, identifying alternative concepts, performing system analysis and definition of the concepts, comparing the concepts and performing programmatic analysis for a reference concept.

Solar Energy Education Packet for Elementary & Secondary Students. Revised Edition.

ERIC Educational Resources Information Center

Center for Renewable Resources, Washington, DC.

The arrangement of this packet is essentially evolutionary, with a conscious effort to alternate reading assignments, activities and experiments. It begins with solar energy facts and terminology as background to introduce the reader to basic concepts. It progresses into a discussion of passive solar systems. This is followed by several projects…

Modeling of biological intelligence for SCM system optimization.

PubMed

Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

2012-01-01

This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

Android malware detection based on evolutionary super-network

NASA Astrophysics Data System (ADS)

Yan, Haisheng; Peng, Lingling

2018-04-01

In the paper, an android malware detection method based on evolutionary super-network is proposed in order to improve the precision of android malware detection. Chi square statistics method is used for selecting characteristics on the basis of analyzing android authority. Boolean weighting is utilized for calculating characteristic weight. Processed characteristic vector is regarded as the system training set and test set; hyper edge alternative strategy is used for training super-network classification model, thereby classifying test set characteristic vectors, and it is compared with traditional classification algorithm. The results show that the detection method proposed in the paper is close to or better than traditional classification algorithm. The proposed method belongs to an effective Android malware detection means.

Modeling of Biological Intelligence for SCM System Optimization

PubMed Central

Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

2012-01-01

This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms. PMID:22162724

Use it or lose it: reproductive implications of ecological specialization in a haematophagous ectoparasite.

PubMed

Arbiv, A; Khokhlova, I S; Ovadia, O; Novoplansky, A; Krasnov, B R

2012-06-01

Using experimentally induced disruptive selection, we tested two hypotheses regarding the evolution of specialization in parasites. The 'trade-off' hypothesis suggests that adaptation to a specific host may come at the expense of a reduced performance when exploiting another host. The alternative 'relaxed selection' hypothesis suggests that the ability to exploit a given host would deteriorate when becoming obsolete. Three replicate populations of a flea Xenopsylla ramesis were maintained on each of two rodent hosts, Meriones crassus and Dipodillus dasyurus, for nine generations. Fleas maintained on a specific host species for a few generations substantially decreased their reproductive performance when transferred to an alternative host species, whereas they generally did not increase their performance on their maintenance host. The results support the 'relaxed selection' hypothesis of the evolution of ecological specialization in haematophagous ectoparasites, while suggesting that trade-offs are unlikely drivers of specialization. Further work is needed to study the extent by which the observed specializations are based on epigenetic or genetic modifications. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

The impact of fishing-induced mortality on the evolution of alternative life-history tactics in brook charr

PubMed Central

Thériault, Véronique; Dunlop, Erin S; Dieckmann, Ulf; Bernatchez, Louis; Dodson, Julian J

2008-01-01

Although contemporary trends indicative of evolutionary change have been detected in the life-history traits of exploited populations, it is not known to what extent fishing influences the evolution of alternative life-history tactics in migratory species such as salmonids. Here, we build a model to predict the evolution of anadromy and residency in an exploited population of brook charr, Salvelinus fontinalis. Our model allows for both phenotypic plasticity and genetic change in the age and size at migration by including migration reaction norms. Using this model, we predict that fishing of anadromous individuals over the course of 100 years causes evolution in the migration reaction norm, resulting in a decrease in average probabilities of migration with increasing harvest rate. Moreover, we show that differences in natural mortalities in freshwater greatly influence the magnitude and rate of evolutionary change. The fishing-induced changes in migration predicted by our model alter population abundances and reproductive output and should be accounted for in the sustainable management of salmonids. PMID:25567640

Pace of life, predators and parasites: predator-induced life-history evolution in Trinidadian guppies predicts decrease in parasite tolerance.

PubMed

Stephenson, J F; van Oosterhout, C; Cable, J

2015-11-01

A common evolutionary response to predation pressure is increased investment in reproduction, ultimately resulting in a fast life history. Theory and comparative studies suggest that short-lived organisms invest less in defence against parasites than those that are longer lived (the pace of life hypothesis). Combining these tenets of evolutionary theory leads to the specific, untested prediction that within species, populations experiencing higher predation pressure invest less in defence against parasites. The Trinidadian guppy, Poecilia reticulata, presents an excellent opportunity to test this prediction: guppy populations in lower courses of rivers experience higher predation pressure, and as a consequence have evolved faster life histories, than those in upper courses. Data from a large-scale field survey showed that fish infected with Gyrodactylus parasites were of a lower body condition (quantified using the scaled mass index) than uninfected fish, but only in lower course populations. Although the evidence we present is correlational, it suggests that upper course guppies sustain lower fitness costs of infection, i.e. are more tolerant, than lower course guppies. The data are therefore consistent with the pace of life hypothesis of parasite defence allocation, and suggest that life-history traits mediate the indirect effect of predators on the parasites of their prey. © 2015 The Author(s).

High School Students' Attitudes towards Spiders: A Cross-Cultural Comparison

ERIC Educational Resources Information Center

Prokop, Pavol; Tolarovicova, Andrea; Camerik, Anne M.; Peterkova, Viera

2010-01-01

Spiders are traditionally considered to be among the least popular of animals. Current evidence suggests that a negative attitude towards spiders could be influenced by both cultural and evolutionary pressures. Some researchers suggest that science education activities could positively influence students' perceptions of spiders. Their evidence is,…

Avian predation pressure as a potential driver of periodical cicada cycle length

Treesearch

Walter E. Koenig; Andrew M. Liebhold

2013-01-01

The extraordinarily long life cycles, synchronous emergences at 13- or 17-year intervals, and complex geographic distribution of periodical cicadas (Magicicada spp.) in eastern North America are a long-standing evolutionary enigma. Although a variety of factors, including satiation of aboveground predators and avoidance of interbrood hybridization,...

Mean protein evolutionary distance: a method for comparative protein evolution and its application.

PubMed

Wise, Michael J

2013-01-01

Proteins are under tight evolutionary constraints, so if a protein changes it can only do so in ways that do not compromise its function. In addition, the proteins in an organism evolve at different rates. Leveraging the history of patristic distance methods, a new method for analysing comparative protein evolution, called Mean Protein Evolutionary Distance (MeaPED), measures differential resistance to evolutionary pressure across viral proteomes and is thereby able to point to the proteins' roles. Different species' proteomes can also be compared because the results, consistent across virus subtypes, concisely reflect the very different lifestyles of the viruses. The MeaPED method is here applied to influenza A virus, hepatitis C virus, human immunodeficiency virus (HIV), dengue virus, rotavirus A, polyomavirus BK and measles, which span the positive and negative single-stranded, doubled-stranded and reverse transcribing RNA viruses, and double-stranded DNA viruses. From this analysis, host interaction proteins including hemagglutinin (influenza), and viroporins agnoprotein (polyomavirus), p7 (hepatitis C) and VPU (HIV) emerge as evolutionary hot-spots. By contrast, RNA-directed RNA polymerase proteins including L (measles), PB1/PB2 (influenza) and VP1 (rotavirus), and internal serine proteases such as NS3 (dengue and hepatitis C virus) emerge as evolutionary cold-spots. The hot spot influenza hemagglutinin protein is contrasted with the related cold spot H protein from measles. It is proposed that evolutionary cold-spot proteins can become significant targets for second-line anti-viral therapeutics, in cases where front-line vaccines are not available or have become ineffective due to mutations in the hot-spot, generally more antigenically exposed proteins. The MeaPED package is available from www.pam1.bcs.uwa.edu.au/~michaelw/ftp/src/meaped.tar.gz.

Mean Protein Evolutionary Distance: A Method for Comparative Protein Evolution and Its Application

PubMed Central

Wise, Michael J.

2013-01-01

Proteins are under tight evolutionary constraints, so if a protein changes it can only do so in ways that do not compromise its function. In addition, the proteins in an organism evolve at different rates. Leveraging the history of patristic distance methods, a new method for analysing comparative protein evolution, called Mean Protein Evolutionary Distance (MeaPED), measures differential resistance to evolutionary pressure across viral proteomes and is thereby able to point to the proteins’ roles. Different species’ proteomes can also be compared because the results, consistent across virus subtypes, concisely reflect the very different lifestyles of the viruses. The MeaPED method is here applied to influenza A virus, hepatitis C virus, human immunodeficiency virus (HIV), dengue virus, rotavirus A, polyomavirus BK and measles, which span the positive and negative single-stranded, doubled-stranded and reverse transcribing RNA viruses, and double-stranded DNA viruses. From this analysis, host interaction proteins including hemagglutinin (influenza), and viroporins agnoprotein (polyomavirus), p7 (hepatitis C) and VPU (HIV) emerge as evolutionary hot-spots. By contrast, RNA-directed RNA polymerase proteins including L (measles), PB1/PB2 (influenza) and VP1 (rotavirus), and internal serine proteases such as NS3 (dengue and hepatitis C virus) emerge as evolutionary cold-spots. The hot spot influenza hemagglutinin protein is contrasted with the related cold spot H protein from measles. It is proposed that evolutionary cold-spot proteins can become significant targets for second-line anti-viral therapeutics, in cases where front-line vaccines are not available or have become ineffective due to mutations in the hot-spot, generally more antigenically exposed proteins. The MeaPED package is available from www.pam1.bcs.uwa.edu.au/~michaelw/ftp/src/meaped.tar.gz. PMID:23613826

The consequences of lifetime and evolutionary exposure to toxic prey: changes in avoidance behaviour through ontogeny.

PubMed

Robbins, T R; Langkilde, T

2012-10-01

Responses to novel threats (e.g. invasive species) can involve genetic changes or plastic shifts in phenotype. There is controversy over the relative importance of these processes for species survival of such perturbations, but we are realizing they are not mutually exclusive. Native eastern fence lizards (Sceloporus undulatus) have adapted to top-down predation pressure imposed by the invasive red imported fire ant (Solenopsis invicta) via changes in adult (but not juvenile) lizard antipredator behaviour. Here, we examine the largely ignored, but potentially equally important, bottom-up effect of fire ants as toxic prey for lizards. We test how fire ant consumption (or avoidance) is affected by lifetime (via plasticity) and evolutionary (via natural selection) exposure to fire ants by comparing field-caught and laboratory-reared lizards, respectively, from fire ant-invaded and uninvaded populations. More naive juveniles from invaded populations ate fire ants than did adults, reflecting a natural ontogenetic dietary shift away from ants. Laboratory-reared lizards from the invaded site were less likely to eat fire ants than were those from the uninvaded site, suggesting a potential evolutionary shift in feeding behaviour. Lifetime and evolutionary exposure interacted across ontogeny, however, and field-caught lizards from the invaded site exhibited opposite ontogenetic trends; adults were more likely to eat fire ants than were juveniles. Our results suggest that plastic and evolutionary processes may both play important roles in permitting species survival of novel threats. We further reveal how complex interactions can shape adaptive responses to multimodal impacts imposed by invaders: in our system, fire ants impose stronger bottom-up selection than top-down selection, with each selection regime changing differently across lizard ontogeny. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling.

PubMed

Vrancken, Bram; Suchard, Marc A; Lemey, Philippe

2017-07-01

Analyses of virus evolution in known transmission chains have the potential to elucidate the impact of transmission dynamics on the viral evolutionary rate and its difference within and between hosts. Lin et al. (2015, Journal of Virology , 89/7: 3512-22) recently investigated the evolutionary history of hepatitis B virus in a transmission chain and postulated that the 'colonization-adaptation-transmission' model can explain the differential impact of transmission on synonymous and non-synonymous substitution rates. Here, we revisit this dataset using a full probabilistic Bayesian phylogenetic framework that adequately accounts for the non-independence of sequence data when estimating evolutionary parameters. Examination of the transmission chain data under a flexible coalescent prior reveals a general inconsistency between the estimated timings and clustering patterns and the known transmission history, highlighting the need to incorporate host transmission information in the analysis. Using an explicit genealogical transmission chain model, we find strong support for a transmission-associated decrease of the overall evolutionary rate. However, in contrast to the initially reported larger transmission effect on non-synonymous substitution rate, we find a similar decrease in both non-synonymous and synonymous substitution rates that cannot be adequately explained by the colonization-adaptation-transmission model. An alternative explanation may involve a transmission/establishment advantage of hepatitis B virus variants that have accumulated fewer within-host substitutions, perhaps by spending more time in the covalently closed circular DNA state between each round of viral replication. More generally, this study illustrates that ignoring phylogenetic relationships can lead to misleading evolutionary estimates.

An analytical approach for estimating fossil record and diversification events in sharks, skates and rays.

PubMed

Guinot, Guillaume; Adnet, Sylvain; Cappetta, Henri

2012-01-01

Modern selachians and their supposed sister group (hybodont sharks) have a long and successful evolutionary history. Yet, although selachian remains are considered relatively common in the fossil record in comparison with other marine vertebrates, little is known about the quality of their fossil record. Similarly, only a few works based on specific time intervals have attempted to identify major events that marked the evolutionary history of this group. Phylogenetic hypotheses concerning modern selachians' interrelationships are numerous but differ significantly and no consensus has been found. The aim of the present study is to take advantage of the range of recent phylogenetic hypotheses in order to assess the fit of the selachian fossil record to phylogenies, according to two different branching methods. Compilation of these data allowed the inference of an estimated range of diversity through time and evolutionary events that marked this group over the past 300 Ma are identified. Results indicate that with the exception of high taxonomic ranks (orders), the selachian fossil record is by far imperfect, particularly for generic and post-Triassic data. Timing and amplitude of the various identified events that marked the selachian evolutionary history are discussed. Some identified diversity events were mentioned in previous works using alternative methods (Early Jurassic, mid-Cretaceous, K/T boundary and late Paleogene diversity drops), thus reinforcing the efficiency of the methodology presented here in inferring evolutionary events. Other events (Permian/Triassic, Early and Late Cretaceous diversifications; Triassic/Jurassic extinction) are newly identified. Relationships between these events and paleoenvironmental characteristics and other groups' evolutionary history are proposed.

Evolutionary consequences of polyploidy in prokaryotes and the origin of mitosis and meiosis.

PubMed

Markov, Alexander V; Kaznacheev, Ilya S

2016-06-08

The origin of eukaryote-specific traits such as mitosis and sexual reproduction remains disputable. There is growing evidence that both mitosis and eukaryotic sex (i.e., the alternation of syngamy and meiosis) may have already existed in the basal eukaryotes. The mating system of the halophilic archaeon Haloferax volcanii probably represents an intermediate stage between typical prokaryotic and eukaryotic sex. H. volcanii is highly polyploid, as well as many other Archaea. Here, we use computer simulation to explore genetic and evolutionary outcomes of polyploidy in amitotic prokaryotes and its possible role in the origin of mitosis, meiosis and eukaryotic sex. Modeling suggests that polyploidy can confer strong short-term evolutionary advantage to amitotic prokaryotes. However, it also promotes the accumulation of recessive deleterious mutations and the risk of extinction in the long term, especially in highly mutagenic environment. There are several possible strategies that amitotic polyploids can use in order to reduce the genetic costs of polyploidy while retaining its benefits. Interestingly, most of these strategies resemble different components or aspects of eukaryotic sex. They include asexual ploidy cycles, equalization of genome copies by gene conversion, high-frequency lateral gene transfer between relatives, chromosome exchange coupled with homologous recombination, and the evolution of more accurate chromosome distribution during cell division (mitosis). Acquisition of mitosis by an amitotic polyploid results in chromosome diversification and specialization. Ultimately, it transforms a polyploid cell into a functionally monoploid one with multiple unique, highly redundant chromosomes. Specialization of chromosomes makes the previously evolved modes of promiscuous chromosome shuffling deleterious. This can result in selective pressure to develop accurate mechanisms of homolog pairing, and, ultimately, meiosis. Emergence of mitosis and the first evolutionary steps towards eukaryotic sex could have taken place in the ancestral polyploid, amitotic proto-eukaryotes, as they were struggling to survive in the highly mutagenic environment of the Early Proterozoic shallow water microbial communities, through the succession of the following stages: (1) acquisition of high-frequency between-individual genetic exchange coupled with homologous recombination; (2) acquisition of mitosis, followed by rapid chromosome diversification and specialization; (3) evolution of homolog synapsis and meiosis. Additional evidence compatible with this scenario includes mass acquisition of new families of paralogous genes by the basal eukaryotes, and recently discovered correlation between polyploidy and the presence of histones in Archaea. This article was reviewed by Eugene Koonin, Uri Gophna and Armen Mulkidjanian. For the full reviews, please go to the Reviewers' comments section.

Cognition, Information Fields and Hologenomic Entanglement: Evolution in Light and Shadow

PubMed Central

Miller, William B.

2016-01-01

As the prime unification of Darwinism and genetics, the Modern Synthesis continues to epitomize mainstay evolutionary theory. Many decades after its formulation, its anchor assumptions remain fixed: conflict between macro organic organisms and selection at that level represent the near totality of any evolutionary narrative. However, intervening research has revealed a less easily appraised cellular and microbial focus for eukaryotic existence. It is now established that all multicellular eukaryotic organisms are holobionts representing complex collaborations between the co-aligned microbiome of each eukaryote and its innate cells into extensive mixed cellular ecologies. Each of these ecological constituents has demonstrated faculties consistent with basal cognition. Consequently, an alternative hologenomic entanglement model is proposed with cognition at its center and conceptualized as Pervasive Information Fields within a quantum framework. Evolutionary development can then be reconsidered as being continuously based upon communication between self-referential constituencies reiterated at every scope and scale. Immunological reactions support and reinforce self-recognition juxtaposed against external environmental stresses. PMID:27213462

Group adaptation, formal darwinism and contextual analysis.

PubMed

Okasha, S; Paternotte, C

2012-06-01

We consider the question: under what circumstances can the concept of adaptation be applied to groups, rather than individuals? Gardner and Grafen (2009, J. Evol. Biol.22: 659-671) develop a novel approach to this question, building on Grafen's 'formal Darwinism' project, which defines adaptation in terms of links between evolutionary dynamics and optimization. They conclude that only clonal groups, and to a lesser extent groups in which reproductive competition is repressed, can be considered as adaptive units. We re-examine the conditions under which the selection-optimization links hold at the group level. We focus on an important distinction between two ways of understanding the links, which have different implications regarding group adaptationism. We show how the formal Darwinism approach can be reconciled with G.C. Williams' famous analysis of group adaptation, and we consider the relationships between group adaptation, the Price equation approach to multi-level selection, and the alternative approach based on contextual analysis. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Multi Sensor Fusion Using Fitness Adaptive Differential Evolution

NASA Astrophysics Data System (ADS)

Giri, Ritwik; Ghosh, Arnob; Chowdhury, Aritra; Das, Swagatam

The rising popularity of multi-source, multi-sensor networks supports real-life applications calls for an efficient and intelligent approach to information fusion. Traditional optimization techniques often fail to meet the demands. The evolutionary approach provides a valuable alternative due to its inherent parallel nature and its ability to deal with difficult problems. We present a new evolutionary approach based on a modified version of Differential Evolution (DE), called Fitness Adaptive Differential Evolution (FiADE). FiADE treats sensors in the network as distributed intelligent agents with various degrees of autonomy. Existing approaches based on intelligent agents cannot completely answer the question of how their agents could coordinate their decisions in a complex environment. The proposed approach is formulated to produce good result for the problems that are high-dimensional, highly nonlinear, and random. The proposed approach gives better result in case of optimal allocation of sensors. The performance of the proposed approach is compared with an evolutionary algorithm coordination generalized particle model (C-GPM).

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

PubMed Central

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

2014-01-01

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

Quantitative genetic models of sexual conflict based on interacting phenotypes.

PubMed

Moore, Allen J; Pizzari, Tommaso

2005-05-01

Evolutionary conflict arises between reproductive partners when alternative reproductive opportunities are available. Sexual conflict can generate sexually antagonistic selection, which mediates sexual selection and intersexual coevolution. However, despite intense interest, the evolutionary implications of sexual conflict remain unresolved. We propose a novel theoretical approach to study the evolution of sexually antagonistic phenotypes based on quantitative genetics and the measure of social selection arising from male-female interactions. We consider the phenotype of one sex as both a genetically influenced evolving trait as well as the (evolving) social environment in which the phenotype of the opposite sex evolves. Several important points emerge from our analysis, including the relationship between direct selection on one sex and indirect effects through selection on the opposite sex. We suggest that the proposed approach may be a valuable tool to complement other theoretical approaches currently used to study sexual conflict. Most importantly, our approach highlights areas where additional empirical data can help clarify the role of sexual conflict in the evolutionary process.

49 CFR 192.620 - Alternative maximum allowable operating pressure for certain steel pipelines.

Code of Federal Regulations, 2014 CFR

2014-10-01

... for certain steel pipelines. 192.620 Section 192.620 Transportation Other Regulations Relating to... STANDARDS Operations § 192.620 Alternative maximum allowable operating pressure for certain steel pipelines..., 2, or 3 location; (2) The pipeline segment is constructed of steel pipe meeting the additional...

40 CFR 65.117 - Alternative means of emission limitation: Batch processes.

Code of Federal Regulations, 2010 CFR

2010-07-01

... (CONTINUED) AIR PROGRAMS (CONTINUED) CONSOLIDATED FEDERAL AIR RULE Equipment Leaks § 65.117 Alternative means... section provide the options of pressure testing or monitoring the equipment for leaks. The owner or... pressure-tested for leaks before regulated material is first fed to the equipment and the equipment is...

Investigation of Aerodynamic and Icing Characteristics of a Flush Alternate Inlet Induction System Air Scoop

NASA Technical Reports Server (NTRS)

Lewis, James P.

1953-01-01

An investigation has been made in the NACA Lewis icing research tunnel to determine the aerodynamic and icing characteristics of a full-scale induction-system air-scoop assembly incorporating a flush alternate inlet. The flush inlet was located immediately downstream of the offset ram inlet and included a 180 deg reversal and a 90 deg elbow in the ducting between inlet and carburetor top deck. The model also had a preheat-air inlet. The investigation was made over a range of mass-air- flow ratios of 0 to 0.8, angles of attack of 0 and 4 deg airspeeds of 150 to 270 miles per hour, air temperatures of 0 and 25 F various liquid-water contents, and droplet sizes. The ram inlet gave good pressure recovery in both clear air and icing but rapid blockage of the top-deck screen occurred during icing. The flush alternate inlet had poor pressure recovery in both clear air and icing. The greatest decreases in the alternate-inlet pressure recovery were obtained at icing conditions of low air temperature and high liquid-water content. No serious screen icing was observed with the alternate inlet. Pressure and temperature distributions on the carburetor top deck were determined using the preheat-air supply with the preheat- and alternate-inlet doors in various positions. No screen icing occurred when the preheat-air system was operated in combination with alternate-inlet air flow.

Genetics of alternative splicing evolution during sunflower domestication.

PubMed

Smith, Chris C R; Tittes, Silas; Mendieta, J Paul; Collier-Zans, Erin; Rowe, Heather C; Rieseberg, Loren H; Kane, Nolan C

2018-06-11

Alternative splicing enables organisms to produce the diversity of proteins necessary for multicellular life by using relatively few protein-coding genes. Although differences in splicing have been identified among divergent taxa, the shorter-term evolution of splicing is understudied. The origins of novel splice forms, and the contributions of alternative splicing to major evolutionary transitions, are largely unknown. This study used transcriptomes of wild and domesticated sunflowers to examine splice differentiation and regulation during domestication. We identified substantial splicing divergence between wild and domesticated sunflowers, mainly in the form of intron retention. Transcripts with divergent splicing were enriched for seed-development functions, suggesting that artificial selection impacted splicing patterns. Mapping of quantitative trait loci (QTLs) associated with 144 differential splicing cases revealed primarily trans -acting variation affecting splicing patterns. A large proportion of identified QTLs contain known spliceosome proteins and are associated with splicing variation in multiple genes. Examining a broader set of wild and domesticated sunflower genotypes revealed that most differential splicing patterns in domesticated sunflowers likely arose from standing variation in wild Helianthus annuus and gained frequency during the domestication process. However, several domesticate-associated splicing patterns appear to be introgressed from other Helianthus species. These results suggest that sunflower domestication involved selection on pleiotropic regulatory alleles. More generally, our findings indicate that substantial differences in isoform abundances arose rapidly during a recent evolutionary transition and appear to contribute to adaptation and population divergence.

How counterfactuals of Red-Queen theory shed light on science and its historiography.

PubMed

Dagg, Joachim L

2017-08-01

A historical episode of evolutionary theory, which has lead to the Red Queen theory of the evolutionary maintenance of sex, includes two striking contingencies. These are used to explore alternative what-if scenarios, in order to test some common opinions about such counterfactuals. This sheds new light on the nature of science and its historiography. One counterfactual leads to an unexpected convergence of its result to that of the actual science but, nevertheless, differs in its causal structure. The other diverges towards an incompatible alternative, but this requires further contingent choices that also diverge from actual science. The convergence in the first counterfactual is due to a horizontal transfer of knowledge. Similar transfers of knowledge are typical for innovations of actual science. This suggests that contingent choices can merge as well as fork research traditions both in actual research and counterfactual history. Neither the paths of the actual history of science nor those of its counterfactual alternatives will form a tree of exclusively diverging bifurcations, but a network instead. Convergencies in counterfactuals may, therefore, be due to the web-structure of science as much as to the aims of the historians in question. Furthermore, the difference in causal structure between the actual science and its convergent counterfactual might become diagnostic for external factors rather than internal aims forcing a historian towards convergence. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tempo and mode of performance evolution across multiple independent origins of adhesive toe pads in lizards.

PubMed

Hagey, Travis J; Uyeda, Josef C; Crandell, Kristen E; Cheney, Jorn A; Autumn, Kellar; Harmon, Luke J

2017-10-01

Understanding macroevolutionary dynamics of trait evolution is an important endeavor in evolutionary biology. Ecological opportunity can liberate a trait as it diversifies through trait space, while genetic and selective constraints can limit diversification. While many studies have examined the dynamics of morphological traits, diverse morphological traits may yield the same or similar performance and as performance is often more proximately the target of selection, examining only morphology may give an incomplete understanding of evolutionary dynamics. Here, we ask whether convergent evolution of pad-bearing lizards has followed similar evolutionary dynamics, or whether independent origins are accompanied by unique constraints and selective pressures over macroevolutionary time. We hypothesized that geckos and anoles each have unique evolutionary tempos and modes. Using performance data from 59 species, we modified Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models to account for repeated origins estimated using Bayesian ancestral state reconstructions. We discovered that adhesive performance in geckos evolved in a fashion consistent with Brownian motion with a trend, whereas anoles evolved in bounded performance space consistent with more constrained evolution (an Ornstein-Uhlenbeck model). Our results suggest that convergent phenotypes can have quite distinctive evolutionary patterns, likely as a result of idiosyncratic constraints or ecological opportunities. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Genetic diversity, virulence and fitness evolution in an obligate fungal parasite of bees.

PubMed

Evison, S E F; Foley, K; Jensen, A B; Hughes, W O H

2015-01-01

Within-host competition is predicted to drive the evolution of virulence in parasites, but the precise outcomes of such interactions are often unpredictable due to many factors including the biology of the host and the parasite, stochastic events and co-evolutionary interactions. Here, we use a serial passage experiment (SPE) with three strains of a heterothallic fungal parasite (Ascosphaera apis) of the Honey bee (Apis mellifera) to assess how evolving under increasing competitive pressure affects parasite virulence and fitness evolution. The results show an increase in virulence after successive generations of selection and consequently faster production of spores. This faster sporulation, however, did not translate into more spores being produced during this longer window of sporulation; rather, it appeared to induce a loss of fitness in terms of total spore production. There was no evidence to suggest that a greater diversity of competing strains was a driver of this increased virulence and subsequent fitness cost, but rather that strain-specific competitive interactions influenced the evolutionary outcomes of mixed infections. It is possible that the parasite may have evolved to avoid competition with multiple strains because of its heterothallic mode of reproduction, which highlights the importance of understanding parasite biology when predicting disease dynamics. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

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.

Natural history collections as windows on evolutionary processes.

PubMed

Holmes, Michael W; Hammond, Talisin T; Wogan, Guinevere O U; Walsh, Rachel E; LaBarbera, Katie; Wommack, Elizabeth A; Martins, Felipe M; Crawford, Jeremy C; Mack, Katya L; Bloch, Luke M; Nachman, Michael W

2016-02-01

Natural history collections provide an immense record of biodiversity on Earth. These repositories have traditionally been used to address fundamental questions in biogeography, systematics and conservation. However, they also hold the potential for studying evolution directly. While some of the best direct observations of evolution have come from long-term field studies or from experimental studies in the laboratory, natural history collections are providing new insights into evolutionary change in natural populations. By comparing phenotypic and genotypic changes in populations through time, natural history collections provide a window into evolutionary processes. Recent studies utilizing this approach have revealed some dramatic instances of phenotypic change over short timescales in response to presumably strong selective pressures. In some instances, evolutionary change can be paired with environmental change, providing a context for potential selective forces. Moreover, in a few cases, the genetic basis of phenotypic change is well understood, allowing for insight into adaptive change at multiple levels. These kinds of studies open the door to a wide range of previously intractable questions by enabling the study of evolution through time, analogous to experimental studies in the laboratory, but amenable to a diversity of species over longer timescales in natural populations. © 2016 John Wiley & Sons Ltd.

Co-niche construction between hosts and symbionts: ideas and evidence.

PubMed

Borges, Renee M

2017-07-01

Symbiosis is a process that can generate evolutionary novelties and can extend the phenotypic niche space of organisms. Symbionts can act together with their hosts to co-construct host organs, within which symbionts are housed. Once established within hosts, symbionts can also influence various aspects of host phenotype, such as resource acquisition, protection from predation by acquisition of toxicity, as well as behaviour. Once symbiosis is established, its fidelity between generations must be ensured. Hosts evolve various mechanisms to screen unwanted symbionts and to facilitate faithful transmission of mutualistic partners between generations. Microbes are the most important symbionts that have influenced plant and animal phenotypes; multicellular organisms engage in developmental symbioses with microbes at many stages in ontogeny. The co-construction of niches may result in composite organisms that are physically nested within each other. While it has been advocated that these composite organisms need new evolutionary theories and perspectives to describe their properties and evolutionary trajectories, it appears that standard evolutionary theories are adequate to explore selection pressures on their composite or individual traits. Recent advances in our understanding of composite organisms open up many important questions regarding the stability and transmission of these units.

Natural history collections as windows on evolutionary processes

PubMed Central

Holmes, Michael W.; Hammond, Talisin T.; Wogan, Guinevere O.U.; Walsh, Rachel E.; LaBarbera, Katie; Wommack, Elizabeth A.; Martins, Felipe M.; Crawford, Jeremy C.; Mack, Katya L.; Bloch, Luke M.; Nachman, Michael W.

2016-01-01

Natural history collections provide an immense record of biodiversity on Earth. These repositories have traditionally been used to address fundamental questions in biogeography, systematics, and conservation. However, they also hold the potential for studying evolution directly. While some of the best direct observations of evolution have come from long-term field studies or from experimental studies in the lab, natural history collections are providing new insights into evolutionary change in natural populations. By comparing phenotypic and genotypic changes in populations through time, natural history collections provide a window into evolutionary processes. Recent studies utilizing this approach have revealed some dramatic instances of phenotypic change over short time scales in response to presumably strong selective pressures. In some instances evolutionary change can be paired with environmental change, providing a context for potential selective forces. Moreover, in a few cases, the genetic basis of phenotypic change is well understood, allowing for insight into adaptive change at multiple levels. These kinds of studies open the door to a wide range of previously intractable questions by enabling the study of evolution through time, analogous to experimental studies in the laboratory, but amenable to a diversity of species over longer timescales in natural populations. PMID:26757135

Complementary and alternative medicine approaches to blood pressure reduction: An evidence-based review.

PubMed

Nahas, Richard

2008-11-01

ABSTRACTOBJECTIVETo review the evidence supporting complementary and alternative medicine approaches used in the treatment of hypertension.QUALITY OF EVIDENCEMEDLINE and EMBASE were searched from January 1966 to May 2008 combining the key words hypertension or blood pressure with acupuncture, chocolate, cocoa, coenzyme Q10, ubiquinone, melatonin, vitamin D, meditation, and stress reduction. Clinical trials, prospective studies, and relevant references were included.MAIN MESSAGEEvidence from systematic reviews supports the blood pressure-lowering effects of coenzyme Q10, polyphenol-rich dark chocolate, Qigong, slow breathing, and transcendental meditation. Vitamin D deficiency is associated with hypertension and cardiovascular risk; supplementation lowered blood pressure in 2 trials. Acupuncture reduced blood pressure in 3 trials; in 1 of these it was no better than an invasive placebo. Melatonin was effective in 2 small trials, but caution is warranted in patients taking pharmacotherapy.CONCLUSIONSeveral complementary and alternative medicine therapies can be considered as part of an evidence-based approach to the treatment of hypertension. The potential benefit of these interventions warrants further research using cardiovascular outcomes.

A Prospective Randomized Clinical Trial of a Novel, Noninvasive Perfusion Enhancement System for the Prevention of Hospital-Acquired Sacral Pressure Injuries.

PubMed

Bharucha, Jitendra B; Seaman, Linda; Powers, Michele; Kelly, Erica; Seaman, Rodney; Forcier, Lea; McGinnis, Janice; Nodiff, Isabel; Pawlak, Brooke; Snyder, Samantha; Nodiff, Susan; Patel, Rohan; Squitieri, Rafael; Wang, Lansheng

2018-06-08

The purpose of this study was to determine the effectiveness of a novel, noninvasive perfusion enhancement system versus beds with integrated alternating pressure capabilities for the prevention of hospital-acquired sacral region (sacral, coccygeal, and ischium) pressure injuries in a high-risk, acute care patient population. A prospective randomized trial of high-risk inpatients without preexisting sacral region pressure injuries was conducted. The sample comprised 431 randomly enrolled adult patients in a 300-bed tertiary care community teaching hospital. Subjects were randomly allocated to one of 2 groups: control and experimental. Both groups received "standard-of-care" pressure injury prevention measures per hospital policy, and both were placed on alternating pressure beds during their hospital stays. In addition, patients in the experimental group used a noninvasive perfusion enhancement system placed on top of their alternating pressure beds and recovery chairs throughout their hospital stay. Fischer's exact probability test was used to compare group differences, and odds ratio (OR) were calculated for comparing pressure injury rates in the experimental and control groups. Three hundred ninety-nine patients completed the trial; 186 patients were allocated to the experimental group and 213 patients to the control group. Eleven patients in the control group versus 2 in the experimental group developed hospital-acquired sacral region pressure injuries (51.6% vs 1.07%; P = .024). Control patients were 5.04 times more likely to develop hospital-acquired sacral region pressure injuries (OR = 0.1996; 95% CI, 0.0437-0.9125). Patients using a noninvasive perfusion enhancement system developed significantly fewer hospital-acquired sacral pressure injuries than those using an alternating pressure bed without the perfusion enhancement system. These findings suggest that a perfusion enhancement system enhances the success of use of pressure redistributing beds for prevention of hospital-acquired sacral pressure injuries.This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal.

Sex Differences: A Resultant of an Evolutionary Pressure?

PubMed

Della Torre, Sara; Maggi, Adriana

2017-03-07

Spurred by current research policy, we are witnessing a significant growth in the number of studies that observe and describe sexual diversities in human physiology and sex prevalence in a large number of pathologies. Yet we are far from the comprehension of the mechanisms underpinning these differences, which are the result of a long evolutionary history. This Essay is meant to underline female reproductive function as a driver for the positive selection of the specific physiological features that explain male and female differential susceptibility to diseases and metabolic disturbances, in particular. A clear understanding of the causes underlying sexual dimorphisms in the physio-pathology is crucial for precision medicine. Copyright © 2017 Elsevier Inc. All rights reserved.

Applications of genetic programming in cancer research.

PubMed

Worzel, William P; Yu, Jianjun; Almal, Arpit A; Chinnaiyan, Arul M

2009-02-01

The theory of Darwinian evolution is the fundamental keystones of modern biology. Late in the last century, computer scientists began adapting its principles, in particular natural selection, to complex computational challenges, leading to the emergence of evolutionary algorithms. The conceptual model of selective pressure and recombination in evolutionary algorithms allow scientists to efficiently search high dimensional space for solutions to complex problems. In the last decade, genetic programming has been developed and extensively applied for analysis of molecular data to classify cancer subtypes and characterize the mechanisms of cancer pathogenesis and development. This article reviews current successes using genetic programming and discusses its potential impact in cancer research and treatment in the near future.

Evolution in response to climate change: in pursuit of the missing evidence.

PubMed

Merilä, Juha

2012-09-01

Climate change is imposing intensified and novel selection pressures on organisms by altering abiotic and biotic environmental conditions on Earth, but studies demonstrating genetic adaptation to climate change mediated selection are still scarce. Evidence is accumulating to indicate that both genetic and ecological constrains may often limit populations' abilities to adapt to large scale effects of climate warming. These constraints may predispose many organisms to respond to climate change with range shifts and phenotypic plasticity, rather than through evolutionary adaptation. In general, broad conclusions about the role of evolutionary adaptation in mitigating climate change induced fitness loss in the wild are as yet difficult to make. Copyright © 2012 WILEY Periodicals, Inc.

Compliant Foil Journal Bearing Performance at Alternate Pressures and Temperatures

NASA Technical Reports Server (NTRS)

Bruckner, Robert J.; Puleo, Bernadette J.

2008-01-01

An experimental test program has been conducted to determine the highly loaded performance of current generation gas foil bearings at alternate pressures and temperatures. Typically foil bearing performance has been reported at temperatures relevant to turbomachinery applications but only at an ambient pressure of one atmosphere. This dearth of data at alternate pressures has motivated the current test program. Two facilities were used in the test program, the ambient pressure rig and the high pressure rig. The test program utilized a 35 mm diameter by 27 mm long foil journal bearing having an uncoated Inconel X-750 top foil running against a shaft with a PS304 coated journal. Load capacity tests were conducted at 3, 6, 9, 12, 15, 18, and 21 krpm at temperatures from 25 to 500 C and at pressures from 0.1 to 2.5 atmospheres. Results show an increase in load capacity with increased ambient pressure and a reduction in load capacity with increased ambient temperature. Below one-half atmosphere of ambient pressure a dramatic loss of load capacity is experienced. Additional lightly loaded foil bearing performance in nitrogen at 25 C and up to 48 atmospheres of ambient pressure has also been reported. In the lightly loaded region of operation the power loss increases for increasing pressure at a fixed load. Knowledge of foil bearing performance at operating conditions found within potential machine applications will reduce program development risk of future foil bearing supported turbomachines.

Anagenesis, Cladogenesis, and Speciation on Islands.

PubMed

Emerson, Brent C; Patiño, Jairo

2018-05-03

Anagenesis and cladogenesis are fundamental evolutionary concepts, but are increasingly being adopted as speciation models in the field of island biogeography. Here, we review the origin of the terms 'anagenetic' and 'cladogenetic' speciation, critique their utility, and finally suggest alternative terminology that better describes the geographical relationships of insular sister species. Copyright © 2018 Elsevier Ltd. All rights reserved.

Stickie removal using neutral enzymatic repulping pressure screening

Treesearch

Marguerite Sykes; John Klungness; Roland Gleisner; Said Abubakr

1998-01-01

Removal of stickie contaminants is currently a major focus of paper recycling research. Medium consistency alkaline repulping followed by pressure screening has proven to be effective for stickie removal. There is, however, an alternate method that is equally effective and more environmentally benign. This study compares the effectiveness of this alternative method,...

A potent synthetic inorganic antibiotic with activity against drug-resistant pathogens.

PubMed

Hubick, Shelby; Jayaraman, Arumugam; McKeen, Alexander; Reid, Shelby; Alcorn, Jane; Stavrinides, John; Sterenberg, Brian T

2017-02-06

The acronymously named "ESKAPE" pathogens represent a group of bacteria that continue to pose a serious threat to human health, not only due to their propensity for repeated emergence, but also due to their ability to "eskape" antibiotic treatment. The evolution of multi-drug resistance in these pathogens alone has greatly outpaced the development of new therapeutics, necessitating an alternative strategy for antibiotic development that considers the evolutionary mechanisms driving antibiotic resistance. In this study, we synthesize a novel inorganic antibiotic, phosphopyricin, which has antibiotic activity against the Gram-positive methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VRE). We show that this potent antibiotic is bactericidal, and exhibits low toxicity in an acute dose assay in mice. As a synthetic compound that does not occur naturally, phosphopyricin would be evolutionarily foreign to microbes, thereby slowing the evolution of resistance. In addition, it loses antibiotic activity upon exposure to light, meaning that the active antibiotic will not accumulate in the general environment where strong selective pressures imposed by antibiotic residuals are known to accelerate resistance. Phosphopyricin represents an innovation in antimicrobials, having a synthetic core, and a photosensitive chemical architecture that would reduce accumulation in the environment.

A potent synthetic inorganic antibiotic with activity against drug-resistant pathogens

PubMed Central

Hubick, Shelby; Jayaraman, Arumugam; McKeen, Alexander; Reid, Shelby; Alcorn, Jane; Stavrinides, John; Sterenberg, Brian T.

2017-01-01

The acronymously named “ESKAPE” pathogens represent a group of bacteria that continue to pose a serious threat to human health, not only due to their propensity for repeated emergence, but also due to their ability to “eskape” antibiotic treatment12. The evolution of multi-drug resistance in these pathogens alone has greatly outpaced the development of new therapeutics, necessitating an alternative strategy for antibiotic development that considers the evolutionary mechanisms driving antibiotic resistance. In this study, we synthesize a novel inorganic antibiotic, phosphopyricin, which has antibiotic activity against the Gram-positive methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VRE). We show that this potent antibiotic is bactericidal, and exhibits low toxicity in an acute dose assay in mice. As a synthetic compound that does not occur naturally, phosphopyricin would be evolutionarily foreign to microbes, thereby slowing the evolution of resistance. In addition, it loses antibiotic activity upon exposure to light, meaning that the active antibiotic will not accumulate in the general environment where strong selective pressures imposed by antibiotic residuals are known to accelerate resistance. Phosphopyricin represents an innovation in antimicrobials, having a synthetic core, and a photosensitive chemical architecture that would reduce accumulation in the environment. PMID:28165020

Cut your losses: self-amputation of injured limbs increases survival.

PubMed

Emberts, Zachary; Miller, Christine W; Kiehl, Daniel; St Mary, Colette M

2017-01-01

Autotomy, self-induced limb loss, is an extreme trait observed throughout the animal kingdom; lizards drop their tails, crickets release their legs, and crabs drop their claws. These repeated evolutionary origins suggest that autotomy is adaptive. Yet, we do not have a firm understanding of the selective pressures that promote and maintain this extreme trait. Although multiple adaptive hypotheses exist, research has generally focused on autotomy's adaptive value as a form of predator escape. However, autotomy could also be selected to reduce the cost of an injured limb, which we investigate here. Previously, this alternative hypothesis has been challenging to directly test because when an injury occurs on an autotomizable limb, that limb is almost always dropped (i.e., autotomy is behaviorally fixed within populations). Recently, however, we have identified a species, Narnia femorata (Insecta: Hemiptera: Coreidae), where some individuals autotomize limbs in response to injury, but some do not. This natural variation allowed us to investigate both the survival costs of retaining an injured limb and the benefits of autotomizing it. In this study, we find a positive association between autotomizing injured limbs and survival, thereby quantifying a new and likely widespread benefit of autotomy-reducing the cost of injury.

Cut your losses: self-amputation of injured limbs increases survival

PubMed Central

Miller, Christine W; Kiehl, Daniel; St. Mary, Colette M

2017-01-01

Abstract Autotomy, self-induced limb loss, is an extreme trait observed throughout the animal kingdom; lizards drop their tails, crickets release their legs, and crabs drop their claws. These repeated evolutionary origins suggest that autotomy is adaptive. Yet, we do not have a firm understanding of the selective pressures that promote and maintain this extreme trait. Although multiple adaptive hypotheses exist, research has generally focused on autotomy’s adaptive value as a form of predator escape. However, autotomy could also be selected to reduce the cost of an injured limb, which we investigate here. Previously, this alternative hypothesis has been challenging to directly test because when an injury occurs on an autotomizable limb, that limb is almost always dropped (i.e., autotomy is behaviorally fixed within populations). Recently, however, we have identified a species, Narnia femorata (Insecta: Hemiptera: Coreidae), where some individuals autotomize limbs in response to injury, but some do not. This natural variation allowed us to investigate both the survival costs of retaining an injured limb and the benefits of autotomizing it. In this study, we find a positive association between autotomizing injured limbs and survival, thereby quantifying a new and likely widespread benefit of autotomy—reducing the cost of injury. PMID:29622925

Mirror neurons in the tree of life: mosaic evolution, plasticity and exaptation of sensorimotor matching responses.

PubMed

Tramacere, Antonella; Pievani, Telmo; Ferrari, Pier F

2017-08-01

Considering the properties of mirror neurons (MNs) in terms of development and phylogeny, we offer a novel, unifying, and testable account of their evolution according to the available data and try to unify apparently discordant research, including the plasticity of MNs during development, their adaptive value and their phylogenetic relationships and continuity. We hypothesize that the MN system reflects a set of interrelated traits, each with an independent natural history due to unique selective pressures, and propose that there are at least three evolutionarily significant trends that gave raise to three subtypes: hand visuomotor, mouth visuomotor, and audio-vocal. Specifically, we put forward a mosaic evolution hypothesis, which posits that different types of MNs may have evolved at different rates within and among species. This evolutionary hypothesis represents an alternative to both adaptationist and associative models. Finally, the review offers a strong heuristic potential in predicting the circumstances under which specific variations and properties of MNs are expected. Such predictive value is critical to test new hypotheses about MN activity and its plastic changes, depending on the species, the neuroanatomical substrates, and the ecological niche. © 2016 Cambridge Philosophical Society.

The Siderophore Metabolome of Azotobacter vinelandii

PubMed Central

Baars, Oliver; Zhang, Xinning

2015-01-01

In this study, we performed a detailed characterization of the siderophore metabolome, or “chelome,” of the agriculturally important and widely studied model organism Azotobacter vinelandii. Using a new high-resolution liquid chromatography-mass spectrometry (LC-MS) approach, we found over 35 metal-binding secondary metabolites, indicative of a vast chelome in A. vinelandii. These include vibrioferrin, a siderophore previously observed only in marine bacteria. Quantitative analyses of siderophore production during diazotrophic growth with different sources and availabilities of Fe showed that, under all tested conditions, vibrioferrin was present at the highest concentration of all siderophores and suggested new roles for vibrioferrin in the soil environment. Bioinformatic searches confirmed the capacity for vibrioferrin production in Azotobacter spp. and other bacteria spanning multiple phyla, habitats, and lifestyles. Moreover, our studies revealed a large number of previously unreported derivatives of all known A. vinelandii siderophores and rationalized their origins based on genomic analyses, with implications for siderophore diversity and evolution. Together, these insights provide clues as to why A. vinelandii harbors multiple siderophore biosynthesis gene clusters. Coupled with the growing evidence for alternative functions of siderophores, the vast chelome in A. vinelandii may be explained by multiple, disparate evolutionary pressures that act on siderophore production. PMID:26452553

Alternating versus synchronous ventilation of left and right lungs in piglets.

PubMed

Versprille, A; Hrachovina, V; Jansen, J R

1995-12-01

We tested whether alternating ventilation (AV) of each lung (i.e. with a phase difference of half a ventilatory cycle) would decrease central venous pressure and so increase cardiac output when compared with simultaneous ventilation (SV) of both lungs. If, during AV, the inflated lung expands partly via compression of the opposite lung, mean lung volume will be smaller during AV than SV. As a consequence, mean intrathoracic pressure (as cited in the literature), and therefore, central venous pressure will be smaller. The experiments were performed in seven anaesthetized and paralyzed piglets using a double-piston ventilator. Minute ventilation was the same during AV and SV. Starting at SV, we alternated three times between AV and SV for periods of 10 min. During AV, central venous pressure was decreased by 0.7 mmHg and cardiac output was increased by 10 +/- 4.4% (mean, +/-SD) compared with SV. AV also resulted in increased arterial pressure. During one-sided inflation with closed outlet of the opposite lung, a pressure rise occurred in the opposite lung, indicating compression. The higher cardiac output during AV than SV can be explained by the fact that central venous pressure is lower during AV. This lower central venous pressure is very probably due to the lower mean intrathoracic pressure caused by compression of the opposite lung during unilateral inflation.

Fixation probabilities on superstars, revisited and revised.

PubMed

Jamieson-Lane, Alastair; Hauert, Christoph

2015-10-07

Population structures can be crucial determinants of evolutionary processes. For the Moran process on graphs certain structures suppress selective pressure, while others amplify it (Lieberman et al., 2005). Evolutionary amplifiers suppress random drift and enhance selection. Recently, some results for the most powerful known evolutionary amplifier, the superstar, have been invalidated by a counter example (Díaz et al., 2013). Here we correct the original proof and derive improved upper and lower bounds, which indicate that the fixation probability remains close to 1-1/(r(4)H) for population size N→∞ and structural parameter H⪢1. This correction resolves the differences between the two aforementioned papers. We also confirm that in the limit N,H→∞ superstars remain capable of eliminating random drift and hence of providing arbitrarily strong selective advantages to any beneficial mutation. In addition, we investigate the robustness of amplification in superstars and find that it appears to be a fragile phenomenon with respect to changes in the selection or mutation processes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Competition among cooperators: Altruism and reciprocity

PubMed Central

Danielson, Peter

2002-01-01

Levine argues that neither self-interest nor altruism explains experimental results in bargaining and public goods games. Subjects' preferences appear also to be sensitive to their opponents' perceived altruism. Sethi and Somanathan provide a general account of reciprocal preferences that survive under evolutionary pressure. Although a wide variety of reciprocal strategies pass this evolutionary test, Sethi and Somanthan conjecture that fewer are likely to survive when reciprocal strategies compete with each other. This paper develops evolutionary agent-based models to test their conjecture in cases where reciprocal preferences can differ in a variety of games. We confirm that reciprocity is necessary but not sufficient for optimal cooperation. We explore the theme of competition among reciprocal cooperators and display three interesting emergent organizations: racing to the “moral high ground,” unstable cycles of preference change, and, when we implement reciprocal mechanisms, hierarchies resulting from exploiting fellow cooperators. If reciprocity is a basic mechanism facilitating cooperation, we can expect interaction that evolves around it to be complex, non-optimal, and resistant to change. PMID:12011403

Ecological and evolutionary drivers of the elevational gradient of diversity.

PubMed

Laiolo, Paola; Pato, Joaquina; Obeso, José Ramón

2018-05-02

Ecological, evolutionary, spatial and neutral theories make distinct predictions and provide distinct explanations for the mechanisms that control the relationship between diversity and the environment. Here, we test predictions of the elevational diversity gradient focusing on Iberian bumblebees, grasshoppers and birds. Processes mediated by local abundance and regional diversity concur in explaining local diversity patterns along elevation. Effects expressed through variation in abundance were similar among taxa and point to the overriding role of a physical factor, temperature. This determines how energy is distributed among individuals and ultimately how the resulting pattern of abundance affects species incidence. Effects expressed through variation in regional species pools depended instead on taxon-specific evolutionary history, and lead to diverging responses under similar environmental pressures. Local filters and regional variation also explain functional diversity gradients, in line with results from species richness that indicate an (local) ecological and (regional) historical unfolding of diversity-elevation relationships. © 2018 John Wiley & Sons Ltd/CNRS.

Adaptive memory: young children show enhanced retention of fitness-related information.

PubMed

Aslan, Alp; Bäuml, Karl-Heinz T

2012-01-01

Evolutionary psychologists propose that human cognition evolved through natural selection to solve adaptive problems related to survival and reproduction, with its ultimate function being the enhancement of reproductive fitness. Following this proposal and the evolutionary-developmental view that ancestral selection pressures operated not only on reproductive adults, but also on pre-reproductive children, the present study examined whether young children show superior memory for information that is processed in terms of its survival value. In two experiments, we found such survival processing to enhance retention in 4- to 10-year-old children, relative to various control conditions that also required deep, meaningful processing but were not related to survival. These results suggest that, already in very young children, survival processing is a special and extraordinarily effective form of memory encoding. The results support the functional-evolutionary proposal that young children's memory is "tuned" to process and retain fitness-related information. Copyright © 2011 Elsevier B.V. All rights reserved.

Ontogenetic Tooth Reduction in Stenopterygius quadriscissus (Reptilia: Ichthyosauria): Negative Allometry, Changes in Growth Rate, and Early Senescence of the Dental Lamina

PubMed Central

Dick, Daniel G.; Maxwell, Erin E.

2015-01-01

We explore the functional, developmental, and evolutionary processes which are argued to produce tooth reduction in the extinct marine reptile Stenopterygius quadriscissus (Reptilia: Ichthyosauria). We analyze the relationship between mandible growth and tooth size, shape, and count, to establish an ontogenetic trend. The pattern in S. quadriscissus is consistent with hypotheses of tooth size reduction by neutral selection, and this unusual morphology (a functionally edentulous rostrum) was produced by a series of different evolutionary developmental changes that are known for other taxa showing tooth reduction and loss. Specifically, this species evolved functional edentulism by evolutionary changes in the growth allometry of the dentition and by altering growth rates through ontogeny. This observation supports previous hypotheses that S. quadriscissus underwent ontogenetic tooth reduction. Tooth reduction in S. quadriscissus may be caused by unique selective pressures resulting from prey choice and feeding behavior, expanding our current understanding of the mechanisms producing tooth reduction. PMID:26579712

Ontogenetic Tooth Reduction in Stenopterygius quadriscissus (Reptilia: Ichthyosauria): Negative Allometry, Changes in Growth Rate, and Early Senescence of the Dental Lamina.

PubMed

Dick, Daniel G; Maxwell, Erin E

2015-01-01

We explore the functional, developmental, and evolutionary processes which are argued to produce tooth reduction in the extinct marine reptile Stenopterygius quadriscissus (Reptilia: Ichthyosauria). We analyze the relationship between mandible growth and tooth size, shape, and count, to establish an ontogenetic trend. The pattern in S. quadriscissus is consistent with hypotheses of tooth size reduction by neutral selection, and this unusual morphology (a functionally edentulous rostrum) was produced by a series of different evolutionary developmental changes that are known for other taxa showing tooth reduction and loss. Specifically, this species evolved functional edentulism by evolutionary changes in the growth allometry of the dentition and by altering growth rates through ontogeny. This observation supports previous hypotheses that S. quadriscissus underwent ontogenetic tooth reduction. Tooth reduction in S. quadriscissus may be caused by unique selective pressures resulting from prey choice and feeding behavior, expanding our current understanding of the mechanisms producing tooth reduction.

Exploration of phase transition in Th2C under pressure: An Ab-initio investigation

NASA Astrophysics Data System (ADS)

Sahoo, B. D.; Joshi, K. D.; Kaushik, T. C.

2018-05-01

With the motivation of searching for new compounds in the Th-C system, we have performed ab initio evolutionary searches for all the stable compounds in this binary system in the pressure range of 0-100 GPa. We have found previously unknown, thermodynamically stable, composition Th2C along with experimentally known ThC, ThC2 and Th2C3 phases at 0 GPa. Interestingly at pressure of 13 GPa the predicted ground state orthorhombic (SG no. 59, Pmmn) phase of Th2C transforms to trigonal (SG no. 164, P-3m1) phase. We also find the mechanical and dynamical stability of both the phases. Further, the theoretically determined equation of state has been utilized to derive various physical quantities such as zero pressure equilibrium volume, bulk modulus, and pressure derivative of bulk modulus of Pmmn phase at ambient conditions.

Pressure induced Ag 2Te polymorphs in conjunction with topological non trivial to metal transition

DOE PAGES

Zhu, J.; Oganov, A. R.; Feng, W. X.; ...

2016-08-01

Silver telluride (Ag 2Te) is well known as superionic conductor and topologica insulator with polymorphs. Pressure induced three phase transitions in Ag 2Te hav been reported in previous. Here, we experimentally identified high pressure phas above 13 GPa of Ag 2Te by using high pressure synchrotron x ray diffraction metho in combination with evolutionary crystal structure prediction, showing it crystallize into a monoclinic structure of space group C2/m with lattice parameters a = 6.081Å b = 5.744Å, c = 6.797 Å, β = 105.53°. The electronic properties measurements of Ag 2Te reveal that the topologically non-trivial semiconducting phase I andmore » semimetalli phase II previously predicated by theory transformed into bulk metals fo high pressure phases in consistent with the first principles calculations« less

Wiener-Hammerstein system identification - an evolutionary approach

NASA Astrophysics Data System (ADS)

Naitali, Abdessamad; Giri, Fouad

2016-01-01

The problem of identifying parametric Wiener-Hammerstein (WH) systems is addressed within the evolutionary optimisation context. Specifically, a hybrid culture identification method is developed that involves model structure adaptation using genetic recombination and model parameter learning using particle swarm optimisation. The method enjoys three interesting features: (1) the risk of premature convergence of model parameter estimates to local optima is significantly reduced, due to the constantly maintained diversity of model candidates; (2) no prior knowledge is needed except for upper bounds on the system structure indices; (3) the method is fully autonomous as no interaction is needed with the user during the optimum search process. The performances of the proposed method will be illustrated and compared to alternative methods using a well-established WH benchmark.

Ancient homology underlies adaptive mimetic diversity across butterflies

PubMed Central

Gallant, Jason R.; Imhoff, Vance E.; Martin, Arnaud; Savage, Wesley K.; Chamberlain, Nicola L.; Pote, Ben L.; Peterson, Chelsea; Smith, Gabriella E.; Evans, Benjamin; Reed, Robert D.; Kronforst, Marcus R.; Mullen, Sean P.

2014-01-01

Convergent evolution provides a rare, natural experiment with which to test the predictability of adaptation at the molecular level. Little is known about the molecular basis of convergence over macro-evolutionary timescales. Here we use a combination of positional cloning, population genomic resequencing, association mapping and developmental data to demonstrate that positionally orthologous nucleotide variants in the upstream region of the same gene, WntA, are responsible for parallel mimetic variation in two butterfly lineages that diverged >65 million years ago. Furthermore, characterization of spatial patterns of WntA expression during development suggests that alternative regulatory mechanisms underlie wing pattern variation in each system. Taken together, our results reveal a strikingly predictable molecular basis for phenotypic convergence over deep evolutionary time. PMID:25198507

Impact of Fluidic Chevrons on Jet Noise

NASA Technical Reports Server (NTRS)

Henderson, Brenda S.; Kinzie, Kevin W.; Whitmire, Julia; Abeysinghe, Amal

2005-01-01

The impact of alternating fluidic core chevrons on the production of jet noise is investigated. Core nozzles for a representative 1/9th scale, bypass ratio 5 model system were manufactured with slots cut near the trailing edges to allow for air injection into the core and fan streams. The injectors followed an alternating pattern around the nozzle perimeter so that the injection alternated between injection into the core stream and injection into the fan stream. For the takeoff condition and a forward flight Mach number of 0.10, the overall sound pressure levels at the peak jet noise angle decrease with increasing injection pressure. Sound pressure levels increase for observation angles less than 110o at higher injection pressures due to increases in high frequency noise. Greater increases in high frequency noise are observed when the number of injectors increases from 8 to 12. When the forward flight Mach number is increased to 0.28, jet noise reduction (relative to the baseline) is observed at aft angles for increasing injection pressure while significant increases in jet noise are observed at forward observation angles due to substantial acoustic radiation at high frequencies. A comparison between inflow and alternating injectors shows that, for equal mass injection rates, the inflow nozzle produces greater low frequency noise reduction (relative to the baseline) than the alternating injectors at 90o and aft observation angles and a forward flight Mach number of 0.28. Preliminary computational fluid dynamic simulations indicate that the spatial decay rate of the hot potential core flow is less for the inflow nozzle than for the alternating nozzles which indicates that gentle mixing may be preferred over sever mixing when fluidic chevrons are used for jet noise reduction.

Fluid Lavage of Open Wounds (FLOW): A Multicenter, Blinded, Factorial Trial Comparing Alternative Irrigating Solutions and Pressures in Patients with Open Fractures

DTIC Science & Technology

2013-10-01

Multicenter, Blinded, Factorial Trial Comparing Alternative Irrigating Solutions and Pressures in Patients with Open Fractures PRINCIPAL...Solutions and Pressures in Patients with Open Fractures 5b. GRANT NUMBER W81XWH-12-1-0530 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Kyle J. Jeray...important initial step in preventing infection in open fractures . However, there is little clinical evidence as to the best irrigation methods and additives

Evolution of precopulatory and post-copulatory strategies of inbreeding avoidance and associated polyandry.

PubMed

Duthie, A B; Bocedi, G; Germain, R R; Reid, J M

2018-01-01

Inbreeding depression is widely hypothesized to drive adaptive evolution of precopulatory and post-copulatory mechanisms of inbreeding avoidance, which in turn are hypothesized to affect evolution of polyandry (i.e. female multiple mating). However, surprisingly little theory or modelling critically examines selection for precopulatory or post-copulatory inbreeding avoidance, or both strategies, given evolutionary constraints and direct costs, or examines how evolution of inbreeding avoidance strategies might feed back to affect evolution of polyandry. Selection for post-copulatory inbreeding avoidance, but not for precopulatory inbreeding avoidance, requires polyandry, whereas interactions between precopulatory and post-copulatory inbreeding avoidance might cause functional redundancy (i.e. 'degeneracy') potentially generating complex evolutionary dynamics among inbreeding strategies and polyandry. We used individual-based modelling to quantify evolution of interacting precopulatory and post-copulatory inbreeding avoidance and associated polyandry given strong inbreeding depression and different evolutionary constraints and direct costs. We found that evolution of post-copulatory inbreeding avoidance increased selection for initially rare polyandry and that evolution of a costly inbreeding avoidance strategy became negligible over time given a lower-cost alternative strategy. Further, fixed precopulatory inbreeding avoidance often completely precluded evolution of polyandry and hence post-copulatory inbreeding avoidance, but fixed post-copulatory inbreeding avoidance did not preclude evolution of precopulatory inbreeding avoidance. Evolution of inbreeding avoidance phenotypes and associated polyandry is therefore affected by evolutionary feedbacks and degeneracy. All else being equal, evolution of precopulatory inbreeding avoidance and resulting low polyandry is more likely when post-copulatory inbreeding avoidance is precluded or costly, and evolution of post-copulatory inbreeding avoidance greatly facilitates evolution of costly polyandry. © The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.

High pressure behaviour of uranium dicarbide (UC{sub 2}): Ab-initio study

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

Sahoo, B. D., E-mail: bdsahoo@barc.gov.in; Mukherjee, D.; Joshi, K. D.

2016-08-28

The structural stability of uranium dicarbide has been examined under hydrostatic compression employing evolutionary structure search algorithm implemented in the universal structure predictor: evolutionary Xtallography (USPEX) code in conjunction with ab-initio electronic band structure calculation method. The ab-initio total energy calculations involved for this purpose have been carried out within both generalized gradient approximations (GGA) and GGA + U approximations. Our calculations under GGA approximation predict the high pressure structural sequence of tetragonal → monoclinic → orthorhombic for this material with transition pressures of ∼8 GPa and 42 GPa, respectively. The same transition sequence is predicted by calculations within GGA + U also with transition pressuresmore » placed at ∼24 GPa and ∼50 GPa, respectively. Further, on the basis of comparison of zero pressure equilibrium volume and equation of state with available experimental data, we find that GGA + U approximation with U = 2.5 eV describes this material better than the simple GGA approximation. The theoretically predicted high pressure structural phase transitions are in disagreement with the only high experimental study by Dancausse et al. [J. Alloys. Compd. 191, 309 (1993)] on this compound which reports a tetragonal to hexagonal phase transition at a pressure of ∼17.6 GPa. Interestingly, during lowest enthalpy structure search using USPEX, we do not see any hexagonal phase to be closer to the predicted monoclinic phase even within 0.2 eV/f. unit. More experiments with varying carbon contents in UC{sub 2} sample are required to resolve this discrepancy. The existence of these high pressure phases predicted by static lattice calculations has been further substantiated by analyzing the elastic and lattice dynamic stability of these structures in the pressure regimes of their structural stability. Additionally, various thermo-physical quantities such as equilibrium volume, bulk modulus, Debye temperature, thermal expansion coefficient, Gruneisen parameter, and heat capacity at ambient conditions have been determined from these calculations and compared with the available experimental data.« less

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

PubMed

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

2016-09-01

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

Tropical forests are both evolutionary cradles and museums of leaf beetle diversity.

PubMed

McKenna, Duane D; Farrell, Brian D

2006-07-18

The high extant species diversity of tropical lineages of organisms is usually portrayed as a relatively recent and rapid development or as a consequence of the gradual accumulation or preservation of species over time. These explanations have led to alternative views of tropical forests as evolutionary "cradles" or "museums" of diversity, depending on the organisms under study. However, biogeographic and fossil evidence implies that the evolutionary histories of diversification among tropical organisms may be expected to exhibit characteristics of both cradle and museum models. This possibility has not been explored in detail for any group of terrestrial tropical organisms. From an extensively sampled molecular phylogeny of herbivorous Neotropical leaf beetles in the genus Cephaloleia, we present evidence for (i) comparatively ancient Paleocene-Eocene adaptive radiation associated with global warming and Cenozoic maximum global temperatures, (ii) moderately ancient lineage-specific diversification coincident with the Oligocene adaptive radiation of Cephaloleia host plants in the genus Heliconia, and (iii) relatively recent Miocene-Pliocene diversification coincident with the collision of the Panama arc with South America and subsequent bridging of the Isthmus of Panama. These results demonstrate that, for Cephaloleia and perhaps other lineages of organisms, tropical forests are at the same time both evolutionary cradles and museums of diversity.

Alternative splicing and the evolution of phenotypic novelty.

PubMed

Bush, Stephen J; Chen, Lu; Tovar-Corona, Jaime M; Urrutia, Araxi O

2017-02-05

Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative splicing to developmental programmes. The role of alternative splicing as a source of transcript diversification has previously been compared to that of gene duplication, with the relationship between the two extensively explored. Alternative splicing is reduced following gene duplication with the retention of duplicate copies higher for genes which were alternatively spliced prior to duplication. Furthermore, and unlike the case for overall gene number, the proportion of alternatively spliced genes has also increased in line with the evolutionary diversification of cell types, suggesting alternative splicing may contribute to the complexity of developmental programmes. Together these observations suggest a prominent role for alternative splicing as a source of functional innovation. However, it is unknown whether the proliferation of alternative splicing events indeed reflects a functional expansion of the transcriptome or instead results from weaker selection acting on larger species, which tend to have a higher number of cell types and lower population sizes.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'. © 2016 The Author(s).

Alternative splicing and the evolution of phenotypic novelty

PubMed Central

Bush, Stephen J.; Chen, Lu; Tovar-Corona, Jaime M.

2017-01-01

Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative splicing to developmental programmes. The role of alternative splicing as a source of transcript diversification has previously been compared to that of gene duplication, with the relationship between the two extensively explored. Alternative splicing is reduced following gene duplication with the retention of duplicate copies higher for genes which were alternatively spliced prior to duplication. Furthermore, and unlike the case for overall gene number, the proportion of alternatively spliced genes has also increased in line with the evolutionary diversification of cell types, suggesting alternative splicing may contribute to the complexity of developmental programmes. Together these observations suggest a prominent role for alternative splicing as a source of functional innovation. However, it is unknown whether the proliferation of alternative splicing events indeed reflects a functional expansion of the transcriptome or instead results from weaker selection acting on larger species, which tend to have a higher number of cell types and lower population sizes. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’. PMID:27994117

Origins of Protein Functions in Cells

NASA Technical Reports Server (NTRS)

Seelig, Burchard; Pohorille, Andrzej

2011-01-01

In modern organisms proteins perform a majority of cellular functions, such as chemical catalysis, energy transduction and transport of material across cell walls. Although great strides have been made towards understanding protein evolution, a meaningful extrapolation from contemporary proteins to their earliest ancestors is virtually impossible. In an alternative approach, the origin of water-soluble proteins was probed through the synthesis and in vitro evolution of very large libraries of random amino acid sequences. In combination with computer modeling and simulations, these experiments allow us to address a number of fundamental questions about the origins of proteins. Can functionality emerge from random sequences of proteins? How did the initial repertoire of functional proteins diversify to facilitate new functions? Did this diversification proceed primarily through drawing novel functionalities from random sequences or through evolution of already existing proto-enzymes? Did protein evolution start from a pool of proteins defined by a frozen accident and other collections of proteins could start a different evolutionary pathway? Although we do not have definitive answers to these questions yet, important clues have been uncovered. In one example (Keefe and Szostak, 2001), novel ATP binding proteins were identified that appear to be unrelated in both sequence and structure to any known ATP binding proteins. One of these proteins was subsequently redesigned computationally to bind GTP through introducing several mutations that introduce targeted structural changes to the protein, improve its binding to guanine and prevent water from accessing the active center. This study facilitates further investigations of individual evolutionary steps that lead to a change of function in primordial proteins. In a second study (Seelig and Szostak, 2007), novel enzymes were generated that can join two pieces of RNA in a reaction for which no natural enzymes are known. Recently it was found that, as in the previous case, the proteins have a structure unknown among modern enzymes. In this case, in vitro evolution started from a small, non-enzymatic protein. A similar selection process initiated from a library of random polypeptides is in progress. These results not only allow for estimating the occurrence of function in random protein assemblies but also provide evidence for the possibility of alternative protein worlds. Extant proteins might simply represent a frozen accident in the world of possible proteins. Alternative collections of proteins, even with similar functions, could originate alternative evolutionary paths.

High pressure structural stability of the Na-Te system

NASA Astrophysics Data System (ADS)

Wang, Youchun; Tian, Fubo; Li, Da; Duan, Defang; Xie, Hui; Liu, Bingbing; Zhou, Qiang; Cui, Tian

2018-03-01

The ab initio evolutionary algorithm is used to search for all thermodynamically stable Na-Te compounds at extreme pressure. In our calculations, several new structures are discovered at high pressure, namely, Imma Na2Te, Pmmm NaTe, Imma Na8Te2 and P4/mmm NaTe3. Like the known structures of Na2Te (Fm-3m, Pnma and P63/mmc), the Pmmm NaTe, Imma Na8Te2 and P4/mmm NaTe3 structures also show semiconductor properties with band-gap decreases when pressure increased. However, we find that the band-gap of Imma Na2Te structure increases with pressure. We presume that the result may be caused by the increasing of splitting between Te p states and Na s, Na p and Te d states. Furthermore, we think that the strong hybridization between Na p state and Te d state result in the band gap increasing with pressure.

Ecological significance of compatible solute accumulation by micro-organisms: from single cells to global climate.

PubMed

Welsh, D T

2000-07-01

The osmoadaptation of most micro-organisms involves the accumulation of K(+) ions and one or more of a restricted range of low molecular mass organic solutes, collectively termed 'compatible solutes'. These solutes are accumulated to high intracellular concentrations, in order to balance the osmotic pressure of the growth medium and maintain cell turgor pressure, which provides the driving force for cell extension growth. In this review, I discuss the alternative roles which compatible solutes may also play as intracellular reserves of carbon, energy and nitrogen, and as more general stress metabolites involved in protection of cells against other environmental stresses including heat, desiccation and freezing. Thus, the evolutionary selection for the accumulation of a specific compatible solute may not depend solely upon its function during osmoadaptation, but also upon the secondary benefits its accumulation provides, such as increased tolerance of other environmental stresses prevalent in the organism's niche or even anti-herbivory or dispersal functions in the case of dimethylsulfoniopropionate (DMSP). In the second part of the review, I discuss the ecological consequences of the release of compatible solutes to the environment, where they can provide sources of compatible solutes, carbon, nitrogen and energy for other members of the micro-flora. Finally, at the global scale the metabolism of specific compatible solutes (betaines and DMSP) in brackish water, marine and hypersaline environments may influence global climate, due to the production of the trace gases, methane and dimethylsulfide (DMS) and in the case of DMS, also couple the marine and terrestrial sulfur cycles.

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

NASA Technical Reports Server (NTRS)

1983-01-01

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

The Myth of the Alpha Male: A New Look at Dominance-Related Beliefs and Behaviors among Adolescent Males and Females

ERIC Educational Resources Information Center

Hawley, Patricia H.; Little, Todd D.; Card, Noel A.

2008-01-01

Evolutionary and biological approaches tend to suggest that social dominance is predominately an aspect of male social organization. Furthermore, when females behave non-normatively, they are less positively evaluated than males engaging in the same behavior. Alternate, less familiar models of females and dominance/aggression underlie the present…

An Alternative to Adaptation by Sexual Selection: Habitat Choice.

PubMed

Porter, Cody K; Akcali, Christopher K

2018-06-09

Adaptation in mating signals and preferences has generally been explained by sexual selection. We propose that adaptation in such mating traits might also arise via a non-mutually exclusive process wherein individuals preferentially disperse to habitats where they experience high mating performance. Here we explore the evolutionary implications of this process. Copyright © 2018 Elsevier Ltd. All rights reserved.

Pressure-induced cation-cation bonding in V 2 O 3

DOE PAGES

Bai, Ligang; Li, Quan; Corr, Serena A.; ...

2015-10-09

A pressure-induced phase transition, associated with the formation of cation-cation bonding, occurs in V 2O 3 by combining synchroton x-ray diffraction in a diamond anvil cell and ab initio evolutionary calculations. The high-pressure phase has a monoclinic structure with a C2/c space group, and it is both energetically and dynamically stable at pressures above 47 GPa to at least 105 GPa. this phase transition can be viewed as a two-dimensional Peierls-like distortion, where the cation-cation dimer chains are connected along the c axis of the monoclinic cell. In conclusion, this finding provides insights into the interplay of electron correlation andmore » lattice distortion in V 2O 3, and it may also help to understand novel properties of other early transition-metal oxides.« less

Tin sulfides and tin selenides at ambient and high pressure conditions

NASA Astrophysics Data System (ADS)

Nguyen Cong, Kien; Gonzalez, Joseph; Steele, Brad; Oleynik, Ivan

The application of high pressure promotes unusual chemical bonding in condensed phase resulting in the synthesis of novel materials, which may be recoverable in metastable states at ambient conditions. First-principles evolutionary crystal structure search is performed to explore novel tin sulfide (SnxSy) and tin selenide (SnxSy) crystals with the goal to discover novel photovoltaic and thermoelectric materials. Variable stoichiometry searches at various pressures are performed and the phase diagrams are constructed in the range of pressures 0-100 GPa, which include both the thermodynamically stable and lowest enthalpy metastable structures. Several new structures are identified and their dynamical stability is investigated. To help experimental synthesis of these novel compounds, Raman spectra and XRD patterns are also calculated. These new materials are also investigated to identify those with promising photovoltaic and thermoelectric properties.

Diversity, evolution and medical applications of insect antimicrobial peptides

PubMed Central

Mylonakis, Eleftherios; Podsiadlowski, Lars; Muhammed, Maged

2016-01-01

Antimicrobial peptides (AMPs) are short proteins with antimicrobial activity. A large portion of known AMPs originate from insects, and the number and diversity of these molecules in different species varies considerably. Insect AMPs represent a potential source of alternative antibiotics to address the limitation of current antibiotics, which has been caused by the emergence and spread of multidrug-resistant pathogens. To get more insight into AMPs, we investigated the diversity and evolution of insect AMPs by mapping their phylogenetic distribution, allowing us to predict the evolutionary origins of selected AMP families and to identify evolutionarily conserved and taxon-specific families. Furthermore, we highlight the use of the nematode Caenorhabditis elegans as a whole-animal model in high-throughput screening methods to identify AMPs with efficacy against human pathogens, including Acinetobacter baumanii and methicillin-resistant Staphylococcus aureus. We also discuss the potential medical applications of AMPs, including their use as alternatives for conventional antibiotics in ectopic therapies, their combined use with antibiotics to restore the susceptibility of multidrug-resistant pathogens, and their use as templates for the rational design of peptidomimetic drugs that overcome the disadvantages of therapeutic peptides. The article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’. PMID:27160593

Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagation.

PubMed

Zeng, Jia; Hannenhalli, Sridhar

2013-01-01

Gene duplication, followed by functional evolution of duplicate genes, is a primary engine of evolutionary innovation. In turn, gene expression evolution is a critical component of overall functional evolution of paralogs. Inferring evolutionary history of gene expression among paralogs is therefore a problem of considerable interest. It also represents significant challenges. The standard approaches of evolutionary reconstruction assume that at an internal node of the duplication tree, the two duplicates evolve independently. However, because of various selection pressures functional evolution of the two paralogs may be coupled. The coupling of paralog evolution corresponds to three major fates of gene duplicates: subfunctionalization (SF), conserved function (CF) or neofunctionalization (NF). Quantitative analysis of these fates is of great interest and clearly influences evolutionary inference of expression. These two interrelated problems of inferring gene expression and evolutionary fates of gene duplicates have not been studied together previously and motivate the present study. Here we propose a novel probabilistic framework and algorithm to simultaneously infer (i) ancestral gene expression and (ii) the likely fate (SF, NF, CF) at each duplication event during the evolution of gene family. Using tissue-specific gene expression data, we develop a nonparametric belief propagation (NBP) algorithm to predict the ancestral expression level as a proxy for function, and describe a novel probabilistic model that relates the predicted and known expression levels to the possible evolutionary fates. We validate our model using simulation and then apply it to a genome-wide set of gene duplicates in human. Our results suggest that SF tends to be more frequent at the earlier stage of gene family expansion, while NF occurs more frequently later on.

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

PubMed Central

Sunagar, Kartik; Moran, Yehu

2015-01-01

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

Evolution in an Afternoon: Rapid Natural Selection and Adaptation of Bacterial Populations

ERIC Educational Resources Information Center

Delpech, Roger

2009-01-01

This paper describes a simple, rapid and low-cost technique for growing bacteria (or other microbes) in an environmental gradient, in order to determine the tolerance of the microbial population to varying concentrations of sodium chloride ions, and suggests how the evolutionary response of a microbial population to the selection pressure of the…

Multiple resistances against diseases and insects in a breeding population of pinus pinaster

Treesearch

Alejandr Solla; Maria Vivas; Elena Cubera; Luis Sampedro; Xoaquin Moreira; Esther Merlo; Raul de la Mata; Rafael Zas

2012-01-01

The different plant defenses existing within a given taxon have been commonly assumed to trade-off among each other because of both evolutionary and physiological reasons. The higher the efficiency of a single defensive trait, the lower selective pressure for other redundant defenses expected. On the other hand, production of multiple defenses might be...

Tracing the role of human civilization in the globalization of plant pathogens

Treesearch

Alberto Santini; Andrew Liebhold; Duccio Migliorini; Steve Woodward

2018-01-01

Co-evolution between plants and parasites, including herbivores and pathogens, has arguably generated much of Earth’s biological diversity. Within an ecosystem, coevolution of plants and pathogens is a stepwise reciprocal evolutionary interaction: epidemics result in intense selection pressures on both host and pathogen populations, ultimately allowing long-term...

Evolution in biodiversity policy – current gaps and future needs

PubMed Central

Santamaría, Luis; Méndez, Pablo F

2012-01-01

The intensity and speed of human alterations to the planet's ecosystems are yielding our static, ahistorical view of biodiversity obsolete. Human actions frequently trigger fast evolutionary responses, affect extant genetic variation and result in the establishment of new communities and co-evolutionary networks for which we lack past analogues. Contemporary evolution interplays with ecological changes to determine the response of organisms and ecosystems to anthropogenic pressures. Examples on wild species include responses to harvest (e.g. fisheries, hunting, angling), habitat loss and fragmentation (e.g. genetic effects of isolation), biotic exchange (e.g. evolutionary responses to control measures), climate change (e.g. local adaptation and its interplay with dispersal processes) and the responses of endangered species to conservation measures. A review of international and EU biodiversity policies showed numerous opportunities for the integration of evolutionary knowledge, with the realistic prospect of improving their efficacy. Such opportunities should be extended to other sectoral policies of direct relevance for biodiversity – notably nature conservation, fisheries, agriculture, water resources, spatial planning and climate change. These avenues for improvement are, however, challenged by the low level of enforcement of biodiversity policies, linked to the nonbinding nature of most biodiversity-policy documents, and the decreasing representation of biodiversity in EU's research policy. PMID:25568042

Engineering the evolution of self-organizing behaviors in swarm robotics: a case study.

PubMed

Trianni, Vito; Nolfi, Stefano

2011-01-01

Evolutionary robotics (ER) is a powerful approach for the automatic synthesis of robot controllers, as it requires little a priori knowledge about the problem to be solved in order to obtain good solutions. This is particularly true for collective and swarm robotics, in which the desired behavior of the group is an indirect result of the control and communication rules followed by each individual. However, the experimenter must make several arbitrary choices in setting up the evolutionary process, in order to define the correct selective pressures that can lead to the desired results. In some cases, only a deep understanding of the obtained results can point to the critical aspects that constrain the system, which can be later modified in order to re-engineer the evolutionary process towards better solutions. In this article, we discuss the problem of engineering the evolutionary machinery that can lead to the desired result in the swarm robotics context. We also present a case study about self-organizing synchronization in a swarm of robots, in which some arbitrarily chosen properties of the communication system hinder the scalability of the behavior to large groups. We show that by modifying the communication system, artificial evolution can synthesize behaviors that scale properly with the group size.

Spatial Selection and Local Adaptation Jointly Shape Life-History Evolution during Range Expansion.

PubMed

Van Petegem, Katrien H P; Boeye, Jeroen; Stoks, Robby; Bonte, Dries

2016-11-01

In the context of climate change and species invasions, range shifts increasingly gain attention because the rates at which they occur in the Anthropocene induce rapid changes in biological assemblages. During range shifts, species experience multiple selection pressures. For poleward expansions in particular, it is difficult to interpret observed evolutionary dynamics because of the joint action of evolutionary processes related to spatial selection and to adaptation toward local climatic conditions. To disentangle the effects of these two processes, we integrated stochastic modeling and data from a common garden experiment, using the spider mite Tetranychus urticae as a model species. By linking the empirical data with those derived form a highly parameterized individual-based model, we infer that both spatial selection and local adaptation contributed to the observed latitudinal life-history divergence. Spatial selection best described variation in dispersal behavior, while variation in development was best explained by adaptation to the local climate. Divergence in life-history traits in species shifting poleward could consequently be jointly determined by contemporary evolutionary dynamics resulting from adaptation to the environmental gradient and from spatial selection. The integration of modeling with common garden experiments provides a powerful tool to study the contribution of these evolutionary processes on life-history evolution during range expansion.

First steps in experimental cancer evolution

PubMed Central

Taylor, Tiffany B; Johnson, Louise J; Jackson, Robert W; Brockhurst, Michael A; Dash, Philip R

2013-01-01

Evolutionary processes play a central role in the development, progression and response to treatment of cancers. The current challenge facing researchers is to harness evolutionary theory to further our understanding of the clinical progression of cancers. Central to this endeavour will be the development of experimental systems and approaches by which theories of cancer evolution can be effectively tested. We argue here that the experimental evolution approach – whereby evolution is observed in real time and which has typically employed microorganisms – can be usefully applied to cancer. This approach allows us to disentangle the ecological causes of natural selection, identify the genetic basis of evolutionary changes and determine their repeatability. Cell cultures used in cancer research share many of the desirable traits that make microorganisms ideal for studying evolution. As such, experimental cancer evolution is feasible and likely to give great insight into the selective pressures driving the evolution of clinically destructive cancer traits. We highlight three areas of evolutionary theory with importance to cancer biology that are amenable to experimental evolution: drug resistance, social evolution and resource competition. Understanding the diversity, persistence and evolution of cancers is vital for treatment and drug development, and an experimental evolution approach could provide strategic directions and focus for future research. PMID:23745144

Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles.

PubMed

Mustafin, Zakhar Sergeevich; Lashin, Sergey Alexandrovich; Matushkin, Yury Georgievich; Gunbin, Konstantin Vladimirovich; Afonnikov, Dmitry Arkadievich

2017-01-27

There are many available software tools for visualization and analysis of biological networks. Among them, Cytoscape ( http://cytoscape.org/ ) is one of the most comprehensive packages, with many plugins and applications which extends its functionality by providing analysis of protein-protein interaction, gene regulatory and gene co-expression networks, metabolic, signaling, neural as well as ecological-type networks including food webs, communities networks etc. Nevertheless, only three plugins tagged 'network evolution' found in Cytoscape official app store and in literature. We have developed a new Cytoscape 3.0 application Orthoscape aimed to facilitate evolutionary analysis of gene networks and visualize the results. Orthoscape aids in analysis of evolutionary information available for gene sets and networks by highlighting: (1) the orthology relationships between genes; (2) the evolutionary origin of gene network components; (3) the evolutionary pressure mode (diversifying or stabilizing, negative or positive selection) of orthologous groups in general and/or branch-oriented mode. The distinctive feature of Orthoscape is the ability to control all data analysis steps via user-friendly interface. Orthoscape allows its users to analyze gene networks or separated gene sets in the context of evolution. At each step of data analysis, Orthoscape also provides for convenient visualization and data manipulation.

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

PubMed

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

2015-02-01

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

Evolutionary and genetic analysis of the VP2 gene of canine parvovirus.

PubMed

Li, Gairu; Ji, Senlin; Zhai, Xiaofeng; Zhang, Yuxiang; Liu, Jie; Zhu, Mengyan; Zhou, Jiyong; Su, Shuo

2017-07-17

Canine parvovirus (CPV) type 2 emerged in 1978 in the USA and quickly spread among dog populations all over the world with high morbidity. Although CPV is a DNA virus, its genomic substitution rate is similar to some RNA viruses. Therefore, it is important to trace the evolution of CPV to monitor the appearance of mutations that might affect vaccine effectiveness. Our analysis shows that the VP2 genes of CPV isolated from 1979 to 2016 are divided into six groups: GI, GII, GIII, GIV, GV, and GVI. Amino acid mutation analysis revealed several undiscovered important mutation sites: F267Y, Y324I, and T440A. Of note, the evolutionary rate of the CPV VP2 gene from Asia and Europe decreased. Codon usage analysis showed that the VP2 gene of CPV exhibits high bias with an ENC ranging from 34.93 to 36.7. Furthermore, we demonstrate that natural selection plays a major role compared to mutation pressure driving CPV evolution. There are few studies on the codon usage of CPV. Here, we comprehensively studied the genetic evolution, codon usage pattern, and evolutionary characterization of the VP2 gene of CPV. The novel findings revealing the evolutionary process of CPV will greatly serve future CPV research.

Darwinian demons, evolutionary complexity, and information maximization.

PubMed

Krakauer, David C

2011-09-01

Natural selection is shown to be an extended instance of a Maxwell's demon device. A demonic selection principle is introduced that states that organisms cannot exceed the complexity of their selective environment. Thermodynamic constraints on error repair impose a fundamental limit to the rate that information can be transferred from the environment (via the selective demon) to the genome. Evolved mechanisms of learning and inference can overcome this limitation, but remain subject to the same fundamental constraint, such that plastic behaviors cannot exceed the complexity of reward signals. A natural measure of evolutionary complexity is provided by mutual information, and niche construction activity--the organismal contribution to the construction of selection pressures--might in principle lead to its increase, bounded by thermodynamic free energy required for error correction.

The Evolutionary Histories of Antiretroviral Proteins SERINC3 and SERINC5 Do Not Support an Evolutionary Arms Race in Primates.

PubMed

Murrell, Ben; Vollbrecht, Thomas; Guatelli, John; Wertheim, Joel O

2016-09-15

Molecular evolutionary arms races between viruses and their hosts are important drivers of adaptation. These Red Queen dynamics have been frequently observed in primate retroviruses and their antagonists, host restriction factor genes, such as APOBEC3F/G, TRIM5-α, SAMHD1, and BST-2. Host restriction factors have experienced some of the most intense and pervasive adaptive evolution documented in primates. Recently, two novel host factors, SERINC3 and SERINC5, were identified as the targets of HIV-1 Nef, a protein crucial for the optimal infectivity of virus particles. Here, we compared the evolutionary fingerprints of SERINC3 and SERINC5 to those of other primate restriction factors and to a set of other genes with diverse functions. SERINC genes evolved in a manner distinct from the canonical arms race dynamics seen in the other restriction factors. Despite their antiviral activity against HIV-1 and other retroviruses, SERINC3 and SERINC5 have a relatively uneventful evolutionary history in primates. Restriction factors are host proteins that block viral infection and replication. Many viruses, like HIV-1 and related retroviruses, evolved accessory proteins to counteract these restriction factors. The importance of these interactions is evidenced by the intense adaptive selection pressures that dominate the evolutionary histories of both the host and viral genes involved in this so-called arms race. The dynamics of these arms races can point to mechanisms by which these viral infections can be prevented. Two human genes, SERINC3 and SERINC5, were recently identified as targets of an HIV-1 accessory protein important for viral infectivity. Unexpectedly, we found that these SERINC genes, unlike other host restriction factor genes, show no evidence of a recent evolutionary arms race with viral pathogens. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates

PubMed Central

Vrancken, Bram; Rambaut, Andrew; Suchard, Marc A.; Drummond, Alexei; Baele, Guy; Derdelinckx, Inge; Van Wijngaerden, Eric; Vandamme, Anne-Mieke; Van Laethem, Kristel; Lemey, Philippe

2014-01-01

Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the ‘store and retrieve’ hypothesis positing that viruses stored early in latently infected cells preferentially transmit or establish new infections upon reactivation. PMID:24699231

Phenotypic landscape inference reveals multiple evolutionary paths to C4 photosynthesis

PubMed Central

Williams, Ben P; Johnston, Iain G; Covshoff, Sarah; Hibberd, Julian M

2013-01-01

C4 photosynthesis has independently evolved from the ancestral C3 pathway in at least 60 plant lineages, but, as with other complex traits, how it evolved is unclear. Here we show that the polyphyletic appearance of C4 photosynthesis is associated with diverse and flexible evolutionary paths that group into four major trajectories. We conducted a meta-analysis of 18 lineages containing species that use C3, C4, or intermediate C3–C4 forms of photosynthesis to parameterise a 16-dimensional phenotypic landscape. We then developed and experimentally verified a novel Bayesian approach based on a hidden Markov model that predicts how the C4 phenotype evolved. The alternative evolutionary histories underlying the appearance of C4 photosynthesis were determined by ancestral lineage and initial phenotypic alterations unrelated to photosynthesis. We conclude that the order of C4 trait acquisition is flexible and driven by non-photosynthetic drivers. This flexibility will have facilitated the convergent evolution of this complex trait. DOI: http://dx.doi.org/10.7554/eLife.00961.001 PMID:24082995

Using protistan examples to dispel the myths of intelligent design.

PubMed

Farmer, Mark A; Habura, Andrea

2010-01-01

In recent years the teaching of the religiously based philosophy of intelligent design (ID) has been proposed as an alternative to modern evolutionary theory. Advocates of ID are largely motivated by their opposition to naturalistic explanations of biological diversity, in accordance with their goal of challenging the philosophy of scientific materialism. Intelligent design has been embraced by a wide variety of creationists who promote highly questionable claims that purport to show the inadequacy of evolutionary theory, which they consider to be a threat to a theistic worldview. We find that examples from protistan biology are well suited for providing evidence of many key evolutionary concepts, and have often been misrepresented or roundly ignored by ID advocates. These include examples of adaptations and radiations that are said to be statistically impossible, as well as examples of speciation both in the laboratory and as documented in the fossil record. Because many biologists may not be familiar with the richness of the protist evolution dataset or with ID-based criticisms of evolution, we provide examples of current ID arguments and specific protistan counter-examples.

Beyond Reasonable Doubt: Evolution from DNA Sequences

PubMed Central

Penny, David

2013-01-01

We demonstrate quantitatively that, as predicted by evolutionary theory, sequences of homologous proteins from different species converge as we go further and further back in time. The converse, a non-evolutionary model can be expressed as probabilities, and the test works for chloroplast, nuclear and mitochondrial sequences, as well as for sequences that diverged at different time depths. Even on our conservative test, the probability that chance could produce the observed levels of ancestral convergence for just one of the eight datasets of 51 proteins is ≈1×10−19 and combined over 8 datasets is ≈1×10−132. By comparison, there are about 1080 protons in the universe, hence the probability that the sequences could have been produced by a process involving unrelated ancestral sequences is about 1050 lower than picking, among all protons, the same proton at random twice in a row. A non-evolutionary control model shows no convergence, and only a small number of parameters are required to account for the observations. It is time that that researchers insisted that doubters put up testable alternatives to evolution. PMID:23950906

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.

Host association influences variation at salivary protein genes in the bat ectoparasite Cimex adjunctus.

PubMed

Talbot, Benoit; Vonhof, Maarten J; Broders, Hugh G; Fenton, Brock; Keyghobadi, Nusha

2018-05-01

Parasite-host relationships create strong selection pressures that can lead to adaptation and increasing specialization of parasites to their hosts. Even in relatively loose host-parasite relationships, such as between generalist ectoparasites and their hosts, we may observe some degree of specialization of parasite populations to one of the multiple potential hosts. Salivary proteins are used by blood-feeding ectoparasites to prevent hemostasis in the host and maximize energy intake. We investigated the influence of association with specific host species on allele frequencies of salivary protein genes in Cimex adjunctus, a generalist blood-feeding ectoparasite of bats in North America. We analysed two salivary protein genes: an apyrase, which hydrolyses ATP at the feeding site and thus inhibits platelet aggregation, and a nitrophorin, which brings nitrous oxide to the feeding site, inhibiting platelet aggregation and vasoconstriction. We observed more variation at both salivary protein genes among parasite populations associated with different host species than among populations from different spatial locations associated with the same host species. The variation in salivary protein genes among populations on different host species was also greater than expected under a neutral scenario of genetic drift and gene flow. Finally, host species was an important predictor of allelic divergence in genotypes of individual C. adjunctus at both salivary protein genes. Our results suggest differing selection pressures on these two salivary protein genes in C. adjunctus depending on the host species. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Migrate small, sound big: functional constraints on body size promote tracheal elongation in cranes.

PubMed

Jones, M R; Witt, C C

2014-06-01

Organismal traits often represent the outcome of opposing selection pressures. Although social or sexual selection can cause the evolution of traits that constrain function or survival (e.g. ornamental feathers), it is unclear how the strength and direction of selection respond to ecological shifts that increase the severity of the constraint. For example, reduced body size might evolve by natural selection to enhance flight performance in migratory birds, but social or sexual selection favouring large body size may provide a countervailing force. Tracheal elongation is a potential outcome of these opposing pressures because it allows birds to convey an auditory signal of exaggerated body size. We predicted that the evolution of migration in cranes has coincided with a reduction in body size and a concomitant intensification of social or sexual selection for apparent large body size via tracheal elongation. We used a phylogenetic comparative approach to examine the relationships among migration distance, body mass and trachea length in cranes. As predicted, we found that migration distance correlated negatively with body size and positively with proportional trachea length. This result was consistent with our hypothesis that evolutionary reductions in body size led to intensified selection for trachea length. The most likely ultimate causes of intensified positive selection on trachea length are the direct benefits of conveying a large body size in intraspecific contests for mates and territories. We conclude that the strength of social or sexual selection on crane body size is linked to the degree of functional constraint. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

The influence of space and time on the evolution of altruistic defence: the case of ant slave rebellion.

PubMed

Metzler, D; Jordan, F; Pamminger, T; Foitzik, S

2016-05-01

How can antiparasite defence traits evolve even if they do not directly benefit their carriers? An example of such an indirect defence is rebellion of enslaved Temnothorax longispinosus ant workers against their social parasite Temnothorax americanus, a slavemaking ant. Ant slaves have been observed to kill their oppressors' offspring, a behaviour from which the sterile slaves cannot profit directly. Parasite brood killing could, however, reduce raiding pressure on related host colonies nearby. We analyse with extensive computer simulations for the Temnothorax slavemaker system under what conditions a hypothetical rebel allele could invade a host population, and in particular, how host-parasite dynamics and population structure influence the rebel allele's success. Exploring a wide range of model parameters, we only found a small number of parameter combinations for which kin selection or multilevel selection could allow a slave rebellion allele to spread in the host population. Furthermore, we did not detect any cases in which the reduction of raiding pressure in the close vicinity of the slavemaker nest would substantially contribute to the inclusive fitness of rebels. This suggests that slave rebellion is not costly and perhaps a side-effect of some other beneficial trait. In some of our simulations, however, even a costly rebellion allele could spread in the population. This was possible when host-parasite interactions led to a metapopulation dynamic with frequent local extinctions and recolonizations of demes by the offspring of few immigrants. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition

PubMed Central

Lefébure, Tristan; Stanhope, Michael J

2007-01-01

Background The genus Streptococcus is one of the most diverse and important human and agricultural pathogens. This study employs comparative evolutionary analyses of 26 Streptococcus genomes to yield an improved understanding of the relative roles of recombination and positive selection in pathogen adaptation to their hosts. Results Streptococcus genomes exhibit extreme levels of evolutionary plasticity, with high levels of gene gain and loss during species and strain evolution. S. agalactiae has a large pan-genome, with little recombination in its core-genome, while S. pyogenes has a smaller pan-genome and much more recombination of its core-genome, perhaps reflecting the greater habitat, and gene pool, diversity for S. agalactiae compared to S. pyogenes. Core-genome recombination was evident in all lineages (18% to 37% of the core-genome judged to be recombinant), while positive selection was mainly observed during species differentiation (from 11% to 34% of the core-genome). Positive selection pressure was unevenly distributed across lineages and biochemical main role categories. S. suis was the lineage with the greatest level of positive selection pressure, the largest number of unique loci selected, and the largest amount of gene gain and loss. Conclusion Recombination is an important evolutionary force in shaping Streptococcus genomes, not only in the acquisition of significant portions of the genome as lineage specific loci, but also in facilitating rapid evolution of the core-genome. Positive selection, although undoubtedly a slower process, has nonetheless played an important role in adaptation of the core-genome of different Streptococcus species to different hosts. PMID:17475002

Cost-effectiveness of pressure-relieving devices for the prevention and treatment of pressure ulcers.

PubMed

Fleurence, Rachael L

2005-01-01

The cost-effectiveness of alternating pressure-relieving devices, mattress replacements, and mattress overlays compared with a standard hospital (high-specification foam mattress) for the prevention and treatment of pressure ulcers in hospital patients in the United Kingdom was investigated. A decision-analytic model was constructed to evaluate different strategies to prevent or treat pressure ulcers. Three scenarios were evaluated: the prevention of pressure ulcers, the treatment of superficial ulcers, and the treatment of severe ulcers. Epidemiological and effectiveness data were obtained from the clinical literature. Expert opinion using a rating scale technique was used to obtain quality of life data. Costs of the devices were obtained from manufacturers, whereas costs of treatment were obtained from the literature. Uncertainty was explored through probabilistic sensitivity analysis. Using 30,000 pounds sterling/QALY (quality-adjusted life year) as the decision-maker's cut off point (the current UK standard), in scenario 1 (prevention), the cost-effective strategy was the mattress overlay at 1, 4, and 12 weeks. In scenarios 2 and 3, the cost-effective strategy was the mattress replacement at 1, 4, and 12 weeks. Standard care was a dominated intervention in all scenarios for values of the decision-maker's ceiling ratio ranging from 5,000 pounds sterling to 100,000 pounds sterling/QALY. However, the probabilistic sensitivity analysis results reflected the high uncertainty surrounding the choice of devices. Current information suggests that alternating pressure mattress overlays may be cost-effective for the prevention of pressure ulcers, whereas alternating pressure mattress replacements appears to be cost-effective for the treatment of superficial and severe pressure ulcers.

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

PubMed

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

2014-03-01

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

Constraining free riding in public goods games: designated solitary punishers can sustain human cooperation

PubMed Central

O'Gorman, Rick; Henrich, Joseph; Van Vugt, Mark

2008-01-01

Much of human cooperation remains an evolutionary riddle. Unlike other animals, people frequently cooperate with non-relatives in large groups. Evolutionary models of large-scale cooperation require not just incentives for cooperation, but also a credible disincentive for free riding. Various theoretical solutions have been proposed and experimentally explored, including reputation monitoring and diffuse punishment. Here, we empirically examine an alternative theoretical proposal: responsibility for punishment can be borne by one specific individual. This experiment shows that allowing a single individual to punish increases cooperation to the same level as allowing each group member to punish and results in greater group profits. These results suggest a potential key function of leadership in human groups and provides further evidence supporting that humans will readily and knowingly behave altruistically. PMID:18812292

Information in the Biosphere: Biological and Digital Worlds.

PubMed

Gillings, Michael R; Hilbert, Martin; Kemp, Darrell J

2016-03-01

Evolution has transformed life through key innovations in information storage and replication, including RNA, DNA, multicellularity, and culture and language. We argue that the carbon-based biosphere has generated a cognitive system (humans) capable of creating technology that will result in a comparable evolutionary transition. Digital information has reached a similar magnitude to information in the biosphere. It increases exponentially, exhibits high-fidelity replication, evolves through differential fitness, is expressed through artificial intelligence (AI), and has facility for virtually limitless recombination. Like previous evolutionary transitions, the potential symbiosis between biological and digital information will reach a critical point where these codes could compete via natural selection. Alternatively, this fusion could create a higher-level superorganism employing a low-conflict division of labor in performing informational tasks. Copyright © 2015 Elsevier Ltd. All rights reserved.

Phylogeny of lion tamarins (Leontopithecus spp) based on interphotoreceptor retinol binding protein intron sequences.

PubMed

Mundy, N I; Kelly, J

2001-05-01

The evolutionary relationships of the lion tamarins (Leontopithecus) were investigated using nuclear interphotoreceptor retinol binding protein (IRBP) intron sequences. Phylogenetic reconstructions strongly support the monophyly of the genus, and a sister relationship between the golden lion tamarin, Leontopithecus rosalia, and the black lion tamarin, L. chrysopygus, to the exclusion of the golden-headed lion tamarin, L. chrysomelas. The most parsimonious evolutionary reconstruction suggests that the ancestral lion tamarin and the common ancestor of L. rosalia and L. chrysopygus had predominantly black coats. This reconstruction is not consistent with a theory of orthogenetic evolution of coat color that was based on coat color evolution in marmosets and tamarins. An alternative reconstruction that is consistent with metachromism requires that ancestral lion tamarins had agouti hairs. Copyright 2001 Wiley-Liss, Inc.

Gender differences in erotic plasticity--evolutionary or sociocultural forces? Comment on Baumeister (2000)

PubMed

Hyde, J S; Durik, A M

2000-05-01

R. F. Baumeister (2000) argued that there are gender differences in erotic plasticity, meaning that women are more influenced by cultural and social factors than men are. He attributed the gender difference in erotic plasticity to evolutionary, biological forces. We propose an alternative account of the data using a multifactor sociocultural model that rests on 4 assertions: (a) Men have more power than women on many levels including the institutional and the interpersonal levels, (b) education increases women's power, (c) groups with less power (women) pay more attention to and adapt their behavior more to the group with more power (men) than the reverse, and (d) gender roles powerfully shape behavior, and heterosexuality is a more important element of the male role than the female role.

Alternative thermodynamic cycle for the Stirling machine

NASA Astrophysics Data System (ADS)

Romanelli, Alejandro

2017-12-01

We develop an alternative thermodynamic cycle for the Stirling machine, where the polytropic process plays a central role. Analytical expressions for pressure and temperatures of the working gas are obtained as a function of the volume and the parameter that characterizes the polytropic process. This approach achieves closer agreement with the experimental pressure-volume diagram and can be adapted to any type of Stirling engine.

A Step-by-Step Design Methodology for a Base Case Vanadium Redox-Flow Battery

ERIC Educational Resources Information Center

Moore, Mark; Counce, Robert M.; Watson, Jack S.; Zawodzinski, Thomas A.; Kamath, Haresh

2012-01-01

The purpose of this work is to develop an evolutionary procedure to be used by Chemical Engineering students for the base-case design of a Vanadium Redox-Flow Battery. The design methodology is based on the work of Douglas (1985) and provides a profitability analysis at each decision level so that more profitable alternatives and directions can be…

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

Cacciari, C.; Clementini, G.

Attention is given to the folowing topics: population I and II variable stars; LP variables, the sun, and mass determination; and predegenerate and degenerate variables. Particular papers are presented on alternative evolutionary approaches to the absolute magnitude of the RR Lyrae variables; the evolution of the Cepheid stars; nonradial pulsations in rapidly rotating Delta Scuti stars; dynamical models of dust shells around Mira variables; and pulsations of central stars of planetary nebulae.

A classification scheme for alternative oxidases reveals the taxonomic distribution and evolutionary history of the enzyme in angiosperms.

PubMed

Costa, José Hélio; McDonald, Allison E; Arnholdt-Schmitt, Birgit; Fernandes de Melo, Dirce

2014-11-01

A classification scheme based on protein phylogenies and sequence harmony method was used to clarify the taxonomic distribution and evolutionary history of the alternative oxidase (AOX) in angiosperms. A large data set analyses showed that AOX1 and AOX2 subfamilies were distributed into 4 phylogenetic clades: AOX1a-c/1e, AOX1d, AOX2a-c and AOX2d. High diversity in AOX family compositions was found. While the AOX2 subfamily was not detected in monocots, the AOX1 subfamily has expanded (AOX1a-e) in the large majority of these plants. In addition, Poales AOX1b and 1d were orthologous to eudicots AOX1d and then renamed as AOX1d1 and 1d2. AOX1 or AOX2 losses were detected in some eudicot plants. Several AOX2 duplications (AOX2a-c) were identified in eudicot species, mainly in the asterids. The AOX2b originally identified in eudicots in the Fabales order (soybean, cowpea) was divergent from AOX2a-c showing some specific amino acids with AOX1d and then it was renamed as AOX2d. AOX1d and AOX2d seem to be stress-responsive, facultative and mutually exclusive among species suggesting a complementary role with an AOX1(a) in stress conditions. Based on the data collected, we present a model for the evolutionary history of AOX in angiosperms and highlight specific areas where further research would be most beneficial. Copyright © 2014 Elsevier B.V. All rights reserved.

God, the Devil, and Darwin - A Critique of Intelligent Design Theory

NASA Astrophysics Data System (ADS)

Shanks, Niall

2007-03-01

In the last fifteen years a controversial new theory of the origins of biological complexity and the nature of the universe has been fomenting bitter debates in education and science policy across North America, Europe, and Australia. Backed by intellectuals at respectable universities, Intelligent Design theory (ID) proposes an alternative to accepted accounts of evolutionary theory: that life is so complex, and that the universe is so fine-tuned for the appearance of life, that the only plausible explanation is the existence of an intelligent designer. For many ID theorists, the designer is taken to be the god of Christianity. Niall Shanks has written the first accessible introduction to, and critique of, this controversial new intellectual movement. Shanks locates the growth of ID in the last two decades of the twentieth century in the growing influence of the American religious right. But as he shows, its roots go back beyond Aquinas to Ancient Greece. After looking at the historical roots of ID, Shanks takes a hard look at its intellectual underpinnings, discussing modern understandings of thermodynamics, and how self-organizing processes lead to complex physical, chemical, and biological systems. He considers cosmological arguments for ID rooted in so-called "anthropic coincidences" and also tackles new biochemical arguments for ID based on "irreducible biological complexity." Throughout he shows how arguments for ID lack cohesion, rest on errors and unfounded suppositions, and generally are grossly inferior to evolutionary explanations. While ID has been proposed as a scientific alternative to evolutionary biology, Shanks argues that ID is in fact "old creationist wine in new designer label bottles" and moreover is a serious threat to the scientific and democratic values that are our cultural and intellectual inheritance from the Enlightenment.

Co-evolutionary interactions between host resistance and pathogen avirulence genes in rice-Magnaporthe oryzae pathosystem.

PubMed

Singh, Pankaj Kumar; Ray, Soham; Thakur, Shallu; Rathour, Rajeev; Sharma, Vinay; Sharma, Tilak Raj

2018-06-01

Rice and Magnaporthe oryzae constitutes an ideal pathosystem for studying host-pathogen interaction in cereals crops. There are two alternative hypotheses, viz. Arms race and Trench warfare, which explain the co-evolutionary dynamics of hosts and pathogens which are under continuous confrontation. Arms race proposes that both R- and Avr- genes of host and pathogen, respectively, undergo positive selection. Alternatively, trench warfare suggests that either R- or Avr- gene in the pathosystem is under balanced selection intending to stabilize the genetic advantage gained over the opposition. Here, we made an attempt to test the above-stated hypotheses in rice-M. oryzae pathosystem at loci of three R-Avr gene pairs, Piz-t-AvrPiz-t, Pi54-AvrPi54 and Pita-AvrPita using allele mining approach. Allele mining is an efficient way to capture allelic variants existing in the population and to study the selective forces imposed on the variants during evolution. Results of nucleotide diversity, neutrality statistics and phylogenetic analyses reveal that Piz-t, Pi54 and AvrPita are diversified and under positive selection at their corresponding loci, while their counterparts, AvrPiz-t, AvrPi54 and Pita are conserved and under balancing selection, in nature. These results imply that rice-M. oryzae populations are engaged in a trench warfare at least at the three R/Avr loci studied. It is a maiden attempt to study the co-evolution of three R-Avr gene pairs in this pathosystem. Knowledge gained from this study will help in understanding the evolutionary dynamics of host-pathogen interaction in a better way and will also aid in developing new durable blast resistant rice varieties in future. Copyright © 2018 Elsevier Inc. All rights reserved.

A New Strategy to Control and Eradicate "Undruggable" Oncogenic K-RAS-Driven Pancreatic Cancer: Molecular Insights and Core Principles Learned from Developmental and Evolutionary Biology.

PubMed

Van Sciver, Robert E; Lee, Michael P; Lee, Caroline Dasom; Lafever, Alex C; Svyatova, Elizaveta; Kanda, Kevin; Colliver, Amber L; Siewertsz van Reesema, Lauren L; Tang-Tan, Angela M; Zheleva, Vasilena; Bwayi, Monicah N; Bian, Minglei; Schmidt, Rebecca L; Matrisian, Lynn M; Petersen, Gloria M; Tang, Amy H

2018-05-14

Oncogenic K-RAS mutations are found in virtually all pancreatic cancers, making K-RAS one of the most targeted oncoproteins for drug development in cancer therapies. Despite intense research efforts over the past three decades, oncogenic K-RAS has remained largely "undruggable". Rather than targeting an upstream component of the RAS signaling pathway (i.e., EGFR/HER2) and/or the midstream effector kinases (i.e., RAF/MEK/ERK/PI3K/mTOR), we propose an alternative strategy to control oncogenic K-RAS signal by targeting its most downstream signaling module, Seven-In-Absentia Homolog (SIAH). SIAH E3 ligase controls the signal output of oncogenic K-RAS hyperactivation that drives unchecked cell proliferation, uncontrolled tumor growth, and rapid cancer cell dissemination in human pancreatic cancer. Therefore, SIAH is an ideal therapeutic target as it is an extraordinarily conserved downstream signaling gatekeeper indispensable for proper RAS signaling. Guided by molecular insights and core principles obtained from developmental and evolutionary biology, we propose an anti-SIAH-centered anti-K-RAS strategy as a logical and alternative anticancer strategy to dampen uncontrolled K-RAS hyperactivation and halt tumor growth and metastasis in pancreatic cancer. The clinical utility of developing SIAH as both a tumor-specific and therapy-responsive biomarker, as well as a viable anti-K-RAS drug target, is logically simple and conceptually innovative. SIAH clearly constitutes a major tumor vulnerability and K-RAS signaling bottleneck in pancreatic ductal adenocarcinoma (PDAC). Given the high degree of evolutionary conservation in the K-RAS/SIAH signaling pathway, an anti-SIAH-based anti-PDAC therapy will synergize with covalent K-RAS inhibitors and direct K-RAS targeted initiatives to control and eradicate pancreatic cancer in the future.

Effects of ovarian fluid and genetic differences on sperm performance and fertilization success of alternative reproductive tactics in Chinook salmon.

PubMed

Lehnert, S J; Butts, I A E; Flannery, E W; Peters, K M; Heath, D D; Pitcher, T E

2017-06-01

In many species, sperm velocity affects variation in the outcome of male competitive fertilization success. In fishes, ovarian fluid (OF) released with the eggs can increase male sperm velocity and potentially facilitate cryptic female choice for males of specific phenotypes and/or genotypes. Therefore, to investigate the effect of OF on fertilization success, we measured sperm velocity and conducted in vitro competitive fertilizations with paired Chinook salmon (Oncorhynchus tshawytscha) males representing two alternative reproductive tactics, jacks (small sneaker males) and hooknoses (large guarding males), in the presence of river water alone and OF mixed with river water. To determine the effect of genetic differences on fertilization success, we genotyped fish at neutral (microsatellites) and functional [major histocompatibility complex (MHC) II ß1] markers. We found that when sperm were competed in river water, jacks sired significantly more offspring than hooknoses; however, in OF, there was no difference in paternity between the tactics. Sperm velocity was significantly correlated with paternity success in river water, but not in ovarian fluid. Paternity success in OF, but not in river water alone, was correlated with genetic relatedness between male and female, where males that were less related to the female attained greater paternity. We found no relationship between MHC II ß1 divergence between mates and paternity success in water or OF. Our results indicate that OF can influence the outcome of sperm competition in Chinook salmon, where OF provides both male tactics with fertilization opportunities, which may in part explain what maintains both tactics in nature. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Vapor Pressure Measurements in a Closed System

ERIC Educational Resources Information Center

Iannone, Mark

2006-01-01

An alternative method that uses a simple apparatus to measure vapor pressure versus temperature in a closed system, in which the total pressure is the vapor pressure of the liquid sample, is described. The use of this apparatus gives students a more direct picture of vapor pressure than the isoteniscope method and results have generally been quite…

When everything is not everywhere but species evolve: an alternative method to model adaptive properties of marine ecosystems

PubMed Central

Sauterey, Boris; Ward, Ben A.; Follows, Michael J.; Bowler, Chris; Claessen, David

2015-01-01

The functional and taxonomic biogeography of marine microbial systems reflects the current state of an evolving system. Current models of marine microbial systems and biogeochemical cycles do not reflect this fundamental organizing principle. Here, we investigate the evolutionary adaptive potential of marine microbial systems under environmental change and introduce explicit Darwinian adaptation into an ocean modelling framework, simulating evolving phytoplankton communities in space and time. To this end, we adopt tools from adaptive dynamics theory, evaluating the fitness of invading mutants over annual timescales, replacing the resident if a fitter mutant arises. Using the evolutionary framework, we examine how community assembly, specifically the emergence of phytoplankton cell size diversity, reflects the combined effects of bottom-up and top-down controls. When compared with a species-selection approach, based on the paradigm that “Everything is everywhere, but the environment selects”, we show that (i) the selected optimal trait values are similar; (ii) the patterns emerging from the adaptive model are more robust, but (iii) the two methods lead to different predictions in terms of emergent diversity. We demonstrate that explicitly evolutionary approaches to modelling marine microbial populations and functionality are feasible and practical in time-varying, space-resolving settings and provide a new tool for exploring evolutionary interactions on a range of timescales in the ocean. PMID:25852217

When everything is not everywhere but species evolve: an alternative method to model adaptive properties of marine ecosystems.

PubMed

Sauterey, Boris; Ward, Ben A; Follows, Michael J; Bowler, Chris; Claessen, David

2015-01-01

The functional and taxonomic biogeography of marine microbial systems reflects the current state of an evolving system. Current models of marine microbial systems and biogeochemical cycles do not reflect this fundamental organizing principle. Here, we investigate the evolutionary adaptive potential of marine microbial systems under environmental change and introduce explicit Darwinian adaptation into an ocean modelling framework, simulating evolving phytoplankton communities in space and time. To this end, we adopt tools from adaptive dynamics theory, evaluating the fitness of invading mutants over annual timescales, replacing the resident if a fitter mutant arises. Using the evolutionary framework, we examine how community assembly, specifically the emergence of phytoplankton cell size diversity, reflects the combined effects of bottom-up and top-down controls. When compared with a species-selection approach, based on the paradigm that "Everything is everywhere, but the environment selects", we show that (i) the selected optimal trait values are similar; (ii) the patterns emerging from the adaptive model are more robust, but (iii) the two methods lead to different predictions in terms of emergent diversity. We demonstrate that explicitly evolutionary approaches to modelling marine microbial populations and functionality are feasible and practical in time-varying, space-resolving settings and provide a new tool for exploring evolutionary interactions on a range of timescales in the ocean.

Evolutionary Effect on the Embodied Beauty of Landscape Architectures.

PubMed

Zhang, Wei; Tang, Xiaoxiang; He, Xianyou; Chen, Guangyao

2018-01-01

According to the framework of evolutionary aesthetics, a sense of beauty is related to environmental adaptation and plasticity of human beings, which has adaptive value and biological foundations. Prior studies have demonstrated that organisms derive benefits from the landscape. In this study, we investigated whether the benefits of landscape might elicit a stronger sense of beauty and what the nature of this sense of beauty is. In two experiments, when viewing classical landscape and nonlandscape architectures photographs, participants rated the aesthetic scores (Experiment 1) and had a two-alternative forced choice aesthetic judgment by pressing the reaction button located near to (15 cm) or far from (45 cm) the presenting stimuli (Experiment 2). The results showed that reaction of aesthetic ratings for classical landscape architectures was faster than those of classical nonlandscape architectures. Furthermore, only the reaction of beautiful judgment of classical landscape architecture photograph was significantly faster when the reaction button was in the near position to the presenting photograph than those in the position of far away from the presenting photograph. This finding suggests a facilitated effect for the aesthetic perception of classical landscape architectures due to their corresponding components including water and green plants with strong evolutionary implications. Furthermore, this sense of beauty for classical landscape architectures might be the embodied approach to beauty based on the viewpoint of evolutionary aesthetics and embodied cognition.

Evolutionary effects of alternative artificial propagation programs: implications for viability of endangered anadromous salmonids

PubMed Central

McClure, Michelle M; Utter, Fred M; Baldwin, Casey; Carmichael, Richard W; Hassemer, Peter F; Howell, Philip J; Spruell, Paul; Cooney, Thomas D; Schaller, Howard A; Petrosky, Charles E

2008-01-01

Most hatchery programs for anadromous salmonids have been initiated to increase the numbers of fish for harvest, to mitigate for habitat losses, or to increase abundance in populations at low abundance. However, the manner in which these programs are implemented can have significant impacts on the evolutionary trajectory and long-term viability of populations. In this paper, we review the potential benefits and risks of hatchery programs relative to the conservation of species listed under the US Endangered Species Act. To illustrate, we present the range of potential effects within a population as well as among populations of Chinook salmon (Oncorhynchus tshawytscha) where changes to major hatchery programs are being considered. We apply evolutionary considerations emerging from these examples to suggest broader principles for hatchery uses that are consistent with conservation goals. We conclude that because of the evolutionary risks posed by artificial propagation programs, they should not be viewed as a substitute for addressing other limiting factors that prevent achieving viability. At the population level, artificial propagation programs that are implemented as a short-term approach to avoid imminent extinction are more likely to achieve long-term population viability than approaches that rely on long-term supplementation. In addition, artificial propagation programs can have out-of-population impacts that should be considered in conservation planning. PMID:25567637

Boron monosulfide: Equation of state and pressure-induced phase transition

NASA Astrophysics Data System (ADS)

Cherednichenko, K. A.; Kruglov, I. A.; Oganov, A. R.; Le Godec, Y.; Mezouar, M.; Solozhenko, V. L.

2018-04-01

Quasi-hydrostatic compression of rhombohedral boron monosulfide (r-BS) has been studied up to 50 GPa at room temperature using diamond-anvil cells and angle-dispersive synchrotron X-ray diffraction. A fit of the experimental P-V data to the Vinet equation of state yields the bulk modulus B0 of 42.2(1.4) GPa and its first pressure derivative B0' of 7.6(2) that are in excellent agreement with our ab initio calculations. Formation of a new high-pressure phase of boron monosulfide (hp-BS) has been observed above 35 GPa. According to ab initio evolutionary crystal structure predictions combined with Rietveld refinement of high-pressure X-ray diffraction data, the structure of hp-BS has trigonal symmetry and belongs to the space group P-3m1. As it follows from the electron density of state calculations, the phase transformation is accompanied by an insulator-metal transition.

A stable compound of helium and sodium at high pressure

DOE PAGES

Dong, Xiao; Oganov, Artem R.; Goncharov, Alexander F.; ...

2017-02-06

Helium is generally understood to be chemically inert and this is due to its extremely stable closed-shell electronic configuration, zero electron affinity and an unsurpassed ionization potential. It is not known to form thermodynamically stable compounds, except a few inclusion compounds. Here, using the ab initio evolutionary algorithm USPEX and subsequent high-pressure synthesis in a diamond anvil cell, we report the discovery of a thermodynamically stable compound of helium and sodium, Na 2He, which has a fluorite-type structure and is stable at pressures >113 GPa. We show that the presence of He atoms causes strong electron localization and makes thismore » material insulating. This phase is an electride, with electron pairs localized in interstices, forming eight-centre two-electron bonds within empty Na 8 cubes. As a result, we also predict the existence of Na 2HeO with a similar structure at pressures above 15 GPa.« less

A stable compound of helium and sodium at high pressure

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

Dong, Xiao; Oganov, Artem R.; Goncharov, Alexander F.

Helium is generally understood to be chemically inert and this is due to its extremely stable closed-shell electronic configuration, zero electron affinity and an unsurpassed ionization potential. It is not known to form thermodynamically stable compounds, except a few inclusion compounds. Here, using the ab initio evolutionary algorithm USPEX and subsequent high-pressure synthesis in a diamond anvil cell, we report the discovery of a thermodynamically stable compound of helium and sodium, Na 2He, which has a fluorite-type structure and is stable at pressures >113 GPa. We show that the presence of He atoms causes strong electron localization and makes thismore » material insulating. This phase is an electride, with electron pairs localized in interstices, forming eight-centre two-electron bonds within empty Na 8 cubes. We also predict the existence of Na 2HeO with a similar structure at pressures above 15 GPa.« less

A stable compound of helium and sodium at high pressure

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

Dong, Xiao; Oganov, Artem R.; Goncharov, Alexander F.

Helium is generally understood to be chemically inert and this is due to its extremely stable closed-shell electronic configuration, zero electron affinity and an unsurpassed ionization potential. It is not known to form thermodynamically stable compounds, except a few inclusion compounds. Here, using the ab initio evolutionary algorithm USPEX and subsequent high-pressure synthesis in a diamond anvil cell, we report the discovery of a thermodynamically stable compound of helium and sodium, Na 2He, which has a fluorite-type structure and is stable at pressures >113 GPa. We show that the presence of He atoms causes strong electron localization and makes thismore » material insulating. This phase is an electride, with electron pairs localized in interstices, forming eight-centre two-electron bonds within empty Na 8 cubes. As a result, we also predict the existence of Na 2HeO with a similar structure at pressures above 15 GPa.« less

CJ concept for advanced aircraft wiring

NASA Technical Reports Server (NTRS)

Redslob, J.

1972-01-01

The techniques and hardware are described which were developed for facilitating the use of flexible flat conductor cable (FFCC) in commercial air transports. The system was designed as an evolutionary transition from the current round wire harnessing to the use of FFCC harnesses. The equipment discussed includes the pressure crimp barrel designed for terminating FFCC, reel-fed applicator, cable connectors and adaptors, and equipment racks.

Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses

USDA-ARS?s Scientific Manuscript database

Two opposing evolutionary constraints exert pressure on pathogens: one to diversify virulence factors in order to evade host defenses, and the other to retain virulence factors critical for maintaining a compatible interaction. To better understand how the diversified arsenals of fungal genes promot...

75 FR 10410 - Alternate Fracture Toughness Requirements for Protection Against Pressurized Thermal Shock Events...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-08

... Toughness Requirements for Protection Against Pressurized Thermal Shock Events; Correcting Amendment AGENCY... Commission (NRC) is revising its regulations to add a table that was inadvertently omitted in a correction... toughness requirements for protection against pressurized thermal shock (PTS) events for pressurized water...

Modeling and measurements of XRD spectra of extended solids under high pressure

NASA Astrophysics Data System (ADS)

Batyrev, I. G.; Coleman, S. P.; Stavrou, E.; Zaug, J. M.; Ciezak-Jenkins, J. A.

2017-06-01

We present results of evolutionary simulations based on density functional calculations of various extended solids: N-Si and N-H using variable and fixed concentration methods of USPEX. Predicted from the evolutionary simulations structures were analyzed in terms of thermo-dynamical stability and agreement with experimental X-ray diffraction spectra. Stability of the predicted system was estimated from convex-hull plots. X-ray diffraction spectra were calculated using a virtual diffraction algorithm which computes kinematic diffraction intensity in three-dimensional reciprocal space before being reduced to a two-theta line profile. Calculations of thousands of XRD spectra were used to search for a structure of extended solids at certain pressures with best fits to experimental data according to experimental XRD peak position, peak intensity and theoretically calculated enthalpy. Comparison of Raman and IR spectra calculated for best fitted structures with available experimental data shows reasonable agreement for certain vibration modes. Part of this work was performed by LLNL, Contract DE-AC52-07NA27344. We thank the Joint DoD / DOE Munitions Technology Development Program, the HE C-II research program at LLNL and Advanced Light Source, supported by BES DOE, Contract No. DE-AC02-05CH112.

Evolutionary pulsational mode dynamics in nonthermal turbulent viscous astrofluids

NASA Astrophysics Data System (ADS)

Karmakar, Pralay Kumar; Dutta, Pranamika

2017-11-01

The pulsational mode of gravitational collapse in a partially ionized self-gravitating inhomogeneous viscous nonthermal nonextensive astrofluid in the presence of turbulence pressure is illustratively analyzed. The constitutive thermal species, lighter electrons and ions, are thermostatistically treated with the nonthermal κ-distribution laws. The inertial species, such as identical heavier neutral and charged dust microspheres, are modelled in the turbulent fluid framework. All the possible linear processes responsible for dust-dust collisions are accounted. The Larson logatropic equations of state relating the dust thermal (linear) and turbulence (nonlinear) pressures with dust densities are included. A regular linear normal perturbation analysis (local) over the complex astrocloud ensues in a generalized quartic dispersion relation with unique nature of plasma-dependent multi-parametric coefficients. A numerical standpoint is provided to showcase the basic mode features in a judicious astronomical paradigm. It is shown that both the kinematic viscosity of the dust fluids and nonthermality parameter (kappa, the power-law tail index) of the thermal species act as stabilizing (damping) agent against the gravity; and so forth. The underlying evolutionary microphysics is explored. The significance of redistributing astrofluid material via waveinduced accretion in dynamic nonhomologic structureless cloud collapse leading to hierarchical astrostructure formation is actualized.

Language at Three Timescales: The Role of Real-Time Processes in Language Development and Evolution.

PubMed

McMurray, Bob

2016-04-01

Evolutionary developmental systems (evo-devo) theory stresses that selection pressures operate on entire developmental systems rather than just genes. This study extends this approach to language evolution, arguing that selection pressure may operate on two quasi-independent timescales. First, children clearly must acquire language successfully (as acknowledged in traditional evo-devo accounts) and evolution must equip them with the tools to do so. Second, while this is developing, they must also communicate with others in the moment using partially developed knowledge. These pressures may require different solutions, and their combination may underlie the evolution of complex mechanisms for language development and processing. I present two case studies to illustrate how the demands of both real-time communication and language acquisition may be subtly different (and interact). The first case study examines infant-directed speech (IDS). A recent view is that IDS underwent cultural to statistical learning mechanisms that infants use to acquire the speech categories of their language. However, recent data suggest is it may not have evolved to enhance development, but rather to serve a more real-time communicative function. The second case study examines the argument for seemingly specialized mechanisms for learning word meanings (e.g., fast-mapping). Both behavioral and computational work suggest that learning may be much slower and served by general-purpose mechanisms like associative learning. Fast-mapping, then, may be a real-time process meant to serve immediate communication, not learning, by augmenting incomplete vocabulary knowledge with constraints from the current context. Together, these studies suggest that evolutionary accounts consider selection pressure arising from both real-time communicative demands and from the need for accurate language development. Copyright © 2016 Cognitive Science Society, Inc.

Comparative Transcriptomes and EVO-DEVO Studies Depending on Next Generation Sequencing.

PubMed

Liu, Tiancheng; Yu, Lin; Liu, Lei; Li, Hong; Li, Yixue

2015-01-01

High throughput technology has prompted the progressive omics studies, including genomics and transcriptomics. We have reviewed the improvement of comparative omic studies, which are attributed to the high throughput measurement of next generation sequencing technology. Comparative genomics have been successfully applied to evolution analysis while comparative transcriptomics are adopted in comparison of expression profile from two subjects by differential expression or differential coexpression, which enables their application in evolutionary developmental biology (EVO-DEVO) studies. EVO-DEVO studies focus on the evolutionary pressure affecting the morphogenesis of development and previous works have been conducted to illustrate the most conserved stages during embryonic development. Old measurements of these studies are based on the morphological similarity from macro view and new technology enables the micro detection of similarity in molecular mechanism. Evolutionary model of embryo development, which includes the "funnel-like" model and the "hourglass" model, has been evaluated by combination of these new comparative transcriptomic methods with prior comparative genomic information. Although the technology has promoted the EVO-DEVO studies into a new era, technological and material limitation still exist and further investigations require more subtle study design and procedure.

Plastic and evolutionary responses to climate change in fish

PubMed Central

Crozier, Lisa G; Hutchings, Jeffrey A

2014-01-01

The physical and ecological ‘fingerprints’ of anthropogenic climate change over the past century are now well documented in many environments and taxa. We reviewed the evidence for phenotypic responses to recent climate change in fish. Changes in the timing of migration and reproduction, age at maturity, age at juvenile migration, growth, survival and fecundity were associated primarily with changes in temperature. Although these traits can evolve rapidly, only two studies attributed phenotypic changes formally to evolutionary mechanisms. The correlation-based methods most frequently employed point largely to ‘fine-grained’ population responses to environmental variability (i.e. rapid phenotypic changes relative to generation time), consistent with plastic mechanisms. Ultimately, many species will likely adapt to long-term warming trends overlaid on natural climate oscillations. Considering the strong plasticity in all traits studied, we recommend development and expanded use of methods capable of detecting evolutionary change, such as the long term study of selection coefficients and temporal shifts in reaction norms, and increased attention to forecasting adaptive change in response to the synergistic interactions of the multiple selection pressures likely to be associated with climate change. PMID:24454549

The association of feeding behaviour with the resistance and tolerance to parasites in recently diverged sticklebacks.

PubMed

Anaya-Rojas, Jaime M; Brunner, Franziska S; Sommer, Nina; Seehausen, Ole; Eizaguirre, Christophe; Matthews, Blake

2016-11-01

Divergent natural selection regimes can contribute to adaptive population divergence, but can be sensitive to human-mediated environmental change. Nutrient loading of aquatic ecosystems, for example, might modify selection pressures by altering the abundance and distribution of resources and the prevalence and infectivity of parasites. Here, we used a mesocosm experiment to test for interactive effects of nutrient loading and parasitism on host condition and feeding ecology. Specifically, we investigated whether the common fish parasite Gyrodactylus sp. differentially affected recently diverged lake and stream ecotypes of three-spined stickleback (Gasterosteus aculeatus). We found that the stream ecotype had a higher resistance to Gyrodactylus sp. infections than the lake ecotype, and that both ecotypes experienced a cost of parasitism, indicated by negative relationships between parasite load and both stomach fullness and body condition. Overall, our results suggest that in the early stages of adaptive population divergence of hosts, parasites can affect host resistance, body condition and diet. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Discovering new materials and new phenomena with evolutionary algorithms

NASA Astrophysics Data System (ADS)

Oganov, Artem

Thanks to powerful evolutionary algorithms, in particular the USPEX method, it is now possible to predict both the stable compounds and their crystal structures at arbitrary conditions, given just the set of chemical elements. Recent developments include major increases of efficiency and extensions to low-dimensional systems and molecular crystals (which allowed large structures to be handled easily, e.g. Mg(BH4)2 and H2O-H2) and new techniques called evolutionary metadynamics and Mendelevian search. Some of the results that I will discuss include: 1. Theoretical and experimental evidence for a new partially ionic phase of boron, γ-B and an insulating and optically transparent form of sodium. 2. Predicted stability of ``impossible'' chemical compounds that become stable under pressure - e.g. Na3Cl, Na2Cl, Na3Cl2, NaCl3, NaCl7, Mg3O2 and MgO2. 3. Novel surface phases (e.g. boron surface reconstructions). 4. Novel dielectric polymers, and novel permanent magnets confirmed by experiment and ready for applications. 5. Prediction of new ultrahard materials and computational proof that diamond is the hardest possible material.

Evolution of Collective Behaviour in an Artificial World Using Linguistic Fuzzy Rule-Based Systems

PubMed Central

Lebar Bajec, Iztok

2017-01-01

Collective behaviour is a fascinating and easily observable phenomenon, attractive to a wide range of researchers. In biology, computational models have been extensively used to investigate various properties of collective behaviour, such as: transfer of information across the group, benefits of grouping (defence against predation, foraging), group decision-making process, and group behaviour types. The question ‘why,’ however remains largely unanswered. Here the interest goes into which pressures led to the evolution of such behaviour, and evolutionary computational models have already been used to test various biological hypotheses. Most of these models use genetic algorithms to tune the parameters of previously presented non-evolutionary models, but very few attempt to evolve collective behaviour from scratch. Of these last, the successful attempts display clumping or swarming behaviour. Empirical evidence suggests that in fish schools there exist three classes of behaviour; swarming, milling and polarized. In this paper we present a novel, artificial life-like evolutionary model, where individual agents are governed by linguistic fuzzy rule-based systems, which is capable of evolving all three classes of behaviour. PMID:28045964

Ultraviolet studies of Cepheids

NASA Technical Reports Server (NTRS)

Boehm-Vitense, Erika

1992-01-01

We discuss whether with new evolutionary tracks we still have a problem fitting the Cepheids and their evolved companions on the appropriate evolutionary tracks. We find that with the Bertelli et al. tracks with convective overshoot by one pressure scale height the problem is essentially removed, though somewhat more mixing would give a better fit. By using the results of recent nonlinear hydrodynamic calculations, we find that we also have no problem matching the observed pulsation periods of the Cepheids with those expected from their new evolutionary masses, provided that Cepheids with periods less than 9 days are overtone pulsators. We investigate possible mass loss of Cepheids from UV studies of the companion spectrum of S Mus and from the ultraviolet spectra of the long period Cepheid l Carinae. For S Mus with a period of 9.6 days we derive an upper limit for the mass loss of M less than 10(exp -9) solar mass, if a standard velocity law is assumed for the wind. For l Carinae with a period of 35.5 days we find a probable mass loss of M is approximately 10(exp -5+/-2) solar mass.

Evolution of Collective Behaviour in an Artificial World Using Linguistic Fuzzy Rule-Based Systems.

PubMed

Demšar, Jure; Lebar Bajec, Iztok

2017-01-01

Collective behaviour is a fascinating and easily observable phenomenon, attractive to a wide range of researchers. In biology, computational models have been extensively used to investigate various properties of collective behaviour, such as: transfer of information across the group, benefits of grouping (defence against predation, foraging), group decision-making process, and group behaviour types. The question 'why,' however remains largely unanswered. Here the interest goes into which pressures led to the evolution of such behaviour, and evolutionary computational models have already been used to test various biological hypotheses. Most of these models use genetic algorithms to tune the parameters of previously presented non-evolutionary models, but very few attempt to evolve collective behaviour from scratch. Of these last, the successful attempts display clumping or swarming behaviour. Empirical evidence suggests that in fish schools there exist three classes of behaviour; swarming, milling and polarized. In this paper we present a novel, artificial life-like evolutionary model, where individual agents are governed by linguistic fuzzy rule-based systems, which is capable of evolving all three classes of behaviour.

Head shape evolution in Gymnophthalmidae: does habitat use constrain the evolution of cranial design in fossorial lizards?

PubMed

Barros, F C; Herrel, A; Kohlsdorf, T

2011-11-01

Habitat usage comprises interactions between ecological parameters and organismal capacities, and the selective pressures that ultimately determine the outcome of such processes in an evolutionary scale may be conflicting when the same morphological structure is recruited for different activities. Here, we investigate the roles of diet and locomotion in the evolution of cranial design in gymnophthalmid lizards and test the hypothesis that microhabitat use drives head shape evolution, particularly in head-first burrowers. Morphological factors were analysed in relation to continuous ecological indexes (prey hardness and substrate compactness) using conventional and phylogenetic approaches. Results suggest that the evolution of head morphology in Gymnophthalmidae was shaped under the influence of microhabitat use rather than diet: burrowers have shorter heads with lower rostral angulation, independently of the prey consumed. Food preferences appear to be relatively conserved throughout the phylogeny of the group, which may have permitted the extensive radiation of gymnophthalmids into fossorial microhabitats. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

Plastic and evolutionary responses to climate change in fish.

PubMed

Crozier, Lisa G; Hutchings, Jeffrey A

2014-01-01

The physical and ecological 'fingerprints' of anthropogenic climate change over the past century are now well documented in many environments and taxa. We reviewed the evidence for phenotypic responses to recent climate change in fish. Changes in the timing of migration and reproduction, age at maturity, age at juvenile migration, growth, survival and fecundity were associated primarily with changes in temperature. Although these traits can evolve rapidly, only two studies attributed phenotypic changes formally to evolutionary mechanisms. The correlation-based methods most frequently employed point largely to 'fine-grained' population responses to environmental variability (i.e. rapid phenotypic changes relative to generation time), consistent with plastic mechanisms. Ultimately, many species will likely adapt to long-term warming trends overlaid on natural climate oscillations. Considering the strong plasticity in all traits studied, we recommend development and expanded use of methods capable of detecting evolutionary change, such as the long term study of selection coefficients and temporal shifts in reaction norms, and increased attention to forecasting adaptive change in response to the synergistic interactions of the multiple selection pressures likely to be associated with climate change.

Test Results for Rotordynamic Coefficients of the SSME HPOTP Turbine Interstage Seal with Two Swirl Brakes

NASA Technical Reports Server (NTRS)

Childs, Dara W.; Baskharone, Erian; Ramsey, Christopher

1991-01-01

Test results are presented for the HPOTP Turbine Interstage Seal with both the current and an alternate, aerodynamically designed, swirl brake. Tests were conducted at speeds out to 16,000 rpm, supply pressures up to 18.3 bars, and the following three inlet tangential velocity conditions: (1) no preswirl; (2) intermediate preswirl in the direction of rotation; and (3) high preswirl in the direction of rotation. The back pressure can be controlled independently and was varied to yield the following four pressure ratios: 0.4, 0.45, 0.56, and 0.67. The central and simplest conclusion to be obtained from the test series is that the alternate swirl brake consistently outperforms the current swirl brake in terms of stability performance. The alternate swirl brake's whirl frequency ratio was generally about one half or less than corresponding values for the current design. In many cases, the alternate design yielded negative whirl frequency ratio values in comparison to positive values for the current design. The alternate design can be directly substituted into the space currently occupied by the current design. There is no change in leakage performance.

Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli.

PubMed

Beauregard-Racine, Julie; Bicep, Cédric; Schliep, Klaus; Lopez, Philippe; Lapointe, François-Joseph; Bapteste, Eric

2011-07-20

We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additional analyses could offer fast heuristic alternatives to standard tree of life (TOL) approaches. We use gene networks to identify genes with atypical modes of evolution, and genome networks to characterize the evolution of genetic partnerships between E. coli and mobile genetic elements. We develop a novel polychromatic quartet method to capture patterns of recombination within E. coli, to update the clanistic toolkit, and to search for the impact of lateral gene transfer and of pathogenicity on gene evolution in two large forests of trees bearing E. coli. We unravel high rates of lateral gene transfer involving E. coli (about 40% of the trees under study), and show that both core genes and shell genes of E. coli are affected by non-tree-like evolutionary processes. We show that pathogenic lifestyle impacted the structure of 30% of the gene trees, and that pathogenic strains are more likely to transfer genes with one another than with non-pathogenic strains. In addition, we propose five groups of genes as candidate mobile modules of pathogenicity. We also present strong evidence for recent lateral gene transfer between E. coli and mobile genetic elements. Depending on which evolutionary questions biologists want to address (i.e. the identification of modules, genetic partnerships, recombination, lateral gene transfer, or genes with atypical evolutionary modes, etc.), forest-based and network-based methods are preferable to the reconstruction of a single tree, because they provide insights and produce hypotheses about the dynamics of genome evolution, rather than the relative branching order of species and lineages. Such a methodological pluralism - the use of woods and webs - is to be encouraged to analyse the evolutionary processes at play in microbial evolution.This manuscript was reviewed by: Ford Doolittle, Tal Pupko, Richard Burian, James McInerney, Didier Raoult, and Yan Boucher.

Is geography an accurate predictor of evolutionary history in the millipede family Xystodesmidae?

PubMed Central

Marek, Paul E.

2017-01-01

For the past several centuries, millipede taxonomists have used the morphology of male copulatory structures (modified legs called gonopods), which are strongly variable and suggestive of species-level differences, as a source to understand taxon relationships. Millipedes in the family Xystodesmidae are blind, dispersal-limited and have narrow habitat requirements. Therefore, geographical proximity may instead be a better predictor of evolutionary relationship than morphology, especially since gonopodal anatomy is extremely divergent and similarities may be masked by evolutionary convergence. Here we provide a phylogenetics-based test of the power of morphological versus geographical character sets for resolving phylogenetic relationships in xystodesmid millipedes. Molecular data from 90 species-group taxa in the family were included in a six-gene phylogenetic analysis to provide the basis for comparing trees generated from these alternative character sets. The molecular phylogeny was compared to topologies representing three hypotheses: (1) a prior classification formulated using morphological and geographical data, (2) hierarchical groupings derived from Euclidean geographical distance, and (3) one based solely on morphological data. Euclidean geographical distance was not found to be a better predictor of evolutionary relationship than the prior classification, the latter of which was the most similar to the molecular topology. However, all three of the alternative topologies were highly divergent (Bayes factor >10) from the molecular topology, with the tree inferred exclusively from morphology being the most divergent. The results of this analysis show that a high degree of morphological convergence from substantial gonopod shape divergence generated spurious phylogenetic relationships. These results indicate the impact that a high degree of morphological homoplasy may have had on prior treatments of the family. Using the results of our phylogenetic analysis, we make several changes to the classification of the family, including transferring the rare state-threatened species Sigmoria whiteheadi Shelley, 1986 to the genus Apheloria Chamberlin, 1921—a relationship not readily apparent based on morphology alone. We show that while gonopod differences are a premier source of taxonomic characters to diagnose species pairwise, the traits should be viewed critically as taxonomic features uniting higher levels. PMID:29038750

As the EBacc Education Beds Down, Pressures Grow for Vocational Alternatives

ERIC Educational Resources Information Center

Allen, Martin

2016-01-01

Though upper secondary education is increasingly dominated by the EBacc, there are growing calls for vocational alternatives and for schools to be more than "exam factories". This short contribution examines whether vocational education provides an alternative way forward.

Lithium hydroxide, LiOH, at elevated densities

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

Hermann, Andreas; Ashcroft, N. W.; Hoffmann, Roald

2014-07-14

We discuss the high-pressure phases of crystalline lithium hydroxide, LiOH. Using first-principles calculations, and assisted by evolutionary structure searches, we reproduce the experimentally known phase transition under pressure, but we suggest that the high-pressure phase LiOH-III be assigned to a new hydrogen-bonded tetragonal structure type that is unique amongst alkali hydroxides. LiOH is at the intersection of both ionic and hydrogen bonding, and we examine the various ensuing structural features and their energetic driving mechanisms. At P = 17 GPa, we predict another phase transition to a new phase, Pbcm-LiOH-IV, which we find to be stable over a wide pressuremore » range. Eventually, at extremely high pressures of 1100 GPa, the ground state of LiOH is predicted to become a polymeric structure with an unusual graphitic oxygen-hydrogen net. However, because of its ionic character, the anticipated metallization of LiOH is much delayed; in fact, its electronic band gap increases monotonically into the TPa pressure range.« less

(Ultra) High Pressure Homogenization for Continuous High Pressure Sterilization of Pumpable Foods – A Review

PubMed Central

Georget, Erika; Miller, Brittany; Callanan, Michael; Heinz, Volker; Mathys, Alexander

2014-01-01

Bacterial spores have a strong resistance to both chemical and physical hurdles and create a risk for the food industry, which has been tackled by applying high thermal intensity treatments to sterilize food. These strong thermal treatments lead to a reduction of the organoleptic and nutritional properties of food and alternatives are actively searched for. Innovative hurdles offer an alternative to inactivate bacterial spores. In particular, recent technological developments have enabled a new generation of high pressure homogenizer working at pressures up to 400 MPa and thus, opening new opportunities for high pressure sterilization of foods. In this short review, we summarize the work conducted on (ultra) high pressure homogenization (U)HPH to inactivate endospores in model and food systems. Specific attention is given to process parameters (pressure, inlet, and valve temperatures). This review gathers the current state of the art and underlines the potential of UHPH sterilization of pumpable foods while highlighting the needs for future work. PMID:25988118

Field test of an alternative longwall gate road design

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

Cox, R.M.; Vandergrift, T.L.; McDonnell, J.P.

1994-01-01

The US Bureau of Mines (USBM) MULSIM/ML modeling technique has been used to analyze anticipated stress distributions for a proposed alternative longwall gate road design for a western Colorado coal mine. The model analyses indicated that the alternative gate road design would reduce stresses in the headgate entry. To test the validity of the alternative gate road design under actual mining conditions, a test section of the alternative system was incorporated into a subsequent set of gate roads developed at the mine. The alternative gate road test section was instrumented with borehole pressure cells, as part of an ongoing USBMmore » research project to monitor ground pressure changes as longwall mining progressed. During the excavation of the adjacent longwall panels, the behavior of the alternative gate road system was monitored continuously using the USBM computer-assisted Ground Control Management System. During these field tests, the alternative gate road system was first monitored and evaluated as a headgate, and later monitored and evaluated as a tailgate. The results of the field tests confirmed the validity of using the MULSIM/NL modeling technique to evaluate mine designs.« less

Accounting for epistatic interactions improves the functional analysis of protein structures.

PubMed

Wilkins, Angela D; Venner, Eric; Marciano, David C; Erdin, Serkan; Atri, Benu; Lua, Rhonald C; Lichtarge, Olivier

2013-11-01

The constraints under which sequence, structure and function coevolve are not fully understood. Bringing this mutual relationship to light can reveal the molecular basis of binding, catalysis and allostery, thereby identifying function and rationally guiding protein redesign. Underlying these relationships are the epistatic interactions that occur when the consequences of a mutation to a protein are determined by the genetic background in which it occurs. Based on prior data, we hypothesize that epistatic forces operate most strongly between residues nearby in the structure, resulting in smooth evolutionary importance across the structure. We find that when residue scores of evolutionary importance are distributed smoothly between nearby residues, functional site prediction accuracy improves. Accordingly, we designed a novel measure of evolutionary importance that focuses on the interaction between pairs of structurally neighboring residues. This measure that we term pair-interaction Evolutionary Trace yields greater functional site overlap and better structure-based proteome-wide functional predictions. Our data show that the structural smoothness of evolutionary importance is a fundamental feature of the coevolution of sequence, structure and function. Mutations operate on individual residues, but selective pressure depends in part on the extent to which a mutation perturbs interactions with neighboring residues. In practice, this principle led us to redefine the importance of a residue in terms of the importance of its epistatic interactions with neighbors, yielding better annotation of functional residues, motivating experimental validation of a novel functional site in LexA and refining protein function prediction. lichtarge@bcm.edu. Supplementary data are available at Bioinformatics online.

Accounting for epistatic interactions improves the functional analysis of protein structures

PubMed Central

Wilkins, Angela D.; Venner, Eric; Marciano, David C.; Erdin, Serkan; Atri, Benu; Lua, Rhonald C.; Lichtarge, Olivier

2013-01-01

Motivation: The constraints under which sequence, structure and function coevolve are not fully understood. Bringing this mutual relationship to light can reveal the molecular basis of binding, catalysis and allostery, thereby identifying function and rationally guiding protein redesign. Underlying these relationships are the epistatic interactions that occur when the consequences of a mutation to a protein are determined by the genetic background in which it occurs. Based on prior data, we hypothesize that epistatic forces operate most strongly between residues nearby in the structure, resulting in smooth evolutionary importance across the structure. Methods and Results: We find that when residue scores of evolutionary importance are distributed smoothly between nearby residues, functional site prediction accuracy improves. Accordingly, we designed a novel measure of evolutionary importance that focuses on the interaction between pairs of structurally neighboring residues. This measure that we term pair-interaction Evolutionary Trace yields greater functional site overlap and better structure-based proteome-wide functional predictions. Conclusions: Our data show that the structural smoothness of evolutionary importance is a fundamental feature of the coevolution of sequence, structure and function. Mutations operate on individual residues, but selective pressure depends in part on the extent to which a mutation perturbs interactions with neighboring residues. In practice, this principle led us to redefine the importance of a residue in terms of the importance of its epistatic interactions with neighbors, yielding better annotation of functional residues, motivating experimental validation of a novel functional site in LexA and refining protein function prediction. Contact: lichtarge@bcm.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24021383

Pressure Ulcer Prevention

PubMed Central

2009-01-01

Executive Summary In April 2008, the Medical Advisory Secretariat began an evidence-based review of the literature concerning pressure ulcers. Please visit the Medical Advisory Secretariat Web site, http://www.health.gov.on.ca/english/providers/program/mas/tech/tech_mn.html to review these titles that are currently available within the Pressure Ulcers series. Pressure ulcer prevention: an evidence based analysis The cost-effectiveness of prevention strategies for pressure ulcers in long-term care homes in Ontario: projections of the Ontario Pressure Ulcer Model (field evaluation) Management of chronic pressure ulcers: an evidence-based analysis (anticipated pubicstion date - mid-2009) Purpose A pressure ulcer, also known as a pressure sore, decubitus ulcer, or bedsore, is defined as a localized injury to the skin/and or underlying tissue occurring most often over a bony prominence and caused by pressure, shear, or friction, alone or in combination. (1) Those at risk for developing pressure ulcers include the elderly and critically ill as well as persons with neurological impairments and those who suffer conditions associated with immobility. Pressure ulcers are graded or staged with a 4-point classification system denoting severity. Stage I represents the beginnings of a pressure ulcer and stage IV, the severest grade, consists of full thickness tissue loss with exposed bone, tendon, and or muscle. (1) In a 2004 survey of Canadian health care settings, Woodbury and Houghton (2) estimated that the prevalence of pressure ulcers at a stage 1 or greater in Ontario ranged between 13.1% and 53% with nonacute health care settings having the highest prevalence rate (Table 1). Executive Summary Table 1: Prevalence of Pressure Ulcers* Setting Canadian Prevalence,% (95% CI) Ontario Prevalence,Range % (n) Acute care 25 (23.8–26.3) 23.9–29.7 (3418) Nonacute care† 30 (29.3–31.4) 30.0–53.3 (1165) Community care 15 (13.4–16.8) 13.2 (91) Mixed health care‡ 22 (20.9–23.4) 13.1–25.7 (3100) All health care settings 26 (25.2–26.8) 13.1–53.3 (7774) * CI indicates confidence interval. † Nonacute care included sub-acute care, chronic care, complex continuing care, long-term care, and nursing home care. ‡ Mixed health care includes a mixture of acute, nonacute, and/or community care health care delivery settings. Pressure ulcers have a considerable economic impact on health care systems. In Australia, the cost of treating a single stage IV ulcer has been estimated to be greater than $61,000 (AUD) (approximately $54,000 CDN), (3) while in the United Kingdom the total cost of pressure ulcers has been estimated at £1.4–£2.1 billion annually or 4% of the National Health Service expenditure. (4) Because of the high physical and economic burden of pressure ulcers, this review was undertaken to determine which interventions are effective at preventing the development of pressure ulcers in an at-risk population. Review Strategy The main objective of this systematic review is to determine the effectiveness of pressure ulcer preventive interventions including Risk Assessment, Distribution Devices, Nutritional Supplementation, Repositioning, and Incontinence Management. A comprehensive literature search was completed for each of the above 5 preventive interventions. The electronic databases searched included MEDLINE, MEDLINE In-Process and Other Non-Indexed Citations, EMBASE, the Cochrane Library, and the Cumulative Index to Nursing and Allied Health Literature. As well, the bibliographic references of selected studies were searched. All studies meeting explicit inclusion and exclusion criteria for each systematic review section were retained and the quality of the body of evidence was determined using the Grading of Recommendation Assessment, Development, and Evaluation (GRADE) system. (5) Where appropriate, a meta-analysis was undertaken to determine the overall estimate of effect of the preventive intervention under review. Summary of Findings Risk Assessment There is very low quality evidence to support the hypothesis that allocating the type of pressure-relieving equipment according to the person’s level of pressure ulcer risk statistically decreases the incidence of pressure ulcer development. Similarly, there is very low quality evidence to support the hypothesis that incorporating a risk assessment into nursing practice increases the number of preventative measures used per person and that these interventions are initiated earlier in the care continuum. Pressure Redistribution Devices There is moderate quality evidence that the use of an alternative foam mattress produces a relative risk reduction (RRR) of 69% in the incidence of pressure ulcers compared with a standard hospital mattress. The evidence does not support the superiority of one particular type of alternative foam mattress. There is very low quality evidence that the use of an alternating pressure mattress is associated with an RRR of 71% in the incidence of grade 1 or 2 pressure ulcers. Similarly, there is low quality evidence that the use of an alternating pressure mattress is associated with an RRR of 68% in the incidence of deteriorating skin changes. There is moderate quality evidence that there is a statistically nonsignificant difference in the incidence of grade 2 pressure ulcers between persons using an alternating pressure mattress and those using an alternating pressure overlay. There is moderate quality evidence that the use of an Australian sheepskin produces an RRR of 58% in the incidence of pressure ulcers grade 1 or greater. There is also evidence that sheepskins are uncomfortable to use. The Pressure Ulcer Advisory Panel noted that, in general, sheepskins are not a useful preventive intervention because they bunch up in a patient’s bed and may contribute to wound infection if not properly cleaned, and this reduces their acceptability as a preventive intervention. There is very low quality evidence that the use of a Micropulse System alternating pressure mattress used intra operatively and postoperatively produces an RRR of 79% in the incidence of pressure ulcers compared with a gel-pad used intraoperatively and a standard hospital mattress used postoperatively (standard care). It is unclear if this effect is due to the use of the alternating pressure mattress intraoperatively or postoperatively or if indeed it must be used in both patient care areas. There is low quality evidence that the use of a vesico-elastic polymer pad (gel pad) on the operating table for surgeries of at least 90 minutes’ duration produces a statistically significant RRR of 47% in the incidence of pressure ulcers grade 1 or greater compared with a standard operating table foam mattress. There is low quality evidence that the use of an air suspension bed in the intensive care unit (ICU) for stays of at least 3 days produces a statistically significant RRR of 76% in the incidence of pressure ulcers compared with a standard ICU bed. There is very low quality evidence that the use of an alternating pressure mattress does not statistically reduce the incidence of pressure ulcers compared with an alternative foam mattress. Nutritional Supplementation There is very low quality evidence supporting an RRR of 15% in the incidence of pressure ulcers when nutritional supplementation is added to a standard hospital diet. Repositioning There is low quality evidence supporting the superiority of a 4-hourly turning schedule with a vesico-elastic polyurethane foam mattress compared with a 2-hourly or 3-hourly turning schedule and a standard foam mattress to reduce the incidence of grade 1 or 2 pressure ulcers. Incontinence Management There is very low quality evidence supporting the benefit of a structured skin care protocol to reduce the incidence of grade 1 or 2 pressure ulcers in persons with urinary and/or fecal incontinence. There is low quality evidence supporting the benefit of a pH-balanced cleanser compared with soap and water to reduce the incidence of grade 1 or 2 pressure ulcers in persons with urinary and fecal incontinence. Conclusions There is moderate quality evidence that an alternative foam mattress is effective in preventing the development of pressure ulcers compared with a standard hospital foam mattress. However, overall there remains a paucity of moderate or higher quality evidence in the literature to support many of the preventive interventions. Until better quality evidence is available, pressure ulcer preventive care must be guided by expert opinion for those interventions where low or very low quality evidence supports the effectiveness of such interventions. Abbreviations CI Confidence interval GRADE Grading of Recommendation Assessment, Development, and Evaluation ICU Intensive care unit MAS Medical Advisory Secretariat NPUAP National Pressure Ulcer Advisory Panel RAS Risk assessment scale RCT Randomized controlled trial RNAO Registered Nurses Association of Ontario RR Relative risk RRR Relative risk reduction PMID:23074524

49 CFR 195.303 - Risk-based alternative to pressure testing older hazardous liquid and carbon dioxide pipelines.

Code of Federal Regulations, 2010 CFR

2010-10-01

... criteria as an alternative to the pressure testing in § 195.302(b)(1)(i)-(iii) and § 195.302(b)(2)(i) of... in paragraph (b) of this section as follows: (1) Risk Classification A if the location indicator is ranked as low or medium risk, the product and volume indicators are ranked as low risk, and the...

49 CFR 195.303 - Risk-based alternative to pressure testing older hazardous liquid and carbon dioxide pipelines.

Code of Federal Regulations, 2011 CFR

2011-10-01

... criteria as an alternative to the pressure testing in § 195.302(b)(1)(i)-(iii) and § 195.302(b)(2)(i) of... in paragraph (b) of this section as follows: (1) Risk Classification A if the location indicator is ranked as low or medium risk, the product and volume indicators are ranked as low risk, and the...

Qualitative similarities in the visual short-term memory of pigeons and people.

PubMed

Gibson, Brett; Wasserman, Edward; Luck, Steven J

2011-10-01

Visual short-term memory plays a key role in guiding behavior, and individual differences in visual short-term memory capacity are strongly predictive of higher cognitive abilities. To provide a broader evolutionary context for understanding this memory system, we directly compared the behavior of pigeons and humans on a change detection task. Although pigeons had a lower storage capacity and a higher lapse rate than humans, both species stored multiple items in short-term memory and conformed to the same basic performance model. Thus, despite their very different evolutionary histories and neural architectures, pigeons and humans have functionally similar visual short-term memory systems, suggesting that the functional properties of visual short-term memory are subject to similar selective pressures across these distant species.

Comparative studies of gene expression and the evolution of gene regulation

PubMed Central

Romero, Irene Gallego; Ruvinsky, Ilya; Gilad, Yoav

2014-01-01

The hypothesis that differences in gene regulation play an important role in speciation and adaptation is more than 40 years old. With the advent of new sequencing technologies, we are able to characterize and study gene expression levels and associated regulatory mechanisms in a large number of individuals and species at unprecedented resolution and scale. We have thus gained new insights into the evolutionary pressures that shape gene expression levels, as well as developed an appreciation for the relative importance of evolutionary changes in different regulatory genetic and epigenetic mechanisms. The current challenge is to link gene regulatory changes to adaptive evolution of complex phenotypes. Here we mainly focus on comparative studies in primates, and how they are complemented by studies in model organisms. PMID:22705669

When the lights go out: the evolutionary fate of free-living colorless green algae.

PubMed

Figueroa-Martinez, Francisco; Nedelcu, Aurora M; Smith, David R; Adrian, Reyes-Prieto

2015-05-01

The endosymbiotic origin of plastids was a launching point for eukaryotic evolution. The autotrophic abilities bestowed by plastids are responsible for much of the eukaryotic diversity we observe today. But despite its many advantages, photosynthesis has been lost numerous times and in disparate lineages throughout eukaryote evolution. For example, among green algae, several groups have lost photosynthesis independently and in response to different selective pressures; these include the parasitic/pathogenic trebouxiophyte genera Helicosporidium and Prototheca, and the free-living chlamydomonadalean genera Polytomella and Polytoma. Here, we examine the published data on colorless green algae and argue that investigations into the different evolutionary routes leading to their current nonphotosynthetic lifestyles provide exceptional opportunities to understand the ecological and genomic factors involved in the loss of photosynthesis.

75 FR 72653 - Alternate Fracture Toughness Requirements for Protection Against Pressurized Thermal Shock Events...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-26

..., Criminal penalties, Fire protection, Intergovernmental relations, Nuclear power plants and reactors... Requirements for Protection Against Pressurized Thermal Shock Events; Correction AGENCY: Nuclear Regulatory... fracture toughness requirements for protection against pressurized thermal shock (PTS) events for...

Integrating evolutionary and functional tests of adaptive hypotheses: a case study of altitudinal differentiation in hemoglobin function in an Andean Sparrow, Zonotrichia capensis.

PubMed

Cheviron, Zachary A; Natarajan, Chandrasekhar; Projecto-Garcia, Joana; Eddy, Douglas K; Jones, Jennifer; Carling, Matthew D; Witt, Christopher C; Moriyama, Hideaki; Weber, Roy E; Fago, Angela; Storz, Jay F

2014-11-01

In air-breathing vertebrates, the physiologically optimal blood-O2 affinity is jointly determined by the prevailing partial pressure of atmospheric O2, the efficacy of pulmonary O2 transfer, and internal metabolic demands. Consequently, genetic variation in the oxygenation properties of hemoglobin (Hb) may be subject to spatially varying selection in species with broad elevational distributions. Here we report the results of a combined functional and evolutionary analysis of Hb polymorphism in the rufous-collared sparrow (Zonotrichia capensis), a species that is continuously distributed across a steep elevational gradient on the Pacific slope of the Peruvian Andes. We integrated a population genomic analysis that included all postnatally expressed Hb genes with functional studies of naturally occurring Hb variants, as well as recombinant Hb (rHb) mutants that were engineered through site-directed mutagenesis. We identified three clinally varying amino acid polymorphisms: Two in the α(A)-globin gene, which encodes the α-chain subunits of the major HbA isoform, and one in the α(D)-globin gene, which encodes the α-chain subunits of the minor HbD isoform. We then constructed and experimentally tested single- and double-mutant rHbs representing each of the alternative α(A)-globin genotypes that predominate at different elevations. Although the locus-specific patterns of altitudinal differentiation suggested a history of spatially varying selection acting on Hb polymorphism, the experimental tests demonstrated that the observed amino acid mutations have no discernible effect on respiratory properties of the HbA or HbD isoforms. These results highlight the importance of experimentally validating the hypothesized effects of genetic changes in protein function to avoid the pitfalls of adaptive storytelling. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Testis-specific glyceraldehyde-3-phosphate dehydrogenase: origin and evolution

PubMed Central

2011-01-01

Background Glyceraldehyde-3-phosphate dehydrogenase (GAPD) catalyses one of the glycolytic reactions and is also involved in a number of non-glycolytic processes, such as endocytosis, DNA excision repair, and induction of apoptosis. Mammals are known to possess two homologous GAPD isoenzymes: GAPD-1, a well-studied protein found in all somatic cells, and GAPD-2, which is expressed solely in testis. GAPD-2 supplies energy required for the movement of spermatozoa and is tightly bound to the sperm tail cytoskeleton by the additional N-terminal proline-rich domain absent in GAPD-1. In this study we investigate the evolutionary history of GAPD and gain some insights into specialization of GAPD-2 as a testis-specific protein. Results A dataset of GAPD sequences was assembled from public databases and used for phylogeny reconstruction by means of the Bayesian method. Since resolution in some clades of the obtained tree was too low, syntenic analysis was carried out to define the evolutionary history of GAPD more precisely. The performed selection tests showed that selective pressure varies across lineages and isoenzymes, as well as across different regions of the same sequences. Conclusions The obtained results suggest that GAPD-1 and GAPD-2 emerged after duplication during the early evolution of chordates. GAPD-2 was subsequently lost by most lineages except lizards, mammals, as well as cartilaginous and bony fishes. In reptilians and mammals, GAPD-2 specialized to a testis-specific protein and acquired the novel N-terminal proline-rich domain anchoring the protein in the sperm tail cytoskeleton. This domain is likely to have originated by exonization of a microsatellite genomic region. Recognition of the proline-rich domain by cytoskeletal proteins seems to be unspecific. Besides testis, GAPD-2 of lizards was also found in some regenerating tissues, but it lacks the proline-rich domain due to tissue-specific alternative splicing. PMID:21663662

Testis-specific glyceraldehyde-3-phosphate dehydrogenase: origin and evolution.

PubMed

Kuravsky, Mikhail L; Aleshin, Vladimir V; Frishman, Dmitrij; Muronetz, Vladimir I

2011-06-10

Glyceraldehyde-3-phosphate dehydrogenase (GAPD) catalyses one of the glycolytic reactions and is also involved in a number of non-glycolytic processes, such as endocytosis, DNA excision repair, and induction of apoptosis. Mammals are known to possess two homologous GAPD isoenzymes: GAPD-1, a well-studied protein found in all somatic cells, and GAPD-2, which is expressed solely in testis. GAPD-2 supplies energy required for the movement of spermatozoa and is tightly bound to the sperm tail cytoskeleton by the additional N-terminal proline-rich domain absent in GAPD-1. In this study we investigate the evolutionary history of GAPD and gain some insights into specialization of GAPD-2 as a testis-specific protein. A dataset of GAPD sequences was assembled from public databases and used for phylogeny reconstruction by means of the Bayesian method. Since resolution in some clades of the obtained tree was too low, syntenic analysis was carried out to define the evolutionary history of GAPD more precisely. The performed selection tests showed that selective pressure varies across lineages and isoenzymes, as well as across different regions of the same sequences. The obtained results suggest that GAPD-1 and GAPD-2 emerged after duplication during the early evolution of chordates. GAPD-2 was subsequently lost by most lineages except lizards, mammals, as well as cartilaginous and bony fishes. In reptilians and mammals, GAPD-2 specialized to a testis-specific protein and acquired the novel N-terminal proline-rich domain anchoring the protein in the sperm tail cytoskeleton. This domain is likely to have originated by exonization of a microsatellite genomic region. Recognition of the proline-rich domain by cytoskeletal proteins seems to be unspecific. Besides testis, GAPD-2 of lizards was also found in some regenerating tissues, but it lacks the proline-rich domain due to tissue-specific alternative splicing.

An adaptive radiation model for the origin of new genefunctions

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

Francino, M. Pilar

2004-10-18

The evolution of new gene functions is one of the keys to evolutionary innovation. Most novel functions result from gene duplication followed by divergence. However, the models hitherto proposed to account for this process are not fully satisfactory. The classic model of neofunctionalization holds that the two paralogous gene copies resulting from a duplication are functionally redundant, such that one of them can evolve under no functional constraints and occasionally acquire a new function. This model lacks a convincing mechanism for the new gene copies to increase in frequency in the population and survive the mutational load expected to accumulatemore » under neutrality, before the acquisition of the rare beneficial mutations that would confer new functionality. The subfunctionalization model has been proposed as an alternative way to generate genes with altered functions. This model also assumes that new paralogous gene copies are functionally redundant and therefore neutral, but it predicts that relaxed selection will affect both gene copies such that some of the capabilities of the parent gene will disappear in one of the copies and be retained in the other. Thus, the functions originally present in a single gene will be partitioned between the two descendant copies. However, although this model can explain increases in gene number, it does not really address the main evolutionary question, which is the development of new biochemical capabilities. Recently, a new concept has been introduced into the gene evolution literature which is most likely to help solve this dilemma. The key point is to allow for a period of natural selection for the duplication per se, before new function evolves, rather than considering gene duplication to be neutral as in the previous models. Here, I suggest a new model that draws on the advantage of postulating selection for gene duplication, and proposes that bursts of adaptive gene amplification in response to specific selection pressures provide the raw material for the evolution of new function.« less

Exotic behavior and crystal structures of calcium under pressure

PubMed Central

Oganov, Artem R.; Ma, Yanming; Xu, Ying; Errea, Ion; Bergara, Aitor; Lyakhov, Andriy O.

2010-01-01

Experimental studies established that calcium undergoes several counterintuitive transitions under pressure: fcc → bcc → simple cubic → Ca-IV → Ca-V, and becomes a good superconductor in the simple cubic and higher-pressure phases. Here, using ab initio evolutionary simulations, we explore the behavior of Ca under pressure and find a number of new phases. Our structural sequence differs from the traditional picture for Ca, but is similar to that for Sr. The β-tin (I41/amd) structure, rather than simple cubic, is predicted to be the theoretical ground state at 0 K and 33–71 GPa. This structure can be represented as a large distortion of the simple cubic structure, just as the higher-pressure phases stable between 71 and 134 GPa. The structure of Ca-V, stable above 134 GPa, is a complex host-guest structure. According to our calculations, the predicted phases are superconductors with Tc increasing under pressure and reaching approximately 20 K at 120 GPa, in good agreement with experiment. PMID:20382865

Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins

PubMed Central

Delcourt, Vivian; Lucier, Jean-François; Gagnon, Jules; Beaudoin, Maxime C; Vanderperre, Benoît; Breton, Marc-André; Motard, Julie; Jacques, Jean-François; Brunelle, Mylène; Gagnon-Arsenault, Isabelle; Fournier, Isabelle; Ouangraoua, Aida; Hunting, Darel J; Cohen, Alan A; Landry, Christian R; Scott, Michelle S

2017-01-01

Recent functional, proteomic and ribosome profiling studies in eukaryotes have concurrently demonstrated the translation of alternative open-reading frames (altORFs) in addition to annotated protein coding sequences (CDSs). We show that a large number of small proteins could in fact be coded by these altORFs. The putative alternative proteins translated from altORFs have orthologs in many species and contain functional domains. Evolutionary analyses indicate that altORFs often show more extreme conservation patterns than their CDSs. Thousands of alternative proteins are detected in proteomic datasets by reanalysis using a database containing predicted alternative proteins. This is illustrated with specific examples, including altMiD51, a 70 amino acid mitochondrial fission-promoting protein encoded in MiD51/Mief1/SMCR7L, a gene encoding an annotated protein promoting mitochondrial fission. Our results suggest that many genes are multicoding genes and code for a large protein and one or several small proteins. PMID:29083303

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

PubMed Central

2008-01-01

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

A simple methodology for characterization of germanium coaxial detectors by using Monte Carlo simulation and evolutionary algorithms.

PubMed

Guerra, J G; Rubiano, J G; Winter, G; Guerra, A G; Alonso, H; Arnedo, M A; Tejera, A; Gil, J M; Rodríguez, R; Martel, P; Bolivar, J P

2015-11-01

The determination in a sample of the activity concentration of a specific radionuclide by gamma spectrometry needs to know the full energy peak efficiency (FEPE) for the energy of interest. The difficulties related to the experimental calibration make it advisable to have alternative methods for FEPE determination, such as the simulation of the transport of photons in the crystal by the Monte Carlo method, which requires an accurate knowledge of the characteristics and geometry of the detector. The characterization process is mainly carried out by Canberra Industries Inc. using proprietary techniques and methodologies developed by that company. It is a costly procedure (due to shipping and to the cost of the process itself) and for some research laboratories an alternative in situ procedure can be very useful. The main goal of this paper is to find an alternative to this costly characterization process, by establishing a method for optimizing the parameters of characterizing the detector, through a computational procedure which could be reproduced at a standard research lab. This method consists in the determination of the detector geometric parameters by using Monte Carlo simulation in parallel with an optimization process, based on evolutionary algorithms, starting from a set of reference FEPEs determined experimentally or computationally. The proposed method has proven to be effective and simple to implement. It provides a set of characterization parameters which it has been successfully validated for different source-detector geometries, and also for a wide range of environmental samples and certified materials. Copyright © 2015 Elsevier Ltd. All rights reserved.

Ecological theatre and the evolutionary game: how environmental and demographic factors determine payoffs in evolutionary games.

PubMed

Argasinski, K; Broom, M

2013-10-01

In the standard approach to evolutionary games and replicator dynamics, differences in fitness can be interpreted as an excess from the mean Malthusian growth rate in the population. In the underlying reasoning, related to an analysis of "costs" and "benefits", there is a silent assumption that fitness can be described in some type of units. However, in most cases these units of measure are not explicitly specified. Then the question arises: are these theories testable? How can we measure "benefit" or "cost"? A natural language, useful for describing and justifying comparisons of strategic "cost" versus "benefits", is the terminology of demography, because the basic events that shape the outcome of natural selection are births and deaths. In this paper, we present the consequences of an explicit analysis of births and deaths in an evolutionary game theoretic framework. We will investigate different types of mortality pressures, their combinations and the possibility of trade-offs between mortality and fertility. We will show that within this new approach it is possible to model how strictly ecological factors such as density dependence and additive background fitness, which seem neutral in classical theory, can affect the outcomes of the game. We consider the example of the Hawk-Dove game, and show that when reformulated in terms of our new approach new details and new biological predictions are produced.

Urban driven phenotypic changes: empirical observations and theoretical implications for eco-evolutionary feedback

PubMed Central

Marzluff, John

2017-01-01

Emerging evidence that cities drive micro-evolution raises the question of whether rapid urbanization of Earth might impact ecosystems by causing systemic changes in functional traits that regulate urban ecosystems' productivity and stability. Intraspecific trait variation—variation in organisms' morphological, physiological or behavioural characteristics stemming from genetic variability and phenotypic plasticity—has significant implications for ecological functions such as nutrient cycling and primary productivity. While it is well established that changes in ecological conditions can drive evolutionary change in species' traits that, in turn, can alter ecosystem function, an understanding of the reciprocal and simultaneous processes associated with such interactions is only beginning to emerge. In urban settings, the potential for rapid trait change may be exacerbated by multiple selection pressures operating simultaneously. This paper reviews evidence on mechanisms linking urban development patterns to rapid phenotypic changes, and differentiates phenotypic changes for which there is evidence of micro-evolution versus phenotypic changes which may represent plasticity. Studying how humans mediate phenotypic trait changes through urbanization could shed light on fundamental concepts in ecological and evolutionary theory. It can also contribute to our understanding of eco-evolutionary feedback and provide insights for maintaining ecosystem function over the long term. This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’. PMID:27920374

Many-to-one form-to-function mapping weakens parallel morphological evolution.

PubMed

Thompson, Cole J; Ahmed, Newaz I; Veen, Thor; Peichel, Catherine L; Hendry, Andrew P; Bolnick, Daniel I; Stuart, Yoel E

2017-11-01

Evolutionary ecologists aim to explain and predict evolutionary change under different selective regimes. Theory suggests that such evolutionary prediction should be more difficult for biomechanical systems in which different trait combinations generate the same functional output: "many-to-one mapping." Many-to-one mapping of phenotype to function enables multiple morphological solutions to meet the same adaptive challenges. Therefore, many-to-one mapping should undermine parallel morphological evolution, and hence evolutionary predictability, even when selection pressures are shared among populations. Studying 16 replicate pairs of lake- and stream-adapted threespine stickleback (Gasterosteus aculeatus), we quantified three parts of the teleost feeding apparatus and used biomechanical models to calculate their expected functional outputs. The three feeding structures differed in their form-to-function relationship from one-to-one (lower jaw lever ratio) to increasingly many-to-one (buccal suction index, opercular 4-bar linkage). We tested for (1) weaker linear correlations between phenotype and calculated function, and (2) less parallel evolution across lake-stream pairs, in the many-to-one systems relative to the one-to-one system. We confirm both predictions, thus supporting the theoretical expectation that increasing many-to-one mapping undermines parallel evolution. Therefore, sole consideration of morphological variation within and among populations might not serve as a proxy for functional variation when multiple adaptive trait combinations exist. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Sex, rebellion and decadence: the scandalous evolutionary history of the human Y chromosome.

PubMed

Navarro-Costa, Paulo

2012-12-01

It can be argued that the Y chromosome brings some of the spirit of rock&roll to our genome. Equal parts degenerate and sex-driven, the Y has boldly rebelled against sexual recombination, one of the sacred pillars of evolution. In evolutionary terms this chromosome also seems to have adopted another of rock&roll's mottos: living fast. Yet, it appears to have refused to die young. In this manuscript the Y chromosome will be analyzed from the intersection between structural, evolutionary and functional biology. Such integrative approach will present the Y as a highly specialized product of a series of remarkable evolutionary processes. These led to the establishment of a sex-specific genomic niche that is maintained by a complex balance between selective pressure and the genetic diversity introduced by intrachromosomal recombination. Central to this equilibrium is the "polish or perish" dilemma faced by the male-specific Y genes: either they are polished by the acquisition of male-related functions or they perish via the accumulation of inactivating mutations. Thus, understanding to what extent the idiosyncrasies of Y recombination may impact this chromosome's role in sex determination and male germline functions should be regarded as essential for added clinical insight into several male infertility phenotypes. This article is part of a Special Issue entitled: Molecular Genetics of Human Reproductive Failure. Copyright © 2012 Elsevier B.V. All rights reserved.

Genomic evidence of gene duplication and adaptive evolution of Toll like receptors (TLR2 and TLR4) in reptiles.

PubMed

Shang, Shuai; Zhong, Huaming; Wu, Xiaoyang; Wei, Qinguo; Zhang, Huanxin; Chen, Jun; Chen, Yao; Tang, Xuexi; Zhang, Honghai

2018-04-01

Toll-like receptors (TLRs) encoded by the TLR multigene family play an important role in initial pathogen recognition in vertebrates. Among the TLRs, TLR2 and TLR4 may be of particular importance to reptiles. In order to study the evolutionary patterns and structural characteristics of TLRs, we explored the available genomes of several representative members of reptiles. 25 TLR2 genes and 19 TLR4 genes from reptiles were obtained in this study. Phylogenetic results showed that the TLR2 gene duplication occurred in several species. Evolutionary analysis by at least two methods identified 30 and 13 common positively selected codons in TLR2 and TLR4, respectively. Most positively selected sites of TLR2 and TLR4 were located in the Leucine-rich repeat (LRRs). Branch model analysis showed that TLR2 genes were under different evolutionary forces in reptiles, while the TLR4 genes showed no significant selection pressure. The different evolutionary adaptation of TLR2 and TLR4 among the reptiles might be due to their different function in recognizing bacteria. Overall, we explored the structure and evolution of TLR2 and TLR4 genes in reptiles for the first time. Our study revealed valuable information regarding TLR2 and TLR4 in reptiles, and provided novel insights into the conservation concern of natural populations. Copyright © 2017 Elsevier B.V. All rights reserved.

Does stress induce (para)sex? Implications for Candida albicans evolution.

PubMed

Berman, Judith; Hadany, Lilach

2012-05-01

Theory predicts that stress is a key factor in explaining the evolutionary role of sex in facultatively sexual organisms, including microorganisms. Organisms capable of reproducing both sexually and asexually are expected to mate more frequently when stressed, and such stress-induced mating is predicted to facilitate adaptation. Here, we propose that stress has an analogous effect on the parasexual cycle in Candida albicans, which involves alternation of generations between diploid and tetraploid cells. The parasexual cycle can generate high levels of diversity, including aneuploidy, yet it apparently occurs only rarely in nature. We review the evidence that stress facilitates four major steps in the parasexual cycle and suggest that parasex occurs much more frequently under stress conditions. This may explain both the evolutionary significance of parasex and its apparent rarity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Bayesian identification of acoustic impedance in treated ducts.

PubMed

Buot de l'Épine, Y; Chazot, J-D; Ville, J-M

2015-07-01

The noise reduction of a liner placed in the nacelle of a turbofan engine is still difficult to predict due to the lack of knowledge of its acoustic impedance that depends on grazing flow profile, mode order, and sound pressure level. An eduction method, based on a Bayesian approach, is presented here to adjust an impedance model of the liner from sound pressures measured in a rectangular treated duct under multimodal propagation and flow. The cost function is regularized with prior information provided by Guess's [J. Sound Vib. 40, 119-137 (1975)] impedance of a perforated plate. The multi-parameter optimization is achieved with an Evolutionary-Markov-Chain-Monte-Carlo algorithm.

What is wrong with intelligent design?

PubMed

Sober, Elliott

2007-03-01

This article reviews two standard criticisms of creationism/intelligent design (ID)): it is unfalsifiable, and it is refuted by the many imperfect adaptations found in nature. Problems with both criticisms are discussed. A conception of testability is described that avoids the defects in Karl Popper's falsifiability criterion. Although ID comes in multiple forms, which call for different criticisms, it emerges that ID fails to constitute a serious alternative to evolutionary theory.

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

PubMed

Matos-Maraví, Pável

2016-07-01

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

The role of peripheral endemism in species diversification: evidence from the coral reef fish genus Anampses (Family: Labridae).

PubMed

Hodge, Jennifer R; Read, Charmaine I; van Herwerden, Lynne; Bellwood, David R

2012-02-01

We examined how peripherally isolated endemic species may have contributed to the biodiversity of the Indo-Australian Archipelago biodiversity hotspot by reconstructing the evolutionary history of the wrasse genus Anampses. We identified three alternate models of diversification: the vicariance-based 'successive division' model, and the dispersal-based 'successive colonisation' and 'peripheral budding' models. The genus was well suited for this study given its relatively high proportion (42%) of endemic species, its reasonably low diversity (12 species), which permitted complete taxon sampling, and its widespread tropical Indo-Pacific distribution. Monophyly of the genus was strongly supported by three phylogenetic analyses: maximum parsimony, maximum likelihood, and Bayesian inference based on mitochondrial CO1 and 12S rRNA and nuclear S7 sequences. Estimates of species divergence times from fossil-calibrated Bayesian inference suggest that Anampses arose in the mid-Eocene and subsequently diversified throughout the Miocene. Evolutionary relationships within the genus, combined with limited spatial and temporal concordance among endemics, offer support for all three alternate models of diversification. Our findings emphasise the importance of peripherally isolated locations in creating and maintaining endemic species and their contribution to the biodiversity of the Indo-Australian Archipelago. Copyright © 2011 Elsevier Inc. All rights reserved.

A morphospace for synthetic organs and organoids: the possible and the actual.

PubMed

Ollé-Vila, Aina; Duran-Nebreda, Salva; Conde-Pueyo, Núria; Montañez, Raúl; Solé, Ricard

2016-04-18

Efforts in evolutionary developmental biology have shed light on how organs are developed and why evolution has selected some structures instead of others. These advances in the understanding of organogenesis along with the most recent techniques of organotypic cultures, tissue bioprinting and synthetic biology provide the tools to hack the physical and genetic constraints in organ development, thus opening new avenues for research in the form of completely designed or merely altered settings. Here we propose a unifying framework that connects the concept of morphospace (i.e. the space of possible structures) with synthetic biology and tissue engineering. We aim for a synthesis that incorporates our understanding of both evolutionary and architectural constraints and can be used as a guide for exploring alternative design principles to build artificial organs and organoids. We present a three-dimensional morphospace incorporating three key features associated to organ and organoid complexity. The axes of this space include the degree of complexity introduced by developmental mechanisms required to build the structure, its potential to store and react to information and the underlying physical state. We suggest that a large fraction of this space is empty, and that the void might offer clues for alternative ways of designing and even inventing new organs.

An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network

PubMed Central

Holden, Brian J; Pinney, John W; Lovell, Simon C; Amoutzias, Grigoris D; Robertson, David L

2007-01-01

Background Alternative representations of biochemical networks emphasise different aspects of the data and contribute to the understanding of complex biological systems. In this study we present a variety of automated methods for visualisation of a protein-protein interaction network, using the basic helix-loop-helix (bHLH) family of transcription factors as an example. Results Network representations that arrange nodes (proteins) according to either continuous or discrete information are investigated, revealing the existence of protein sub-families and the retention of interactions following gene duplication events. Methods of network visualisation in conjunction with a phylogenetic tree are presented, highlighting the evolutionary relationships between proteins, and clarifying the context of network hubs and interaction clusters. Finally, an optimisation technique is used to create a three-dimensional layout of the phylogenetic tree upon which the protein-protein interactions may be projected. Conclusion We show that by incorporating secondary genomic, functional or phylogenetic information into network visualisation, it is possible to move beyond simple layout algorithms based on network topology towards more biologically meaningful representations. These new visualisations can give structure to complex networks and will greatly help in interpreting their evolutionary origins and functional implications. Three open source software packages (InterView, TVi and OptiMage) implementing our methods are available. PMID:17683601

Chromosomal targeting by CRISPR-Cas systems can contribute to genome plasticity in bacteria

PubMed Central

Dy, Ron L; Pitman, Andrew R; Fineran, Peter C

2013-01-01

The clustered regularly interspaced short palindromic repeats (CRISPR) and their associated (Cas) proteins form adaptive immune systems in bacteria to combat phage and other foreign genetic elements. Typically, short spacer sequences are acquired from the invader DNA and incorporated into CRISPR arrays in the bacterial genome. Small RNAs are generated that contain these spacer sequences and enable sequence-specific destruction of the foreign nucleic acids. Occasionally, spacers are acquired from the chromosome, which instead leads to targeting of the host genome. Chromosomal targeting is highly toxic to the bacterium, providing a strong selective pressure for a variety of evolutionary routes that enable host cell survival. Mutations that inactivate the CRISPR-Cas functionality, such as within the cas genes, CRISPR repeat, protospacer adjacent motifs (PAM), and target sequence, mediate escape from toxicity. This self-targeting might provide some explanation for the incomplete distribution of CRISPR-Cas systems in less than half of sequenced bacterial genomes. More importantly, self-genome targeting can cause large-scale genomic alterations, including remodeling or deletion of pathogenicity islands and other non-mobile chromosomal regions. While control of horizontal gene transfer is perceived as their main function, our recent work illuminates an alternative role of CRISPR-Cas systems in causing host genomic changes and influencing bacterial evolution. PMID:24251073

Biophysical modeling of the temporal niche: from first principles to the evolution of activity patterns.

PubMed

Levy, Ofir; Dayan, Tamar; Kronfeld-Schor, Noga; Porter, Warren P

2012-06-01

Most mammals can be characterized as nocturnal or diurnal. However infrequently, species may overcome evolutionary constraints and alter their activity patterns. We modeled the fundamental temporal niche of a diurnal desert rodent, the golden spiny mouse, Acomys russatus. This species can shift into nocturnal activity in the absence of its congener, the common spiny mouse, Acomys cahirinus, suggesting that it was competitively driven into diurnality and that this shift in a small desert rodent may involve physiological costs. Therefore, we compared metabolic costs of diurnal versus nocturnal activity using a biophysical model to evaluate the preferred temporal niche of this species. The model predicted that energy expenditure during foraging is almost always lower during the day except during midday in summer at the less sheltered microhabitat. We also found that a shift in summer to foraging in less sheltered microhabitats in response to predation pressure and food availability involves a significant physiological cost moderated by midday reduction in activity. Thus, adaptation to diurnality may reflect the "ghost of competition past"; climate-driven diurnality is an alternative but less likely hypothesis. While climate is considered to play a major role in the physiology and evolution of mammals, this is the first study to model its potential to affect the evolution of activity patterns of mammals.

CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription

PubMed Central

Carlson, Jonathan; Yan, Jiyu; Akinsiku, Olusimidele T.; Schaefer, Malinda; Sabbaj, Steffanie; Bet, Anne; Levy, David N.; Heath, Sonya; Tang, Jianming; Kaslow, Richard A.; Walker, Bruce D.; Ndung’u, Thumbi; Goulder, Philip J.; Heckerman, David; Hunter, Eric; Goepfert, Paul A.

2010-01-01

Retroviruses pack multiple genes into relatively small genomes by encoding several genes in the same genomic region with overlapping reading frames. Both sense and antisense HIV-1 transcripts contain open reading frames for known functional proteins as well as numerous alternative reading frames (ARFs). At least some ARFs have the potential to encode proteins of unknown function, and their antigenic properties can be considered as cryptic epitopes (CEs). To examine the extent of active immune response to virally encoded CEs, we analyzed human leukocyte antigen class I–associated polymorphisms in HIV-1 gag, pol, and nef genes from a large cohort of South Africans with chronic infection. In all, 391 CEs and 168 conventional epitopes were predicted, with the majority (307; 79%) of CEs derived from antisense transcripts. In further evaluation of CD8 T cell responses to a subset of the predicted CEs in patients with primary or chronic infection, both sense- and antisense-encoded CEs were immunogenic at both stages of infection. In addition, CEs often mutated during the first year of infection, which was consistent with immune selection for escape variants. These findings indicate that the HIV-1 genome might encode and deploy a large potential repertoire of unconventional epitopes to enhance vaccine-induced antiviral immunity. PMID:20065064

Caspase-12 and the inflammatory response to Yersinia pestis.

PubMed

Ferwerda, Bart; McCall, Matthew B B; de Vries, Maaike C; Hopman, Joost; Maiga, Boubacar; Dolo, Amagana; Doumbo, Ogobara; Daou, Modibo; de Jong, Dirk; Joosten, Leo A B; Tissingh, Rudi A; Reubsaet, Frans A G; Sauerwein, Robert; van der Meer, Jos W M; van der Ven, André J A M; Netea, Mihai G

2009-09-01

Caspase-12 functions as an antiinflammatory enzyme inhibiting caspase-1 and the NOD2/RIP2 pathways. Due to increased susceptibility to sepsis in individuals with functional caspase-12, an early-stop mutation leading to the loss of caspase-12 has replaced the ancient genotype in Eurasia and a significant proportion of individuals from African populations. In African-Americans, it has been shown that caspase-12 inhibits the pro-inflammatory cytokine production. We assessed whether similar mechanisms are present in African individuals, and whether evolutionary pressures due to plague may have led to the present caspase-12 genotype population frequencies. No difference in cytokine induction through the caspase-1 and/or NOD2/RIP2 pathways was observed in two independent African populations, among individuals with either an intact or absent caspase-12. In addition, stimulations with Yersinia pestis and two other species of Yersinia were preformed to investigate whether caspase-12 modulates the inflammatory reaction induced by Yersinia. We found that caspase-12 did not modulate cytokine production induced by Yersinia spp. Our experiments demonstrate for the first time the involvement of the NOD2/RIP2 pathway for recognition of Yersinia. However, caspase-12 does not modulate innate host defense against Y. pestis and alternative explanations for the geographical distribution of caspase-12 should be sought.

The History of Nontraditional or Ectopic Placement of Reservoirs in Prosthetic Urology.

PubMed

Perito, Paul; Wilson, Steven

2016-04-01

Reservoir placement during implantation of prosthetic urology devices has been problematic throughout the history of the surgical treatment of erectile dysfunction and urinary incontinence. We thought it would be interesting to review the history of reservoir placement leading up to current surgical techniques. To provide an overview of the past and present techniques for reservoir placement and discuss the evolutionary process leading to safe and effective placement of prosthetic reservoirs. We reviewed data pertaining to inflatable penile prosthesis (IPP) reservoirs and pressure-regulating balloons (PRB) in a chronological fashion, spanning 25 years. Main outcomes included a historical review of techniques for IPP reservoir and PRB placement leading to the subsequent incremental improvements in safety and efficacy when performing penile implants and artificial urinary sphincters. Prosthetic urologic reservoirs have traditionally been placed in the retropubic space. Over the years, urologists have attempted use of alternative spaces including peritoneal, epigastric, "ectopic," posterior to transversalis, and high submuscular. Current advances in prosthetic urologic reservoir placement allow safe and effective abdominal wall placement of reservoirs. These novel approaches appear to be so effective that urologists may now be able to cease using the traditional retropubic space for reservoir placement, even in the case of virgin pelves. Copyright © 2016 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

Insights on the evolution of metabolic networks of unicellular translationally biased organisms from transcriptomic data and sequence analysis.

PubMed

Carbone, Alessandra; Madden, Richard

2005-10-01

Codon bias is related to metabolic functions in translationally biased organisms, and two facts are argued about. First, genes with high codon bias describe in meaningful ways the metabolic characteristics of the organism; important metabolic pathways corresponding to crucial characteristics of the lifestyle of an organism, such as photosynthesis, nitrification, anaerobic versus aerobic respiration, sulfate reduction, methanogenesis, and others, happen to involve especially biased genes. Second, gene transcriptional levels of sets of experiments representing a significant variation of biological conditions strikingly confirm, in the case of Saccharomyces cerevisiae, that metabolic preferences are detectable by purely statistical analysis: the high metabolic activity of yeast during fermentation is encoded in the high bias of enzymes involved in the associated pathways, suggesting that this genome was affected by a strong evolutionary pressure that favored a predominantly fermentative metabolism of yeast in the wild. The ensemble of metabolic pathways involving enzymes with high codon bias is rather well defined and remains consistent across many species, even those that have not been considered as translationally biased, such as Helicobacter pylori, for instance, reveal some weak form of translational bias for this genome. We provide numerical evidence, supported by experimental data, of these facts and conclude that the metabolic networks of translationally biased genomes, observable today as projections of eons of evolutionary pressure, can be analyzed numerically and predictions of the role of specific pathways during evolution can be derived. The new concepts of Comparative Pathway Index, used to compare organisms with respect to their metabolic networks, and Evolutionary Pathway Index, used to detect evolutionarily meaningful bias in the genetic code from transcriptional data, are introduced.

Parallel and nonparallel behavioural evolution in response to parasitism and predation in Trinidadian guppies.

PubMed

Jacquin, L; Reader, S M; Boniface, A; Mateluna, J; Patalas, I; Pérez-Jvostov, F; Hendry, A P

2016-07-01

Natural enemies such as predators and parasites are known to shape intraspecific variability of behaviour and personality in natural populations, yet several key questions remain: (i) What is the relative importance of predation vs. parasitism in shaping intraspecific variation of behaviour across generations? (ii) What are the contributions of genetic and plastic effects to this behavioural divergence? (iii) And to what extent are responses to predation and parasitism repeatable across independent evolutionary lineages? We addressed these questions using Trinidadian guppies (Poecilia reticulata) (i) varying in their exposure to dangerous fish predators and Gyrodactylus ectoparasites for (ii) both wild-caught F0 and laboratory-reared F2 individuals and coming from (iii) multiple independent evolutionary lineages (i.e. independent drainages). Several key findings emerged. First, a population's history of predation and parasitism influenced behavioural profiles, but to different extent depending on the behaviour considered (activity, shoaling or boldness). Second, we had evidence for some genetic effects of predation regime on behaviour, with differences in activity of F2 laboratory-reared individuals, but not for parasitism, which had only plastic effects on the boldness of wild-caught F0 individuals. Third, the two lineages showed a mixture of parallel and nonparallel responses to predation/parasitism, with parallel responses being stronger for predation than for parasitism and for activity and boldness than for shoaling. These findings suggest that different sets of behaviours provide different pay-offs in alternative predation/parasitism environments and that parasitism has more transient effects in shaping intraspecific variation of behaviour than does predation. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

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

PubMed

Julien, Clavel; Leandro, Aristide; Hélène, Morlon

2018-06-19

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

Ideal Gas with a Varying (Negative Absolute) Temperature: an Alternative to Dark Energy?

NASA Astrophysics Data System (ADS)

Saha, Subhajit; Mondal, Anindita; Corda, Christian

2018-02-01

The present work is an attempt to investigate whether the evolutionary history of the Universe from the offset of inflation can be described by assuming the cosmic fluid to be an ideal gas with a specific gas constant but a varying negative absolute temperature (NAT). The motivation of this work is to search for an alternative to the "exotic" and "supernatural" dark energy (DE). In fact, the NAT works as an "effective quintessence" and there is need to deal neither with exotic matter like DE nor with modified gravity theories. For the sake of completeness, we release some clarifications on NATs in Section 3 of the paper.

Foot-and-Mouth Disease in the Middle East Caused by an A/ASIA/G-VII Virus Lineage, 2015-2016.

PubMed

Bachanek-Bankowska, Katarzyna; Di Nardo, Antonello; Wadsworth, Jemma; Henry, Elisabeth K M; Parlak, Ünal; Timina, Anna; Mischenko, Alexey; Qasim, Ibrahim Ahmad; Abdollahi, Darab; Sultana, Munawar; Hossain, M Anwar; King, Donald P; Knowles, Nick J

2018-06-01

Phylogenetic analyses of foot-and-mouth disease type A viruses in the Middle East during 2015-2016 identified viruses belonging to the A/ASIA/G-VII lineage, which originated in the Indian subcontinent. Changes in a critical antigenic site within capsid viral protein 1 suggest possible evolutionary pressure caused by an intensive vaccination program.

Genetic variation of lodgepole pine physical and chemical defenses associated with each step in host selection behavior sequence by mountain pine beetle

Treesearch

Kimberly F. Wallin; Daniel S. Ott; Alvin D. Yanchuk

2012-01-01

Abiotic and biotic stressors exert selective pressures on plants, and over evolutionary time lead to the development of specialized adaptations and specific responses to stresses (Safranyik and Carroll 2006, Wallin and Raffa 2002). In this way, the environment in which plants evolve shapes their life cycles, range, growth, reproduction, and defenses. Insects and...

Adaptive molecular evolution of the two-pore channel 1 gene TPC1 in the karst-adapted genus Primulina (Gesneriaceae)

PubMed Central

Tao, Junjie; Feng, Chao; Ai, Bin; Kang, Ming

2016-01-01

Background and Aims Limestone karst areas possess high floral diversity and endemism. The genus Primulina, which contributes to the unique calcicole flora, has high species richness and exhibit specific soil-based habitat associations that are mainly distributed on calcareous karst soils. The adaptive molecular evolutionary mechanism of the genus to karst calcium-rich environments is still not well understood. The Ca2+-permeable channel TPC1 was used in this study to test whether its gene is involved in the local adaptation of Primulina to karst high-calcium soil environments. Methods Specific amplification and sequencing primers were designed and used to amplify the full-length coding sequences of TPC1 from cDNA of 76 Primulina species. The sequence alignment without recombination and the corresponding reconstructed phylogeny tree were used in molecular evolutionary analyses at the nucleic acid level and amino acid level, respectively. Finally, the identified sites under positive selection were labelled on the predicted secondary structure of TPC1. Key Results Seventy-six full-length coding sequences of Primulina TPC1 were obtained. The length of the sequences varied between 2220 and 2286 bp and the insertion/deletion was located at the 5′ end of the sequences. No signal of substitution saturation was detected in the sequences, while significant recombination breakpoints were detected. The molecular evolutionary analyses showed that TPC1 was dominated by purifying selection and the selective pressures were not significantly different among species lineages. However, significant signals of positive selection were detected at both TPC1 codon level and amino acid level, and five sites under positive selective pressure were identified by at least three different methods. Conclusions The Ca2+-permeable channel TPC1 may be involved in the local adaptation of Primulina to karst Ca2+-rich environments. Different species lineages suffered similar selective pressure associated with calcium in karst environments, and episodic diversifying selection at a few sites may play a major role in the molecular evolution of Primulina TPC1. PMID:27582362

Evolutionary Dynamics of West Nile Virus in the United States, 1999–2011: Phylogeny, Selection Pressure and Evolutionary Time-Scale Analysis

PubMed Central

Chancey, Caren; Ball, Christopher; Akolkar, Namita; Land, Kevin J.; Winkelman, Valerie; Stramer, Susan L.; Kramer, Laura D.; Rios, Maria

2013-01-01

West Nile virus (WNV), an arbovirus maintained in a bird-mosquito enzootic cycle, can infect other vertebrates including humans. WNV was first reported in the US in 1999 where, to date, three genotypes belonging to WNV lineage I have been described (NY99, WN02, SW/WN03). We report here the WNV sequences obtained from two birds, one mosquito, and 29 selected human samples acquired during the US epidemics from 2006–2011 and our examination of the evolutionary dynamics in the open-reading frame of WNV isolates reported from 1999–2011. Maximum-likelihood and Bayesian methods were used to perform the phylogenetic analyses and selection pressure analyses were conducted with the HyPhy package. Phylogenetic analysis identified human WNV isolates within the main WNV genotypes that have circulated in the US. Within genotype SW/WN03, we have identified a cluster with strains derived from blood donors and birds from Idaho and North Dakota collected during 2006–2007, termed here MW/WN06. Using different codon-based and branch-site selection models, we detected a number of codons subjected to positive pressure in WNV genes. The mean nucleotide substitution rate for WNV isolates obtained from humans was calculated to be 5.06×10−4 substitutions/site/year (s/s/y). The Bayesian skyline plot shows that after a period of high genetic variability following the introduction of WNV into the US, the WNV population appears to have reached genetic stability. The establishment of WNV in the US represents a unique opportunity to understand how an arbovirus adapts and evolves in a naïve environment. We describe a novel, well-supported cluster of WNV formed by strains collected from humans and birds from Idaho and North Dakota. Adequate genetic surveillance is essential to public health since new mutants could potentially affect viral pathogenesis, decrease performance of diagnostic assays, and negatively impact the efficacy of vaccines and the development of specific therapies. PMID:23738027

Elevated Rate of Fixation of Endogenous Retroviral Elements in Haplorhini TRIM5 and TRIM22 Genomic Sequences: Impact on Transcriptional Regulation

PubMed Central

Diehl, William E.; Johnson, Welkin E.; Hunter, Eric

2013-01-01

All genes in the TRIM6/TRIM34/TRIM5/TRIM22 locus are type I interferon inducible, with TRIM5 and TRIM22 possessing antiviral properties. Evolutionary studies involving the TRIM6/34/5/22 locus have predominantly focused on the coding sequence of the genes, finding that TRIM5 and TRIM22 have undergone high rates of both non-synonymous nucleotide replacements and in-frame insertions and deletions. We sought to understand if divergent evolutionary pressures on TRIM6/34/5/22 coding regions have selected for modifications in the non-coding regions of these genes and explore whether such non-coding changes may influence the biological function of these genes. The transcribed genomic regions, including the introns, of TRIM6, TRIM34, TRIM5, and TRIM22 from ten Haplorhini primates and one prosimian species were analyzed for transposable element content. In Haplorhini species, TRIM5 displayed an exaggerated interspecies variability, predominantly resulting from changes in the composition of transposable elements in the large first and fourth introns. Multiple lineage-specific endogenous retroviral long terminal repeats (LTRs) were identified in the first intron of TRIM5 and TRIM22. In the prosimian genome, we identified a duplication of TRIM5 with a concomitant loss of TRIM22. The transposable element content of the prosimian TRIM5 genes appears to largely represent the shared Haplorhini/prosimian ancestral state for this gene. Furthermore, we demonstrated that one such differentially fixed LTR provides for species-specific transcriptional regulation of TRIM22 in response to p53 activation. Our results identify a previously unrecognized source of species-specific variation in the antiviral TRIM genes, which can lead to alterations in their transcriptional regulation. These observations suggest that there has existed long-term pressure for exaptation of retroviral LTRs in the non-coding regions of these genes. This likely resulted from serial viral challenges and provided a mechanism for rapid alteration of transcriptional regulation. To our knowledge, this represents the first report of persistent evolutionary pressure for the capture of retroviral LTR insertions. PMID:23516500

Evolutionary divergence in sexual signals: Insights from within and among barn swallow populations

NASA Astrophysics Data System (ADS)

Wilkins, Matthew Reed

A wealth of studies across diverse animal groups indicate the importance of sexual selection in shaping phenotypes within and across breeding populations. In recent decades, much research has focused on how divergent sexual selection pressures among populations may lead to speciation. For my first dissertation chapter, I performed a literature review on the causes and consequences of evolutionary divergence in acoustic signals and developed the acoustic window conceptual framework for understanding the contributions of selection, genetic drift, and evolutionary constraint to signal divergence. Further, I found that sexual selection explains acoustic differences between recently diverged populations of the best-studied taxa. However, the relative contributions of ecological selection, sexual selection, and drift to acoustic divergence have not typically been considered within the same study systems. The remainder of my dissertation used the Northern Hemisphere-distributed barn swallow ( Hirundo rustica) species complex as a model system to study sender-receiver dynamics, intra- and intersexual selection pressures, and visual and acoustic signal interactions at the local scale, and signal divergence across populations at the global scale. From song recordings taken across 19 sampling sites, spanning five of six described subspecies, I demonstrated considerable conservation in song structure. However, temporal traits were highly divergent across subspecies, and in particular, the speed of the terminal trill of songs. In a detailed study of the multimodal communication system of the barn swallow (including visual and acoustic traits), I demonstrated that males and females use different types of signals to mediate competition and mate choice. One of the only exceptions to this rule was trill rate, which was also implicated in song divergence across populations. In order to test the function of trill rate in communication, I performed a two-year playback study within the North American subspecies, H. r. erythrogaster. Contrary to expectations, males did not have stronger responses to faster trilling (high performance) simulated intruders. Instead, resident males had stronger responses to the high performance stimulus only when the intruder was also darker than the resident. Collectively, my dissertation offers novel insight into the evolutionary dynamics of complex sexual signaling at multiple spatial scales.

The Potential Feasibility of Chlorinic Photosynthesis on Extrasolar Planets

NASA Astrophysics Data System (ADS)

Haas, Johnson

2009-09-01

It is highly likely that the first convincing evidence of extrasolar life will arrive in the form of atmospheric absorption spectra. The modern search for life-bearing extrasolar planets emphasizes the potential detection of O2 and O3 absorption spectra in exoplanetary atmospheres as archetypal signatures of biology. However, oxygenic photosynthesis apparently failed to evolve independently more than once on Earth, and is thus unlikely to be reliably ubiquitous throughout the universe. Alternative evolutionary paths may yield planetary atmospheres tinted with the waste products of other dominant metabolisms, including potentially exotic biochemistries. This study examines the potential feasibility of one such exotic metabolism: chlorinic photosynthesis (CPS), defined as biologically-mediated halogenation of aqueous chloride to HClO, Cl2 or partially-oxidized intermediates (e.g. haloalkanes, haloacids, haloaromatics), coupled with photosynthetic CO2 fixation. This metabolic couple is feasible thermodynamically and appears to be geochemically plausible under approximately terrestrial conditions. This study hypothesizes that planetary biospheres dominated by CPS would develop atmospheres enriched with dihalogens and other halogenated compounds, evolve a highly oxidizing surface geochemical environment, and foster biological selection pressures favoring halogen resistance and eventual metazoan heterotrophy based on dihalogen and halocarbon respiration. Planets favoring the evolution of CPS would probably receive equivalent or greater surface UV flux than Earth did in the Paleoarchean (promoting abiotic photo-oxidation of aqueous halides, and establishing a strong biological selective pressure toward their accommodation), and would orbit stars having equivalent or greater bulk metallicities (promoting greater planetary halide abundances) relative to the Sun. Directed searches for such worlds should probably focus on A, F and G0 spectral class stars having bulk metallicities of +0.0 Dex or greater.

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

PubMed

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

2016-12-01

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

Evolutionary Ensemble for In Silico Prediction of Ames Test Mutagenicity

NASA Astrophysics Data System (ADS)

Chen, Huanhuan; Yao, Xin

Driven by new regulations and animal welfare, the need to develop in silico models has increased recently as alternative approaches to safety assessment of chemicals without animal testing. This paper describes a novel machine learning ensemble approach to building an in silico model for the prediction of the Ames test mutagenicity, one of a battery of the most commonly used experimental in vitro and in vivo genotoxicity tests for safety evaluation of chemicals. Evolutionary random neural ensemble with negative correlation learning (ERNE) [1] was developed based on neural networks and evolutionary algorithms. ERNE combines the method of bootstrap sampling on training data with the method of random subspace feature selection to ensure diversity in creating individuals within an initial ensemble. Furthermore, while evolving individuals within the ensemble, it makes use of the negative correlation learning, enabling individual NNs to be trained as accurate as possible while still manage to maintain them as diverse as possible. Therefore, the resulting individuals in the final ensemble are capable of cooperating collectively to achieve better generalization of prediction. The empirical experiment suggest that ERNE is an effective ensemble approach for predicting the Ames test mutagenicity of chemicals.

Endangered Species Hold Clues to Human Evolution

PubMed Central

Bejerano, Gill; Salama, Sofie R.; Haussler, David

2010-01-01

We report that 18 conserved, and by extension functional, elements in the human genome are the result of retroposon insertions that are evolving under purifying selection in mammals. We show evidence that 1 of the 18 elements regulates the expression of ASXL3 during development by encoding an alternatively spliced exon that causes nonsense-mediated decay of the transcript. The retroposon that gave rise to these functional elements was quickly inactivated in the mammalian ancestor, and all traces of it have been lost due to neutral decay. However, the tuatara has maintained a near-ancestral version of this retroposon in its extant genome, which allows us to connect the 18 human elements to the evolutionary events that created them. We propose that conservation efforts over more than 100 years may not have only prevented the tuatara from going extinct but could have preserved our ability to understand the evolutionary history of functional elements in the human genome. Through simulations, we argue that species with historically low population sizes are more likely to harbor ancient mobile elements for long periods of time and in near-ancestral states, making these species indispensable in understanding the evolutionary origin of functional elements in the human genome. PMID:20332163

Mathematics and evolutionary biology make bioinformatics education comprehensible.

PubMed

Jungck, John R; Weisstein, Anton E

2013-09-01

The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes-the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software-the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a 'two-culture' problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses.

Mathematics and evolutionary biology make bioinformatics education comprehensible

PubMed Central

Weisstein, Anton E.

2013-01-01

The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes—the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software—the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a ‘two-culture’ problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses. PMID:23821621

Investigation of SSME alternate high pressure fuel turbopump lift-off seal fluid and structural dynamic interaction

NASA Technical Reports Server (NTRS)

Elrod, David A.

1989-01-01

The Space Shuttle main engine (SSME) alternate turbopump development program (ATD) high pressure fuel turbopump (HPFTP) design utilizes an innovative lift-off seal (LOS) design that is located in close proximity to the turbine end bearing. Cooling flow exiting the bearing passes through the lift-off seal during steady state operation. The potential for fluid excitation of lift-off seal structural resonances is investigated. No fluid excitation of LOS resonances is predicted. However, if predicted LOS natural frequencies are significantly lowered by the presence of the coolant, pressure oscillations caused by synchronous whirl of the HPFTP rotor may excite a resonance.

Equation of state of U2Mo up-to Mbar pressure range: Ab-initio study

NASA Astrophysics Data System (ADS)

Mukherjee, D.; Sahoo, B. D.; Joshi, K. D.; Kaushik, T. C.

2018-04-01

Experimentally, U2Mo is known to exist in tetragonal structure at ambient conditions. In contrast to experimental reports, the past theoretical studies carried out in this material do not find this phase to be stable structure at zero pressure. In order to examine this discrepancy between experiment and theory, we have performed ab-initio electronic band structure calculations on this material. In our theoretical study, we have attempted to search for lowest enthalpy structure at ambient as well at high pressure up to 200 GPa, employing evolutionary structure search algorithm in conjunction with ab-inito method. Our investigations suggest that a hexagonal structure with space group symmetry P6/mmm is the lowest enthalpy structure not only at ambient pressure but also up to pressure range of ˜200 GPa. To further, substantiate the results of these static lattice calculations the elastic and lattice dynamical stability has also been analysed. The theoretical isotherm derived from these calculations has been utilized to determine the Hugoniot of this material. Various physical properties such as zero pressure equilibrium volume, bulk modulus and its pressure derivative has also been derived from theoretical isotherm.

Lifetime prediction for organic coating under alternating hydrostatic pressure by artificial neural network

PubMed Central

Tian, Wenliang; Meng, Fandi; Liu, Li; Li, Ying; Wang, Fuhui

2017-01-01

A concept for prediction of organic coatings, based on the alternating hydrostatic pressure (AHP) accelerated tests, has been presented. An AHP accelerated test with different pressure values has been employed to evaluate coating degradation. And a back-propagation artificial neural network (BP-ANN) has been established to predict the service property and the service lifetime of coatings. The pressure value (P), immersion time (t) and service property (impedance modulus |Z|) are utilized as the parameters of the network. The average accuracies of the predicted service property and immersion time by the established network are 98.6% and 84.8%, respectively. The combination of accelerated test and prediction method by BP-ANN is promising to evaluate and predict coating property used in deep sea. PMID:28094340

[Evolutionary medicine: an introduction. Evolutionary biology, a missing element in medical teaching].

PubMed

Swynghedauw, Bernard

2009-05-01

The aim of this brief review article is to help to reconcile medicine with evolutionary biology, a subject that should be taught in medical school. Evolutionary medicine takes the view that contemporary ills are related to an incompatibility between the environment in which humans currently live and their genomes, which have been shaped by diferent environmental conditions during biological evolution. Human activity has recently induced acute environmental modifications that have profoundly changed the medical landscape. Evolutionary biology is an irreversible, ongoing and discontinuous process characterized by periods of stasis followed by accelerations. Evolutionary biology is determined by genetic mutations, which are selected either by Darwinian selective pressure or randomly by genetic drift. Most medical events result from a genome/environment conflict. Some may be purely genetic, as in monogenic diseases, and others purely environmental, such as traffic accidents. Nevertheless, in most common diseases the clinical landscape is determined by the conflict between these two factors, the genetic elements of which are gradually being unraveled Three examples are examined in depth:--The medical consequences of the greenhouse effect. The absence of excess mortality during recent heat waves suggests that the main determinant of mortality in the 2003 heatwave was heatstroke and old age. The projected long-term effects of global warming call for research on thermolysis, a forgotten branch of physiology.--The hygiene hypothesis postulates that the exponential rise in autoimmune and allergic diseases is linked to lesser exposure to infectious agents, possibly involving counter-regulatory factors such as IL-10.--The recent rise in the incidence of obesity and type 2 diabetes in rich countries can be considered to result from a conflict between a calorie-rich environment and gene variants that control appetite. These variants are currently being identified by genome-wide analysis. Biological evolution should be taken into account in future holistic health policies.

Protein interface classification by evolutionary analysis

PubMed Central

2012-01-01

Background Distinguishing biologically relevant interfaces from lattice contacts in protein crystals is a fundamental problem in structural biology. Despite efforts towards the computational prediction of interface character, many issues are still unresolved. Results We present here a protein-protein interface classifier that relies on evolutionary data to detect the biological character of interfaces. The classifier uses a simple geometric measure, number of core residues, and two evolutionary indicators based on the sequence entropy of homolog sequences. Both aim at detecting differential selection pressure between interface core and rim or rest of surface. The core residues, defined as fully buried residues (>95% burial), appear to be fundamental determinants of biological interfaces: their number is in itself a powerful discriminator of interface character and together with the evolutionary measures it is able to clearly distinguish evolved biological contacts from crystal ones. We demonstrate that this definition of core residues leads to distinctively better results than earlier definitions from the literature. The stringent selection and quality filtering of structural and sequence data was key to the success of the method. Most importantly we demonstrate that a more conservative selection of homolog sequences - with relatively high sequence identities to the query - is able to produce a clearer signal than previous attempts. Conclusions An evolutionary approach like the one presented here is key to the advancement of the field, which so far was missing an effective method exploiting the evolutionary character of protein interfaces. Its coverage and performance will only improve over time thanks to the incessant growth of sequence databases. Currently our method reaches an accuracy of 89% in classifying interfaces of the Ponstingl 2003 datasets and it lends itself to a variety of useful applications in structural biology and bioinformatics. We made the corresponding software implementation available to the community as an easy-to-use graphical web interface at http://www.eppic-web.org. PMID:23259833

Time to Evolve? Potential Evolutionary Responses of Fraser River Sockeye Salmon to Climate Change and Effects on Persistence

PubMed Central

Reed, Thomas E.; Schindler, Daniel E.; Hague, Merran J.; Patterson, David A.; Meir, Eli; Waples, Robin S.; Hinch, Scott G.

2011-01-01

Evolutionary adaptation affects demographic resilience to climate change but few studies have attempted to project changes in selective pressures or quantify impacts of trait responses on population dynamics and extinction risk. We used a novel individual-based model to explore potential evolutionary changes in migration timing and the consequences for population persistence in sockeye salmon Oncorhynchus nerka in the Fraser River, Canada, under scenarios of future climate warming. Adult sockeye salmon are highly sensitive to increases in water temperature during their arduous upriver migration, raising concerns about the fate of these ecologically, culturally, and commercially important fish in a warmer future. Our results suggest that evolution of upriver migration timing could allow these salmon to avoid increasingly frequent stressful temperatures, with the odds of population persistence increasing in proportion to the trait heritability and phenotypic variance. With a simulated 2°C increase in average summer river temperatures by 2100, adult migration timing from the ocean to the river advanced by ∼10 days when the heritability was 0.5, while the risk of quasi-extinction was only 17% of that faced by populations with zero evolutionary potential (i.e., heritability fixed at zero). The rates of evolution required to maintain persistence under simulated scenarios of moderate to rapid warming are plausible based on estimated heritabilities and rates of microevolution of timing traits in salmon and related species, although further empirical work is required to assess potential genetic and ecophysiological constraints on phenological adaptation. These results highlight the benefits to salmon management of maintaining evolutionary potential within populations, in addition to conserving key habitats and minimizing additional stressors where possible, as a means to build resilience to ongoing climate change. More generally, they demonstrate the importance and feasibility of considering evolutionary processes, in addition to ecology and demography, when projecting population responses to environmental change. PMID:21738573

Artificial evolution by viability rather than competition.

PubMed

Maesani, Andrea; Fernando, Pradeep Ruben; Floreano, Dario

2014-01-01

Evolutionary algorithms are widespread heuristic methods inspired by natural evolution to solve difficult problems for which analytical approaches are not suitable. In many domains experimenters are not only interested in discovering optimal solutions, but also in finding the largest number of different solutions satisfying minimal requirements. However, the formulation of an effective performance measure describing these requirements, also known as fitness function, represents a major challenge. The difficulty of combining and weighting multiple problem objectives and constraints of possibly varying nature and scale into a single fitness function often leads to unsatisfactory solutions. Furthermore, selective reproduction of the fittest solutions, which is inspired by competition-based selection in nature, leads to loss of diversity within the evolving population and premature convergence of the algorithm, hindering the discovery of many different solutions. Here we present an alternative abstraction of artificial evolution, which does not require the formulation of a composite fitness function. Inspired from viability theory in dynamical systems, natural evolution and ethology, the proposed method puts emphasis on the elimination of individuals that do not meet a set of changing criteria, which are defined on the problem objectives and constraints. Experimental results show that the proposed method maintains higher diversity in the evolving population and generates more unique solutions when compared to classical competition-based evolutionary algorithms. Our findings suggest that incorporating viability principles into evolutionary algorithms can significantly improve the applicability and effectiveness of evolutionary methods to numerous complex problems of science and engineering, ranging from protein structure prediction to aircraft wing design.

The many voices of Darwin's descendants: reply to Schmitt (2014).

PubMed

Eastwick, Paul W; Luchies, Laura B; Finkel, Eli J; Hunt, Lucy L

2014-05-01

This article elaborates on evolutionary perspectives relevant to the meta-analytic portion of our recent review (Eastwick, Luchies, Finkel, & Hunt, 2014). We suggested that if men and women evolved sex-differentiated ideals (i.e., mate preferences), then they should exhibit sex-differentiated desires (e.g., romantic attraction) and/or relational outcomes (e.g., relationship satisfaction) with respect to live opposite-sex targets. Our meta-analysis revealed no support for these sex-differentiated desires and relational outcomes in either established relationship or mate selection contexts. With respect to established relationships, Schmitt (2014) has objected to the idea that relationship quality (one of our primarily romantic evaluation dependent measures) has functional relevance. In doing so, he neglects myriad evolutionary perspectives on the adaptive importance of the pair-bond and the wealth of data suggesting that relationship quality predicts the dissolution of pair-bonds. With respect to mate selection, Schmitt (2014) has continued to suggest that sex-differentiated patterns should emerge in these contexts despite the fact that our meta-analysis included this literature and found no sex differences. Schmitt (2014) also generated several novel sex-differentiated predictions with respect to attractiveness and earning prospects, but neither the existing literature nor reanalyses of our meta-analytic data reveal any support for his "proper" function-related hypotheses. In short, there are diverse evolutionary perspectives relevant to mating, including our own synthesis; Schmitt's (2014) conceptual analysis is not the one-and-only evolutionary psychological view, and his alternative explanations for our meta-analytic data remain speculative.

Plant polyadenylation factors: conservation and variety in the polyadenylation complex in plants.

PubMed

Hunt, Arthur G; Xing, Denghui; Li, Qingshun Q

2012-11-20

Polyadenylation, an essential step in eukaryotic gene expression, requires both cis-elements and a plethora of trans-acting polyadenylation factors. The polyadenylation factors are largely conserved across mammals and fungi. The conservation seems also extended to plants based on the analyses of Arabidopsis polyadenylation factors. To extend this observation, we systemically identified the orthologs of yeast and human polyadenylation factors from 10 plant species chosen based on both the availability of their genome sequences and their positions in the evolutionary tree, which render them representatives of different plant lineages. The evolutionary trajectories revealed several interesting features of plant polyadenylation factors. First, the number of genes encoding plant polyadenylation factors was clearly increased from "lower" to "higher" plants. Second, the gene expansion in higher plants was biased to some polyadenylation factors, particularly those involved in RNA binding. Finally, while there are clear commonalities, the differences in the polyadenylation apparatus were obvious across different species, suggesting an ongoing process of evolutionary change. These features lead to a model in which the plant polyadenylation complex consists of a conserved core, which is rather rigid in terms of evolutionary conservation, and a panoply of peripheral subunits, which are less conserved and associated with the core in various combinations, forming a collection of somewhat distinct complex assemblies. The multiple forms of plant polyadenylation complex, together with the diversified polyA signals may explain the intensive alternative polyadenylation (APA) and its regulatory role in biological functions of higher plants.

49 CFR 192.328 - Additional construction requirements for steel pipe using alternative maximum allowable operating...

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 3 2012-10-01 2012-10-01 false Additional construction requirements for steel pipe using alternative maximum allowable operating pressure. 192.328 Section 192.328 Transportation... Lines and Mains § 192.328 Additional construction requirements for steel pipe using alternative maximum...

49 CFR 192.328 - Additional construction requirements for steel pipe using alternative maximum allowable operating...

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 3 2014-10-01 2014-10-01 false Additional construction requirements for steel pipe using alternative maximum allowable operating pressure. 192.328 Section 192.328 Transportation... Lines and Mains § 192.328 Additional construction requirements for steel pipe using alternative maximum...

Replacement of salt by a novel potassium- and magnesium-enriched salt alternative improves the cardiovascular effects of ramipril.

PubMed Central

Mervaala, E. M.; Paakkari, I.; Laakso, J.; Nevala, R.; Teräväinen, T. M.; Fyhrquist, F.; Vapaatalo, H.; Karppanen, H.

1994-01-01

1. The influence of salt (sodium chloride; NaCl) (an additional 6% in the diet) and that of a novel sodium-reduced, potassium-, magnesium-, and L-lysine-enriched salt alternative on the cardiovascular effects of ramipril was studied in stroke-prone spontaneously hypertensive rats in a 6-week study. The intake of sodium chloride was adjusted to the same level by adding the salt alternative at a 1.75 times higher amount than regular salt. 2. Salt produced a marked rise in blood pressure and induced cardiac hypertrophy and significant mortality, while the salt alternative neither increased blood pressure nor caused any mortality and produced less cardiac hypertrophy than salt. 3. Ramipril treatment at a daily dose of 3 mg kg-1 normalized blood pressure and prevented the development of cardiac hypertrophy of rats on control diet. These effects of ramipril were blocked by the addition of salt but were only slightly attenuated by the addition of the salt alternative. The mortality in the salt group was prevented by ramipril. 4. Responses of mesenteric arterial rings in vitro were examined at the end of the study. Salt, but not the salt alternative, increased vascular contractile responses to noradrenaline. Ramipril treatment improved the arterial relaxation responses to acetylcholine and to sodium nitroprusside. The vascular relaxation enhancing effect of ramipril was blocked by salt but only slightly attenuated by the salt alternative. 5. Ramipril treatment did not significantly increase plasma renin activity in the presence or in the absence of salt supplementation. The salt alternative did not cause hyperkalaemia, either alone or in combination with ramipril treatment.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8032605

21 CFR 868.5935 - External negative pressure ventilator.

Code of Federal Regulations, 2010 CFR

2010-04-01

... ventilator. (a) Identification. An external negative pressure ventilator (e.g., iron lung, cuirass) is a device chamber that is intended to support a patient's ventilation by alternately applying and releasing external negative pressure over the diaphragm and upper trunk of the patient. (b) Classification. Class II...

Giant pandas are not an evolutionary cul-de-sac: evidence from multidisciplinary research.

PubMed

Wei, Fuwen; Hu, Yibo; Yan, Li; Nie, Yonggang; Wu, Qi; Zhang, Zejun

2015-01-01

The giant panda (Ailuropoda melanoleuca) is one of the world's most endangered mammals and remains threatened by environmental and anthropogenic pressure. It is commonly argued that giant pandas are an evolutionary cul-de-sac because of their specialized bamboo diet, phylogenetic changes in body size, small population, low genetic diversity, and low reproductive rate. This notion is incorrect, arose from a poor understanding or appreciation of giant panda biology, and is in need of correction. In this review, we summarize research across morphology, ecology, and genetics to dispel the idea, once and for all, that giant pandas are evolutionary dead-end. The latest and most advanced research shows that giant pandas are successful animals highly adapted to a specialized bamboo diet via morphological, ecological, and genetic adaptations and coadaptation of gut microbiota. We also debunk misconceptions around population size, population growth rate, and genetic variation. During their evolutionary history spanning 8 My, giant pandas have survived diet specialization, massive bamboo flowering and die off, and rapid climate oscillations. Now, they are suffering from enormous human interference. Fortunately, continued conservation effort is greatly reducing impacts from anthropogenic interference and allowing giant panda populations and habitat to recover. Previous ideas of a giant panda evolutionary cul-de-sac resulted from an unsystematic and unsophisticated understanding of their biology and it is time to shed this baggage and focus on the survival and maintenance of this high-profile species. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

PubMed

Maslo, Brooke; Fefferman, Nina H

2015-08-01

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

Upon Accounting for the Impact of Isoenzyme Loss, Gene Deletion Costs Anticorrelate with Their Evolutionary Rates.

PubMed

Jacobs, Christopher; Lambourne, Luke; Xia, Yu; Segrè, Daniel

2017-01-01

System-level metabolic network models enable the computation of growth and metabolic phenotypes from an organism's genome. In particular, flux balance approaches have been used to estimate the contribution of individual metabolic genes to organismal fitness, offering the opportunity to test whether such contributions carry information about the evolutionary pressure on the corresponding genes. Previous failure to identify the expected negative correlation between such computed gene-loss cost and sequence-derived evolutionary rates in Saccharomyces cerevisiae has been ascribed to a real biological gap between a gene's fitness contribution to an organism "here and now" and the same gene's historical importance as evidenced by its accumulated mutations over millions of years of evolution. Here we show that this negative correlation does exist, and can be exposed by revisiting a broadly employed assumption of flux balance models. In particular, we introduce a new metric that we call "function-loss cost", which estimates the cost of a gene loss event as the total potential functional impairment caused by that loss. This new metric displays significant negative correlation with evolutionary rate, across several thousand minimal environments. We demonstrate that the improvement gained using function-loss cost over gene-loss cost is explained by replacing the base assumption that isoenzymes provide unlimited capacity for backup with the assumption that isoenzymes are completely non-redundant. We further show that this change of the assumption regarding isoenzymes increases the recall of epistatic interactions predicted by the flux balance model at the cost of a reduction in the precision of the predictions. In addition to suggesting that the gene-to-reaction mapping in genome-scale flux balance models should be used with caution, our analysis provides new evidence that evolutionary gene importance captures much more than strict essentiality.

Peer pressure: enhancement of cooperation through mutual punishment.

PubMed

Yang, Han-Xin; Wu, Zhi-Xi; Rong, Zhihai; Lai, Ying-Cheng

2015-02-01

An open problem in evolutionary game dynamics is to understand the effect of peer pressure on cooperation in a quantitative manner. Peer pressure can be modeled by punishment, which has been proved to be an effective mechanism to sustain cooperation among selfish individuals. We investigate a symmetric punishment strategy, in which an individual will punish each neighbor if their strategies are different, and vice versa. Because of the symmetry in imposing the punishment, one might intuitively expect the strategy to have little effect on cooperation. Utilizing the prisoner's dilemma game as a prototypical model of interactions at the individual level, we find, through simulation and theoretical analysis, that proper punishment, when even symmetrically imposed on individuals, can enhance cooperation. Also, we find that the initial density of cooperators plays an important role in the evolution of cooperation driven by mutual punishment.

Peer pressure: Enhancement of cooperation through mutual punishment

NASA Astrophysics Data System (ADS)

Yang, Han-Xin; Wu, Zhi-Xi; Rong, Zhihai; Lai, Ying-Cheng

2015-02-01

An open problem in evolutionary game dynamics is to understand the effect of peer pressure on cooperation in a quantitative manner. Peer pressure can be modeled by punishment, which has been proved to be an effective mechanism to sustain cooperation among selfish individuals. We investigate a symmetric punishment strategy, in which an individual will punish each neighbor if their strategies are different, and vice versa. Because of the symmetry in imposing the punishment, one might intuitively expect the strategy to have little effect on cooperation. Utilizing the prisoner's dilemma game as a prototypical model of interactions at the individual level, we find, through simulation and theoretical analysis, that proper punishment, when even symmetrically imposed on individuals, can enhance cooperation. Also, we find that the initial density of cooperators plays an important role in the evolution of cooperation driven by mutual punishment.

An observational study of the effectiveness of alternative care providers in the management of obstructive sleep apnea.

PubMed

Pendharkar, Sachin R; Dechant, Anthony; Bischak, Diane P; Tsai, Willis H; Stevenson, Ann-Marie; Hanly, Patrick J

2016-04-01

Alternative care providers have been proposed as a substitute for physician-based management of obstructive sleep apnea. The purpose of this study was to describe the clinical course of patients with a new diagnosis of obstructive sleep apnea who were treated with continuous positive airway pressure and followed by alternative care providers at a tertiary care sleep clinic. It was hypothesized that care by alternative care providers would result in improvement of daytime sleepiness and satisfactory treatment adherence, and that a specific number of follow-up visits could be identified after which clinical outcomes no longer improved. The Epworth Sleepiness Scale score was measured for each patient at baseline and at each alternative care provider visit. Patients were discharged when they demonstrated a significant improvement in sleepiness and were adherent to therapy. The Epworth Sleepiness Scale score decreased by 3.9 points from baseline to discharge. Patients with three or more visits required more follow-up time to achieve the same clinical improvement as those with only two visits. Continuous positive airway pressure adherence was comparable to previous studies of physician-led care and improved with ongoing alternative care provider follow-up. The current results suggest that clinical care by alternative care providers leads to continued improvements in sleepiness in patients with obstructive sleep apnea who are treated with continuous positive airway pressure, and that a minority of patients require longer follow-up to achieve a satisfactory clinical response to therapy. © 2015 European Sleep Research Society.

Pressure-Letdown Machine for a Coal Reactor

NASA Technical Reports Server (NTRS)

Perkins, G. S.; Mabe, W. B.

1986-01-01

Pumps operating in reverse generate power. Conceptual pressure-letdown machine for coal-liquefaction system extracts energy from expansion of product fluid. Mud pumps, originally intended for use in oil drilling, operated in reverse so their motors act as generators. Several pumps operated in alternating phase to obtain multiple stages of letdown from inlet pressure to outlet pressure. About 75 percent of work generates inlet pressure recoverable as electrical energy.